Mercurial > repos > jankanis > blast2html

--- a/Blast output page example.html	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2071 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head>
-
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
-<meta name="jig" content="ncbitoggler ncbiautocomplete ncbilocalnav ncbigrid ncbipopper">
-<meta name="ncbitoggler" content="animation:'none'">
-<meta name="ncbipopper" content="animation:'none',closeEvent: 'click',openEvent: 'click',destPosition: 'top right',triggerPosition: 'bottom right'">
-
-<meta name="ncbi_app" content="blast">
-<meta name="ncbi_pdid" content="blastresults">
-<meta name="ncbi_stat" content="false">
-<meta name="ncbi_sessionid" content="8A8E11EE2CABF371_0000SID">
-<meta name="ncbi_phid" content="5AAB74D7368F2C81000000000000C9C8">
-<script type="text/javascript"> var ncbi_startTime = new Date(); </script>
-<title>NCBI Blast:Nucleotide Sequence (16 letters)</title>
-<script type="text/javascript" src="Blast%20output%20page%20example_files/jig.js"></script><link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example_files/jig.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_002.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery_005.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_004.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery_004.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_007.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery_003.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery_007.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_003.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery_008.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_008.js"></script><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_005.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_009.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery_006.css"><script type="text/javascript" src="Blast%20output%20page%20example_files/jquery_006.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example_files/jquery_002.css">
-<script type="text/javascript">    jQuery.getScript("/core/alerts/alerts.js", function() {
-        galert(['div#header', 'body > *:nth-child(1)'])
-    });</script>
-<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example_files/main.css" media="screen">
-<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example_files/blastRes.css" media="screen">
-<!--[if IE]>
-<link rel="stylesheet" type="text/css" href="css/descriptionsIE.css" media="screen" />
-<![endif]-->
-<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example_files/print.css" media="print">
-<!--[if lte IE 6]>
-<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
-<![endif]-->
-<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example_files/blastReq.css" media="screen">
-<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example_files/results.css" media="screen">
-<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example_files/dynFormatRes.css" media="screen">
-
-<style media="print" type="text/css">.print-log { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }.print-log li { list-style-image: url('/stat?jsevent=print&ncbi_app=blast&ncbi_pdid=blastresults&ncbi_phid=5AAB74D7368F2C81000000000000C9C8'); }</style><style type="text/css">.print-log { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }</style></head>
-
-<body id="type-a" class="noToggleCheck ">
-<div id="wrap">
-			<div id="header">
-		<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov/" title="NCBI Home Page"><img src="Blast%20output%20page%20example_files/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page"></a>BLAST <span id="trdm"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
-		</div>
-		<div id="search">
-
-<div>
-<script language="JavaScript" type="text/javascript"><!--
-// --></script><table class="medium1" style="border:2px solid #336699;" id="myncbi_off" cellpadding="2" cellspacing="0"><tbody><tr><td align="left" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td align="right" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img src="Blast%20output%20page%20example_files/myncbihelpicon.gif" alt="My NCBI help" border="0"></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to sign in" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Sign In]</a> <a href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to register for an account" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Register]</a></td></tr></tbody></table></div>
-		</div>
-		<a class="skp" href="#content-wrap">Jump to Page Content</a>
-		<ul id="nav">
-                <li class="first "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
-                <li class="recent "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&amp;RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
-                <li class="saved "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
-                <li class="last documentation "> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>
-                </ul>
-    </div>
-
-        <div id="content-wrap">
-
-                <div id="breadcrumb" class="inlineDiv">
-                   <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
-                   <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome">BLAST</a>/
-                   <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&amp;PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=">blastn suite</a>/
-                   <strong>Formatting Results - PHWP1JNZ014</strong>
-                </div>
-                <div class="inlineDiv resHeader resPage">
-
-                </div>
-                <ul class="print-log-res"><li></li></ul>
-
-                <!-- CDD info for old design -->
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-
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-                <div id="content">
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-                <!--<ul id="msg" class="msg"><li class="info"><p class=""></p><p class=""></p><p class=""></p></li></ul>-->
-                <ul id="msg" class="msg"><li class="info"><p class="info">Your search parameters were adjusted to search for a short input sequence.</p></li></ul>
-                <a href="#" class="resLink resPage" id="searchOptions" submitform="setSavedOptions">Edit and Resubmit</a>
-<a href="#" class="resLink resPage hidden" id="saveSearchOptions" submitform="saveOptions">Save Search Strategies</a>
-<span class="reslink  resPage">[Sign in above to save your search strategy]</span>
-<a aria-expanded="false" role="button" aria-disabled="false" id="showFormat" class="resLink resPage resArrowLinkB ui-ncbitoggler jig-ncbitoggler ui-widget" data-ncbitoggler-toggles="FormatForm" href="#">
-<span class="ui-ncbitoggler-master-text">Formatting options </span>
-<span class="ui-icon ui-icon-triangle-1-e"></span>
-</a>
-<a aria-expanded="false" role="button" aria-disabled="false" id="showDownload" class="resLink resPage resArrowLinkB jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="FormatDownload" href="#">
-<span class="ui-ncbitoggler-master-text">Download</span>
-<span class="ui-icon ui-icon-triangle-1-e"></span>
-</a>
-<span id="hnr">
-<a id="ytb" class="ytb " title="External link to YouTube" href="http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq" target="lnkPHWP1JNZ014">How to read this page</a>
-<a id="brFtp" class="" title="Blast report description" href="ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_NewBLAST.pdf" target="lnkPHWP1JNZ014">Blast report description</a>
-</span>
-                <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
-                <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden"><input name="ALIGNMENTS" value="100" type="hidden"><input name="ALIGNMENT_VIEW" value="Pairwise" type="hidden"><input name="BLAST_PROGRAMS" value="blastn" type="hidden"><input name="CLIENT" value="web" type="hidden"><input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden"><input name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden"><input name="DATABASE" value="pdb" type="hidden"><input name="DBTYPE" value="gc" type="hidden"><input name="DEFAULT_PROG" value="megaBlast" type="hidden"><input name="DESCRIPTIONS" value="100" type="hidden"><input name="DYNAMIC_FORMAT" value="on" type="hidden"><input name="EQ_OP" value="AND" type="hidden"><input name="EXPECT" value="1000" type="hidden"><input name="FORMAT_NUM_ORG" value="1" type="hidden"><input name="FORMAT_OBJECT" value="Alignment" type="hidden"><input name="FORMAT_TYPE" value="HTML" type="hidden"><input name="FULL_DBNAME" value="pdb" type="hidden"><input name="GAPCOSTS" value="5 2" type="hidden"><input name="GET_SEQUENCE" value="on" type="hidden"><input name="HSP_RANGE_MAX" value="0" type="hidden"><input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="LAYOUT" value="OneWindow" type="hidden"><input name="LINE_LENGTH" value="60" type="hidden"><input name="MASK_CHAR" value="2" type="hidden"><input name="MASK_COLOR" value="1" type="hidden"><input name="MATCH_SCORES" value="1,-3" type="hidden"><input name="MAX_NUM_SEQ" value="100" type="hidden"><input name="NUCL_PENALTY" value="-2" type="hidden"><input name="NUCL_REWARD" value="1" type="hidden"><input name="NUM_DIFFS" value="1" type="hidden"><input name="NUM_OPTS_DIFFS" value="0" type="hidden"><input name="NUM_ORG" value="1" type="hidden"><input name="NUM_OVERVIEW" value="100" type="hidden"><input name="OLD_BLAST" value="false" type="hidden"><input name="OLD_VIEW" value="false" type="hidden"><input name="PAGE" value="Nucleotides" type="hidden"><input name="PAGE_TYPE" value="BlastSearch" type="hidden"><input name="PROGRAM" value="blastn" type="hidden"><input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="QUERY_LENGTH" value="16" type="hidden"><input name="REPEATS" value="repeat_9606" type="hidden"><input name="RID" value="PHWP1JNZ014" type="hidden"><input name="RTOE" value="42" type="hidden"><input name="SEARCH_DB_STATUS" value="43" type="hidden"><input name="SELECTED_PROG_TYPE" value="megaBlast" type="hidden"><input name="SERVICE" value="plain" type="hidden"><input name="SHORT_QUERY_ADJUST" value="on" type="hidden"><input name="SHOW_LINKOUT" value="on" type="hidden"><input name="SHOW_OVERVIEW" value="on" type="hidden"><input name="USER_DEFAULT_MATCH_SCORES" value="0" type="hidden"><input name="USER_DEFAULT_PROG_TYPE" value="megaBlast" type="hidden"><input name="USER_TYPE" value="2" type="hidden"><input name="WORD_SIZE" value="7" type="hidden"><input name="_PGR" value="2" type="hidden"><input name="db" value="nucleotide" type="hidden"><input name="stype" value="nucleotide" type="hidden">
-                <input name="QUERY_INDEX" value="0" type="hidden">
-                <input name="_PGR" value="2" type="hidden">
-                <input id="seqViewUrl" value="http://www.ncbi.nlm.nih.gov/projects/sviewer" type="hidden">
-                <input name="CMD" value="Get" type="hidden">
-                </form>
-                <!-- Reformat and downlaod for new design -->
-                <div class="ui-helper-reset" aria-live="assertive">
-<form aria-hidden="true" action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="FormatForm" id="FormatForm" class="resbox ui-ncbitoggler-slave  ui-ncbitoggler">
-<table class="options blastn ">
-<tbody><tr>
-<td class="frh" colspan="2">
-<div class="fi">
-<div class="tb">Formatting options</div>
-<input id="onPageReformat" src="Blast%20output%20page%20example_files/reformat.jpg" class="blastbutton" alt="Reformat" mouseovimg="css/images/reformatOver.jpg" mouseoutimg="css/images/reformat.jpg" mousedownimg="css/images/reformatDown.jpg" mouseupimg="css/images/reformatOver.jpg" border="0" type="image">
-</div>
-</td></tr>
-<tr class="paramSet xgl">
-<td class="hd"><label for="FORMAT_OBJECT">Show</label></td>
-<td>
-<div class="fi">
-<input id="FORMAT_OBJECT" value="Alignment" name="FORMAT_OBJECT" type="hidden">
-<label for="FORMAT_TYPE" id="nft">Alignment as</label>
-<select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defval="HTML">
-<option value="HTML" selected="selected">HTML</option>
-<option value="Text">Plain text</option>
-
-</select>
-
-<span id="advView" class="">
-<span class=""><input name="OLD_VIEW" id="OLD_VIEW" class="cb reset" defval="unchecked" false="" type="checkbox">
-<label for="OLD_VIEW">Old View</label></span>
-</span>
-<a class="resetAll" id="resetAll">Reset form to defaults</a>
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments object formatting help" id="formatHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp1">
-These options control formatting of alignments in results pages. The
-default is HTML, but other formats (including plain text) are available.
-PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
-The Advanced view option allows the database descriptions to be sorted by various indices in a table.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a>
-</p>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-
-<tr class="odd paramSet">
-<td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td>
-<td>
-<div class="fi">
-<select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defval="Pairwise" class="reset">
-<option value="Pairwise" selected="selected">Pairwise</option>
-<option value="PairwiseWithIdentities">Pairwise with dots for identities</option>
-<option value="QueryAnchored">Query-anchored with dots for identities</option>
-<option value="QueryAnchoredNoIdentities">Query-anchored with letters for identities</option>
-<option value="FlatQueryAnchored">Flat query-anchored with dots for identities</option>
-<option value="FlatQueryAnchoredNoIdentities">Flat query-anchored with letters for identities</option>
-
-</select>
-
-
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments view options help" id="alnViewHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp2">
-Choose how to view alignments.
-The default "pairwise" view shows how each subject sequence aligns
-individually to the query sequence. The "query-anchored" view shows how
-all subject sequences align to the query sequence. For each view type,
-you can choose to show "identities" (matching residues) as letters or
-dots.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a>
-</p>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-
-<tr class="paramSet">
-<td class="hd"><label>Display</label></td>
-<td class="cb">
-<div class="fi">
-<input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" class="cb reset" defval="checked" checked="checked" type="checkbox">
-<label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label>
-
-<span class="hidden" id="shl">
-<input name="SHOW_LINKOUT" id="SHOW_LINKOUT" class="cb reset" defval="checked" checked="checked" type="checkbox">
-<label class="rb" for="SHOW_LINKOUT">Linkout</label>
-</span>
-<span class="hidden" id="gts">
-<input name="GET_SEQUENCE" id="GET_SEQUENCE" class="cb reset" defval="checked" checked="checked" type="checkbox">
-<label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label>
-</span>
-
-<input name="NCBI_GI" id="NCBI_GI" class="cb reset" defval="unchecked" type="checkbox">
-<label class="rb" for="NCBI_GI">NCBI-gi</label>
-<span id="scf">
-<input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" class="cb reset blastn" defval="unchecked" type="checkbox">
-<label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label>
-</span>
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments display options help" id="displayHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp3">
-<li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to  query.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a>
-</li>
-<li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin">more...</a>
-</li>
-<li>Sequence Retrieval: Show buttons to download matching sequences.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin">more...</a>
-</li>
-<li>NCBI-gi: Show NCBI gi identifiers.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin">more...</a>
-</li>
-<li>CDS feature: Show annotated coding region and translation.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin">more...</a>
-</li></ul>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-
-
-<tr class="paramSet odd xgl">
-<td class="hd"><label>Masking</label></td>
-<td>
-<div class="fi">
-<label for="MASK_CHAR"> Character: </label>
-<select name="MASK_CHAR" id="MASK_CHAR" class="reset" defval="2">
-<option value="0">X for protein, n for nucleotide</option>
-<option value="2" selected="selected">Lower Case</option>
-</select>
-<label for="MASK_COLOR"> Color:</label>
-<select name="MASK_COLOR" id="MASK_COLOR" class="reset" defval="1">
-<option value="0">Black
-</option>
-
-<option value="1" selected="selected">Grey
-</option>
-
-<option value="2">Red
-</option>
-
-</select>
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments masking help" id="maskingHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp4">
-<li>Masking Character: Display masked (filtered) sequence regions as
-lower-case or as specific letters (N for nucleotide, P for protein).
-</li>
-<li>Masking Color: Display masked sequence regions in the given color.</li>
-</ul>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-
-
-<tr id="lr" class="paramSet xgl">
-<td class="hd"><label>Limit results</label></td>
-<td>
-<div class="fi">
-<label for="FRM_DESCRIPTIONS">Descriptions:</label>
-<select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defval="100">
-
-<option value="10">10</option>
-<option value="50">50</option>
-<option value="100" selected="selected">100</option>
-
-
-
-
-
-
-</select>
-
-<label for="FRM_NUM_OVERVIEW">Graphical overview:</label>
-<select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defval="100">
-<option value="0">0</option>
-<option value="10">10</option>
-<option value="50">50</option>
-<option value="100" selected="selected">100</option>
-
-
-
-</select>
-<span class="hidden" id="frmAln">
-<label for="FRM_ALIGNMENTS">Alignments:</label>
-<select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defval="100">
-<option value="0">0</option>
-<option value="10">10</option>
-<option value="50">50</option>
-<option value="100" selected="selected">100</option>
-
-
-
-
-
-
-</select>
-</span>
-<label for="FRM_LINE_LENGTH">Line length:</label>
-<select name="LINE_LENGTH" id="FRM_LINE_LENGTH" class="reset" defval="60">
-<option value="60" selected="selected">60</option>
-<option value="90">90</option>
-<option value="120">120</option>
-<option value="150">150</option>
-</select>
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit number of descriptions/alignments help" id="numHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp5">
-<li>Descriptions: Show short descriptions for up to the given number of  sequences.</li>
-<li>Alignments:  Show alignments for up to the given number of sequences, in order of statistical significance.</li>
-<li>Line lenghth:  ....</li>
-</ul>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-
-<tr class="paramSet odd xgl ">
-<td class="hd"></td>
-<td>
-<div class="">
-<label for="qorganism">Organism</label>
-<span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br>
-<input role="textbox" aria-autocomplete="list" aria-haspopup="true" title="Use up and down arrows to choose an item from the autocomplete." name="FORMAT_ORGANISM" size="55" id="qorganism" value="Enter organism name or id--completions will be suggested" data-jigconfig="dictionary:'taxids_sg'" autocomplete="off" class="jig-ncbiautocomplete reset orgHint" type="text">
-<input name="FORMAT_ORG_EXCLUDE" class="oExclR cb" id="orgExcl" type="checkbox">
-<input value="1" name="FORMAT_NUM_ORG" id="numOrg" type="hidden">
-<label for="orgExcl" class="right">Exclude</label>
-<a href="#" title="Add organism" id="addOrg"><img src="Blast%20output%20page%20example_files/addOrg.jpg" id="addOrgIm" alt="Add organism" mouseovimg="css/images/addOrgOver.jpg" mouseoutimg="css/images/addOrg.jpg" mousedownimg="css/images/addOrgDown.jpg" mouseupimg="css/images/addOrgOver.jpg" border="0"></a>
-<div id="orgs">
-
-</div>
-<div class="fi">
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by organism help" id="organismHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp6">
-Show only sequences from the given organism.
-</p>
-</div><!-- ARIA -->
-</div>
-</div>
-</td>
-</tr>
-
-<tr class="paramSet xgl ">
-<td class="hd"></td>
-<td>
-<div class="fi">
-<label for="FORMAT_EQ_TEXT">Entrez query:</label>
-<input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" class="reset" type="text">
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by Entrez query help" id="entrezHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp7">
-Show only those sequences that match the given Entrez query.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#limit_result" target="helpWin" title="Additional limit results by Entrez query help">more...</a>
-</p>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-
-
-<tr class="paramSet odd xgl">
-<td class="hd"></td>
-<td>
-<div class="fi">
-<label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" class="reset" type="text">
-<label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" class="reset" type="text">
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by expect value range help" id="expectHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp8">
-Show only sequences with expect values in the given range.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect_range" target="helpWin" title="Additional limit results by expect value range help">more...</a>
-</p>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-<tr class="paramSet xgl">
-<td class="hd"></td>
-<td>
- <div class="fi">
-<label for="PERC_IDENT_LOW">Percent Identity Min:</label> <input name="PERC_IDENT_LOW" id="PERC_IDENT_LOW" size="10" class="reset" type="text">
-<label for="PERC_IDENT_HIGH">Percent Identity Max:</label> <input name="PERC_IDENT_HIGH" id="PERC_IDENT_HIGH" size="10" class="reset" type="text">
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by percent identity range help" id="percIdentHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp10">
- Show only sequences with percent identity values in the given range.
-</p>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-<tr class="psiBlast odd paramSet xgl">
-<td class="hd"><label>Format for</label></td>
-<td>
-<div class="fi">
-<input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" class="cb psiBlast" type="checkbox">
-<label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label>
-<label for="I_THRESH">with inclusion threshold:</label>
-<input name="I_THRESH" id="I_THRESH" size="10" defval="0.005" type="text">
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="PSI BLAST formatting help" id="psiHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-<div class="ui-helper-reset" aria-live="assertive">
-<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp9">
-<li>Format for PSI-BLAST: The Position-Specific Iterated BLAST
-(PSI-BLAST) program performs iterative searches with a protein query,
-in which sequences found in one round of search are used to build a
-custom score model for the next round.
-<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a>
-</li>
-<li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used
-by PSI-BLAST to create the PSSM on the next iteration.</li>
-</ul>
-</div><!-- ARIA -->
-</div>
-</td>
-</tr>
-</tbody></table>
-
-
-<input name="ViewReport" value="ViewReport" type="hidden">
-<input name="REFORMAT_REPORT" value="shown" type="hidden">
-<input name="RID" value="PHWP1JNZ014" type="hidden">
-<input name="CDD_RID" value="" type="hidden">
-<input name="CDD_SEARCH_STATE" value="" type="hidden">
-
-<input name="STEP_NUMBER" value="" id="stepNumber" type="hidden">
-<input name="CMD" value="Get" type="hidden">
-<input name="FORMAT_EQ_OP" value="AND" type="hidden">
-<input name="RESULTS_PAGE_TARGET" id="resPageTarget" value="" type="hidden">
-<!-- <input name="QUERY_INFO" type="hidden" value="Nucleotide Sequence (16 letters)" /> -->
-<!-- <input name="ENTREZ_QUERY" type="hidden" value="" /> -->
-<input name="QUERY_INDEX" value="0" type="hidden">
-<input name="NUM_QUERIES" value="1" type="hidden">
-<input name="PHI_PTTRN_INDEX" value="" type="hidden">
-<input id="cfcDsSave" name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden">
-<!-- Those params are set in the template (blastn.dat, blastp.dat etc. -->
-<input name="BLAST_PROGRAMS" value="blastn" type="hidden">
-<input name="PAGE" value="Nucleotides" type="hidden">
-<input name="PROGRAM" value="blastn" type="hidden">
-<input name="MEGABLAST" value="" type="hidden">
-<input name="RUN_PSIBLAST" value="" type="hidden">
-<input name="BLAST_SPEC" id="blastSpec" value="" type="hidden">
-
-
-<input name="QUERY" value="" type="hidden">
-<input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden">
-<input name="QUERY_TO" value="" type="hidden">
-<input name="QUERY_FROM" value="" type="hidden">
-<input name="EQ_TEXT" value="" type="hidden">
-<input name="ORGN" value="" type="hidden">
-<input name="EQ_MENU" value="" type="hidden">
-<input name="ORG_EXCLUDE" value="" type="hidden">
-<input name="PHI_PATTERN" value="" type="hidden">
-<input name="EXPECT" value="1000" type="hidden">
-<input name="DATABASE" value="pdb" type="hidden">
-<input name="DB_GROUP" value="" type="hidden">
-<input name="SUBGROUP_NAME" value="" type="hidden">
-
-<input name="GENETIC_CODE" value="" type="hidden">
-<input name="WORD_SIZE" value="7" type="hidden">
-<input name="MATCH_SCORES" value="1,-3" type="hidden">
-<input name="MATRIX_NAME" value="" type="hidden">
-<input name="GAPCOSTS" value="5 2" type="hidden">
-<input name="MAX_NUM_SEQ" id="maxNumSeq" value="100" type="hidden">
-<input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden">
-<input name="NEWWIN" value="" type="hidden">
-<input name="SHORT_QUERY_ADJUST" value="on" type="hidden">
-<input name="FILTER" value="" type="hidden">
-<input name="REPEATS" value="repeat_9606" type="hidden">
-<input name="ID_FOR_PSSM" value="" type="hidden">
-<input name="EXCLUDE_MODELS" value="" type="hidden">
-<input name="EXCLUDE_SEQ_UNCULT" value="" type="hidden">
-<input name="WP_PROTEINS" value="" type="hidden">
-<input name="SEQ_FROM_TYPE" value="" type="hidden">
-<input name="ENTREZ_QUERY_PRESET" value="" type="hidden">
-<input name="ENTREZ_QUERY_PRESET_EXCL" value="" type="hidden">
-<input name="NUM_ORG" value="1" type="hidden">
-
-<!-- PSSM -->
-<input name="LCASE_MASK" value="" type="hidden">
-<input name="TEMPLATE_TYPE" value="" type="hidden">
-<input name="TEMPLATE_LENGTH" value="" type="hidden">
-<input name="I_THRESH" value="" type="hidden">
-<input name="PSI_PSEUDOCOUNT" value="" type="hidden">
-<input name="DI_THRESH" id="diThresh" value="" type="hidden">
-<input name="HSP_RANGE_MAX" value="0" type="hidden">
-
-
-
-<input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden">
-<input name="MIXED_QUERIES" value="" type="hidden">
-<input name="MIXED_DATABASE" id="mixedDb" value="" type="hidden">
-<input name="BUILD_NAME" value="" type="hidden">
-<input name="ORG_DBS" value="" type="hidden">
-
-</form>
-</div> <!-- aria -->
-                <div class="ui-helper-reset" aria-live="assertive">
-<form aria-hidden="true" name="FormatDownload" id="FormatDownload" class="resbox ui-ncbitoggler-slave ui-ncbitoggler">
-<table class="options dwnl ">
-<tbody><tr><td class="frh" colspan="6"><div class="tb">Download</div></td></tr>
-<tr>
-<td id="tdal">
-<div class="dnHeader">Alignment</div>
-<div class="dnLinks">
-<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;DESCRIPTIONS=100&amp;ALIGNMENTS=100&amp;CMD=Get">Text</a>
-<a class="xgl" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=XML&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get">XML</a>
-<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get">ASN.1</a>
-<a id="hitText" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get">Hit Table(text)</a>
-<a id="hitCvs" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=CSV&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get">Hit Table(csv)</a>
-</div>
-</td>
-<td class="dnl xgl">
-<div class="dnHeader">Search Strategies</div>
-<div class="dnLinks">
-<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&amp;RECENT_RESULTS=on&amp;RID=PHWP1JNZ014&amp;DOWNLOAD_OPTIONS=true">ASN.1</a>
-</div>
-</td>
-<td class="dnl hidden" id="dnPSSMPar">
-<div class="dnHeader">PssmWithParameters</div>
-<div class="dnLinks">
-<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=PSSM_Scoremat&amp;CMD=Get">ASN.1</a>
-</div>
-</td>
-<td>
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Download help" data-ncbitoggler-toggles="hlp11" id="dnHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-</td>
-</tr>
-</tbody></table>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp11">
-  The Download link provides BLAST output that may be used as input to
-another program.
-  This includes parseable formats such as the tabular report or XML as
-well as the Search Strategy files read by the BLAST+ applications.
-  More details on the parseable (XML, tabular, and ASN.1) reports can be
- found at
-  <a href="http://www.ncbi.nlm.nih.gov/books/NBK21097/" target="helpWin">http://www.ncbi.nlm.nih.gov/books/NBK21097/</a><br>
-  <br>
-  The following formats are offered under the Alignment section:<br>
-    1). "Text". Non-HTML standard BLAST report.<br>
-
-    2). "XML". XML report based upon the DTD at <a href="http://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd" target="helpWin">http://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd</a><br>
-
-    3). "ASN.1" Alignment. This is the alignment written out in Abstract Syntax Notation 1.<br>
-
-    4). "Hit Table(text)". The tabular report as text.<br>
-
-    5). "Hit Table(csv)". The tabular report ready for import into spread-sheet programs like Excel.<br>
-  <br>
-  The following report is offered under the Search Strategy section:<br>
-
-  1). "ASN.1" Search Strategy. A record of the parameters, query, and
-database used in the search. This file can be used to start a
-stand-alone BLAST search, see
-  <a href="http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra" target="helpWin">http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra</a>
-</p>
-</div><!-- ARIA -->
-</form>
-</div> <!-- aria -->
-                <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" name="overview0">
-                <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden"><input name="ALIGNMENTS" value="100" type="hidden"><input name="ALIGNMENT_VIEW" value="Pairwise" type="hidden"><input name="BLAST_PROGRAMS" value="blastn" type="hidden"><input name="CLIENT" value="web" type="hidden"><input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden"><input name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden"><input name="DATABASE" value="pdb" type="hidden"><input name="DBTYPE" value="gc" type="hidden"><input name="DEFAULT_PROG" value="megaBlast" type="hidden"><input name="DESCRIPTIONS" value="100" type="hidden"><input name="DYNAMIC_FORMAT" value="on" type="hidden"><input name="EQ_OP" value="AND" type="hidden"><input name="EXPECT" value="1000" type="hidden"><input name="FORMAT_NUM_ORG" value="1" type="hidden"><input name="FORMAT_OBJECT" value="Alignment" type="hidden"><input name="FORMAT_TYPE" value="HTML" type="hidden"><input name="FULL_DBNAME" value="pdb" type="hidden"><input name="GAPCOSTS" value="5 2" type="hidden"><input name="GET_SEQUENCE" value="on" type="hidden"><input name="HSP_RANGE_MAX" value="0" type="hidden"><input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="LAYOUT" value="OneWindow" type="hidden"><input name="LINE_LENGTH" value="60" type="hidden"><input name="MASK_CHAR" value="2" type="hidden"><input name="MASK_COLOR" value="1" type="hidden"><input name="MATCH_SCORES" value="1,-3" type="hidden"><input name="MAX_NUM_SEQ" value="100" type="hidden"><input name="NUCL_PENALTY" value="-2" type="hidden"><input name="NUCL_REWARD" value="1" type="hidden"><input name="NUM_DIFFS" value="1" type="hidden"><input name="NUM_OPTS_DIFFS" value="0" type="hidden"><input name="NUM_ORG" value="1" type="hidden"><input name="NUM_OVERVIEW" value="100" type="hidden"><input name="OLD_BLAST" value="false" type="hidden"><input name="OLD_VIEW" value="false" type="hidden"><input name="PAGE" value="Nucleotides" type="hidden"><input name="PAGE_TYPE" value="BlastSearch" type="hidden"><input name="PROGRAM" value="blastn" type="hidden"><input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="QUERY_LENGTH" value="16" type="hidden"><input name="REPEATS" value="repeat_9606" type="hidden"><input name="RID" value="PHWP1JNZ014" type="hidden"><input name="RTOE" value="42" type="hidden"><input name="SEARCH_DB_STATUS" value="43" type="hidden"><input name="SELECTED_PROG_TYPE" value="megaBlast" type="hidden"><input name="SERVICE" value="plain" type="hidden"><input name="SHORT_QUERY_ADJUST" value="on" type="hidden"><input name="SHOW_LINKOUT" value="on" type="hidden"><input name="SHOW_OVERVIEW" value="on" type="hidden"><input name="USER_DEFAULT_MATCH_SCORES" value="0" type="hidden"><input name="USER_DEFAULT_PROG_TYPE" value="megaBlast" type="hidden"><input name="USER_TYPE" value="2" type="hidden"><input name="WORD_SIZE" value="7" type="hidden"><input name="_PGR" value="2" type="hidden"><input name="db" value="nucleotide" type="hidden"><input name="stype" value="nucleotide" type="hidden">
-                <input name="CMD" value="Get" type="hidden">
-                <p id="qb"><!--
-QBlastInfoBegin
-	Status=READY
-QBlastInfoEnd
---></p>
-<div id="page">
-
-<div id="summary" class="">
-<div id="ht"></div>
-<h1>Nucleotide Sequence (16 letters) <span id="hdTitle" class="shownInl"></span></h1>
-<div>
-<div id="multipleSeqs" class="hidden">
-<label for="queryList">Results for:</label>
-<select id="queryList" name="queryList">
-<option value="0" selected="selected" class="">lcl|59987 None(16bp)</option>
-</select>
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="queryInfo" title="Multiple quries help" id="queryHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a>
-</div><!--/#multipleSeqs"-->
-
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" id="queryInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
-Your BLAST job specified more than one input sequence.
-This box lets you choose which input sequence to show BLAST results for.
-</p>
-</div><!-- ARIA -->
-</div>
-<div id="summarylists">
-<dl>
-<dt>RID</dt>
-<dd>
-<a title="BLAST search request ID" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014">PHWP1JNZ014</a> (Expires on 05-07 22:33 pm)
-</dd>
-</dl>
-<div id="querysummary">
-<dl>
-<dt>Query ID</dt>
-<dd class="hidden">
-<a title="Find query in Entrez" href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&amp;db=nucleotide&amp;term=59987&amp;dopt=GenBank" target="lnkPHWP1JNZ014">lcl|59987</a>
-</dd>
-<dd class="">lcl|59987</dd>
-<dt>Description</dt>
-<dd>None</dd>
-<dt>Molecule type</dt>
-<dd>nucleic acid</dd>
-<dt>Query Length</dt>
-<dd>16</dd>
-</dl>
-</div><!--/#querysummary-->
-
-<div id="dbsummary">
-<dl>
-<dt>   </dt><dd>   </dd>
-<dt>Database Name</dt>
-<dd>pdb</dd>
-<dt>Description</dt>
-<dd>PDB nucleotide database <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="See multiple databases detailed information" class="jtg resArrowLinkB hidden  jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="dbDetails" id="showDetails"><span class="ui-ncbitoggler-master-text">See details</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd> <!-- -- Database or subject info ---->
-<dt class="xgl">Program</dt>
-<dd class="xgl">BLASTN 2.2.29+ <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="How to cite BLAST in publications" class="resArrowLinkB hidden shown jig-ncbitoggler ui-ncbitoggler jtg ui-widget" data-ncbitoggler-toggles="refInfo" id="showRefs"><span class="ui-ncbitoggler-master-text">Citation</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd>
-</dl>
-</div><!--/#dbsummary-->
-</div><!--/#summarylists -->
-<br>
-<div class="ui-helper-reset" aria-live="assertive">
-<div aria-hidden="true" id="dbDetails" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
- <!-- multiple databases or subjects table -->
-</div>
-</div> <!-- aria end -->
-<div class="ui-helper-reset" aria-live="assertive">
-<div aria-hidden="true" id="refInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
-<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Retrieve&amp;list_uids=9254694&amp;dopt=Citation">Reference </a>
-<div>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer,
-Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
-"Gapped BLAST and PSI-BLAST: a new generation of protein database search
- programs", Nucleic Acids Res. 25:3389-3402.</div>
- </div>  <!-- refInfo -->
-</div> <!-- aria end -->
-
-<div id="seealso">
-<label>Other reports:</label>
- <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="Show statistics" class="resArrowLinkB jtg jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="resStat" id="showStat"><span class="ui-ncbitoggler-master-text">Search Summary</span><span class="ui-icon ui-icon-triangle-1-e"></span></a>
- <span class="xgl">
- <a id="tax" class="hidden shown" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=PHWP1JNZ014&amp;FORMAT_OBJECT=TaxBlast&amp;NCBI_GI=off&amp;DESCRIPTIONS=100&amp;ALIGNMENTS=100&amp;FORMAT_BLOCK_ON_RESPAGE=Top&amp;MASK_COLOR=1&amp;MASK_CHAR=2" target="lnkPHWP1JNZ014" title="See results arranged by taxonomy">[Taxonomy reports]</a>
- <a href="http://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl%7C59987&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;ns=100" class="" id="TreeViewlcl|59987" onclick="ViewTree('TreeViewlcl|59987');return false;" target="lnkPHWP1JNZ014" title="See a distance tree of these pairwise comparisons">[Distance tree of results]</a>
-
-
-
- </span>
-</div> <!-- seealso -->
-
-<div class="ui-helper-reset" aria-live="assertive">
-<div aria-hidden="true" id="resStat" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
- <table id="params" class="dbInfo">
- <caption>Search Parameters</caption>
- <tbody><tr><th><div>Search parameter name</div></th><th><div>Search parameter value</div></th></tr>
- <tr><td>Program</td><td>blastn</td></tr><tr><td>Word size</td><td>7</td></tr><tr><td>Expect value</td><td>1000</td></tr><tr><td>Hitlist size</td><td>100</td></tr><tr><td>Match/Mismatch scores</td><td>1,-3</td></tr><tr><td>Gapcosts</td><td>5,2</td></tr><tr><td>Filter string </td><td>F</td></tr><tr><td>Genetic Code</td><td>1</td></tr>
- </tbody></table>
-  <table id="dbStat" class="dbInfo">
- <caption>Database</caption>
- <tbody><tr><th><div>Database parameter name</div></th><th><div>Database parameter value</div></th></tr>
- <tr><td>Posted date</td><td>Apr 29, 2014  3:14 AM</td></tr>
- <tr><td>Number of letters</td><td>885,284</td></tr>
- <tr><td>Number of sequences</td><td>8,975</td></tr>
- <tr><td>Entrez query</td><td>none</td></tr>
- </tbody></table>
-
- <table id="Kappa" class="dbInfo show xgl">
-<caption>Karlin-Altschul statistics</caption>
- <tbody><tr><th><div>Params</div></th><th><div>Ungapped</div></th><th><div>Gapped</div></th></tr>
- <tr><td>Lambda</td><td>1.37406</td><td>1.37406</td></tr>
- <tr><td>K</td><td>0.710603</td><td>0.710603</td></tr>
- <tr><td>H</td><td>1.30725</td><td>1.30725</td></tr>
-
- </tbody></table>
-
-
- <table class="dbInfo show">
- <caption>Results Statistics</caption>
- <tbody><tr><th><div>Results Statistics parameter name</div></th><th><div>Results Statistics parameter value</div></th></tr>
- <tr><td>Length adjustment</td><td> 11</td></tr><tr><td>Effective length of query</td><td> 5</td></tr><tr><td>Effective length of database</td><td> 786559</td></tr><tr><td>Effective search space</td><td> 3932795</td></tr><tr><td>Effective search space used</td><td> 3932795</td></tr>
- </tbody></table>
- <!-- Results statistics -->
- </div>  <!-- resStat -->
- </div> <!-- aria end -->
-</div><!--/#summary-->
-</div><!--/#page-->
-<iframe id="RSIFrameDesc" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="Blast%20output%20page%20example_files/plinkcgi.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe>
-
-<div id="grView" class="hidden shown">
-<h2 class="resArr">
-<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showGraphic" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="graphicInfo" title="Show/hide Graphic Summary">
-<span class="ui-ncbitoggler-master-text">Graphic Summary</span>
-<span class="ui-icon ui-icon-plus-minus-big-open"></span>
-</a>
-</h2>
-<div class="ui-helper-reset" aria-live="assertive">
-<div aria-hidden="false" id="graphicInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
-
-
-<div id="graphic" class="hidden shown">
-<h3>Distribution of 45 Blast Hits on the Query Sequence
-<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Graphic summary help" id="grHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
-<span class="ui-icon ui-icon-triangle-1-e"></span></a></h3>
-<div class="ui-helper-reset" aria-live="assertive">
-<p aria-hidden="true" id="ovrInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
-An overview of the database sequences aligned to the query sequence is
-shown. The score of each alignment is indicated by one of five
-different colors, which divides the range of scores into five groups.
-Multiple alignments on the same database sequence are connected
-by a striped line. <span class="hl">Mousing over</span> a hit sequence causes the definition and score to be shown in the window at the top,
-<span class="hl">clicking</span> on a hit sequence takes the user to the associated alignments.
-New:
-This graphic is an overview of database sequences aligned to the query sequence.
-Alignments are color-coded by score, within one of five score ranges.
-Multiple alignments on the same database sequence are connected by a dashed line.
-<span class="hl">Mousing</span> over an alignment shows the alignment definition and score in the box at the top.
-<span class="hl">Clicking</span> an alignment displays the alignment detail.
-</p>
-</div><!-- ARIA -->
-<center><input name="defline" size="85" value="Mouse-over to show defline and scores, click to show alignments" type="text"><table bordercolordark="#0000FF" bordercolorlight="#0000FF" border="1" cellpadding="10" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/score.gif" height="40" width="500"></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/query_no_scale.gif" height="10" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="51"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/scale.gif" height="10" width="2"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="91"></td>
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-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/scale.gif" height="10" width="2"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="91"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/scale.gif" height="10" width="2"></td>
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-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/scale.gif" height="10" width="2"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="91"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/scale.gif" height="10" width="2"></td>
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-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="83"></td>
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-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="83"></td>
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-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="73"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/1.gif" height="13" width="10"></td>
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-<td align="LEFT" valign="CENTER"><a href="#557804451" onclick='DisplayAlignFromGraphics("557804451",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J5A_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="500"></a></td>
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-<td align="LEFT" valign="CENTER"><a href="#557804283" onclick='DisplayAlignFromGraphics("557804283",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J54_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="500"></a></td>
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-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><a href="#557804227" onclick='DisplayAlignFromGraphics("557804227",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J52_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="500"></a></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><a href="#557804195" onclick='DisplayAlignFromGraphics("557804195",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J51_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="500"></a></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><a href="#557804163" onclick='DisplayAlignFromGraphics("557804163",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J50_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="500"></a></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><a href="#557804083" onclick='DisplayAlignFromGraphics("557804083",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J4X_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="500"></a></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="250"></a></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/black.gif" height="6" width="1"></td>
-<td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=18 E=12'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="124"></a></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/black.gif" height="6" width="1"></td>
-<td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="124"></a></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 14" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=14 E=1.9e+02'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="219"></a></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/black.gif" height="6" width="1"></td>
-<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=18 E=12'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="155"></a></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/black.gif" height="6" width="1"></td>
-<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=16 E=47'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="124"></a></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="50"></td>
-<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="94"></td>
-<td align="LEFT" valign="CENTER"><a href="#357380483" onclick='DisplayAlignFromGraphics("357380483",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J0O_8 Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex .. S=18 E=12'" src="Blast%20output%20page%20example_files/black.gif" height="4" border="0" width="281"></a></td>
-</tr></tbody></table>
-<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
-</td></tr></tbody></table>
-</center><hr>
-</div><!--/#graphic-->
-</div><!-- graphicInfo -->
-</div><!-- ARIA -->
-</div>
-<!--HITMATRIX_VIEW - only for bl2seq -->
-
-<div id="dscrView" class="hidden shown">
-<h2 class="resArr">
-<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showDescr" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="descrInfo" title="Show/hide Descriptions">
-<span class="ui-ncbitoggler-master-text">Descriptions</span>
-<span class="ui-icon ui-icon-plus-minus-big-open"></span>
-</a>
-</h2>
-<div class="ui-helper-reset" aria-live="assertive">
-<div aria-hidden="false" id="descrInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
- <!-- legend to links to other resources -->
-<a name="sort_mark"></a>
-
-
-<div id="debug">, Reading indexes 1-5, displaying indexes 1-5</div>
-<input id="Rid" value="PHWP1JNZ014" type="hidden">
-<input id="useAlignDB" name="useAlignDB" value="" type="hidden">
-<input id="dbType" value="GenBank" type="hidden"><!-- Indicates genbank, etc -->
-<input id="serviceType" value="plain" type="hidden">
-<input id="clientType" value="web" type="hidden">
-<input id="currQuery" value="" type="hidden">
-<input id="minDispAlnLen" value="2000" type="hidden">
-<input id="maxDispAlnLen" value="20000" type="hidden">
-<div class="hidden" id="dynHspTmpl"><div class="alnParLinks moreHsps" id="@moreHspsID@"><a class="gbd toolsCtr navNext" title="Load matches @segs@ out of @totalHSP@ for @accs@" onmouseover="scan(this)" ref="range=@segs@&amp;currseq=@alnSeqGi@" onclick="ReadNextHSPSet(@argstring@);"><span>Load next set</span></a><a class="gbd toolsCtr navPrev" title="Go to previous match #@aln_prev_num@ for @accs@" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a></div></div>
-<div id="descriptions" class="blRes">
-<!--<pre> -->
-<div class="cap">Sequences producing significant alignments:</div>
-<a id="shcl" href="#" onclick="showAllCol(event,this)" class="shcl hidden">
-Show all columns <span class="accsb"> of the table presenting sequences producing significant alignments </span>
-</a>
-<span id="cntDesc">
-<span>Select:<a href="#" id="cntSelA" sel="all">All</a><a href="#" id="cntSelN" sel="n">None</a></span>
-<span>Selected:<span id="slcNum">0</span></span>
-</span>
-
-<div id="descTblCtrl" class="cnf">
-<a href="#alignInfo" id="alnNav" class="toolsCtr alnNav" title="Go to alignments"><span>Alignments</span></a>
-<a aria-haspopup="true" aria-expanded="false" role="button" href="#dsDownload" minslct="1" class="jig-ncbipopper toolsCtr dnld dialog " data-jigconfig="hasArrow:'true',arrowDirection:'top'" id="dscDwnld" disabled="disabled" title="Download information for selected sequences"><span>Download</span></a>
-
-<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsDownload" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
-<div class=""><input name="dwn" checked="checked" id="dwFST" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST">FASTA (complete sequence)</label></div>
-<div class=""><input name="dwn" id="dwFSTAl" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl">FASTA (aligned sequences)</label></div>
-<div class=""><input name="dwn" id="dwGenBank" getgi="on" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class=" shownInl" for="dwGenBank">GenBank (complete sequence)</label></div>
-<div><input name="dwn" id="dwHitText" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get" type="radio"><label class="shownInl" for="dwHitText">Hit Table (text)</label></div>
-<div><input name="dwn" id="dwHitCsv" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=CSV&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get" type="radio"><label class="shownInl" for="dwHitCsv">Hit Table (CSV)</label></div>
-<div><input name="dwn" id="dwText" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get" type="radio"><label class="shownInl" for="dwText">Text</label></div>
-<div><input name="dwn" id="dwXML" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=XML&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get" type="radio"><label class="shownInl" for="dwXML">XML</label></div>
-<div><input name="dwn" id="dwASN" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get" type="radio"><label class="shownInl" for="dwASN">ASN.1</label></div>
-<div>
-<button class="cfg" id="dw_cont">Continue</button>
-<button class="cfg cnc">Cancel</button>
-</div>
-</div> <!-- dsDownload -->
-
-
-
-
-
-<a href="#" class="toolsCtr" minslct="1" view="dflt" frm="submitterTop" seqlist="selSeqs" title="See genbank report for selected sequences" disabled="disabled">GenBank</a> <!-- genbank or Traces -->
-<a href="#" class="toolsCtr " minslct="1" view="graph" title="See graphic representation for selected sequences" disabled="disabled">Graphics</a>
-<a href="#" class="toolsCtr hidden shown" view="tree" minslct="1" frm="sbmtTreeView" seqlist="selSeqsTr" disabled="disabled" title="See a distance tree of pairwise comparisons for the selected sequences">Distance tree of results</a>
-<a href="#" class="toolsCtr hidden " view="dflt" minslct="2" frm="sbmtMultiAln" seqlist="selSeqsMl" disabled="disabled" title="See multple alignment of query and target sequences for the selected sequences with expect value better than 0.001">Multiple alignment</a>
-
-<a aria-haspopup="true" aria-expanded="false" role="button" class="jig-ncbipopper button_config" title="Show/hide columns" id="button_config" href="#dsConfig"><span class="accsb">Show/hide columns of the table presenting sequences producing significant alignments </span></a>
-
-<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsConfig" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
-<div class="tl">Available columns</div>
-<input checked="checked" id="chkDs" value="2" type="checkbox"><label class="shownInl" for="chkDs">Description</label><br>
-<input checked="checked" id="chkMS" value="3" type="checkbox"><label class="shownInl" for="chkMs">Max Score</label><br>
-<input checked="checked" id="chkTS" value="4" type="checkbox"><label class="shownInl" for="chkTs">Total Score</label><br>
-<input checked="checked" id="chkCov" value="5" type="checkbox"><label class="shownInl" for="chkCov">Coverage</label><br>
-<input checked="checked" id="chkEval" value="6" type="checkbox"><label class="shownInl" for="chkEval">E-value</label><br>
-<input checked="checked" id="chkIdnt" value="7" type="checkbox"><label class="shownInl" for="chkIdnt"><span class="">Ident</span><span class="hidden">N</span></label><br>
-<input checked="checked" id="chkAcc" value="8" type="checkbox"><label class="shownInl" for="chkAcc">Accession</label><br>
-<button class="cfg rdf" id="dscRsDf">Restore Defaults</button>
-<button class="cfg" id="dscOk">Ok</button>
-<button class="cfg cnc" id="dscCnc">Cancel</button>
-</div> <!-- dsConfig -->
-
-<input id="cfcDsInf" defval="2,3,4,5,6,7,8" value="2,3,4,5,6,7,8" type="hidden">
-</div>
-<div class="ui-ncbigrid-outer-div caption-exists">
-<div class="ui-ncbigrid-inner-div">
-<table id="dscTable" class="jig-ncbigrid  ui-ncbigrid" data-jigconfig="" cellpadding="0" cellspacing="0">
-<caption class="hdnHeader">Sequences producing significant alignments:</caption>
-<thead>
-<tr class="first">
-  <th class="c0" id="c0"><span>Select for downloading or viewing reports</span></th>
-  <th class="dflnDth c2" id="c2">Description</th>
-  <th class=" c3" id="c3">
-
-  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=1&amp;HSP_SORT=1" class="dcs" title="Sort by max score">Max score</a>
-  </th>
-  <th class=" c4" id="c4">
-  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=2&amp;HSP_SORT=1" class="dcs" title="Sort by total score">Total score</a>
-  </th>
-  <th class=" c5" id="c5">
-  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=4&amp;HSP_SORT=0" class="dcs" title="Sort by query coverage">Query cover</a>
-  </th>
-  <th class="sel c6" id="c6">
-  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=0&amp;HSP_SORT=0" class="dcs" title="Sort by E value">E value</a>
-  </th>
-  <th class="c7" id="c7">
-<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;DISPLAY_SORT=3&amp;HSP_SORT=3" class="dcs" title="Sort by ident">Ident</a>
-</th>
-
-  <th class="c1" id="c8">Accession</th>
-</tr>
-</thead>
-<tbody>
-<tr id="dtr_557804451" ind="1" class="odd dflLnk">
-<td class="l c0"><span class="ind">1</span><input id="chk_1" class="cb" name="getSeqGi" value="557804451" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_1" class="accsb">Select seq pdb|3J5A|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="1" accs="pdb|3J5A|A" seqfsta="gi|557804451" gi="557804451" seqid="557804451" id="deflnDesc_1" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804451">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nucltop&amp;blast_rank=1&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J5A_A">3J5A_A</a>
-</td>
-</tr><tr id="dtr_557804395" ind="2" class="even dflLnk">
-<td class="l c0"><span class="ind">2</span><input id="chk_2" class="cb" name="getSeqGi" value="557804395" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_2" class="accsb">Select seq pdb|3J58|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="2" accs="pdb|3J58|A" seqfsta="gi|557804395" gi="557804395" seqid="557804395" id="deflnDesc_2" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804395">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nucltop&amp;blast_rank=2&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J58_A">3J58_A</a>
-</td>
-</tr><tr id="dtr_557804339" ind="3" class="odd dflLnk">
-<td class="l c0"><span class="ind">3</span><input id="chk_3" class="cb" name="getSeqGi" value="557804339" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_3" class="accsb">Select seq pdb|3J56|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="3" accs="pdb|3J56|A" seqfsta="gi|557804339" gi="557804339" seqid="557804339" id="deflnDesc_3" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804339">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nucltop&amp;blast_rank=3&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J56_A">3J56_A</a>
-</td>
-</tr><tr id="dtr_557804283" ind="4" class="even dflLnk">
-<td class="l c0"><span class="ind">4</span><input id="chk_4" class="cb" name="getSeqGi" value="557804283" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_4" class="accsb">Select seq pdb|3J54|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="4" accs="pdb|3J54|A" seqfsta="gi|557804283" gi="557804283" seqid="557804283" id="deflnDesc_4" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804283">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nucltop&amp;blast_rank=4&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J54_A">3J54_A</a>
-</td>
-</tr><tr id="dtr_557804227" ind="5" class="odd dflLnk">
-<td class="l c0"><span class="ind">5</span><input id="chk_5" class="cb" name="getSeqGi" value="557804227" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_5" class="accsb">Select seq pdb|3J52|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="5" accs="pdb|3J52|A" seqfsta="gi|557804227" gi="557804227" seqid="557804227" id="deflnDesc_5" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804227">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nucltop&amp;blast_rank=5&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J52_A">3J52_A</a>
-</td>
-</tr><tr id="dtr_557804195" ind="6" class="even dflLnk">
-<td class="l c0"><span class="ind">6</span><input id="chk_6" class="cb" name="getSeqGi" value="557804195" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_6" class="accsb">Select seq pdb|3J51|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="6" accs="pdb|3J51|A" seqfsta="gi|557804195" gi="557804195" seqid="557804195" id="deflnDesc_6" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804195">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804195?report=genbank&amp;log$=nucltop&amp;blast_rank=6&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J51_A">3J51_A</a>
-</td>
-</tr><tr id="dtr_557804163" ind="7" class="odd dflLnk">
-<td class="l c0"><span class="ind">7</span><input id="chk_7" class="cb" name="getSeqGi" value="557804163" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_7" class="accsb">Select seq pdb|3J50|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="7" accs="pdb|3J50|A" seqfsta="gi|557804163" gi="557804163" seqid="557804163" id="deflnDesc_7" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804163">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804163?report=genbank&amp;log$=nucltop&amp;blast_rank=7&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J50_A">3J50_A</a>
-</td>
-</tr><tr id="dtr_557804083" ind="8" class="even dflLnk">
-<td class="l c0"><span class="ind">8</span><input id="chk_8" class="cb" name="getSeqGi" value="557804083" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_8" class="accsb">Select seq pdb|3J4X|A</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="8" accs="pdb|3J4X|A" seqfsta="gi|557804083" gi="557804083" seqid="557804083" id="deflnDesc_8" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804083">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)</a>
-</div>
-</td>
-<td class="c3">32.2</td>
-<td class="c4">77.3</td>
-<td class="c5">100%</td>
-<td class="c6">8e-04</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804083?report=genbank&amp;log$=nucltop&amp;blast_rank=8&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J4X_A">3J4X_A</a>
-</td>
-</tr><tr id="dtr_485601478" ind="9" class="odd dflLnk">
-<td class="l c0"><span class="ind">9</span><input id="chk_9" class="cb" name="getSeqGi" value="485601478" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_9" class="accsb">Select seq pdb|3J3F|5</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a title="Go to alignment for Chain 5, Structure Of The H. Sapiens 60s Rrna" class="deflnDesc" hsp="8" len="63" ind="9" accs="pdb|3J3F|5" seqfsta="gi|485601478" gi="485601478" seqid="485601478" id="deflnDesc_9" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601478">Chain 5, Structure Of The H. Sapiens 60s Rrna</a>
-</div>
-</td>
-<td class="c3">18.3</td>
-<td class="c4">  128</td>
-<td class="c5">100%</td>
-<td class="c6">   12</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601478?report=genbank&amp;log$=nucltop&amp;blast_rank=9&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3F_5">3J3F_5</a>
-</td>
-</tr><tr id="dtr_485601474" ind="10" class="even dflLnk">
-<td class="l c0"><span class="ind">10</span><input id="chk_10" class="cb" name="getSeqGi" value="485601474" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_10" class="accsb">Select seq pdb|3J3E|5</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a title="Go to alignment for Chain 5, Structure Of The D. Melanogaster 60s Rrna" class="deflnDesc" hsp="4" len="31" ind="10" accs="pdb|3J3E|5" seqfsta="gi|485601474" gi="485601474" seqid="485601474" id="deflnDesc_10" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601474">Chain 5, Structure Of The D. Melanogaster 60s Rrna</a>
-</div>
-</td>
-<td class="c3">18.3</td>
-<td class="c4">63.4</td>
-<td class="c5">100%</td>
-<td class="c6">   12</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601474?report=genbank&amp;log$=nucltop&amp;blast_rank=10&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3E_5">3J3E_5</a>
-</td>
-</tr><tr id="dtr_357380483" ind="11" class="odd dflLnk">
-<td class="l c0"><span class="ind">11</span><input id="chk_11" class="cb" name="getSeqGi" value="357380483" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_11" class="accsb">Select seq pdb|3J0O|8</label></td>
-<td class="lim l c2">
-<div class="lim n">
-<a title="Go to alignment for Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2" class="deflnDesc" hsp="1" len="9" ind="11" accs="pdb|3J0O|8" seqfsta="gi|357380483" gi="357380483" seqid="357380483" id="deflnDesc_11" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_357380483">Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2</a>
-</div>
-</td>
-<td class="c3">18.3</td>
-<td class="c4">18.3</td>
-<td class="c5">56%</td>
-<td class="c6">   12</td><td class="c7">100%</td>
-<td class="c1 l lim">
-<a href="http://www.ncbi.nlm.nih.gov/nucleotide/357380483?report=genbank&amp;log$=nucltop&amp;blast_rank=11&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J0O_8">3J0O_8</a>
-</td>
-</tr>
-</tbody>
-</table>
-</div></div>
-<!--</pre>  -->
-</div><!--/#descriptions-->
-</div><!-- descrInfo -->
-</div><!--ARIA-->
-</div>
-</form><!-- this is the end tag for the <form in blastcgi templates -->
-<form id="dwdlSubmit" action="" method="post" class="getseq">
-<input name="" value="" id="selDnSeqs" type="hidden">
-</form>
-<form class="getseq" method="post" seqsform="getSeqAlignment1" action="http://www.ncbi.nlm.nih.gov/sites/entrez" target="lnkPHWP1JNZ014" id="submitterTop">
-<input name="db" value="Nucleotide" type="hidden">
-<input id="selSeqs" name="term" value="" type="hidden">
-<input name="doptcmdl" value="docsum" type="hidden">
-<input name="cmd" value="search" type="hidden">
-</form>
-<form class="getseq" method="get" action="http://www.ncbi.nlm.nih.gov/projects/sviewer/" target="lnkPHWP1JNZ014" id="sbmtGraphics">
-<input id="ridParam" value="PHWP1JNZ014" type="hidden">
-<input id="seqViewParams" name="RID" value="" type="hidden">
-<input name="appname" value="ncbiblast" type="hidden">
-<input name="link_loc" value="fromDescr" type="hidden">
-<input name="tracks" value="[key:sequence_track,ShowLabel:true]" type="hidden">
-<input name="id" value="" type="hidden">
-</form>
-<form class="getseq" method="post" action="http://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl|59987&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;ns=100" id="sbmtTreeView" target="lnkPHWP1JNZ014">
-<input id="selSeqsTr" name="sequenceSet" value="" type="hidden">
-<input id="scrWidth" name="screenWidth" value="" type="hidden">
-<input id="scrHeight" name="screenHeight" value="" type="hidden">
-</form>
-<form class="getseq" method="post" action="?CMD=submit&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl|59987&amp;numSeqs=100" id="sbmtMultiAln" target="lnkPHWP1JNZ014">
-<input id="selSeqsMl" name="sequenceSet" value="" type="hidden">
-</form>
-<form class="getseq" enctype="text/plain" method="post" action="http://blast.ncbi.nlm.nih.gov/blast/SEQDUMP/seqdump.cgi" id="sbmtFASTA">
-<input name="RID" value="PHWP1JNZ014" type="hidden">
-<input name="DATABASE" value="" type="hidden">
-<input name="ALIGNDB_BATCH_ID" value="" type="hidden">
-<input name="ALIGNDB_MASTER_ALIAS" value="" type="hidden">
-<input name="ALIGNDB_CGI_HOST" value="" type="hidden">
-<input name="ALIGNDB_CGI_PATH" value="" type="hidden">
-<input name="SERVICE_TYPE" value="plain" type="hidden">
-<input name="DBTYPE" value="nucl" type="hidden">
-<input name="DOWNLOAD_TYPE" value="" type="hidden">
-<input name="ALIGN_SEQ_LIST" value="" type="hidden">
-</form><!-- used in redesign -->
-<iframe id="RSIFrameAln" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="Blast%20output%20page%20example_files/plinkcgi_002.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe>
-<div id="alignView" class=" ">
-<h2 class="resArr">
-<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showAlign" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="alignInfo" title="Show/hide Alignments">
-<span class="ui-ncbitoggler-master-text">Alignments</span>
-<span class="ui-icon ui-icon-plus-minus-big-open"></span>
-</a>
-</h2>
-
-<div class="ui-helper-reset" aria-live="assertive">
-<div aria-hidden="false" id="alignInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
-<div id="alignments" class="blRes">
-<span id="alnStart"></span><div seqlist="gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227" indexes="1-5" id="alnShow_1" class="alnMsg"><div class="alnMsgS hidden" id="alnMsg_1">Loading alignment...<span class="db"> for sequences gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227 Reading indexes 1-5</span></div><div id="alnShowReal_1" class="alnMsgR"><form name="getSeqAlignment1">
-<div class="alnHdr cnf" id="alnHdr_557804451" seqid="557804451" accs="pdb|3J5A|A">
-<a name="557804451"></a>
-<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804451" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804451" title="Download information for pdb|3J5A|A"><span>Download</span></a>
-<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804451" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
-<div><input seqfsta="gi|557804451" name="dwn_557804451" checked="checked" id="dwFST_557804451" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804451">FASTA (complete sequence)</label></div>
-<div><input seqfsta="gi|557804451" name="dwn_557804451" id="dwFSTAl_557804451" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804451">FASTA (aligned sequences)</label></div>
-<div class=""><input name="dwn_557804451" id="dwGenBank_557804451" getgi="557804451" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804451">GenBank (complete sequence)</label></div>
-<div>
-<button class="cfg" id="dw_cont_557804451">Continue</button>
-<button class="cfg cnc">Cancel</button>
-</div>
-</div> <!-- dsDownload -->
-<span class="csLinks" id="csLinks_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics">Graphics</a></span>
-
-<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
-<select id="sa_557804451" onchange="SortHSPAlnSel(event,this)">
-<option selected="selected" value="0">E value</option>
-<option value="1"> Score</option>
-<option value="3">Percent identity</option>
-<option value="2">Query start position</option>
-<option value="4">Subject start position</option>
-</select>
-</div>
-<span class="alnSeqLinks">
-<a title="Go to next alignment for pdb|3J58|A" class="gbd toolsCtr navNext" ref="ordinalpos=1&amp;currseq=557804451" id="alnNxt_557804451" onclick="goToNextAlign('dtr_557804451',true);"><span>Next</span></a>
-<a disabled="disabled" class="gbd toolsCtr navPrev" ref="ordinalpos=1&amp;currseq=557804451" id="alnPrv_557804451" onclick="goToNextAlign('dtr_557804451',false);"><span>Previous</span></a>
-<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J5A|A" id="alnDsc_557804451" onclick="goToDefLine('dtr_557804451');" href="#dtr_557804451"><span>Descriptions</span></a>
-</span>
-</div>
-<div class="oneSeqAln" id="aln_557804451">
-<div id="dln_557804451">
-<div class="dlfRow">
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)
-<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J5A|A">pdb|3J5A|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
-</div>
-</div>
-<div class="relInf" id="relInf_557804451"><label>Related Information</label></div>
-<!--
-<pre>
-<@aln_gene_info@>
-</pre>
--->
-<div class="alnAll" id="alnAll_557804451"><div id="hd_557804451_1">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
-<span id="hsp557804451_1" class="alnParLinks">
-<a init="on" class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack hidden" href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #1</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>32.2 bits(16)</td>
-<td>8e-04<span class="sumN ">()</span></td>
-<td>16/16(100%)</td>
-<td>0/16(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804451_1">
-<pre>Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-</pre>
-</div>
-<div id="hd_557804451_2">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
-<span id="hsp557804451_2" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #2</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>16.4 bits(8)</td>
-<td>   47<span class="sumN ">()</span></td>
-<td>8/8(100%)</td>
-<td>0/8(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804451_2">
-<pre>Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-</pre>
-</div>
-<div id="hd_557804451_3">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
-<span id="hsp557804451_3" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #3</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804451_3">
-<pre>Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-</pre>
-</div>
-<div id="hd_557804451_4">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
-<span id="hsp557804451_4" class="alnParLinks">
-<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #4</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804451_4">
-<pre>Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-</pre>
-</div>
-</div> <!-- alnAll_557804451 -->
-</div> <!-- aln_557804451 -->
-<div class="alnHdr cnf" id="alnHdr_557804395" seqid="557804395" accs="pdb|3J58|A">
-<a name="557804395"></a>
-<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804395" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804395" title="Download information for pdb|3J58|A"><span>Download</span></a>
-<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804395" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
-<div><input seqfsta="gi|557804395" name="dwn_557804395" checked="checked" id="dwFST_557804395" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804395">FASTA (complete sequence)</label></div>
-<div><input seqfsta="gi|557804395" name="dwn_557804395" id="dwFSTAl_557804395" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804395">FASTA (aligned sequences)</label></div>
-<div class=""><input name="dwn_557804395" id="dwGenBank_557804395" getgi="557804395" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804395">GenBank (complete sequence)</label></div>
-<div>
-<button class="cfg" id="dw_cont_557804395">Continue</button>
-<button class="cfg cnc">Cancel</button>
-</div>
-</div> <!-- dsDownload -->
-<span class="csLinks" id="csLinks_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics">Graphics</a></span>
-
-<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
-<select id="sa_557804395" onchange="SortHSPAlnSel(event,this)">
-<option selected="selected" value="0">E value</option>
-<option value="1"> Score</option>
-<option value="3">Percent identity</option>
-<option value="2">Query start position</option>
-<option value="4">Subject start position</option>
-</select>
-</div>
-<span class="alnSeqLinks">
-<a title="Go to next alignment for pdb|3J56|A" class="gbd toolsCtr navNext" ref="ordinalpos=2&amp;currseq=557804395" id="alnNxt_557804395" onclick="goToNextAlign('dtr_557804395',true);"><span>Next</span></a>
-<a title="Go to previous alignment for pdb|3J5A|A" class="gbd toolsCtr navPrev" ref="ordinalpos=2&amp;currseq=557804395" id="alnPrv_557804395" onclick="goToNextAlign('dtr_557804395',false);"><span>Previous</span></a>
-<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J58|A" id="alnDsc_557804395" onclick="goToDefLine('dtr_557804395');" href="#dtr_557804395"><span>Descriptions</span></a>
-</span>
-</div>
-<div class="oneSeqAln" id="aln_557804395">
-<div id="dln_557804395">
-<div class="dlfRow">
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)
-<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J58|A">pdb|3J58|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
-</div>
-</div>
-<div class="relInf" id="relInf_557804395"><label>Related Information</label></div>
-<!--
-<pre>
-<@aln_gene_info@>
-</pre>
--->
-<div class="alnAll" id="alnAll_557804395"><div id="hd_557804395_1">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
-<span id="hsp557804395_1" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack hidden" href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #1</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>32.2 bits(16)</td>
-<td>8e-04<span class="sumN ">()</span></td>
-<td>16/16(100%)</td>
-<td>0/16(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804395_1">
-<pre>Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-</pre>
-</div>
-<div id="hd_557804395_2">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
-<span id="hsp557804395_2" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #2</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>16.4 bits(8)</td>
-<td>   47<span class="sumN ">()</span></td>
-<td>8/8(100%)</td>
-<td>0/8(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804395_2">
-<pre>Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-</pre>
-</div>
-<div id="hd_557804395_3">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
-<span id="hsp557804395_3" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #3</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804395_3">
-<pre>Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-</pre>
-</div>
-<div id="hd_557804395_4">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
-<span id="hsp557804395_4" class="alnParLinks">
-<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #4</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804395_4">
-<pre>Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-</pre>
-</div>
-</div> <!-- alnAll_557804395 -->
-</div> <!-- aln_557804395 -->
-<div class="alnHdr cnf" id="alnHdr_557804339" seqid="557804339" accs="pdb|3J56|A">
-<a name="557804339"></a>
-<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804339" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804339" title="Download information for pdb|3J56|A"><span>Download</span></a>
-<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804339" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
-<div><input seqfsta="gi|557804339" name="dwn_557804339" checked="checked" id="dwFST_557804339" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804339">FASTA (complete sequence)</label></div>
-<div><input seqfsta="gi|557804339" name="dwn_557804339" id="dwFSTAl_557804339" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804339">FASTA (aligned sequences)</label></div>
-<div class=""><input name="dwn_557804339" id="dwGenBank_557804339" getgi="557804339" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804339">GenBank (complete sequence)</label></div>
-<div>
-<button class="cfg" id="dw_cont_557804339">Continue</button>
-<button class="cfg cnc">Cancel</button>
-</div>
-</div> <!-- dsDownload -->
-<span class="csLinks" id="csLinks_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics">Graphics</a></span>
-
-<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
-<select id="sa_557804339" onchange="SortHSPAlnSel(event,this)">
-<option selected="selected" value="0">E value</option>
-<option value="1"> Score</option>
-<option value="3">Percent identity</option>
-<option value="2">Query start position</option>
-<option value="4">Subject start position</option>
-</select>
-</div>
-<span class="alnSeqLinks">
-<a title="Go to next alignment for pdb|3J54|A" class="gbd toolsCtr navNext" ref="ordinalpos=3&amp;currseq=557804339" id="alnNxt_557804339" onclick="goToNextAlign('dtr_557804339',true);"><span>Next</span></a>
-<a title="Go to previous alignment for pdb|3J58|A" class="gbd toolsCtr navPrev" ref="ordinalpos=3&amp;currseq=557804339" id="alnPrv_557804339" onclick="goToNextAlign('dtr_557804339',false);"><span>Previous</span></a>
-<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J56|A" id="alnDsc_557804339" onclick="goToDefLine('dtr_557804339');" href="#dtr_557804339"><span>Descriptions</span></a>
-</span>
-</div>
-<div class="oneSeqAln" id="aln_557804339">
-<div id="dln_557804339">
-<div class="dlfRow">
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)
-<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J56|A">pdb|3J56|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
-</div>
-</div>
-<div class="relInf" id="relInf_557804339"><label>Related Information</label></div>
-<!--
-<pre>
-<@aln_gene_info@>
-</pre>
--->
-<div class="alnAll" id="alnAll_557804339"><div id="hd_557804339_1">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
-<span id="hsp557804339_1" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack hidden" href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #1</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>32.2 bits(16)</td>
-<td>8e-04<span class="sumN ">()</span></td>
-<td>16/16(100%)</td>
-<td>0/16(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804339_1">
-<pre>Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-</pre>
-</div>
-<div id="hd_557804339_2">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
-<span id="hsp557804339_2" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #2</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>16.4 bits(8)</td>
-<td>   47<span class="sumN ">()</span></td>
-<td>8/8(100%)</td>
-<td>0/8(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804339_2">
-<pre>Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-</pre>
-</div>
-<div id="hd_557804339_3">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
-<span id="hsp557804339_3" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #3</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804339_3">
-<pre>Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-</pre>
-</div>
-<div id="hd_557804339_4">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
-<span id="hsp557804339_4" class="alnParLinks">
-<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #4</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804339_4">
-<pre>Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-</pre>
-</div>
-</div> <!-- alnAll_557804339 -->
-</div> <!-- aln_557804339 -->
-<div class="alnHdr cnf" id="alnHdr_557804283" seqid="557804283" accs="pdb|3J54|A">
-<a name="557804283"></a>
-<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804283" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804283" title="Download information for pdb|3J54|A"><span>Download</span></a>
-<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804283" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
-<div><input seqfsta="gi|557804283" name="dwn_557804283" checked="checked" id="dwFST_557804283" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804283">FASTA (complete sequence)</label></div>
-<div><input seqfsta="gi|557804283" name="dwn_557804283" id="dwFSTAl_557804283" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804283">FASTA (aligned sequences)</label></div>
-<div class=""><input name="dwn_557804283" id="dwGenBank_557804283" getgi="557804283" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804283">GenBank (complete sequence)</label></div>
-<div>
-<button class="cfg" id="dw_cont_557804283">Continue</button>
-<button class="cfg cnc">Cancel</button>
-</div>
-</div> <!-- dsDownload -->
-<span class="csLinks" id="csLinks_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics">Graphics</a></span>
-
-<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
-<select id="sa_557804283" onchange="SortHSPAlnSel(event,this)">
-<option selected="selected" value="0">E value</option>
-<option value="1"> Score</option>
-<option value="3">Percent identity</option>
-<option value="2">Query start position</option>
-<option value="4">Subject start position</option>
-</select>
-</div>
-<span class="alnSeqLinks">
-<a title="Go to next alignment for pdb|3J52|A" class="gbd toolsCtr navNext" ref="ordinalpos=4&amp;currseq=557804283" id="alnNxt_557804283" onclick="goToNextAlign('dtr_557804283',true);"><span>Next</span></a>
-<a title="Go to previous alignment for pdb|3J56|A" class="gbd toolsCtr navPrev" ref="ordinalpos=4&amp;currseq=557804283" id="alnPrv_557804283" onclick="goToNextAlign('dtr_557804283',false);"><span>Previous</span></a>
-<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J54|A" id="alnDsc_557804283" onclick="goToDefLine('dtr_557804283');" href="#dtr_557804283"><span>Descriptions</span></a>
-</span>
-</div>
-<div class="oneSeqAln" id="aln_557804283">
-<div id="dln_557804283">
-<div class="dlfRow">
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)
-<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J54|A">pdb|3J54|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
-</div>
-</div>
-<div class="relInf" id="relInf_557804283"><label>Related Information</label></div>
-<!--
-<pre>
-<@aln_gene_info@>
-</pre>
--->
-<div class="alnAll" id="alnAll_557804283"><div id="hd_557804283_1">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
-<span id="hsp557804283_1" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack hidden" href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #1</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>32.2 bits(16)</td>
-<td>8e-04<span class="sumN ">()</span></td>
-<td>16/16(100%)</td>
-<td>0/16(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804283_1">
-<pre>Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-</pre>
-</div>
-<div id="hd_557804283_2">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
-<span id="hsp557804283_2" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #2</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>16.4 bits(8)</td>
-<td>   47<span class="sumN ">()</span></td>
-<td>8/8(100%)</td>
-<td>0/8(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804283_2">
-<pre>Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-</pre>
-</div>
-<div id="hd_557804283_3">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
-<span id="hsp557804283_3" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #3</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804283_3">
-<pre>Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-</pre>
-</div>
-<div id="hd_557804283_4">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
-<span id="hsp557804283_4" class="alnParLinks">
-<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #4</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804283_4">
-<pre>Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-</pre>
-</div>
-</div> <!-- alnAll_557804283 -->
-</div> <!-- aln_557804283 -->
-<div class="alnHdr cnf" id="alnHdr_557804227" seqid="557804227" accs="pdb|3J52|A">
-<a name="557804227"></a>
-<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804227" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804227" title="Download information for pdb|3J52|A"><span>Download</span></a>
-<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804227" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
-<div><input seqfsta="gi|557804227" name="dwn_557804227" checked="checked" id="dwFST_557804227" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804227">FASTA (complete sequence)</label></div>
-<div><input seqfsta="gi|557804227" name="dwn_557804227" id="dwFSTAl_557804227" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804227">FASTA (aligned sequences)</label></div>
-<div class=""><input name="dwn_557804227" id="dwGenBank_557804227" getgi="557804227" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804227">GenBank (complete sequence)</label></div>
-<div>
-<button class="cfg" id="dw_cont_557804227">Continue</button>
-<button class="cfg cnc">Cancel</button>
-</div>
-</div> <!-- dsDownload -->
-<span class="csLinks" id="csLinks_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics">Graphics</a></span>
-
-<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
-<select id="sa_557804227" onchange="SortHSPAlnSel(event,this)">
-<option selected="selected" value="0">E value</option>
-<option value="1"> Score</option>
-<option value="3">Percent identity</option>
-<option value="2">Query start position</option>
-<option value="4">Subject start position</option>
-</select>
-</div>
-<span class="alnSeqLinks">
-<a title="Go to next alignment for pdb|3J51|A" class="gbd toolsCtr navNext" ref="ordinalpos=5&amp;currseq=557804227" id="alnNxt_557804227" onclick="goToNextAlign('dtr_557804227',true);"><span>Next</span></a>
-<a title="Go to previous alignment for pdb|3J54|A" class="gbd toolsCtr navPrev" ref="ordinalpos=5&amp;currseq=557804227" id="alnPrv_557804227" onclick="goToNextAlign('dtr_557804227',false);"><span>Previous</span></a>
-<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J52|A" id="alnDsc_557804227" onclick="goToDefLine('dtr_557804227');" href="#dtr_557804227"><span>Descriptions</span></a>
-</span>
-</div>
-<div class="oneSeqAln" id="aln_557804227">
-<div id="dln_557804227">
-<div class="dlfRow">
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)
-<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J52|A">pdb|3J52|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
-</div>
-</div>
-<div class="relInf" id="relInf_557804227"><label>Related Information</label></div>
-<!--
-<pre>
-<@aln_gene_info@>
-</pre>
--->
-<div class="alnAll" id="alnAll_557804227"><div id="hd_557804227_1">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
-<span id="hsp557804227_1" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack hidden" href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #1</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>32.2 bits(16)</td>
-<td>8e-04<span class="sumN ">()</span></td>
-<td>16/16(100%)</td>
-<td>0/16(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804227_1">
-<pre>Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-</pre>
-</div>
-<div id="hd_557804227_2">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
-<span id="hsp557804227_2" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #2</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>16.4 bits(8)</td>
-<td>   47<span class="sumN ">()</span></td>
-<td>8/8(100%)</td>
-<td>0/8(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804227_2">
-<pre>Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-</pre>
-</div>
-<div id="hd_557804227_3">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
-<span id="hsp557804227_3" class="alnParLinks">
-<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #3</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804227_3">
-<pre>Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-</pre>
-</div>
-<div id="hd_557804227_4">
-<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
-<span id="hsp557804227_4" class="alnParLinks">
-<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
-<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
-<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
-</span>
-</div>
-<table class="alnParams">
-<caption class="hdnHeader">Alignment statistics for match #4</caption>
-<tbody><tr>
-<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
-</tr>
-<tr>
-<td>14.4 bits(7)</td>
-<td>  186<span class="sumN ">()</span></td>
-<td>7/7(100%)</td>
-<td>0/7(0%)</td>
-<td>Plus/Plus</td>
-<td class="aln_frame "></td>
-</tr></tbody></table>
-<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
-</div>
-<div id="ar_557804227_4">
-<pre>Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-</pre>
-</div>
-</div> <!-- alnAll_557804227 -->
-</div> <!-- aln_557804227 -->
-</form>
-
-</div></div>
-<pre>
-</pre>
-</div><!--/#alignments-->
-</div><!-- alignInfo -->
-</div><!--ARIA-->
-
-</div><!-- alignView -->
-<form><!-- this is the start tag for the </form in blastcgi templates - needs to be changed-->
-<!-- not used - verify -->
-<!-- not used - verify -->
-
-
-                </form>
-				</div><!-- /#content -->
-				<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="reformat" id="reformat">
-				   <input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden">
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-				   <input name="PAGE_TYPE" value="BlastFormatting" type="hidden">
-
-				   <!-- TO DO: test all of those changes -->
-				   <!-- Psi blast params  PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> -->
-				   <!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> -->
-				   <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
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-					<input name="CMD" value="Web" type="hidden">
-					<!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
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-					<input name="SAVE" value="true" type="hidden">
-					<input name="CMD" value="GetSaved" type="hidden">
-					<!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from formatter> -->
-				</form>
-        </div><!-- /#content-wrap -->
-
-
-<div id="footer">
-   <div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
-   <p id="orgns">
-      <a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
-      <a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
-      <a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
-      <a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
-   </p>
-
-   <p>
-      <a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html" title="NCBI intellectual property statement">Copyright</a> |
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-      <a href="mailto:blast-help@ncbi.nlm.nih.gov" title="How to get help, submit data, or provide feedback">Send feedback</a>
-   </p>
-</div>
-   </div><!--/#wrap-->
-
-<script type="text/javascript" src="Blast%20output%20page%20example_files/utils.js"></script>
-<script type="text/javascript" src="Blast%20output%20page%20example_files/toggle.js"></script>
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\ No newline at end of file
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--- a/Blast output page example_files/InstrumentPageStarterJS.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-jQuery(c.target).parents("#disc_col a").length==0&&ncbi.sg.getInstance().setCookie("hovernext","")})}});
-
-;
-// This code creates window.console if it doesn't exist.
-// It also creates stub functions for those functions that are missing in window.console.
-// (Safari implements some but not all of the firebug window.console methods--this implements the rest.)
-(function() {
-    var names = [ "log", "debug", "info", "warn", "error", "assert", "dir", "dirxml", "group",
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-
-    if (typeof(console) === 'undefined' || typeof console === "function" ) {
-      //"typeof function" is needed see PP-769
-      console = {};
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-       if (typeof(console[names[i]]) === 'undefined') {
-          console[names[i]] = function() { return false; };
-       }
-    }
-    ncbi.sg.getInstance().init();
-})();
Binary file Blast output page example_files/addOrg.jpg has changed
Binary file Blast output page example_files/black.gif has changed
--- a/Blast output page example_files/blast.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,308 +0,0 @@
-
-function printfire()
-{
-    // Firefox
-    if (document.createEvent && window.dispatchEvent) {
-        printfire.args = arguments;
-        var ev = document.createEvent("Events");
-        ev.initEvent("printfire", false, true);
-        window.dispatchEvent(ev);
-    }
-}
-//This functions handle setting defaults for protein or nulcleotide suite  search page when
-//one of blast program radio buttons is clicked - not used now
-function AdjustMoreOptionsStyle()
-{
-	var optsEl = document.getElementById("moreopts");
-	if(optsEl && optsEl.style.height != "0px") {
-		optsEl.style.height = optsEl.scrollHeight + "px";
-	}
-}
-
-//Strip (taxid:XXX) from organism list selection
-//sgRunFunc="AdjustOrganism();"
-function AdjustOrganism()
-{
-	var words = $("qorganism").value.split(" (taxid");
-	$("qorganism").value = words[0];
-}
-
-
-/* JS Common to all BLAST pages */
-
-
-function setResultsTarget()
-{
-	//var newWin = $("newwin");
-	var newWin = this;
-	var searchFrm = $(newWin.getAttribute("form"));
-	if(newWin && newWin.checked == true) {
-		if(newWin.getAttribute("winType") == "random") {
-			searchFrm.target = "Blast_Results_for_" + Math.floor(Math.pow(10,10) *Math.random());
-		}
-		else {
-			searchFrm.target = $("resPageTarget").value;
-		}
-	}
-	else {
-		searchFrm.target = "";
-	}
-}
-
-function diffFromDefault(elem)
-{
-    var currentVal = "";
-    var ret = 0;
-
-    if (!(elem)) return;
-    var defVal = elem.getAttribute("defVal"); //Default value
-    var elShowDiff = utils.getParent(elem);
-    if(!elem.type) {//div element for example
-        //Check if parent elem has "hide" class
-        if(utils.hasClass(utils.getParent(elem), "hide")) {
-            currentVal = "hide";
-        }
-        else {
-            currentVal = "show";
-        }
-        elShowDiff = elem;
-    }
-    else if(elem.type == "select-one") {
-        if(elem[elem.selectedIndex].value) currentVal = elem[elem.selectedIndex].value;
-        //If Default value is not specified - the first one in the selection list is the default
-        if (!defVal && elem[0].value) defVal = elem[0].value;
-    }
-    else if(elem.type == "select-multiple") {
-	    currentVal = "";//for now
-    }
-    else if(elem.type == "checkbox") {
-        //alert("defVal1=" + elem.id + " " + defVal);
-        //var defVal = elem.defVal; //Default value
-        //alert("defVal2=" + defVal);
-        if(elem.checked == true) currentVal = "checked"
-        else  currentVal = "unchecked";
-    }
-    else {
-        currentVal = elem.value;
-    }
-
-
-    var numdiff = parseInt($("NUM_DIFFS").value,10);
-    var optsNumDiff = parseInt($("NUM_OPTS_DIFFS").value,10);
-    if(defVal != currentVal) {
-        if(!utils.hasClass(elShowDiff, "nondef")) {
-            utils.addClass(elShowDiff, "nondef");
-            numdiff++;
-            if(utils.hasClass(elem,"opts")) optsNumDiff++;
-        }
-        ret = 1;
-    }
-    else {
-        if(utils.hasClass(elShowDiff, "nondef")) {
-            utils.removeClass(elShowDiff, "nondef");
-            //alert("noDiff-" + elem.id);
-            if(numdiff != 0) numdiff--;
-            if(utils.hasClass(elem,"opts")) optsNumDiff--;
-        }
-        ret=0;
-    }
-    $("NUM_DIFFS").value = numdiff;
-    $("NUM_OPTS_DIFFS").value = optsNumDiff;
-    if(numdiff > 0) {
-        $("diffMes").style.display = "inline";
-    }
-    else {
-        $("diffMes").style.display = "none";
-    }
-    //alert(elem.id + " " + $("NUM_DIFFS").value);
-    return ret;
-}
-
-function setDefalValue(elem)
-{
-    var currentVal;
-    var defVal = elem.getAttribute("defVal"); //Default value
-    if(elem.type == "select-one") {
-        //If Default value is not specified - the first one in the selection list is the default
-        if(!defVal) defVal = elem[0].value;
-        for(j=0; j < elem.options.length; j++) {
-		    if(elem.options[j].value == defVal) {
-		        elem.options[j].selected = true;
-		        break;
-		    }
-        }
-    }
-    else if(elem.type == "checkbox" || elem.type == "radio") {
-        if(!defVal) defVal = "checked";
-        if(defVal == "checked") elem.checked = true
-        else elem.checked = false;
-    }
-    else {
-        if(!defVal) defVal = "";
-        elem.value = defVal;
-    }
-
-    var elShowDiff = utils.getParent(elem);
-    if(utils.hasClass(elShowDiff, "nondef")) {
-        utils.removeClass(elShowDiff, "nondef");
-    }
-    //alert(elem.id + " " + $("NUM_DIFFS").value);
-}
-
-function newResultsWinInit() {
-    jQuery("[class='newwin']").each(function(index) {
-        utils.addEvent(this, "click", setResultsTarget, false);
-    });
-}
-
-function resetOrganismSuggest(orgEntryElem)
-{
-    //suggestHint is in the hidden field used for SRA
-    var defaultMessage = ($("suggestHint")) ? $("suggestHint").value : "Enter organism name or id--completions will be suggested";
-    var suggestHint = $("qorganism").getAttribute("suggestHint");
-    if(suggestHint) defaultMessage = suggestHint;
-    if(orgEntryElem.value == "") {
-        orgEntryElem.value = defaultMessage;
-    }
-    if(orgEntryElem.value == defaultMessage) {
-        utils.addClass(orgEntryElem,"orgHint");
-    }
-}
-
-function setupOrganismSuggest(orgEntryElem)
-{
-    resetOrganismSuggest(orgEntryElem);
-    utils.addEvent(orgEntryElem, "focus", function() {
-        clearOrgSuggest(orgEntryElem);
-     }, false);
-}
-
-function clearOrgSuggest(orgEntryElem)
-{
-    if(utils.hasClass(orgEntryElem,"orgHint")) {
-        orgEntryElem.value="";
-        utils.removeClass(orgEntryElem,"orgHint");
-    }
-}
-
-function InitCustomButton(bn)
-{
-  utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
-  utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
-  utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
-  utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);
-}
-
-function showHideElem(id,hide)
-{
-  if($(id)) {
-    if(hide) {
-	    if(!utils.hasClass($(id),"hidden")) utils.addClass($(id), "hidden");
-	}
-	else {
-	    if(utils.hasClass($(id),"hidden")) utils.removeClass($(id), "hidden");
-	}
-  }
-}
-
-function resetOrganismControls(orgEntryElem) {
-    resetOrganismSuggest(orgEntryElem);
-    if ($("orgExcl")) $("orgExcl").checked = false;
-    utils.replaceInHtml("", $("orgs"));
-    if ($("frOrgs")) utils.replaceInHtml("", $("frOrgs"));
-    if ($("numOrg")) $("numOrg").value = 1;
-}
-
-function AddOrgRow(e,orgName,exclName) {
-    e = e || window.event;
-    utils.preventDefault(e);
-    var checkedExclude = new Array();
-    var orgDict = jQuery($($("qorganism"))).ncbiautocomplete("option","dictionary");
-    orgDict = (!orgDict || orgDict == "") ? "taxids_sg" : orgDict;
-    var len = $("qorganism").getAttribute("size");
-
-    var newOrgFieldID = "qorganism" + $("numOrg").value;
-    var newOrgField = " <div><input name=\"" + orgName + $("numOrg").value + "\" size=\"" + len + "\" id=\"" + newOrgFieldID +
-                       "\" type=\"text\" data-jigconfig=\"dictionary:'" + orgDict + "'\" autocomplete=\"off\" class=\"jig-ncbiautocomplete multiOrg\" />";
-    if (exclName != "") {
-        newOrgField += "<span class=\"orgExcl\">" +
-                       "<input type=\"checkbox\" name=\"" + exclName + $("numOrg").value + "\" class=\"oExcl cb\" id=\"orgExcl" + $("numOrg").value + "\" />" +
-                       "<label for=\"orgExcl" + $("numOrg").value + "\" class=\"right oExclRl\">Exclude</label></span>";
-    }
-    newOrgField += "</div>";
-    if (navigator.userAgent.match(/ie/i)) {
-        for (i = 1; i < $("numOrg").value; i++) {
-            if ($("orgExcl" + i)) checkedExclude[i] = $("orgExcl" + i).checked;
-        }
-    }
-    if (!navigator.userAgent.match(/firefox/i)) {
-        jQuery($($(orgs))).append(newOrgField,true);
-    }
-    else {
-        utils.insertInHtml(newOrgField, $("orgs"));
-    }
-
-    if (navigator.userAgent.match(/ie/i)) {
-        for (i = 1; i < $("numOrg").value; i++) {
-            if ($("orgExcl" + i)) $("orgExcl" + i).checked = checkedExclude[i];
-        }
-    }
-    setupOrganismSuggest($(newOrgFieldID));
-    jQuery($($(newOrgFieldID))).ncbiautocomplete();
-    $("numOrg").value++;
-}
-
-function adjustOrgVal(orgEntryElem)
-{
-    //if (utils.hasClass($("searchForm").EQ_MENU, "orgHint")) $("searchForm").EQ_MENU.value = "";
-    clearOrgSuggest(orgEntryElem);
-    if ($("numOrg")) {
-        for (i = 1; i < $("numOrg").value; i++) {
-            if ($("qorganism" + i)) {
-                clearOrgSuggest($("qorganism" + i));
-            }
-        }
-    }
-}
-
-function getUrlCompForEntryField(elem) {
-    var url = "";
-    if (elem && elem.value != "") {
-        url = "&" + elem.name + "=" + escape(elem.value);
-    }
-    return url;
-}
-
-
-function getUrlCompForCheckedField(elem) {
-    var url = "";
-    if (elem && elem.checked) {
-        url = "&" + elem.name + "=" + elem.value;
-    }
-    return url;
-
-}
-
-function getUrlCompForOptionsField(elem) {
-    var url = "";
-    if (elem) {
-        url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
-    }
-    return url;
-}
-
-function getUrlCompForMultiOptionsField(elem) {
-    var url = "";
-    if (elem) {
-        for (i = 0; i < elem.options.length; i++) {
-            if (elem.options[i].selected) {
-                url += "&" + elem.name + "=" + elem.options[i].value;
-            }
-        }
-    }
-    return url;
-}
-
-
-utils.addEvent(window, 'load', newResultsWinInit, false);
-
--- a/Blast output page example_files/blastReq.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,332 +0,0 @@
-#msgR .info {
-background-color: #dfd;
-padding: 4px;
-border: solid 1px green;
-color: green;
-}
-
-dl.summary dt {
-float: left;
-width: 8em;
-clear:left;
-margin: 0;
-text-align: right;
-padding-right: 1em;
-color: #666;
-}
-
-dl.summary dd {
-padding-left: 0.5em;
-display: block;
-margin-left: 7em !important;
-margin: 0;
-}
-dl.summary dt, dl.summary dd {
-margin-bottom: 0.5em;
-}
-a.help
-{
-float:right;
-font-size: 110%;
-}
-
-dl.summary label {
-display: inline;
-}
-
-dl.summary tr th label {
-padding: 0;
-margin-right:0;
-}
-table.options {
-border: solid 1px #ccc;
-border-right: solid 1px #ccc;
-}
-
-table.options td,
-table.options td.frh {
-font-size: 90%;
-_font-size: 85%;
-}
-
-table.options label.rb {
-border-right: solid 1px #ccc;
-margin-right: 0.5em;
-padding-right: 2.0em;
-}
-
-table.options tr td {
-_font-size: 90%;
-padding-left: 0.5em;
-}
-
-table.options {
-/*border-collapse: collapse;*/
-margin-left: 0;
-padding-left: 0;
-width: 62em;
-}
-
-table.options td label {
-font-size: 90%;
-}
-
-table.options th label,
-table.options td label {
-margin-right: 0;
-_position: relative;
-_top: -0.1em;
-}
-
-table.options tr.hdr td,
-table.options tr.hdr th {
-padding: 2px;
-border: solid 1px #ccc;
-background-color: #ddd;
-}
-
-table.options td, table.options td.frh {
-padding: 0.25em 0;
-vertical-align: center;
-}
-
-table.options th {
-padding-right: 1em;
-text-align: right;
-padding-left: 1em;
-}
-
-/*
-*:focus{
-background-color: white !important;
-}
-*/
-
-table.options select,table.options input, #graphic input{
-border: solid 1px #888;
-padding: 1px;
-}
-
-select {
-font-size: 90%;
-}
-
-select option {
-padding-right: 0.5em;
-}
-
-input.cb, table.options input.cb {
-border: none;
-}
-
-select {
-margin-right:1em;
-}
-
-table.options tr {
-background-color: #eee;
-}
-
-table.options tr.odd {
-background-color: #e0e0e0;
-}
-
-table.options th {
-
-background-color: white;
-}
-
-table.options tr.paramSet td
-{
-	border-top: solid 2px white;
-}
-
-
-
-
-.resetAll
-{
-font-weight: normal;
-padding: 0.5em;
-font-size: 90%;
-margin-left:5em;
-}
-
-.button {
-background-color: #ccc;
-padding: 0.25em 0.25em;
-color: black;
-border: outset 3px #eee;
-_border: outset 3px #eee;
-font-size: 90%;
-_padding:0;
-font-weight: bold;
-height:25px;
-_height:22px;
-}
-
-.fbtn {
-margin-bottom: 0.5em;
-}
-
-.note {
-font-size: 80%;
-color: green;
-background-color: #ffc;
-margin-left: 2em;
-padding: 3px;
-}
-.instr {
-   margin-left: 1em;
-   color: #666;
-font-size: 90%;
-}
-.smaller {
-font-size: 90%;
-font-weight: normal;
-}
-
-/* Results Page styles */
-
-#ridRes
-{
-	background-color: #FC9;
-	padding:5px 5px;
-}
-
-
-span dd.hidden,dt.hidden,dd.hidden span
-{
-	display:none;
-}
-
-dl.query .query,
-dl.title .title,
-dl.entrez .entrez,
-dl.db .db
-{
-	display:block;
-}
-
-
-dl.entrez span.entrez
-{
-	display:inline;
-}
-
-.hidden {
-display: none;
-}
-.hide {
-display: none;
-}
-.shown {
-display: block;
-}
-
-
-
-table.megaBlast tr.psiBlast,
-table.blastn tr.psiBlast,
-table.blastx tr.psiBlast,
-table.tblastn tr.psiBlast,
-table.tblastx tr.psiBlast,
-table.discoMegablast tr.psiBlast
-{
-display: none;
-}
-
-
-table.GlobalAln .xgl,
-body.GlobalAln div.xgl,
-body.GlobalAln dt.xgl,
-body.GlobalAln dd.xgl,
-body.GlobalAln span.xgl,
-body.GlobalAln table.xgl
-{
-display: none;
-}
-
-.dispType
-{
-	/*background-color:White;
-	border:solid 1px black;*/
-	border-top:solid 2px gray;
-	border-left:solid 2px gray;
-	font-size:90%;
-	padding-left:2px;
-
-}
-
-.newwin {
-border: none;
-}
-
-table.options .helplink
-{
-    font-weight:bold;
-    position:absolute;
-    right:0;
-}
-
-div#query label
-{
-    display: inline;
-    font-weight:bold;
-    padding-right:1em;
-}
-#NEW_VIEW
-{
-    _margin-left:-2px;
-}
-
-
-table.blastp *.blastn,
-table.psiBlast *.blastn,
-table.phiBlast *.blastn,
-table.blastx *.blastn,
-table.tblastn *.blastn,
-table.tblastx *.blastn
-{
-display: none;
-}
-
-#formatTable th.col1 {
-width: 8em;
-vertical-align: top;
-}
-/*
-#formatTable .helplink span {
-position: relative;
-}
-*/
-#org
-{
-    margin-top:2em;
-}
-#qorganism
-{
-    /*display:block;*/
-}
-.fi
-{
-    position:relative;
-}
-
-a#organismHelp
-{
-    margin-top:-1.5em;
-}
-
-table.options tr.paramSet td.hd {
-padding-right: 1em;
-text-align: right;
-padding-left: 1em;
-background-color:White;
-font-weight:bold;
-border-top:none;
-}
-.oExcl
-{
-    margin-left:2px;
-}
--- a/Blast output page example_files/blastRes.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,262 +0,0 @@
-a#refPage
-{
-	margin-left:3em;
-}
-
-a.resLink
-{
-	margin-left:1em;
-	display:none;
-}
-
-a.resLinkhidden
-{
-	display:none;
-}
-
-
-#cddResults
-{
-	float:right;
-	margin-top:-2em;
-	margin-right:1em;
-	color:#336699;
-    font-size:100%;
-}
-
-#cddResults.showing {
-   background-image: url(images/down.gif);
-}
-
-
-
-div.inlineDiv
-{
-	display:inline;
-}
-
-span.reslink
-{
-	display:none;
-}
-
-div.statPage *.statPage,
-div.resPage *.resPage
-{
-	display:inline;
-}
-
-div.resHeader *.hidden
-{
-	display:none;
-}
-
-#cddInfo
-{
-    text-align:center;
-}
-#cddDesc
-{
-    font-weight:bold;
-}
-div#desctbl
-{
-border: solid 1px #018aac;
-/*min-width: 1000px;*/
-margin: none;
-width: 100%;
-background-color:White;
-/*line-height:0;
-_line-height:0;*/
-}
-
-table#descs
-{
-font-family: Verdana, Sans-Serif;
-font-size: 90%;
-_font-size: 86%;
-border-collapse: collapse;
-/*min-width: 600px;*/
-width: 100%;
-}
-
-table#descs th a {
-text-decoration: none;
-color: #00c;
-}
-
-table#descs th a:visited {
-color: #00c;
-}
-
-table#descs th a:hover {position: relative;
-text-decoration: underline;
-}
-
-table#descs tr th.l,
-table#descs tr td.l {
-text-align: left;
-}
-
-table#descs tr th.sp {
-background-color: #def;
-}
-
-table#descs tr th,
-table#descs tr td {
-text-align: center;
-padding: 1px 4px;
-}
-
-table#descs tr.first th {
-padding-left:18px;
-border-left: solid 1px #A0ceff;
-border-top: solid 1px #A0ceff;
-border-bottom: solid 1px #018aac;
-border-right: solid 1px #018aac;
-padding-right: 8px;
-/*background-color: #01d5ff;*/
-background-color: #9cf;
-/*font-size: 92%;*/
-white-space:normal;
-line-height: 1.2em
-}
-
-
-table#descs td {
-border: solid 1px #ccc;
-border-width: 0px 1px;
-white-space:nowrap;
-overflow: hidden;
-}
-
-.slink {
-font-size: 90%;
-font-weight: normal;
-}
-
-table#descs tr.first th.sel {
-background: #9cf url(images/up.gif) no-repeat center left;
-padding-left: 18px;
-padding-right: 18px;
-}
-
-div.lim
-{
-/*overflow: hidden;-this used to work in Firefox 2- comment for now and set the width */
-width: 35em;
-display: inline-block;
-height: 1.3em;
-}
-
-table#descs tr:hover {
-background-color: #def;
-}
-
-pre
-{
-	font-size:110%;
-	_font-size:100%;
-	line-height:1;
-}
-
-#msg
-{
-    white-space:normal;
-    border-color:#cccccc;
-    padding:0;
-    margin: 0;
-    margin-top:2px;
-}
-#msg li
-{
-    display:none;
-    padding:0;
-    margin: 0;
-    text-indent: 0;
-}
-#msg li.warning, #msg li.error ,#msg li.info
-{
-    display:block;
-}
-
-#msg ul
-{
-    margin:0;
-    padding:0;
-}
-
-table#statInfo
-{
-    border: solid 1px #ccc;
-    background-color: #eee;
-    width: 100%;
-}
-
-table#statInfo tr.odd {
-background-color: #e0e0e0;
-}
-
-.READY, .UNKNOWN
-{
-    display:none;
-}
-
-p.WAITING
-{
-    margin-top:1em;
-}
-
-#frmPage
-{
-	margin-left:1em;
-}
-
-span.Gene_PubMedLinks
-{
-    color: Green; font-weight: bold;
-}
-
-ul.msg li p
-{
-    display:none;
-}
-
-.msg li p.warning, .msg li p.error, .msg li p.success,.msg li p.info
-{
-    display:block;
-}
-
-.mdlbox
-{
-    white-space:pre;
-    background-color:Transparent;
-    border:none;
-}
-
-#blastErr
-{
-    white-space:normal;
-}
-
-
-
-#RSIFrameNoRes,#RSIFrameDesc,#RSIFrameAln
-{
-    border:none;
-    width:519px;
-    height:35px;
-    margin:0px auto;
-}
-
-
-a.ui-ncbitoggler.hidden, a.ui-ncbitoggler-open.hidden
-{
-    display:none;
-}
-
-.smn {
-  display: inline-block;
-  height: 16px;
-  width: 16px;
-}
--- a/Blast output page example_files/dynFormatRes.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,623 +0,0 @@
-/* style changes for redesign begin*/
-a.gbd
-{
-    text-decoration:none;
-}
-
-tr.dflLnk td span
-{
-    font-size:78%;
-    display:none;
-    text-align:center;
-}
-a.dflSeq
-{
-    color:#369;
-    text-decoration:underline;
-    width:auto;
-}
-table.defln tr.dflLnk a
-{
-	margin-right:auto;
-	padding-left:0;
-}
-
-.alnParLinks
-{
-    float:right;
-}
-
-.alnSeqLinks
-{
-    float:right;
-    margin-right:1em;
-}
-
-
-.seqlinks select
-{
-    padding:0;
-}
-
-.dlfRow div
-{
-    font-size:90%;
-}
-
-.dlfRow
-{
-    display:inline;
-    font-size:110%;
-}
-
-.dlfRow.hidden
-{
-    display:none;
-}
-.dlfRow label
-{
-    font-size:87%;
-    display:inline;
-    color:#606060;
-    font-weight:bold;
-}
-
-.dlfRow span.r label
-{
-    padding-left:0.8em;
-}
-
-
-div.relInf
-{
-    font-family: Verdana, Sans-Serif;
-    font-size: 80%;
-    float:right;
-    width:21%;
-    border-top:solid 2px gray;
-    margin-top:-1em;
-    margin-right:3.5em;
-    left:3em;
-    max-width:25em;
-    padding-left:1em;
-    position:relative;
-    white-space:normal;
-}
-
-div.relInf a
-{
-    padding-right:0.2em;
-}
-
-.rlLink
-{
-    padding-left:0.2em;
-}
-.relInf label
-{
-    font-size:110%;
-    color:brown;
-    font-weight:bold;
-}
-div#content
-{
-    min-width:70em;
-}
-
-.dflLnk a
-{
-	font-size:90%;
-}
-a.dflSeq
-{
-    width:auto;
-    font-weight:normal;
-}
-
-
-#cntDesc,#cntDesc_psiw
-{
-    margin-bottom:0.2em;
-    display:inline-block;
-    width:20em;
-}
-#cntDesc span,#cntDesc_psiw span
-{
-    margin-right:0.5em;
-}
-
-#cntDesc a,#cntDesc input,#cntDesc_psiw a,#cntDesc_psiw input
-{
-    margin-left:0.5em;
-}
-
-#cntSelNone,#cntShAll
-{
-    margin-left:0.2em;
-}
-
-.toolsCtr
-{
-    color:Blue;
-}
-
-table.ui-ncbigrid th span.slink a
-{
-  display:inline;
-  padding-right: 0;
-}
-table.ui-ncbigrid th.sp
-{
-    font-weight:bold;
-}
-
-table.ui-ncbigrid th span.slink
-{
-    margin-left:0.2em;
-}
-
-table.ui-ncbigrid td {
- white-space:nowrap;
-}
-table.ui-ncbigrid td.c3
-{
-    /*padding-left:0.8em;*/
-}
-table.ui-ncbigrid caption
-{
-    font-size:0;
-    line-height:0;
-}
-#content h3.cap,#content h3.cap a.ui-ncbitoggler.ui-widget, #content h3.cap a.ui-ncbitoggler-open
-{
-    color:#4d4d4d;
-    text-align:left;
-    margin:0 0 0.5em 0;
-}
-
-#content div.cap,#content div.cap a.ui-ncbitoggler.ui-widget, #content div.cap a.ui-ncbitoggler-open
-{
-    color:#4d4d4d;
-    text-align:left;
-    margin:0 0 0.5em 0;
-    letter-spacing:-1px;
-    font-size:110%;
-    font-weight:bold;
-}
-
-#descriptions div.caption-exists {
-  margin: 0;
-}
-
-/**********decrition toolbar styles *********/
-
-div.cnf {
-  -moz-border-bottom-colors: none;
-  -moz-border-image: none;
-  -moz-border-left-colors: none;
-  -moz-border-right-colors: none;
-  -moz-border-top-colors: none;
-  background: url("images/cnf.png") repeat scroll 0 0 transparent;
-  border-style: solid none none;
-  border-width: 1px medium medium;
-  /*clear: left;*/
-  height: 22px;
-  /*overflow: auto;*/
-  width: 100%;
-}
-
-ul.ui-ncbilocalnav li.has-child a.button_config {
-  background: url("/portal/portal3rc.fcgi/3493904/img/81796") no-repeat scroll right center transparent !important;
-  width: 22px;
-  height:22px;
-  margin-left:12em;
-}
-
-#li-config
-{
-    float:right;
-    width:17em;
-}
-div#descTblCtrl ul.ui-ncbilocalnav li
-{
-    border-right:none;
-}
-
-
-.cfg
-{
-    font-size:90%;
-}
-
-
-.oneSeqAln .hsp label
-{
-    color:#606060;
-    font-size:95%;
-    padding-right:0.5em;
-}
-
-.oneSeqAln pre
-{
-    margin-top:0.5em;
-}
-
-.aln_feat label
-{
-  color: #606060;
-  font-size: 95%;
-  padding-right: 0.5em;
-}
-.oneSeqAln .dflLnk.aln_feat
-{
-    padding-bottom:1em;
-}
-div.oneSeqAln h4
-{
-    border:none;
-    font-size:100%;
-    font-weight:normal;
-    letter-spacing:normal;
-    margin:0;
-}
-
-.oneSeqAln .dflLnk
-{
-    width:56em;
-}
-.aln_feat a
-{
-    margin-left:1em;
-    display:block;
-}
-.dflLnk.aln_feat div
-{
-  /*display:inline-block;  */
-  margin-left:5em;
-  margin-top:-1em;
-}
-.aln_frame.shown
-{
-    display:block;
-}
-/*align params styles change */
-
-table.alnParams
-{
-    border-left:none;
-    border-right:none;
-    margin-top:0.5em;
-    width:49em;
-}
-
-table.alnParams th
-{
-    background-color:Transparent;
-    border:none;
-    text-align:left;
-}
-
-table.alnParams td
-{
-   border:none;
-}
-
-
-.alnAll
-{
-    line-height:normal;
-    margin-top:1em;
-}
-
-.alnAll div
-{
-    width:70%;
-}
-
-/**new config staff begin**/
-.popDl
-{
-    display:none;
-}
-.popDl div
-{
-    margin-top:0.5em;
-}
-.popDl div.tl
-{
-    margin-top:0;
-    font-weight:bold;
-}
-a.button_config {
-  background: url("images/cnfButn.png") no-repeat scroll right center transparent !important;
-  width: 22px;
-  height:22px;
-  margin-left:12em;
-  float:right;
-}
-
-a.toolsCtr,span.csLinks a
-{
-    margin-left:8px;
-    float:left;
-    cursor:pointer;
-}
-
-a.toolsCtr[disabled] {
-  cursor: default;
-}
-
-
-a.toolsCtr SPAN
-{
-	color: #14376c;
-	/*line-height: 22px;*/
-	padding-left: 15px;
-	background-repeat: no-repeat;
-	background-position:left center;
-}
-
-a.toolsCtr[disabled] SPAN,a.toolsCtr[disabled]
-{
-    color:#C2C2C2;
-}
-
-a.dnld span
-{
-	background-image: url("images/dndl.png");
-}
-
-a.dnld[disabled] span
-{
-	background-image: url("images/dndl_dsb.png");
-}
-
-a.dialog
-{
-	padding-right: 18px;
-	background:transparent url(images/dialog.png) no-repeat scroll right center;
-	text-decoration:none;
-}
-
-a.dialog[disabled] {
-    background-image: url("images/dialog_dsb.png");
-}
-
-
-a.alnNav span
-{
-	background-image: url("images/align_Normal.png");
-}
-
-a.alnNav
-{
-    text-decoration:none;
-}
-
-
-a.navNext span
-{
-	background-image: url("images/next_Normal.png");
-}
-
-
-a.navNext[disabled] span
-{
-	background-image: url("images/next_Inactive.png");
-}
-
-
-a.navPrev span
-{
-	background-image: url("images/prev_Normal.png");
-}
-
-
-a.navPrev[disabled] span
-{
-	background-image: url("images/prev_Inactive.png");
-}
-
-
-a.navBack span
-{
-	background-image: url("images/table_Normal.png");
-}
-
-.alnRn
-{
-    float:left;
-}
-
-
-/* styles to change per discusssion with Mark begin*/
-.dflLnk a
-{
-	padding-left:0;
-}
-
-
-table.ui-ncbigrid th {
-  padding-left:0.3em;
-  padding-right:0;
-  text-align:center;
-}
-
-table.ui-ncbigrid td {
-  padding-left:0.4em;
-  padding-right:0.4em;
-  text-align:center;
-}
-
-table.ui-ncbigrid td.c2,table.ui-ncbigrid td.c1 {
-  text-align:left;
-}
-
-table.ui-ncbigrid td.c3{
-  padding:0.363em 0.25em;
-}
-
-
-table.ui-ncbigrid th a {
-  padding-right: 5px;
-}
-table.ui-ncbigrid th.c0
-{
-    width:25px;
-    padding:0;
-}
-
-.dflnDth
-{
-    width:100%;
-}
-div.lim {
-  width: 14em;
-}
-
-table.ui-ncbigrid th.c8,table.ui-ncbigrid th.c9 {
-  padding-right: 0.3em;
-}
-.c8,.c9
-{
-    font-size:80%;
-}
-
-
-td.lim.l.c2,td.lim.l.c1
-{
-    overflow:hidden;
-}
-a.spr
-{
-    border-right:none;
-}
-
-
-.psiInp
-{
-    margin-left:1em;
-    margin-top:0.5em;
-}
-
-
-.c8 input
-{
-    border:none;
-}
-table.ui-ncbigrid td.c8
-{
-    padding-left:1.5em;
-}
-
-tr.psi_new td
-{
-    background-color:#FFFF99;
-    border-top:solid 4px white;
-    border-spacing:3px;
-    border-collapse:collapse;
-    line-height:normal;
-}
-/* accessibility setting */
-tr.dflLnk td span.psiNw,tr.first th span,a.button_config span, a span.accsb,.dflLnk label.accsb
-{
-    display:inline;
-    position:absolute;
-    left:-9999px;
-}
-
-div.tgl
-{
-    margin-top:-1em;
-}
-.shcl
-{
-    float:right;
-}
-
-/* styles to change per discusssion with Mark end*/
-
-.alnRn a
-{
-    padding-right:1em;
-}
-.alnAll .moreHsps
-{
-    font-family: Verdana, Sans-Serif;
-    font-size: 75%;
-    margin-top:-2.5em;
-    width:58%;
-}
-.erm
-{
-    background-color:#FFFFCC;
-    padding:0.5em;
-}
-
-#debug,.ind,.alnMsgS .db,.erm .db
-{
-    display:none;
-}
-
-.tmsAln label
-{
-    font-size:93%;
-    display:inline;
-    color:#606060;
-    font-weight:bold;
-}
-.alnAll .tmsAln, .tmsAln div
-{
-    width:100%;
-    margin-bottom:-1em;
-}
-.tmsAlnPar
-{
-    margin-top:-1em;
-}
-/*debug info styles begin */
-
-
-/* use those styles only in debug version
-
-.alnMsg
-{
-    border:solid 1px black;
-}
-
-.alnMsgS.hidden,.alnMsgS .db
-{
-    display:block;
-}
-
-.oneSeqAln
-{
-    border:1px solid #C8C8C8;
-}
-
-#debug,tr.dflLnk td span.ind
-{
-    display:inline;
-}
-.c0
-{
-    width:30px;
-}
-/*debug info styles end */
-
-
-
-/**new config staff end**/
-/*
-ul.ui-ncbilocalnav li, ul.ui-ncbilocalnav {
-  background-color: #F4F4F4;
-  background-image: -moz-linear-gradient(center top , #FFFFFF, #F4F4F4);
-}
-ul.ui-ncbilocalnav li {
-  border-right: 1px solid #C4C4C4;
-}
-*/
-/**********decrition toolbar styles end*********/
-
-
-/* style chenges for redesign end*/
--- a/Blast output page example_files/firefox-descriptions.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-table.dbInfo caption {
-
-}
\ No newline at end of file
--- a/Blast output page example_files/format.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,270 +0,0 @@
-
-function UpdateDisplayTypes(displayTypes) {
-    dispMenu = displayTypes.options;
-    for(i=0; i < dispMenu.length; i++) {
-	    //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") ||
-	    if($("stepNumber").value == "" || $("stepNumber").value < 2) {
-			if(dispMenu[i].value.indexOf("PSSM") != -1) {
-				dispMenu[i--] = null;
-				//break;
-			}
-		}
-	}
-}
-
-function GetIndexByValue(selectElem,val) {
-    var idx = 0;
-    var opts = selectElem.options;
-    for(i=0; i < opts.length; i++) {
-        if(opts[i].value == val) {
-            idx = i;
-            break;
-        }
-    }
-    return idx;
-}
-
-function resetAdvView(show)
-{
-    var advView = $("advView");
-    if(show) {
-        if(utils.hasClass(advView, "hidden")) {
-            utils.removeClass(advView, "hidden");
-        }
-    }
-    else {
-        utils.addClass(advView, "hidden");
-    }
-}
-
-
-function ShowOrHide(hide,elem)
-{
-    if(hide) {
-        if(!utils.hasClass(elem, "hidden")) {
-            utils.addClass(elem, "hidden");
-        }
-    }
-    else {
-        if(utils.hasClass(elem, "hidden")) {
-            utils.removeClass(elem, "hidden");
-        }
-    }
-}
-
-function UpdateFormatTypes(form) {
-    var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value;
-    var hideAdvView = false;
-    bioseqFormatHide = true;
-    pssmFormatHide = true;
-    pssmScFormatHide = true;
-    formatTypeHide = true;
-	if (selectedObjType == "Alignment") {
-		formatObjectSelectedIndex = 0; //HTML
-		formatTypeHide = false;
-		hideAdvView = true;
-	}
-    if (selectedObjType == "PSSM") {
-		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text");
-		pssmFormatHide = false;
-    }
-    if (selectedObjType == "PSSM_Scoremat") {
-		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");
-		pssmScFormatHide = false;
-    }
-    else if (selectedObjType == "Bioseq") {
-		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");
-		bioseqFormatHide = false;
-    }
-    form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex;
-	ShowOrHide(formatTypeHide,form.FORMAT_TYPE);
-	if ($("bioseqFormat")) {
-	    ShowOrHide(bioseqFormatHide,$("bioseqFormat"));
-	    $("bioseqFormat").readOnly=true;
-	}
-	if ($("pssmFormat")) {
-	    ShowOrHide(pssmFormatHide,$("pssmFormat"));
-	    $("pssmFormat").readOnly=true;
-	}
-	if ($("pssmScFormat")) {
-	    ShowOrHide(pssmScFormatHide,$("pssmScFormat"));
-	    $("pssmScFormat").readOnly=true;
-	}
-	resetAdvView(hideAdvView);
-}
-
-function ResetForm()
-{
-    //var defValNodes = cssQuery(".reset");
-    defValNodes = $("FormatForm").elements;
-	for(i=0; i < defValNodes.length; i++) {
-	  if(utils.hasClass(defValNodes[i],"reset"))
-	                 setDefalValue(defValNodes[i]);
-	}
-	if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
-	    UpdateFormatTypes($("FormatForm"));
-	    UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
-	}
-	if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH)
-	else $("FormatForm").I_THRESH.value="";
-	//resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
-	resetOrganismControls($("FormatForm").FORMAT_ORGANISM);
-	//TO DO: add threshold
-}
-
-function LimitByHitlistSize(list)
-{
-    var listBreak = false;
-    var optSel = false;
-    for(i=0; i < list.options.length; i++) {
-        var optVal = parseInt(list.options[i].value ,10);
-        var hitListSize = parseInt($("maxNumSeq").value ,10);
-        if(list.options[i].selected) optSel = true;
-        if(optVal >= hitListSize)  {
-            if(!optSel) {list.options[i].selected = true;}
-            list.options.length = i + 1;
-            break;
-        }
-    }
-}
-
-function AddFormatOrgField(e) {
-    AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE");
-}
-
-function initSubmit() {
-
-
-}
-
-function adjustFormatOptions()
-{
-    var alignView = $("FormatForm").ALIGNMENT_VIEW;
-    var formatType = $("FormatForm").FORMAT_TYPE;
-    var queryAnch =  formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
-    var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch;
-    dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities");
-
-    UpdateDescriptions(dynFormatPW);
-    if (dynFormatPW) {
-        jQuery("#frmAln").addClass("hidden");
-        if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
-        jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE
-        jQuery("#scf").removeClass("hidden");//show CDS_FEAT
-        $("FormatForm").SHOW_LINKOUT.checked = true;
-    }
-    else {
-        if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex;
-
-        jQuery("#frmAln").removeClass("hidden");
-        if (dynFormatQA) {
-            if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
-        }
-        else {
-            jQuery("#shl").removeClass("hidden");
-        }
-        if (queryAnch) {
-            jQuery("#scf").addClass("hidden"); //hide CDS_FEAT
-        }
-        else {//pairwise old_view=false
-            jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT
-        }
-        jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE
-    }
-    if ($("blastSpec").value == "VecScreen") {
-        adjustVecscreen(dynFormatPW);
-    }
-}
-
-function adjustVecscreen(dynFormatPW)
-{
-    var dfltDescrInd = 0; //0
-    var dfltDynDescrInd = 5; //1000
-    var dfltAlnInd = 6; //1000
-    if (dynFormatPW) {
-        utils.addClass($("lr"), "hidden");
-        $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd;
-    }
-    else {
-        utils.removeClass($("lr"), "hidden");
-        $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd;
-    }
-    $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd;
-}
-
-
-function UpdateDescriptions(removeZero)
-{
-    if (removeZero) {
-        dispMenu = $("FormatForm").DESCRIPTIONS;
-        dispMenu.remove(0);
-    }
-    else {
-        dispMenu = $("FormatForm").DESCRIPTIONS;
-        if (dispMenu.options[0].value != "0") {
-            if (navigator.userAgent.match(/ie/i)) {
-                dispMenu.add(new Option("0", "0"), 0);
-            }
-            else {
-                dispMenu.add(new Option("0", "0"), dispMenu[0]);
-            }
-        }
-	}
-}
-
-function InitDynFormatOptions()
-{
-    if ($("OLD_VIEW")) {
-        utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false);
-        utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false);
-        utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false);
-        adjustFormatOptions();
-    }
-}
-
-function InitFormatPage()
-{
-    if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
-        UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
-        UpdateFormatTypes($("FormatForm"));
-        list = $("FormatForm").FORMAT_OBJECT;
-        utils.addEvent(list, "change", function() {
-            UpdateFormatTypes($("FormatForm"));
-                               },
-	                           false);
-    }
-    utils.addEvent($("resetAll"), "click",  ResetForm, false);
-    if($("maxNumSeq") != null) {
-    if($("maxNumSeq").value != "") {
-        LimitByHitlistSize($("FormatForm").DESCRIPTIONS);
-        LimitByHitlistSize($("FormatForm").ALIGNMENTS);
-        LimitByHitlistSize($("FormatForm").NUM_OVERVIEW);
-    }
-    }
-    setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
-    utils.addEvent($("FormatForm"), "submit", function() {
-                            adjustOrgVal($("FormatForm").FORMAT_ORGANISM);},
-                    false);
-
-    if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false);
-    InitDynFormatOptions();
-	/* add this code if decide image for View Report
-	var imgButtons = jQuery("[class='viewReport']");
-    for (var i = 0; i < imgButtons.length; i++) {
-      var l = imgButtons[i];
-      utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false);
-      utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false);
-      utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false);
-      utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false);
-      utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false);
-   }
-   */
-}
-
-utils.addEvent(window, 'load', InitFormatPage, false);
-
-
-
-
-
-
--- a/Blast output page example_files/formatRes.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1542 +0,0 @@
-// JScript source code
-/*************************new code begin *******************************************************/
-
-function getHiddenFieldVal(elemName) {
-    var val;
-    var elem = document.getElementsByName(elemName);
-    if (elem) {
-        val = (elem.length > 1) ? elem[0].value : elem.value;
-    }
-    return val;
-}
-
-function getHiddenFieldParamString(elemName) {
-    var ret = "";
-    var val = getHiddenFieldVal(elemName);
-    if (val) {
-        ret = "&" + elemName + "=" + val;
-    }
-    return ret;
-}
-
-function elementInViewport(el) {
-    if (!el) return;
-    var rect = el.getBoundingClientRect();
-
-    var myWidth = 0, myHeight = 0;
-    if (typeof (window.innerWidth) == 'number') {
-        //Non-IE
-        myWidth = window.innerWidth;
-        myHeight = window.innerHeight;
-    } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) {
-        //IE 6+ in 'standards compliant mode'
-        myWidth = document.documentElement.clientWidth;
-        myHeight = document.documentElement.clientHeight;
-    } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) {
-        //IE 4 compatible
-        myWidth = document.body.clientWidth;
-        myHeight = document.body.clientHeight;
-    }
-    //window.alert('Width = ' + myWidth);
-    //window.alert('Height = ' + myHeight);
-
-
-    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth)
-    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth)
-    return (rect.top >= 0 && rect.bottom <= myHeight);
-}
-
-function DisplayAlignFromDescription(elem) {
-    var alignView = $("FormatForm").ALIGNMENT_VIEW;
-    if (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities") {
-        DisplayDynamicAlign(elem);
-    }
-    else {
-        location.href = "#" + elem.getAttribute("seqID");
-    }
-}
-
-//<a class="deflnDesc" hsp=<hsp_num> ind="<index>" gi="<gi>" id="deflnDesc_gi" href="#AlnHdrgi">desc</a>
-//<div class="alnHdr" gi="<gi>" id="alnHdr_<index>">
-function DisplayDynamicAlign(elem) {
-    var currGi = elem.getAttribute("gi");
-    var currInd = elem.getAttribute("ind");
-    var stat = elem.getAttribute("stat");
-    if (!currInd || !currGi) return;
-
-    if (!stat || stat == "") {
-        //Get 4(5) aligns before currInd and 4(5) aligns after
-        ReadCurrentSeqAligns(currInd, 5);
-    }
-    else if (stat == "read") {
-        var indexes = getCurrIndexRange(currInd);
-        if (indexes) {
-            var msgID = "alnShow_" + indexes[0];
-            location.href = "#" + msgID;
-        }
-    }
-    else {
-        //error status handling
-    }
-}
-
-
-function goToNextAlign(dtrID, next) {
-    var currInd = parseInt($(dtrID).getAttribute("ind"));
-    var rid = $("Rid").value;
-    nextInd = (next) ? currInd + 1 : currInd - 1;
-
-    if ($("deflnDesc_" + nextInd)) {
-        currGi = $("deflnDesc_" + nextInd).getAttribute("seqID");
-        scrollToGI = currGi;
-        if (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "") {
-
-            if (!next) {
-                ReadPrevSeqAligns(currInd, 5, scrollToGI);
-            }
-            else {
-                //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!!
-                ReadNextSeqAligns(currInd, 5, scrollToGI);
-            }
-
-        }
-        else {
-            location.href = "#" + scrollToGI;
-        }
-    }
-}
-
-function goToDefLine(dtrID) {
-    if ($("psiInp")) {
-        var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table
-        togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1";
-        jQuery($(togglerID)).ncbitoggler("open");
-    }
-}
-
-/*
-readAln.rid = rid;
-readAln.startIndex = parseInt(currInd);
-readAln.numSeq = parseInt(maxNumAligns);
-
-readAln.insertAfterID = insertAfterID;
-readAln.seqList = giList;
-readAln.scrollToSeqID = scrollToGI;
-*/
-function ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) {
-    var lastDispIdx = 0;
-    var rid = $("Rid").value;
-
-    var readAln = new Object();
-    readAln.seqList = ""; //giList
-    readAln.rid = rid;
-
-    currInd = parseInt(currInd);
-
-    if (currInd != 0 && $("deflnDesc_" + currInd)) {
-        var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_<ind>
-        //alert(par.id);
-        if (par) par = utils.getParent(par); //"alnShow_<ind>
-        //alert(par.id);
-        if (par) readAln.insertAfterID = par.id;
-    }
-    else {
-        readAln.insertAfterID = "alnStart";
-    }
-
-
-
-    readAln.startIndex = currInd + 1;
-    readAln.numSeq = maxNumAligns;
-
-    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next");
-
-    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : "";
-    readAln.hspSort = 0;
-    ReadSeqAlignByIndex(readAln);
-}
-
-function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) {
-    var lastDispIdx = 0;
-    var rid = $("Rid").value;
-
-    var readAln = new Object();
-    readAln.seqList = ""; //giList
-    readAln.rid = rid;
-
-    currInd = parseInt(currInd);
-
-
-    //sets readAln.insertAfterID and returns lastDispIdx;
-    //Find the index of the previously displayed alignment
-    lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
-
-    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
-    readAln.numSeq = currInd - readAln.startIndex;    //stopIndex = currInd
-
-    checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev");
-
-    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID");
-    readAln.hspSort = 0;
-    ReadSeqAlignByIndex(readAln);
-}
-
-//When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd
-function ReadCurrentSeqAligns(currInd, maxNumAligns) {
-    var rid = $("Rid").value;
-    var readAln = new Object();
-    readAln.seqList = ""; //giList
-    readAln.rid = rid;
-
-    currInd = parseInt(currInd);
-
-
-    //sets readAln.insertAfterID and returns lastDispIdx;
-    //Find the index of the previously displayed alignment
-    var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
-
-    //lastDispIdx = parseInt(lastDispIdx);
-    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
-    readAln.numSeq = parseInt(maxNumAligns * 2);
-
-    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr");
-
-    readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID");
-    readAln.hspSort = 0;
-    ReadSeqAlignByIndex(readAln);
-    g_DisableAutoCheck = true;
-    location.href = "#alnShow_" + readAln.startIndex;
-}
-
-
-
-
-function setupDynHSPParams(readAln)
-{
-    var currSeqInd = readAln.startIndex;
-    hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp"));
-    alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len"));
-    var maxDispLen = parseInt($("maxDispAlnLen").value);//20000
-    var minDispLen = parseInt($("minDispAlnLen").value);//2000
-    if (alnLen > maxDispLen) {
-        var lenPerMatch = alnLen / hspNum;
-        readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch);
-        readAln.AlignDbPageNum = 0;
-        $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize);
-    }
-}
-
-
-
-function getCurrSeqsAlnLen(currSeqInd)
-{
-    var alnLen = 0;
-    if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") || $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) {
-        alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len");
-    }
-    alnLen = (alnLen) ? parseInt(alnLen) : 0;
-    return alnLen;
-}
-
-function checkTotalAlignLen(startIndex,stopIndex)
-{
-    var dispAlnLen = 0;
-    var maxDispLen = parseInt($("maxDispAlnLen").value);
-    for (var i = startIndex; i <= stopIndex; i++) {
-        alnLen = getCurrSeqsAlnLen(i);
-        if (alnLen == 0) break;
-        dispAlnLen += alnLen;
-    }
-    return dispAlnLen;
-}
-//Get total align length for seq currSeqInd and
-//"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs
-function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType)
-{
-    var startIndex = readAln.startIndex;
-    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
-    if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current
-        startIndex = Math.max(startIndex, currSeqInd - countSeqs);
-        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs);
-    }
-    else if(dispType == "prev") {
-        startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs);
-        stopIndex = currSeqInd - 1;
-    }
-    else {//next
-        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1);
-    }
-    var totAlnLen = checkTotalAlignLen(startIndex,stopIndex);
-    return totAlnLen;
-}
-
-function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType)
-{
-    var maxDispLen = parseInt($("maxDispAlnLen").value);
-    var totAlnLen = 0;
-    var exc = false;
-    for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) {
-        totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType);
-        if(totAlnLen > maxDispLen) {
-            break;
-        }
-    }
-    if (totAlnLen > maxDispLen) {
-        if (numSeq != 0) numSeq--;
-        if (dispType == "curr") {
-            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq);
-            //prev + 1(curr) + next
-            readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq;
-        }
-        else if (dispType == "prev") {
-            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq);
-            readAln.numSeq = numSeq + 1;
-        }
-        else { //"next" - readAln.startIndex stays
-            readAln.numSeq = numSeq + 1;
-        }
-
-        if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") {
-            setupDynHSPParams(readAln);
-        }
-
-        exc = true;
-    }
-    return exc;
-}
-
-
-//readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set
-function ReadSeqAlignByIndex(readAln) {
-    var numAligns = 0;
-    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
-
-        if (!$("deflnDesc_" + i)) {
-            break;
-        }
-        if (!$("deflnDesc_" + i).getAttribute("stat") || $("deflnDesc_" + i).getAttribute("stat") == "") {
-            currGi = $("deflnDesc_" + i).getAttribute("seqFSTA");
-            if (readAln.seqList != "") readAln.seqList += ",";
-            readAln.seqList += currGi;
-            numAligns++;
-        }
-        else {
-            break;
-        }
-    }
-    if (readAln.seqList != "") {
-        readAln.numSeq = parseInt(numAligns);
-        ReadSeqAlignForSeqList(readAln);
-    }
-}
-
-
-var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2...
-//Find the range of indexes of displayed alignments for currAlnInd
-//Returns array of 2 startIndex, stopIndex
-function getCurrIndexRange(currAlinInd) {
-    var currRange;
-    var ranges = g_DisplayeAlignsRanges.split(",");
-    for (var i = 0; i < ranges.length; i++) {
-        var indexes = ranges[i].split("-");
-        if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) {
-            currRange = indexes;
-            break;
-        }
-    }
-    return currRange;
-}
-
-
-//Find the index of the previous  displayed alignment
-function getPrevDisplyedAlignInfo(currInd, readAln) {
-    readAln.insertAfterID = "alnStart";
-    lastDispIdx = 0;
-    for (var i = currInd - 1; i >= 1; i--) {
-        indexes = getCurrIndexRange(i);
-        if (indexes) {
-            lastDispIdx = indexes[1];
-            readAln.insertAfterID = "alnShow_" + indexes[0];
-            break;
-        }
-    }
-    return parseInt(lastDispIdx);
-}
-
-
-//setReadStatus
-function setSeqAlnReadStatus(readAln, status) {
-    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
-        if ($("deflnDesc_" + i)) {
-            jQuery($($("deflnDesc_" + i))).attr("stat", status);
-            if (status == "disp") {
-                g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex;
-            }
-        }
-    }
-}
-
-/*
-readAln.rid = rid;
-readAln.seqList = giList;
-readAln.startIndex = parseInt(idx);
-readAln.insertAfterID = insertAfterID;
-readAln.numSeq = parseInt(numSeq);
-readAln.scrollToSeqID = scrollToGI;
-*/
-function SendReadSeqAlinRequest(readAln) {
-    blastUrl = "t2g.cgi";
-
-    var rp = new RemoteDataProvider(blastUrl);
-
-
-    rp.onSuccess = function(obj) {
-        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
-
-        if ($("alnShow_" + readAln.startIndex)) {
-            var moreHspsLink = getNextHspsLink(readAln);
-            jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, {
-                'widgets': ['ncbipopper', 'ncbitoggler'],
-                'configs': {
-                    'ncbipopper': { hasArrow: true, arrowDirection: 'top' }
-                }
-            });
-            setSeqAlnReadStatus(readAln, "disp");
-            jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
-            //Saves start and stop indexes of loaded alignments in global variables
-            saveIdxesForAutomaticLoad(readAln);
-            jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) {
-                var seqID = this.getAttribute("seqID");
-                if(seqID) initAlignBatch(seqID);
-            });
-
-        }
-
-        if (readAln.scrollToSeqID) {
-            location.href = "#" + readAln.scrollToSeqID;
-        }
-
-    };
-    rp.onError = function(obj) {
-        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
-        jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
-        $("alnShowReal_" + readAln.startIndex).innerHTML = "<div class=\"erm\" id=\"erm_" + readAln.startIndex + "\">Error loading alignment ...<span class=\"db\">requests:" + this.iActiveRequests + " status:" + obj.status +
-                          "</span><a class=\"gbd\" href=\"#\" onclick=\"ReSubmitReadSeqAligns(event," + readAln.startIndex + ")\">Try again<\a></div>";
-    }
-    var params = constructURLParams(readAln);
-    if (readAln.numSeq == 1) {
-        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
-    }
-    params += "&SEQ_LIST_START=" + readAln.startIndex;
-
-    var formatParams = constructFormatParams();
-    params += formatParams;
-
-    //alert(params);
-    rp.Request(params);
-}
-
-
-function constructURLParams(readAln) {
-    var params;
-
-    if ($("useAlignDB") && $("useAlignDB").value == "true") {
-
-        var alignDbParams = "&USE_ALIGNDB=true";
-        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
-        if (batchID) {
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID");
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS");
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST");
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH");
-        }
-        alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList;
-        alignDbParams += "&HSP_SORT=" + readAln.hspSort;
-
-        if (readAln.hasOwnProperty("AlignDbPageNum")) {
-            alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum;
-            alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize;
-            alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum;
-        }
-
-        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams;
-    }
-    else {
-        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort;
-    }
-    if ($("phiPtInd")) {
-        params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value;
-    }
-    return params;
-}
-
-/*
-readAln.rid = rid;
-readAln.seqList = giList;
-readAln.startIndex = parseInt(idx);
-readAln.insertAfterID = insertAfterID;
-readAln.numSeq = parseInt(numSeq);
-readAln.scrollToSeqID = scrollToGI;
-*/
-/*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes
-2. Insert another div with id="alnShowReal_index and class="alnMsgR"
-3. For "alnShow_index" set atrr indexes="startInd-stopInd"
-4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this
-5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes
-6. Send read request
-*/
-
-function ReadSeqAlignForSeqList(readAln) {
-    var text = "<div id=\"alnShow_" + readAln.startIndex + "\" class=\"alnMsg\"><div class=\"alnMsgS\" id=\"alnMsg_" + readAln.startIndex + "\">Loading alignment...<span class=\"db\"> for sequences " + readAln.seqList;
-    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
-    var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : "";
-    text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "</span></div>";
-    text += "<div id=\"alnShowReal_" + readAln.startIndex + "\" class=\"alnMsgR\"></div></div>";
-    var debugControl = "<div id=\"debug\"></div>";
-    if (!$("debug")) {
-        jQuery($($("descriptions"))).before(debugControl);
-    }
-    if (!$("alnShow_" + readAln.startIndex)) {
-        jQuery($($(readAln.insertAfterID))).after(text);
-        jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex);
-        jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList);
-        g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex;
-        setSeqAlnReadStatus(readAln, "read");
-        $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex;
-
-        if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ",";
-        g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex;
-
-        SendReadSeqAlinRequest(readAln);
-    }
-    else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) {
-        jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden");
-        jQuery($("erm_" + readAln.startIndex)).remove();
-        SendReadSeqAlinRequest(readAln);
-    }
-}
-
-
-function ReSubmitReadSeqAligns(e,currInd) {
-    var rid = $("Rid").value;
-    if ($("alnShow_" + currInd)) {
-        var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes");
-        var range = indexRange.split("-");
-
-
-        var readAln = new Object();
-        readAln.seqList = ""; //giList
-        readAln.rid = rid;
-        readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist");
-        readAln.startIndex = parseInt(range[0]);
-        readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1;
-        readAln.hspSort = 0;
-        ReadSeqAlignForSeqList(readAln);
-        utils.preventDefault(e);
-    }
-}
-
-
-var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read"
-var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N
-var g_DisableAutoCheck = false;
-
-var g_autoStartIdx = new Array();
-var g_autoStopIdx = new Array();
-
-function saveIdxesForAutomaticLoad(readAln) {
-    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
-    g_autoStartIdx.push(readAln.startIndex); //1,20,25
-    g_autoStopIdx.push(stopIndex);  //4,24,29
-    $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex;
-}
-
-function getNextHspsLink(readAln)
-{
-    var moreHspsLink = ""
-    if (readAln.hasOwnProperty("AlignDbPageNum")) {
-        var nextPageNum = readAln.AlignDbPageNum + 1;
-        var currHspInd = readAln.AlignDbPageSize * nextPageNum;
-        var argstring = readAln.startIndex + "," + currHspInd;
-        var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId");
-        var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs");
-        var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
-        var prevHspInd = readAln.AlignDbPageSize * nextPageNum;
-        var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize);
-        var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1);
-
-        moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID);
-        moreHspsLink = moreHspsLink.replace(/@accs@/g, accs);
-        moreHspsLink = moreHspsLink.replace("@argstring@", argstring);
-        moreHspsLink = moreHspsLink.replace(/@segs@/g, segs);
-        moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps);
-        moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize);
-        moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd);
-        moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi);
-    }
-    return moreHspsLink;
-}
-
-
-function ReadNextHSPSet(currSeqInd, currHSPNum) {
-    var readAln = new Object();
-
-    readAln.rid = $("Rid").value;
-    readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA");
-    readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId");
-    dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps");
-    readAln.startIndex = currSeqInd;
-    readAln.numSeq = 1;
-    if (dynHsps) {
-        readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps);
-        readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve
-    }
-    if (currHSPNum != 0) {
-        readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1);
-        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum;
-    }
-    var sortLink = $("sa_" + readAln.gi);
-    readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0;
-    SendReadSeqAlinSortHSPRequest(readAln);
-}
-
-function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) {
-    ReadNextHSPSet(currSeqInd, currHSPNum);
-    utils.preventDefault(e);
-}
-
-
-
-function checkAutoAlignArray() {
-    var stop = false;
-    var start = false;
-    var currAlignViewPos = $("alignView").getBoundingClientRect().top;
-    if (currAlignViewPos < g_alignViewPos) {//scrolling down
-        g_alignViewPos = currAlignViewPos;
-        if (g_DisableAutoCheck) {
-            g_DisableAutoCheck = false;
-            return;
-        }
-        for (i = 0; i < g_autoStopIdx.length; i++) {
-            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) {
-                //alert("Reading more aligns scrolling down!");
-                var nextInd = parseInt(g_autoStopIdx[i] + 1);
-                var currInd = g_autoStopIdx[i];
-                if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "")) {
-                    ReadNextSeqAligns(currInd, 5);
-                    stop = true;
-                    break;
-                }
-            }
-        }
-        if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array
-    }
-    else if (currAlignViewPos > g_alignViewPos) {//scrolling up
-        g_alignViewPos = currAlignViewPos;
-        //here maybe return if autoStop found!!!
-        /* commenting automic read when scroll up */
-        for (i = 0; i < g_autoStartIdx.length; i++) {
-            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) {
-                //alert("Reading more aligns scrolling up!");
-                var currInd = g_autoStartIdx[i];
-                //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!!
-                if (currInd > 1) {
-                    ReadPrevSeqAligns(currInd, 5);
-                    start = true;
-                    break;
-                }
-            }
-        }
-        if (start) g_autoStartIdx.splice(i, 1);
-    }
-    /*end of comment*/
-}
-
-var g_alignViewPos = 0;
-
-function checkAutoAlignLoad() {
-
-
-    checkAutoAlignArray();
-
-    if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) {
-        //alert("bottom!");
-
-        if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") {
-            //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex
-            ReadNextSeqAligns(g_MaxDisplayedIndex, 5);
-        }
-    }
-}
-
-
-function GetPatternLocResults()
-{
-    form = $("results");
-    if (!form.PHI_PTTRN_INDEX) {
-        var el = document.createElement("input");
-        el.name = "PHI_PTTRN_INDEX";
-        el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
-        form.appendChild(el);
-    }
-    else {
-        form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
-    }
-    form.submit();
-}
-
-function goToNextHSP(elem, next) {
-    var par = jQuery(elem).parent(); //parent span with class="alnParLinks"
-    var parts = par[0].id.split("_"); //"hsp<seqid>_hspnum "hsp207524544_2"
-    if (parts[0].indexOf("nxHsp") != -1) {
-        parts[0] = parts[0].replace("nxHsp", "hsp");
-    }
-    nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1)
-
-    gotoElem = jQuery($(nextID));
-    if (gotoElem[0]) {
-        a = jQuery(gotoElem).offset();
-        window.scroll(0, a.top);
-    }
-
-    else {
-        retrieveNextHSP(parts[0],parts[1]);
-    }
-
-}
-
-
-//parts[0]//hsp<seqid>,    parts[1] hspnum
-function retrieveNextHSP(currLinkID, currHSPNum)
-{
-    var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id
-    var currSeqInd, totalHsps;
-    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
-        currSeqInd = parseInt(this.getAttribute("ind"));
-        totalHsps = parseInt(this.getAttribute("hsp"));
-        dynHsps = this.getAttribute("dynHsps");
-    });
-    currHSPNum = parseInt(currHSPNum);
-    if (currHSPNum < totalHsps && dynHsps) {
-        ReadNextHSPSet(currSeqInd, currHSPNum);
-    }
-}
-/********Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error********************************/
-function getUrlCompForEntryField(elem) {
-    var url = "";
-    if (elem && elem.value != "") {
-        url = "&" + elem.name + "=" + escape(elem.value);
-    }
-    return url;
-}
-
-
-function getUrlCompForCheckedField(elem) {
-    var url = "";
-    if (elem && elem.checked) {
-        url = "&" + elem.name + "=" + elem.value;
-    }
-    return url;
-
-}
-
-function getUrlCompForOptionsField(elem) {
-    var url = "";
-    if (elem) {
-        url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
-    }
-    return url;
-}
-/****************************************/
-
-function constructFormatParams() {
-    var formatParams = "";
-
-    if ($("queryList")) {
-        formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value;
-    }
-
-
-    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT);
-    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE);
-    formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI);
-    formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW);
-    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR);
-    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR);
-    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW);
-    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH);
-    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW);
-    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH);
-    formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH);
-
-
-    formatParams += getHiddenFieldParamString("BUILD_NAME");
-
-    var serviceType = "";
-    if ($("serviceType").value == "sra") {
-        serviceType = "sra";
-    }
-    else if ($("clientType").value == "TMSmart_restricted") {
-        serviceType = "restricted";
-    }
-    if (serviceType != "") {
-        formatParams += "&BOBJSRVC=" + serviceType;
-    }
-    if ($("currQuery").value != "") {
-        formatParams += "&CURR_QUERY_ID=" + $("currQuery").value;
-    }
-
-    return formatParams;
-}
-
-//readAln.seqList contains one gi only for this
-function SendReadSeqAlinSortHSPRequest(readAln) {
-    blastUrl = "t2g.cgi";
-    var rp = new RemoteDataProvider(blastUrl);
-
-
-    rp.onSuccess = function(obj) {
-        var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : "";
-        var alnHtml = obj.responseText + moreHspsLink;
-        initHSPRequest(readAln, obj.responseText + moreHspsLink,false);
-        if (readAln.scrollToSeqID) {
-            location.href = "#" + readAln.scrollToSeqID;
-        }
-    };
-    rp.onError = function(obj) {
-        var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
-        var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
-        if (!$(msgID)) {
-            var msg = "<div class=\"erm\" att=\"1\" id=\"" + msgID + "\">Error loading alignment ...<span class=\"db\">status:" + obj.status +
-                          "</span><a class=\"gbd\" href=\"#\" onclick=\"ReadNextHSPSetEvt(event," + readAln.startIndex + "," + currHspInd +
-                          ")\">Try again <span class=\"attmt\"></span> <\a></div>";
-            initHSPRequest(readAln, msg, true);
-        }
-        else {
-            var attNum = parseInt($(msgID).getAttribute("att")) + 1;
-            $(msgID).setAttribute("att", attNum);
-            jQuery($(msgID)).find(".attmt").each(function(index) {
-                jQuery(this).html(", attempt " + attNum);
-            });
-        }
-    }
-
-    var params = constructURLParams(readAln);
-    if (readAln.AlignDbPageSize) {
-        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
-    }
-    params += "&SORT_ONE_ALN=on";
-    var formatParams = constructFormatParams();
-
-    params += formatParams;
-
-    //alert(params);
-    rp.Request(params);
-}
-function initHSPRequest(readAln, alnHtml, err) {
-    var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
-    if (currHspInd != 0) {
-        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd;
-        jQuery($(readAln.insertAfterID)).after(alnHtml);
-        moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1);
-        jQuery($(moreHspsID)).remove();
-        if (!err) {
-            errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
-            jQuery($(errMsgID)).remove();
-        }
-    }
-    else {
-        jQuery($("alnAll_" + readAln.gi)).html(alnHtml);
-    }
-}
-
-function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544"
-    var readAln = new Object();
-
-
-    var desLineID = sortLink.id.replace("sa", "dtr"); //tr id
-    var seqInd;
-
-    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
-        seqInd = this.getAttribute("ind");
-    });
-
-    ReadNextHSPSet(parseInt(seqInd), 0);
-}
-
-
-function configDescriptions(e,btn,dlgId)
-{
-    var suffix = PsiBelowThresh(dlgId);
-    var colmnsInfId = "cfcDsInf" + suffix;
-    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
-    var showAllColId = "shcl" + suffix;
-    var chkBoxes = $C("checkbox", "type", $(dlgId), "input");
-    if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = "";
-    for (i = 0; i < chkBoxes.length; i++) {
-        var check;
-        if (utils.hasClass(btn, "cnc")) {//cancel
-            if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) {
-                check = true;
-            }
-            else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) {
-                check = false;
-            }
-        }
-        else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) {
-            check = true;
-        }
-        if (typeof (check) != 'undefined') {
-            chkBoxes[i].checked = check;
-            showHideCol(tblID,parseInt(chkBoxes[i].value), !check);
-        }
-        if (!utils.hasClass(btn, "cnc")) {
-            if (chkBoxes[i].checked) { //OK
-                if ($(colmnsInfId).value != "") $(colmnsInfId).value += ",";
-                $(colmnsInfId).value += chkBoxes[i].value;
-            }
-        }
-    }
-    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
-        jQuery($(showAllColId)).removeClass("hidden");
-    }
-    else {
-        jQuery($(showAllColId)).addClass("hidden");
-    }
-
-    var chConfig = $("cfcDsSave").value != $(colmnsInfId).value;
-
-    var cfds = document.getElementsByName("CONFIG_DESCR");
-    if (cfds) {
-        for (i = 0; i < cfds.length; i++) {
-            cfds[i].value = $(colmnsInfId).value;
-        }
-    }
-    $("cfcDsSave").value = $(colmnsInfId).value;
-    if (chConfig) SaveConfigTable();
-    jQuery(document.body).click();
-    utils.preventDefault(e);
-}
-
-
-
-function initDescConfig()
-{
-    initConfigColumns("dsConfig");
-    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
-        initConfigColumns("dsConfig_psiw");
-    }
-}
-
-
-function initConfigColumns(cnfDlgID)
-{
-    var suffix = PsiBelowThresh(cnfDlgID);
-    //cnfDlgID is "dsConfig[_psiw]"
-    var colmnsInfId = "cfcDsInf" + suffix;
-    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
-    var showAllColId = "shcl" + suffix;
-
-    if (navigator.userAgent.match(/ie/i)) {
-        if ($("FormatForm").NCBI_GI.checked || $("serviceType").value == "sra") {
-            jQuery($(tblID)).find("th.c1").each(function(index) {
-                db = getHiddenFieldVal("DATABASE");
-                var width = (db.match(/WGS/i) || db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em";
-                jQuery(this).css("width", width);
-            });
-        }
-    }
-
-    jQuery($(tblID)).find("tr.first").each(function(index) {
-        jQuery(this).find("a.dcs").each(function(index) {
-           jQuery(this).bind("click", function(e) { checkConfig(this); });
-        });
-    });
-
-    jQuery($(cnfDlgID)).find("button").each(function(index) {
-        jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); });
-    });
-
-
-    jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); });
-
-    $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR");
-    if ($(colmnsInfId).value == "" || $(colmnsInfId).value == "undefined") {
-        $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval");
-    }
-    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
-        jQuery($(showAllColId)).removeClass("hidden");
-    }
-    else {
-        jQuery($(showAllColId)).addClass("hidden");
-    }
-    var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input")
-    for (i = 0; i < chkBoxes.length; i++) {
-        jQuery(chkBoxes[i]).bind("click", configColumn);
-        if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) {
-            chkBoxes[i].checked = true;
-        }
-        else {
-            //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value);
-            showHideCol($(tblID), chkBoxes[i].value, true);
-        }
-    }
-}
-function showAllCol(e,elem)
-{
-    var suffix = PsiBelowThresh(elem.id);
-    var rdf = "dscRsDf" + suffix;
-    jQuery($(rdf)).click();//click "restore defaults'
-    utils.preventDefault(e);
-}
-
-
-function configColumn() {
-    var suffix = PsiBelowThresh(this.id);
-    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
-
-    cCls = "c" + this.value;
-    if (this.checked) {//show
-        showHideCol(tblID,parseInt(this.value), false);
-    }
-    else {
-        showHideCol(tblID,parseInt(this.value), true);
-    }
-}
-
-function showHideCol(tblID, columnIndex, hide) {
-
-    if ($("Transcr")) {
-        colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden");
-        hide = hide && !colHidden;
-        show = !hide && colHidden;
-    }
-    else {
-        show = !hide;
-    }
-    if (hide) {
-        jQuery($(tblID)).ncbigrid("hideColumn", columnIndex);
-    }
-    else if (show) {
-        jQuery($(tblID)).ncbigrid("showColumn", columnIndex);
-    }
-    if ($("Transcr") && (hide || show) ) {
-        var colsp = parseInt($("Transcr").getAttribute("colspan"));
-        colsp = (hide) ? colsp - 1 : colsp + 1;
-        $("Transcr").setAttribute("colSpan", colsp);
-        if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp);
-    }
-}
-
-function checkConfig(lnk) {
-    var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value;
-    lnk.href = lnk.href + cnfCol + "#sort_mark";
-}
-
-function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists
-{
-    var dflLineLinks = $C(seqID, "gi", document, "a");
-    for (i = 0; i < dflLineLinks.length; i++) {
-        jQuery(dflLineLinks[i]).click();
-        break;
-    }
-    location.href = dflLineLinks[i].href;
-}
-
-
-
-function initDescSelect()
-{
-
-    jQuery("#cntDesc").find("a").each(function(index) {
-        jQuery(this).bind("click", configDescrSelect);
-    });
-    jQuery("#cntSelN").click();
-    jQuery("#descTblCtrl").find("a[view]").each(function(index) {
-        jQuery(this).bind("click", DisplaySelectedView);
-    });
-    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
-        jQuery("#cntDesc_psiw").find("a").each(function(index) {
-            jQuery(this).bind("click", configDescrSelect);
-        });
-        jQuery("#cntSelN_psiw").click();
-        jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) {
-            jQuery(this).bind("click", DisplaySelectedView);
-        });
-    }
-
-
-    //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });??
-
-}
-
-function DisplaySelectedView(e) {
-    if (this.getAttribute("view") == "graph") {    //seqviewer
-        ViewSelectedSeqViewer(e,this);
-    }
-    else {
-        if (this.getAttribute("view") == "tree") {    //seqviewer
-            $("scrWidth").value = screen.width;
-            $("scrHeight").value = screen.height;
-        }
-        ViewSelectedSeqsEx(e, this);
-    }
-}
-
-function PsiBelowThresh(elemID)
-{
-    var suffix = "";
-    if (elemID.indexOf("_psiw") != -1) {
-        suffix = "_psiw";
-    }
-    return suffix;
-}
-
-function ViewSelectedSeqsEx(e,elem) {
-    var sbmForm = elem.getAttribute("frm");
-    var seqList = elem.getAttribute("seqList");
-
-    var cnfElem = utils.getParent(elem); //.cnf div
-    var suffix = PsiBelowThresh(cnfElem.id);
-    var tblID = "dscTable" + suffix;
-
-    $(seqList).value = createSelseqString(tblID,true);
-    $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces
-    if ($(seqList).value.indexOf("dbSNP") != -1) {
-        $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp
-        elem.href = $(sbmForm).action + $(seqList).value;
-        elem.target = "new";
-    }
-    else {
-        $(sbmForm).submit();
-        utils.preventDefault(e);
-    }
-}
-
-function ViewSelectedSeqsTree(e) {
-    $("scrWidth").value = screen.width;
-    $("scrHeight").value = screen.height;
-}
-
-function initSeqViewerGet(seqList) {
-    if (seqList.length >= 2000) {
-        seqList = seqList.substr(0,2000);
-        lastComma = seqList.lastIndexOf(",");
-        seqList = seqList.substr(0,lastComma);
-    }
-    $("seqViewParams").name = "RID";
-    $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]";
-}
-
-function ViewSelectedSeqViewer(e, elem)
-{
-    var cnfElem = utils.getParent(elem); //.cnf div
-    var suffix = PsiBelowThresh(cnfElem.id);
-    var tblID = "dscTable" + suffix;
-
-    //change to false when new verison of seqVier is installed in production
-    var seqList = createSelseqString(tblID, false);
-    $("sbmtGraphics").action = $("seqViewUrl").value;
-
-    var rp = new RemoteDataProvider("url2nc.cgi");
-    rp.onSuccess = function(obj) {
-        var jsnResp = JSON.parse(obj.responseText);
-        ncid = jsnResp.ncid;
-
-        if (ncid != "") {
-            $("seqViewParams").name = "rkey";
-            $("seqViewParams").value = ncid;
-        }
-        else {
-            initSeqViewerGet(seqList);
-        }
-        $("sbmtGraphics").submit();
-    };
-    rp.onError = function(obj) {
-        initSeqViewerGet(seqList);
-        $("sbmtGraphics").submit();
-        utils.preventDefault(e);
-    }
-    var params = $("ridParam").value + "[" + seqList + "]";
-    rp.Request(params, "POST");
-    utils.preventDefault(e);
-}
-
-function configDescrSelect(e) {
-    var sel = this.getAttribute("sel");
-    if (sel) {
-        var selNum = 0;
-        var check = (sel == "all") ? true : false;
-
-        var suffix = PsiBelowThresh(this.id);
-        var tblID = "dscTable" + suffix;
-        var toolbarID = "descTblCtrl" + suffix;
-        var selElID = "slcNum" + suffix;
-
-        jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
-            jQuery(this)[0].checked = check;
-            if (check) selNum++;
-        });
-        enableDescrLinks(selNum, toolbarID, selElID);
-    }
-    utils.preventDefault(e);
-}
-
-
-
-function enableDescrLinks(selNum, toolbarID, selElID) {
-    jQuery($(toolbarID)).find("a[minSlct]").each(function(index) {
-        var minSelected = this.getAttribute("minSlct");
-        minSelected = parseInt(minSelected);
-        if (selNum >= minSelected) {
-            this.removeAttribute("disabled");
-        }
-        else {
-            this.setAttribute("disabled", "disabled");
-        }
-    });
-    $(selElID).innerHTML = selNum;
-}
-
-
-
-function configDescrLinks(e, elem)
-{
-
-    ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false");
-    var par = jQuery(elem).parents(".jig-ncbigrid");//parent table
-    if (par) {
-        var suffix = PsiBelowThresh(par[0].id);
-        var tblID = "dscTable" + suffix;
-        var toolbarID = "descTblCtrl" + suffix;
-        var selElID = "slcNum" + suffix;
-
-        var currSelNum = parseInt($(selElID).innerHTML);
-        var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1;
-        enableDescrLinks(selNum, toolbarID, selElID);
-    }
-}
-/***Download code begin****/
-
-function initDownLoadPopup(dwnDialog) {
-
-    jQuery(dwnDialog).find("button").each(function(index) {
-        jQuery(this).bind("click", execDownLoad);
-    });
-
-    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
-}
-
-function initDescDownLoad() {
-    initDownLoadPopup($("dsDownload"));
-
-    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
-        initDownLoadPopup($("dsDownload_psiw"));
-    }
-}
-
-function initAlignDownLoad(navObj)
-{
-    var seqID = navObj.seqID;
-    var dwnDialog = $("dlgDwnl_" + seqID);
-    jQuery(dwnDialog).find("button").each(function(index) {
-        jQuery(this).bind("click", execDownLoad);
-    });
-
-    var dwnFSTW = $("dwFST_" + seqID);//whole seq
-    var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions
-
-    if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID);
-    if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID);
-
-    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
-}
-
-
-function execDownLoad(e) {
-    if (!utils.hasClass(this, "cnc")) {
-        par = utils.getParent(this);
-        dwnDialog = utils.getParent(par); //parent dialog with popDl class
-        var descr = (this.id == "dw_cont" || this.id == "dw_cont_psiw") ? true : false;
-        jQuery(dwnDialog).find("input").each(function(index) {
-            if (this.checked) {
-                submitDownLoad(this, descr);
-            }
-        });
-    }
-    jQuery(document.body).click();
-    utils.preventDefault(e);
-}
-
-function submitDownLoad(radioElem, descr) {
-    var toolURL = radioElem.getAttribute("url");
-    if (toolURL) {
-        if (descr) {
-            var getGi = radioElem.getAttribute("getGi");
-            getGi = (getGi) ? true : false;
-
-            var tblID = "dscTable";
-            var suffix = PsiBelowThresh(radioElem.id);
-            tblID += suffix;
-
-            $("selDnSeqs").value = createSelseqString(tblID,getGi);
-        }
-        else {
-            var seqfsta = radioElem.getAttribute("seqfsta");
-            $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi");
-        }
-        var addParams = "";
-        if (radioElem.getAttribute("addParam")) {
-            addParams = addDwnlParams();
-        }
-        var submitName = radioElem.getAttribute("sbName")
-        $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST";
-        $("dwdlSubmit").action = toolURL + addParams;
-        $("dwdlSubmit").submit();
-    }
-    else {
-        var sbFunction = radioElem.getAttribute("sbFunc");
-        if (sbFunction) {
-            eval(sbFunction + "(radioElem, descr)");
-        }
-    }
-}
-
-
-function initDownLoadFSTA(radioElem, descr)
-{
-    if (descr) {
-
-        var tblID = "dscTable";
-        var suffix = PsiBelowThresh(radioElem.id);
-        tblID += suffix;
-
-        $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false);
-    }
-    else {
-        $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta");
-    }
-    $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType");
-
-    $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE");
-    if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox
-        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
-        if (batchID) {
-            $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID");
-            $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS");
-            $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST");
-            $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH");
-        }
-    }
-    $("sbmtFASTA").submit();
-}
-
-function createSelseqString(tblID,getGi) {
-    var selSeqs = "";
-    jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
-        if (jQuery(this)[0].checked) {
-            if (selSeqs != "") selSeqs += ",";
-            if (getGi) {
-                selSeqs += jQuery(this)[0].value;
-            }
-            else {
-                var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc");
-                selSeqs += $(linkID).getAttribute("seqFSTA");
-            }
-        }
-    });
-    return selSeqs;
-}
-
-/***Download code end****/
-
-/***Init navigation code begin **/
-
-function initNavigation(navObj) {
-    initNextAlnLink(navObj, true);
-    initNextAlnLink(navObj, false);
-}
-
-
-function initNavInfo(navObj) {
-    var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind"));
-    nextInd = currInd + 1;
-    prevInd = currInd - 1;
-
-    navObj.currSeqID = "";
-    navObj.nextSeqID = "";
-    navObj.prevSeqID = "";
-
-    if ($("deflnDesc_" + nextInd)) {
-        navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs");
-        if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA");
-    }
-    if ($("deflnDesc_" + prevInd)) {
-        navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs");
-        if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA");
-    }
-    if ($("deflnDesc_" + currInd)) {
-        navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA");
-    }
-}
-
-
-function initNextAlnLink(navObj, next) {
-
-    var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID);
-    var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID;
-
-    if (nextLinkEl) {
-        if (nextSeqid != "") {
-            var text = (next) ? "next" : "previous";
-            nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid);
-        }
-        else {
-            nextLinkEl.setAttribute("disabled", "disabled");
-        }
-    }
-}
-function scan(link) {
-    var init = link.getAttribute("init");
-    if (!init) {
-        ncbi.sg.scanLinks(link);
-        link.setAttribute("init","on");
-    }
-}
-
-function initWidth(seqID) {
-    var lineLengthElem = $("FormatForm").LINE_LENGTH;
-    var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
-    if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
-
-    var relWidth = (lineLength > 90) ? "12%" : "15%";
-    var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
-    lineLength = (lineLength + parseInt(17)) * charWidth;
-    var width = lineLength + "px";
-    jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) {
-        jQuery(this).css("width", width);
-    });
-    jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) {
-        jQuery(this).css("width", width);
-    });
-    jQuery($("relInf_" + seqID)).css("width", relWidth);
-}
-
-
-/***Init navigation code end **/
-function initAlignBatch(seqID)
-{
-    var navObj = new Object();
-    navObj.seqID = seqID;
-    initNavInfo(navObj);
-
-    initAlignDownLoad(navObj);
-    initNavigation(navObj);
-    ncbi.sg.scanLinks($("alnNxt_" + seqID));
-    ncbi.sg.scanLinks($("alnPrv_" + seqID));
-    if ($("serviceType").value == "vecscreen") {
-        utils.addClass($("alnDsc_" + seqID), "hidden");
-    }
-    ncbi.sg.scanLinks($("alnDwnld_" + seqID));
-    jQuery($("csLinks_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("relInf_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("rng_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("dln_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    initWidth(seqID);
-/*
-    jQuery($("alnHdr_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("aln_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-*/
-}
-
-function SaveConfigTable() {
-    blastUrl = "fmtsave.cgi";
-
-
-    var rp = new RemoteDataProvider(blastUrl);
-
-
-    rp.onSuccess = function(obj) {
-        //alert("success");
-    };
-    rp.onError = function(obj) {
-        //alert("error");
-    }
-
-    var program = getHiddenFieldVal("PROGRAM");
-    var rid = getHiddenFieldVal("RID");
-    var blastSpec = getHiddenFieldVal("BLAST_SPEC");
-    var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value;
-    if(blastSpec) {
-        params += "&BLAST_SPEC=" + blastSpec;
-    }
-    rp.Request(params,"POST");
-}
-
-function removeRID() {
-    var rid = document.getElementsByName("RID");
-    for (var i = 0; i <= rid.length; i++) {
-        jQuery(rid[i]).remove();
-    }
-}
-
-function initAdvancedView()
-{
-    if ($("dsConfig")) {
-
-        var alnView = getHiddenFieldVal("ALIGNMENT_VIEW");
-        if (alnView == "Pairwise" || alnView == "PairwiseWithIdentities") {
-            var rid = getHiddenFieldVal("RID");
-            ReadNextSeqAligns(0, 5);
-            g_alignViewPos = $("alignView").getBoundingClientRect().top;
-            utils.addEvent(window, "scroll", checkAutoAlignLoad, false);
-        }
-        list = $("phiPtInd");
-        if (list) {
-            utils.addEvent(list, "change", GetPatternLocResults, false);
-        }
-        initDescConfig();
-        initDescSelect();
-        initDescDownLoad();
-        if ($("psiInp")) {
-            var nextIter = document.getElementsByName("NEXT_I");
-            for (var i = 0; i < nextIter.length; i++) {
-                utils.addEvent(nextIter[i], "click", removeRID, false);
-            }
-        }
-    }
-}
-
-//takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4"
-function initjQry()
-{
-    var oldCreate = jQuery.ui.ncbipopper.prototype._create;
-    jQuery.ui.ncbipopper.prototype._create = function() {
-        var destSelector = this.options.destSelector || this.options.sourceSelector || this.element.prop("hash");
-        this.options.destSelector = destSelector.replace(/\./g, "\\.");
-        oldCreate.apply(this, arguments);
-    }
-}
-utils.addEvent(window,
-				"load", initAdvancedView,
-				false);
-
-initjQry()
-
-/* If user agent has "safari" in it, include safari-specific stylesheet. */
-if (navigator.userAgent.match(/ie/i)) {
-    document.write("<link rel='stylesheet' type='text/css' href='css/ie-descriptions.css'  media='screen'/>");
-}
-/*****************************new code end*********************************************************************/
Binary file Blast output page example_files/helix.gif has changed
--- a/Blast output page example_files/jig.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-.ui-helper-hidden{display:none;}.ui-helper-hidden-accessible{position:absolute;left:-99999999px;}.ui-helper-reset{margin:0;padding:0;border:0;outline:0;line-height:1.3;text-decoration:none;font-size:100%;list-style:none;}.ui-helper-clearfix:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-helper-clearfix{display:inline-block;}/* required comment for clearfix to work in Opera \*/ * html .ui-helper-clearfix{height:1%;}.ui-helper-clearfix{display:block;}/* end clearfix */ .ui-helper-zfix{width:100%;height:100%;top:0;left:0;position:absolute;opacity:0;filter:Alpha(Opacity=0);}.ui-state-disabled{cursor:default!important;}.ui-icon{display:block;text-indent:-99999px;overflow:hidden;background-repeat:no-repeat;}.ui-widget-overlay{position:absolute;top:0;left:0;width:100%;height:100%;}.ui-widget{font-size:1.1em;}.ui-widget-content{border:1px solid #aaa;background:#fff url(images/ui-bg_flat_75_ffffff_40x100.png) 50% 50% repeat-x;color:#222;}.ui-widget-content a{color:#222;}.ui-widget-header{border:1px solid #aaa;background:#ccc url(images/ui-bg_highlight-soft_75_cccccc_1x100.png) 50% 50% repeat-x;color:#222;font-weight:bold;}.ui-widget-header a{color:#222;}.ui-state-default,.ui-widget-content .ui-state-default{border:1px solid #d3d3d3;background:#e6e6e6 url(images/ui-bg_glass_75_e6e6e6_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#555;}.ui-state-default a,.ui-state-default a:link,.ui-state-default a:visited{color:#555;text-decoration:none;}.ui-state-hover,.ui-widget-content .ui-state-hover,.ui-state-focus,.ui-widget-content .ui-state-focus{border:1px solid #999;background:#dadada url(images/ui-bg_glass_75_dadada_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#212121;}.ui-state-hover a,.ui-state-hover a:hover{color:#212121;text-decoration:none;}.ui-state-active,.ui-widget-content .ui-state-active{border:1px solid #aaa;background:#fff url(images/ui-bg_glass_65_ffffff_1x400.png) 50% 50% 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--- a/Blast output page example_files/jquery.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
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\ No newline at end of file
--- a/Blast output page example_files/jquery.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
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-over:function(){if(a._isActive){var b=jQuery(this),c=b.parent();if(c.has("ul").length===0){c=c.siblings("li.selected").removeClass("selected");a.closeSub(c);b.focus()}else c.hasClass("selected")||b.focus().click()}},out:function(){}};this.element.find(">li:not(:has(ul))>a,li:has(ul)>a").hoverIntent(d)}},_destroyEvents:function(){jQuery(window).off("click",this._windowClickFnc);this._windowClickFnc=null;this.element.off("blur","a",this._blurFnc);this._blurFnc=null;this.element.find(">li:not(:has(ul))>a,li:has(ul)>a").unbind("mouseover mouseoff");
-this.element.find("li").not(":has(ul)").find("a").off("click",this._unselectEverythingFnc)},_addAjaxEvents:function(){if(this.element.find(">li:has(a.expandDown)").not(":has(ul)").length>0){var a=this;this._ajaxEnterFnc=function(){a._loadAjaxContent()};this.element.on("mouseenter",this._ajaxEnterFnc)}},_loadAjaxContent:function(){var a=this;this.element.off("mouseenter",this._ajaxEnterFnc);this._ajaxEnterFnc=null;var d=this.element.find("a.expandDown"),b=d.eq(0).prop("href").split("#");jQuery("<div/>").load(b[0],
-function(){a._handleAjaxLoadCallback(this,d)})},_handleAjaxLoadCallback:function(a,d){var b=jQuery(a);d.each(function(){var c=jQuery(this),e=c.prop("href").split("#")[1];e=b.find("#"+e);if(e[0].tagName.toLowerCase()==="li")e=e.find(">ul");c.parent().append(e)});this._createMenus();this._addEvents()},_checkFocus:function(){function a(){d.element.find("a:focus").length===0&&d._unselectEverything()}var d=this;window.setTimeout(a,10)},_addListeners:function(){var a=this;this.element.find(">ul").andSelf().on("ncbibasicmenuunselected",
-function(d,b,c,e){e==="click"&&a.closeSub(c)}).on("ncbibasicmenuselected",function(d,b,c,e){if(e==="click")a.openSub(c);else{d=c.siblings().find("ul:visible");if(d.length>0){d.each(function(){a.closeSub(jQuery(this))});c.parent("ul").hasClass("ui-ncbimenu")&&a.openSub(c)}}}).on("ncbibasicmenuactiondown ncbibasicmenuactionright",function(d,b){b=jQuery(b);var c=b.find(">ul");if(b.hasClass("selected"))c.length===1&&c.not(":visible")&&a.openSub(b);else b.find(">a").click();c.length===1&&window.setTimeout(function(){c.ncbibasicmenu("selectFirstItem")},
-10)}).on("ncbibasicmenuactionup ncbibasicmenuactionleft ncbibasicmenuescape",function(d,b){b=jQuery(b);d=b.find(">ul");if(d.length>0&&d.is(":visible"))a.closeSub(jQuery(b));else{b=b.parent("ul").parent("li");b.find(">a").focus();a.closeSub(b)}})},_destroyListeners:function(){this.element.find("ul").andSelf().off("ncbibasicmenuunselected").off("ncbibasicmenuselected")},openSub:function(a){var d=a.find(">ul");if(d.length===1){this._isActive=true;var b=a.parent().find("li:has(ul:visible)");b.length>
-0&&this.closeSub(b);if(a.parent().hasClass("orientation_hort")){b="left bottom";var c="fit flip"}else{b="right center";c="flip fit"}d.show().position({of:a,my:"left top",at:b,collision:c}).attr("aria-hidden","false")}},closeSub:function(a){(a.is("li")?a.find("ul"):a).find("ul").andSelf().not(".ui-ncbimenu").hide().attr("aria-hidden","true").end().ncbibasicmenu("removeAllSelections").find("li.selected").removeClass("selected")},_unselectEverything:function(){this.closeSub(this.element.find("ul:visible").andSelf());
-this._isActive=false}});
--- a/Blast output page example_files/jquery_002.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-.ui-ncbigrid-outer-div{min-width:300px;}table.ui-ncbigrid td{padding:.363em .637em;}table.ui-ncbigrid th{padding:.308em .539em;text-align:left;border-left:0;border-top:0;font-weight:normal;}table.ui-ncbigrid thead th{border-bottom:1px solid #d4dfe9;border-right:1px solid #cfcfcf;background:#F0F0F0;background:-moz-linear-gradient(top,#FFF 0,#F0F0F0 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#F0F0F0));}table.ui-ncbigrid tbody th{line-height:1.333em;color:#333;font-size:.923em;border-bottom:1px solid #d4dfe9;border-right:1px solid #cfcfcf;background:#FAFAFA;background:-moz-linear-gradient(top,#FFF 0,#FAFAFA 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#FAFAFA));}table.ui-ncbigrid th:last-child{border-right:0;*margin-right:-1px;}table.ui-ncbigrid td{border:0;}table.ui-ncbigrid td input[type="checkbox"]{margin:0;}table.ui-ncbigrid thead,table.ui-ncbigrid tbody,table.ui-ncbigrid colgroup,table.ui-ncbigrid col,table.ui-ncbigrid tr{border:0!important;}table.ui-ncbigrid,table.ui-ncbigrid thead,table.ui-ncbigrid caption{margin:0;}.ui-ncbigrid-outer-div{position:relative;zoom:1;margin:1em 0 2.8em 0;}div.caption-exists,div.filterToolbar-exists{margin:3em 0;}table.ui-ncbigrid{border-width:0;}.ui-ncbigrid-inner-div{border-color:#97b0c8;border-style:solid;}.ui-ncbigrid-inner-div{border-width:0 0 1px 0;clear:both;}.ui-ncbigrid-outer-div{border:1px solid #97b0c8;}.ui-ncbigrid-outer-div:after{clear:both;content:'.';display:block;height:0;visibility:hidden;font-size:0;}.ui-ncbigrid-header-wrapper{height:auto;max-width:100%;}.ui-ncbigrid-header-wrapper table.ui-ncbigrid{border:0;height:auto;}.ui-ncbigrid-header-wrapper thead{border-width:1px 0 0 0;}table.ui-ncbigrid caption{color:#4D4D4D;font-size:.923em;font-weight:bold;padding:0;position:absolute;text-align:left;top:-2.077em;zoom:1;}.ui-ncbigrid-filter-toolbar{clear:both;display:block;font-size:.923em;line-height:27px;position:absolute;right:0;text-align:right;top:-2.417em;width:auto;}.ui-ncbigrid-filter-toolbar input[type="text"]{font-size:inherit!important;height:1.091em;padding:0;margin-right:-1px;}.ui-ncbigrid-paged-toolbar{display:block;clear:both;width:100%;}.ui-ncbigrid-paged-countItems,.ui-ncbigrid-checkbox-toolbar{font-size:.923em;}.ui-ncbigrid-paged-toolbar div{float:left;display:inline-block;width:auto;margin-right:1em;}.ui-ncbigrid-paged-toolbar .ui-ncbigrid-paged-pageControl{margin-right:0;}.ui-ncbigrid-paged-countItems{text-align:center;}.ui-ncbigrid-paged-pageControl{text-align:right;font-size:.923em;}.ui-ncbigrid-paged-pageControl .prev{margin-left:.2em;margin-right:.6em;}.ui-ncbigrid-paged-pageControl .next{margin-left:.6em;margin-right:.2em;}.ui-ncbigrid-paged-toolbar-bottom{border-top:0;}.ui-ncbigrid-select-question{clear:both;text-align:center;display:none;padding:.385em 0 .308em;border-style:solid;border-color:#d4dfe9;border-width:1px 0;background:-moz-linear-gradient(top,#FFF 0,#F5F5F5 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#F5F5F5));font-size:.923em;}.ui-ncbigrid-select-question-footer{background:#fff;border-bottom:0;}.ui-ncbigrid-select-question .ui-ncbigrid-select-row-count{font-weight:bold;}.ui-ncbigrid-select-question a{margin-left:.583em;}.ui-ncbigrid-checkbox-toolbar label{margin-left:1em;}.ui-ncbigrid-checkbox-toolbar label:first-child{margin-left:0;}.ui-ncbigrid-checkbox-toolbar a,.ui-ncbigrid-checkbox-toolbar a:visited{color:#369;}.ui-ncbigrid-checkbox-toolbar,.ui-ncbigrid-paged-toolbar{width:auto;}.ui-ncbigrid-checkbox-toolbar{float:left;clear:left;padding:.416em .416em .416em .583em;line-height:1.75em;}.ui-ncbigrid-paged-toolbar{float:right;clear:right;padding:.385em .385em .385em .539em;line-height:1.615em;}table.ui-ncbigrid{border-collapse:separate;width:100%;}div.ui-ncbigrid-scroll{height:20em;overflow-y:auto;overflow-x:hidden;}div.ui-ncbigrid-scroll table.ui-ncbigrid{border-top:0;border-bottom:0;width:100%;}div.ui-ncbigrid-scroll table.ui-ncbigrid caption,div.ui-ncbigrid-scroll>table.ui-ncbigrid>thead>tr>th{visibility:hidden;line-height:0;border-bottom:0;border-top:0;padding-top:0;padding-bottom:0;}div.ui-ncbigrid-scroll table.ui-ncbigrid tbody tr:first-child td{border-top:0;}div.ui-ncbigrid-header-wrapper{width:100%;overflow:hidden;}div.ui-ncbigrid-hort-scroll{overflow-x:auto;}tr.ui-ncbigrid-rowHidden{display:none;}table.ui-ncbigrid th.sortAsc a,table.ui-ncbigrid th.sortDsc a,table.ui-ncbigrid th.sortNone a{padding-right:21px;background-repeat:no-repeat;background-position:right center;color:#333;}table.ui-ncbigrid th.sortAsc,table.ui-ncbigrid th.sortDsc{background:#fff;}table.ui-ncbigrid th.sortAsc a{background-image:url('../img/sorted_asc.gif');}table.ui-ncbigrid th.sortDsc a{background-image:url('../img/sorted_dsc.gif');}table.ui-ncbigrid th.sortNone a{background-image:none;color:#14376c;}table.ui-ncbigrid th.sortNone a:hover{background-image:url('../img/sorted_non.gif');color:#985735;}table.ui-ncbigrid th a{display:block;text-decoration:none;_width:100%;padding-right:21px;border:0;}table.ui-ncbigrid th a:hover,table.ui-ncbigrid th a,table.ui-ncbigrid th a:active{border:0!important;}table.ui-ncbigrid th,table.ui-ncbigrid th a{color:#14376c;}table.ui-ncbigrid tbody tr.ui-ncbigrid-checkbox-selected td,table.ui-ncbigrid tr.ui-ncbigrid-row-selected td{background-color:#eaf0f4;}table.ui-ncbigrid tbody tr.ui-ncbigrid-checkbox-hover td,table.ui-ncbigrid tr.ui-ncbigrid-row-hover>td{background-color:#D5DEE3;}table.ui-ncbigrid tr.ncbigrid-row-filtered{display:none;}td.ui-ncbigrid-column-hidden,th.ui-ncbigrid-column-hidden{display:none;}table.ui-ncbigrid tbody tr.ui-ncbigrid-high>td{background-color:#eaf0f4;}.ui-ncbigrid-paged-pageControl{margin-top:0;}.ui-ncbigrid-paged-pageControl input[type="text"]{height:1.091em;font-size:inherit!important;padding:0;}.ui-ncbigrid-paged-pageControl span.page_link{color:#ccc;padding:1px 7px;}.ui-ncbigrid-paged-pageControl a.page_link{border:1px solid #ddd;padding:2px 6px;*padding:0 4px;white-space:nowrap;text-decoration:none;}.ui-ncbigrid-paged-pageControl a.page_link:hover{color:#985735;}.ui-ncbigrid tbody tr.collapsed{display:none;}.ui-ncbigrid tbody tr th span.collapsableTbodyIcon{float:left;margin-right:.833em;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big{background-position:left -30px;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big-open{background-position:left 0;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big,.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big-open{background-color:transparent;background-image:url("../img/ncbitoggler-plus-minus-big.gif");background-repeat:no-repeat;margin-left:-0.1em;top:.2em;}.ui-ncbigrid-collapsable,.ui-ncbigrid-collapsable span{cursor:pointer;}table.ui-ncbigrid .ignoreCollapse{cursor:default;}.ui-ncbigrid-outer-div .ui-ncbigrid-outer-div{margin:0;*position:static;}
\ No newline at end of file
--- a/Blast output page example_files/jquery_002.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-(function(e){e.widget("ui.ncbitoggler",{styles:{ariaWrapper:"ui-ncbitoggler-live",groupMasterReplaceNode:"span.ui-ncbitoggler-group-replace-txt",groupMasterStateClose:"ui-ncbitoggler-group-master-to-close",groupMasterStateOpen:"ui-ncbitoggler-group-master-to-open",master:"ui-ncbitoggler",masterOpen:"ui-ncbitoggler-open",target:"ui-ncbitoggler-slave",targetOpen:"ui-ncbitoggler-slave-open",icon:"ui-icon-triangle-1-e",iconOpen:"ui-icon-triangle-1-s",iconPlusMinusBig:"ui-icon-plus-minus-big",iconPlusMinusBigOpen:"ui-icon-plus-minus-big-open",
-iconArrowStop:"ui-icon-arrowthickstop-1-s",iconArrowStopOpen:"ui-icon-arrowthickstop-1-n"},options:{animation:"slide",closedAppendText:"",cookieNamePrefix:"jig-tog-rem-",indicator:"small-arrow",initOpen:false,isIcon:true,liveRegions:true,openedAppendText:"",remember:false,speed:50,targets:""},_cachedTargetData:{},_create:function(){this._setOption("disabled",false);this.appendTextNode=this.initTargetsClass=this.iconSpan=this.startOpen=this.rememberCookie=this.remember=this.cookieName=this.addedHref=
-null;var a=this.element,b=a[0],c=this.styles,d=this,f=this.options.isIcon;a.data("isOpen",false);a.addClass("ui-widget ui-ncbitoggler");f||a.addClass("ui-ncbitoggler-no-icon");var g=a.attr("href");!g?(this.addedHref=true):(this.addedHref=false);this._validate(g);a.children("span.ui-ncbitoggler-master-text").length===0&&a.contents().filter(function(){return this.nodeType===3}).each(function(){var h=e(this);jQuery.trim(this.nodeValue).length>0&&h.wrap('<span class="ui-ncbitoggler-master-text"></span>')});
-if(this.options.openedAppendText!==""||this.options.closedAppendText!==""){this.appendTextNode=a.children("span.ui-ncbitoggler-appended-text");if(this.appendTextNode.length===0)if(!this.initOpen){this.appendTextNode=e('<span class="ui-ncbitoggler-appended-text">'+this.options.closedAppendText+"</span>");a.find(".ui-ncbitoggler-master-text").after(this.appendTextNode)}}if(this.remember=this.options.remember||false){g=this.element.attr("id");if(!g){window.console&&console.error&&console.error("ncbitoggler: master node "+
-b+" must have a unique id attribute when remembering state");return}this.cookieName=this.options.cookieNamePrefix+g;this.rememberCookie=e.cookie(this.cookieName)}if(this.startOpen=this.rememberCookie?this.rememberCookie==="open"?true:false:a.hasClass("jig-ncbitoggler-open")||a.hasClass(c.masterOpen)||this.options.initOpen?true:false){this.element.data("isOpen",true);a.removeClass(this.styles.master);a.addClass(c.masterOpen);this._targetsOpen=true}else{this.element.data("isOpen",false);a.removeClass(this.styles.masterOpen);
-a.addClass(c.master)}f&&this._initMasterIcon();this.targets=this._getTargets();this.targets.addClass("ui-ncbitoggler").removeClass("ui-ncbitoggler-disabled ui-state-disabled");if(this.startOpen){this.targets.removeClass(c.target);this.targets.addClass(c.targetOpen);this.initTargetsClass=c.targetOpen}else{this.targets.removeClass(c.targetOpen);this.targets.addClass(c.target);this.initTargetsClass=c.target}this._initAria();this._doGrouping();a.click(function(h){d.toggle(h,d)});this._saveReferences()},
-_getGroupMaster:function(){for(var a=this.styles,b=this.element[0].className.split(/\s+/),c=0;c<b.length;c++){var d=b[c].match(/ui-ncbitoggler-group-(.+)$/);if(d){d=d[1];var f=e("a.ui-ncbitoggler-group-open-"+d+", a.ui-ncbitoggler-group-close-"+d,this.options.contextNode);if(f.length===1){f.hasClass("ui-ncbitoggler-group-open-"+d)&&f.addClass(a.groupMasterStateOpen);f.hasClass("ui-ncbitoggler-group-close-"+d)&&f.addClass(a.groupMasterStateClose);return f}}}},_doGrouping:function(){var a=this._getGroupMaster();
-if(a){var b=this,c=this.styles,d=a.data("togglers");this.element.id||e.ui.jig._generateId(this.widgetName);if(!this.element[0].id)this.element[0].id=e.ui.jig._generateId(this.widgetName);if(typeof d==="undefined"){a.data("togglers",[]);a.data("togglers").push(this.element)}else d.push(this.element);var f=a.find(c.groupMasterReplaceNode);a.click(function(g){g.preventDefault();g=a.data("togglers");g=g[g.length-1][0];if(a.hasClass(c.groupMasterStateOpen)){b.open();f.length>0&&f.text(b.options.groupMasterCloseReplaceText);
-b.element[0]===g&&a.removeClass(c.groupMasterStateOpen).addClass(c.groupMasterStateClose)}else{b.close();f.length>0&&f.text(b.options.groupMasterOpenReplaceText);b.element[0]===g&&a.removeClass(c.groupMasterStateClose).addClass(c.groupMasterStateOpen)}})}},_initAria:function(){var a=this.startOpen;this.element.attr({role:"button","aria-expanded":a});this.options.liveRegions&&this.targets.each(function(){var b=e(this);b.find("table").length===0&&!b.parent("div").hasClass("ui-helper-reset")&&b.wrap('<div class="ui-helper-reset" aria-live="assertive">');
-b.attr("aria-hidden",a?"false":"true")})},_validate:function(a){var b=this.element,c=["a"],d=b[0].tagName.toLowerCase();if(e.inArray(d,c)===-1)throw new Error("ncbitoggler: master node must be one of the following elements: "+c.toString());a||b.attr("href","#")},_initMasterIcon:function(){var a=this.element,b=this.styles;if(this.options.indicator=="plus-minus-big"){this.iconOpenClass=b.iconPlusMinusBigOpen;this.iconCloseClass=b.iconPlusMinusBig}else if(this.options.indicator=="arrow-stop"){this.iconOpenClass=
-b.iconArrowStopOpen;this.iconCloseClass=b.iconArrowStop}else{this.iconOpenClass=b.iconOpen;this.iconCloseClass=b.icon}this.iconSpan=a.find("span.ui-icon");if(this.iconSpan.length===0){this.iconSpan=e('<span class="ui-icon"></span>');this.startOpen?this.iconSpan.addClass(this.iconOpenClass):this.iconSpan.addClass(this.iconCloseClass);a.append(this.iconSpan)}else if(this.startOpen){this.iconSpan.removeClass(this.iconCloseClass);this.iconSpan.addClass(this.iconOpenClass)}},getSlaves:function(){return this._targets},
-getTargets:function(){return this.getSlaves()},_getTargets:function(){var a=this.element,b=a.attr("toggles")||a.attr("data-ncbitoggler-toggles");if(b)jQuery.ui.jig._isConsole("warn")&&console.warn('The attributes "toggles" and "data-ncbitoggler-toggles" are deprecated. Please use the "targets" attribute instead (see documentation).');else b=this.options.targets;if(b&&typeof b=="object"){b=b;a="";for(var c in b)a+=c+", ";a=a.replace(/,\s$/,"");c=e(a)}else if(b){c=e(b);if(c.length===0){this.isSibling=
-false;c=b.split(/ +/);b="";for(a=0;a<c.length;a++)b+=a!==c.length-1?"#"+c[a]+",":"#"+c[a];c=e(b)}}else if(a.parent(":header").length>0){a.parent(":header").parent().css("zoom","1");this.isSibling=true;c=a.parent(":header").css("zoom","1").next()}else{this.isSibling=true;c=a.next()}return this._targets=this._normalizeTargets(c)},_normalizeTargets:function(a){var b=[];a.each(function(){var c=this,d=e(this);if(d.hasClass("ui-helper-reset"))c=d.children().get(0);b.push(c)});return ret=e(b)},_getCachedTargetData:function(a){return this._cachedTargetData[a]},
-_cacheTargetData:function(a,b){this._cachedTargetData[a]=b},_openAjaxTarget:function(a,b){var c=this,d=this._getCachedTargetData(a);d?e(a).html(d):e.get(b,function(f){c._cacheTargetData(a,f);e(a).html(f)})},_openTargets:function(){if(!(this._targetsOpening||this._targetsClosing||this._targetOpen)){this._targetsOpening=true;var a=this.targets,b=this.styles;a.removeClass(b.target).addClass(b.targetOpen).attr("aria-hidden","false");var c=this.options.targets;if(typeof c=="object"){var d=this;for(targetSel in c)(function(f){d._openAjaxTarget(f,
-c[f])})(targetSel)}b=this.options.openedAppendText;b!==""&&this.appendTextNode.html(b);a.css("display","");this._targetsOpening=false;this._targetsOpen=true}},_closeTargets:function(){if(!(this._targetsOpening||this._targetsClosing||!this._targetsOpen)){this._targetsClosing=true;var a=this.targets,b=this.styles;a.removeClass(b.targetOpen).addClass(b.target).attr("aria-hidden","true");b=this.options.closedAppendText;b!==""&&this.appendTextNode.html(b);a.css("display","");this._targetsOpen=this._targetsClosing=
-false}},_fixHasLayout:function(a){window.setTimeout(function(){a.targets.addClass("foo").removeClass("foo")},1)},open:function(a){var b=this.element,c=this;if(!b.hasClass(this.styles.master))return b;this.updateState("open");if(this.options.animation==="slide")this.targets.slideToggle(this.options.speed,function(){c._openTargets();e.browser.msie&&c._fixHasLayout(c);b.data("isOpen",true);b.trigger("ncbitoggleropen");a&&a()});else{this._openTargets();e.browser.msie&&c._fixHasLayout(c);b.data("isOpen",
-true);b.trigger("ncbitoggleropen");a&&a()}this._updateReferences("open");return b},close:function(a){var b=this.element,c=this;if(!b.hasClass(this.styles.masterOpen))return b;this.updateState("closed");if(this.options.animation==="slide")this.targets.slideToggle(this.options.speed,function(){c._closeTargets();b.trigger("ncbitogglerclosed").trigger("ncbitogglerclose");b.data("isOpen",false);a&&a()});else{this._closeTargets();b.data("isOpen",false);b.trigger("ncbitogglerclosed");a&&a()}this._updateReferences("closed");
-return b},toggle:function(a,b,c){var d=arguments.length;if(d===0||d===1){b=this;if(d===1)c=arguments[0]}else a.preventDefault();this.element.hasClass(this.styles.master)?b.open(c):b.close(c)},updateState:function(a){var b=this.element;a||(a=b.hasClass(styles.master)?"open":"closed");var c=this.styles.master,d=this.styles.masterOpen,f=this.iconCloseClass,g=this.iconOpenClass;if(a=="closed"){c=this.styles.masterOpen;d=this.styles.master;f=this.iconOpenClass;g=this.iconCloseClass}b.removeClass(c).addClass(d).attr("aria-expanded",
-a=="closed"?"false":"true");this.options.isIcon&&this.iconSpan.removeClass(f).addClass(g);this.remember&&e.cookie(this.cookieName,a)},_removeHandlers:function(){this.element.unbind("click")},destroy:function(){e.Widget.prototype.destroy.apply(this,arguments);var a=this.element,b=this.styles;a.removeClass(b.master+" "+b.masterOpen+" ui-state-disabled ui-widget ui-ncbitoggler-disabled").removeAttr("role").removeAttr("aria-expanded");this.targets.removeClass("ui-ncbitoggler ui-ncbitoggler-slave ui-ncbitoggler-slave-open ui-state-disabled ui-ncbitoggler-disabled");
-this.targets.removeAttr("aria-hidden");if(this.options.isIcon){b=a.find("span.ui-icon")[0];a[0].removeChild(b)}this.targets.each(function(){var d=jQuery(this),f=d.parent("div.ui-helper-reset");if(f.length>0){d.insertBefore(f);f.remove()}});b=a.find("span.ui-ncbitoggler-master-text");var c=b.html();b.remove();a.html(c);this._removeHandlers();return this},disable:function(){e.Widget.prototype.disable.apply(this,arguments);this._removeHandlers();this.targets.addClass("ui-ncbitoggler-disabled ui-state-disabled");
-return this},enable:function(){e.Widget.prototype.enable.apply(this,arguments);this.targets.removeClass("ui-ncbitoggler-disabled ui-state-disabled");var a=this;this.element.click(function(b){a.toggle(b,a)});return this},_saveReferences:function(){var a=this;this._targets.each(function(){typeof e(this).data("ncbitoggler-masters")==="undefined"&&e(this).data("ncbitoggler-masters",[]);e(this).data("ncbitoggler-masters").push(a.element)})},_updateReferences:function(a){var b=this;e.each(this._targets.data("ncbitoggler-masters"),
-function(){b.element!=this&&e(this).ncbitoggler("updateState",a)})}})})(jQuery);
--- a/Blast output page example_files/jquery_003.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-.ui-ncbibasicmenu{list-style-type:none;min-width:200px;}.ui-ncbibasicmenu,.ui-ncbibasicmenu>li{padding:0;margin:0;}.ui-ncbibasicmenu li ul li{background-color:#FFF;}.ui-ncbibasicmenu li ul li a:hover,.ui-ncbibasicmenu li ul li.selected a:hover{background-color:#4C96DF;color:#FFF;}.oneLevel li a,.ui-ncbibasicmenu li a{display:block;text-decoration:none;background-color:#FCFCFC;border:1px solid #FCFCFC;border-width:1px 0;color:#14376C;font-size:13px;font-weight:normal;margin:0;padding:.2em .9em;text-decoration:none;}.oneLevel li a:hover,.ui-ncbibasicmenu>li>a:hover{background-color:#E3F8FF;}.oneLevel li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbibasicmenu>li.ui-ncbimenu-item-no-hlt>a:hover,.oneLevel li.ui-ncbimenu-item-skip a:hover,.ui-ncbibasicmenu>li.ui-ncbimenu-item-skip>a:hover{background-color:#FCFCFC;}.oneLevel li a:focus,.ui-ncbibasicmenu>li>a:focus{outline:1px dashed #000;}.oneLevel li.selected a,.ui-ncbibasicmenu>li.selected>a{color:#FFF;background-color:#4C96DF;}.oneLevel li.selected a:hover,.ui-ncbibasicmenu>li.selected>a:hover{color:#FFF;}.oneLevel li.selected.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbibasicmenu>li.selected.ui-ncbimenu-item-no-hlt>a:hover,.oneLevel li.selected.ui-ncbimenu-item-skip a:hover,.ui-ncbibasicmenu>li.selected.ui-ncbimenu-item-skip>a:hover{color:inherit;background-color:#FCFCFC;}.orientation_hort>li{display:inline;float:left;}
\ No newline at end of file
--- a/Blast output page example_files/jquery_003.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-(function(){jQuery.widget("ui.ncbilocalnav",jQuery.ui.ncbimenu,{_create:function(){this.options.isSubMenuLimited=true;jQuery.ui.ncbimenu.prototype._create.apply(this,arguments)},_addClasses:function(){this.element.addClass("ui-ncbilocalnav");jQuery.ui.ncbimenu.prototype._addClasses.apply(this,arguments)},_destroyClasses:function(){this.element.removeClass("ui-ncbilocalnav");jQuery.ui.ncbimenu.prototype._destroyClasses.apply(this,arguments)}})})();
--- a/Blast output page example_files/jquery_004.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-div.ui-ncbiautocomplete-holder{position:absolute;top:0;left:0;border:1px solid #5a5a5a;display:none;font-family:Arial,helvetica,sans-serif;font-size:inherit;border-style:solid;border-color:#777;border-width:1px;}ul.ui-ncbiautocomplete-options{height:218px;overflow:auto;overflow-x:hidden;overflow-y:auto;width:100%;margin:0;padding:0;list-style-type:none;font-weight:normal;cursor:pointer;background-color:#FFF;}ul.ui-ncbiautocomplete-options li span{font-weight:normal;}ul.ui-ncbiautocomplete-options li{padding:.2em;padding-left:.8em;padding:.231em .461em;white-space:nowrap;overflow:hidden;width:100%;color:#14376c;text-overflow:ellipsis;}ul.ui-ncbiautocomplete-options li:last-child{padding-bottom:.6em;}ul.ui-ncbiautocomplete-options li.ui-ncbiautocomplete-options-high{background-color:#DAEEF4;text-decoration:none;color:#015;}.ui-ncbiautocomplete-actions{background-color:#CECECE;line-height:inherit;padding:5px;border:1px solid #777;*zoom:1;*display:block;margin:1px -1px 0 -1px;min-height:15px;}.ui-ncbiautocomplete-actions:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-ncbiautocomplete-actions{display:inline-block;}.ui-ncbiautocomplete-actions a{display:inline;float:left;color:#015;text-decoration:none;}.ui-ncbiautocomplete-actions .ui-ncbiautocomplete-link-pref-right{text-align:right;float:right;}.ui-ncbiautocomplete-link-pref{text-indent:-9999px;background:url("../img/gear.png") no-repeat;width:15px;height:16px;}a.ui-ncbiautocomplete-link-off:hover,a.ui-ncbiautocomplete-link-pref:hover{text-decoration:underline;color:#015;}li.ui-ncbiautocomplete-show-more{width:100%!important;background:#C3D2DB!important;border-top:1px solid #5A5A5A;}li.ui-ncbiautocomplete-show-more.ui-ncbiautocomplete-options-high{text-decoration:underline!important;}iframe.ui-ncbiautocomplete-iframe{position:absolute;top:0;left:0;height:200px;z-index:1000;display:none;filter:alpha(opacity=1);}.shadow{-webkit-box-shadow:.4em .4em .5em rgba(153,153,153,.9);-moz-box-shadow:.4em .4em .5em rgba(153,153,153,.9);box-shadow:.4em .4em .5em rgba(153,153,153,.9);}
\ No newline at end of file
--- a/Blast output page example_files/jquery_004.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-jQuery.widget("ui.ncbiautocomplete",{options:{webserviceUrl:"/portal/utils/autocomp.fcgi",isUrlRelative:false,dictionary:"",responseFormat:"old",disableUrl:null,prefUrl:null,zIndex:1001,isEnabled:true,hasRelatedMatches:false,minLength:2,expandPauseTime:400,maxListLimit:null,isCrossDomain:false,disableCache:false,requireValidation:false,queryParameter:"q"},_create:function(){if(this.options.localData&&!this.options.dictionary)this.options.dictionary="local";this._storeTitleAttribute();this._createOptionsBox();
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-optionIndex:-1,optionsCount:-1}},_addAttributes:function(){this.element.attr({title:"Use up and down arrows to choose an item from the autocomplete.","aria-haspopup":true,"aria-autocomplete":"list",role:"textbox"})},_setHandlers:function(){var a=this;jQuery(this.element).focus(function(){a._focused()}).keypress(function(c){a._keyPress(c,"press")}).keydown(function(c){a._keyPress(c,"down")}).keyup(function(c){a._keyUp(c)}).bind("cut paste",function(){a._changeFired()}).attr("AUTOCOMPLETE","OFF");var b=
-jQuery(this.element)[0];b.autocomplete="off";b.AUTOCOMPLETE="OFF";jQuery(window).resize(function(){a._isActive&&a._positionOptionsBox()});jQuery(document).click(function(c){a._checkClickEvent(c)});jQuery(this._gol.optionsBox).hover(function(){if(a._isActive)a._isOptionsBoxFocused=true},function(){if(a._isActive)a._isOptionsBoxFocused=false})},_isOptionsBoxFocused:false,_createOptionsBox:function(){if(jQuery.ui.ncbiautocomplete._globalOptionsList===null){jQuery.ui.ncbiautocomplete._globalOptionsList=
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-null)c=false;else{if(b){b=b;if(typeof this._localCache[this.options.dictionary]==="undefined")this._localCache[this.options.dictionary]={};else if(typeof this._localCache[this.options.dictionary][e]==="undefined")this._localCache[this.options.dictionary][e]={}}else b=this._localCache[this.options.dictionary][e][a];b.matchedText=a;var d=this.options.minLength===0&&a.length===0;if(!this.options.hasRelatedMatches){c=a.replace(/([\^\$\\\?\(\)\[\]\*\+\{\}\|\/\.\,])/g,"\\$1");c=new RegExp(c,"ig");for(var f=
-b.matches.join("!!!~~~!!!").split("!!!~~~!!!"),i=f.length-1;i>=0;i--)!d&&f[i].match(c)===null&&f.splice(i,1);b.matches=f;this._localCache[this.options.dictionary][e][a]=b;c=f.length>0}}c?this._displayOptions(this._localCache[this.options.dictionary][e][a]):this._hideOptions()},_removeHighlight:function(a){if(!(a==="mouse"&&new Date-this._lastKeyPressDwnUpScroll<100)){var b=this;jQuery("li",this._gol.optionsList).removeClass("ui-ncbiautocomplete-options-high").each(function(){b._collapseOption(this)})}},
-_addHightlightMouse:function(a){if(new Date-this._lastKeyPressDwnUpScroll>100){this._resetCurrentIndex();this._currIndex=jQuery(a).prevAll("li").length;this._addHightlight(a)}},_addHightlight:function(a){this._removeHighlight();jQuery(a).addClass("ui-ncbiautocomplete-options-high");var b=this;this._expandTimer&&window.clearTimeout(this._expandTimer);this._expandTimer=window.setTimeout(function(){b._expandOption(a)},this.options.expandPauseTime)},_expandOption:function(a){if(jQuery(a).hasClass("ui-ncbiautocomplete-options-high")){a=
-jQuery(a).attr("isExpanded",true);var b=a.attr("fullText");if(a.html()!==b||a.attr("isIEExpand")){a.html(b).css("text-overflow","").css("white-space","normal").css("-o-text-overflow","");this._scrollIntoView()}}},_collapseOption:function(a){a=jQuery(a);a.attr("isIEExpand")?a.css("text-overflow","ellipsis").css("white-space","nowrap").css("-o-text-overflow","ellipsis"):a.css("white-space","nowrap").html(a.attr("partialText"))},_optionClicked:function(a){a=jQuery(a);if(a.hasClass("ui-ncbiautocomplete-show-more"))this._gotoShowAll();
-else{var b=this._cleanUpSelectionText(a);a=a.attr("valueId")||null;this.sgData.optionSelected=b;this.sgData.optionIndex=this._currIndex;this.sgData.valueId=a;this.sgData.selectionAction="click";this._sgSend();b=jQuery(this.element).val(b);b.attr("valueid",a);b.trigger("ncbiautocompleteoptionclick",this.sgData);b.trigger("ncbiautocompletechange",this.sgData)}this._isOptionsBoxFocused=false;this._hideOptions()},isOptionsBoxOpen:function(){return jQuery(this._gol.optionsBox).css("display")==="block"},
-_hideOptions:function(a){this._gol.activeElement=null;if(!(this._isOptionsBoxFocused&&!a)){var b=jQuery(this._gol.optionsBox);a&&jQuery(this._gol.optionsBox).css("display","none");b.attr("aria-activedescendant")===this.element.attr("id")&&b.attr("aria-activedescendant","");this._gol.isIE6&&jQuery(this._gol.optionsBox.iframe).css("display","none");this._resetCurrentIndex();this._isActive=false;this._lastEnteredTerm=null;b=jQuery(this._gol.optionsBox);var c=jQuery(this._gol.optionsList);b.css("display",
-"none");c.html("");this._lastTextInTextbox=b=this.element.val();if(this.options.requireValidation&&b.length>0&&this.options.isEnabled&&(!this.element.is(":focus")||a))this._trigger((b.length<this.options.minLength?false:this.isInDictionary(b))?"validselection":"invalidselection")}},_setTextCursorToEnd:function(a){var b=this.element;jQuery(b).val(a);if(b.createTextRange){a=b.createTextRange();a.moveStart("character",b.value.length);a.collapse();a.select()}},_resetCurrentIndex:function(){this._currIndex=
--1},_cleanUpSelectionText:function(a){return jQuery.trim(a.attr("acValue")).replace(/&amp;/gi,"&").replace(/\\"/g,'"')},_currIndex:-1,_moveSelection:function(a){if(this._isActive){this.sgData.usedArrows=true;var b=jQuery("li",this._gol.optionsList).length;this._currIndex+=a;this._removeHighlight();a=this._lastEnteredTerm;var c="";if(!(a===null||a.length<this.options.minLength)){if(this._currIndex<0||this._currIndex>=b)this._currIndex=this._currIndex===-2?b-1:-1;if(this._currIndex!==-1){b=jQuery("li:eq("+
-this._currIndex+")",this._gol.optionsList);this._addHightlight(b);if(this._currIndex===this.options.maxListLimit){this.sgData.optionSelected="";this.sgData.valueId=""}else{a=this._cleanUpSelectionText(b);c=b.attr("valueId")||null;this.sgData.optionSelected=a;this.sgData.valueId=c}}else{this.sgData.optionSelected="";this.sgData.valueId=""}this.element.attr("_optValue",c);this.element.attr("valueId",c);this._setTextCursorToEnd(a);this._scrollIntoView();this.sgData.optionIndex=this._currIndex}}},_scrollIntoView:function(){var a=
-jQuery("li:eq("+this._currIndex+")",this._gol.optionsList);if(a.length!==0){var b=jQuery(this._gol.optionsList),c=b.height(),e=b.scrollTop(),d=a[0].offsetTop;a=a.height();if(d-c+a>e){e=jQuery("li:eq("+(this._currIndex+1)+")",this._gol.optionsList);b.scrollTop((e.length===1?e[0].offsetTop:d+a+10)-c)}else d<e&&b.scrollTop(d)}},enableAutocomnplete:function(){this.options.isEnabled=true},disableAutocomnplete:function(){this.disableAutocomplete()},disableAutocomplete:function(){this._isOptionsBoxFocused=
-this.options.isEnabled=false;this._hideOptions()},turnOff:function(a){this.disableAutocomplete();var b=this.element.data("ncbiautocompleteOriginalTitle");b&&this.element.attr("title",b);if(!a){typeof ncbi!=="undefined"&&ncbi.sg&&ncbi.sg.ping&&ncbi.sg.ping(this.element[0],"autocompleteoffclick","dictionary="+this.options.dictionary);this.element.trigger("ncbiautocompletedisableclicked");a=this.options.disableUrl;if(a!==null&&a.length>0){b=jQuery.ui.jig._getFncFromStr(a);typeof b==="function"?b():jQuery.get(a)}}},
-_prefLinkClick:function(){typeof ncbi!=="undefined"&&ncbi.sg&&ncbi.sg.ping&&ncbi.sg.ping(this.element[0],"autocompleteprefclick","dictionary="+this.options.dictionary)},_checkClickEvent:function(a){if(this._isActive)if(jQuery(this.element)[0]!=a.target){this._isActive=this._isOptionsBoxFocused=false;this._hideOptions()}},_sgSend:function(){typeof ncbi!=="undefined"&&typeof ncbi.sg!=="undefined"&&typeof ncbi.sg.ping!=="undefined"&&ncbi.sg.ping(this.sgData,false)},getSgData:function(){return this.sgData},
-_gotoShowAll:function(){var a=jQuery(this.element),b=a.val();a.trigger("ncbiautocompleteshowall",{value:b,dictionary:this.options.dictionary})},_hideOptionsIfOffPage:function(){if(this.options.maxListLimit){var a=this,b=jQuery(".ui-ncbiautocomplete-options li"),c=b.eq(0).outerHeight()||20,e=jQuery(this._gol.optionsBox),d=jQuery(window).height(),f=e.position().top,i=f+e.outerHeight()-(document.body.scrollTop||document.documentElement.scrollTop||window.pageYOffset||0);if(b.last().hasClass("ui-ncbiautocomplete-show-more")){var k=
-f+"-"+d+"-"+i;if(!this.choppedDetails)this.choppedDetails={};var h=this.choppedDetails[k],m=0,q=function(){i=f+e.outerHeight()-(document.body.scrollTop||document.documentElement.scrollTop||window.pageYOffset||0);if(i>d){b=jQuery(".ui-ncbiautocomplete-options li");var r=b.length-2;if(r>=0){b.eq(r).remove();sz=c*(b.length-1);b.closest(".ui-ncbiautocomplete-holder").height(sz).css("min-height",sz+"px");b.closest(".ui-ncbiautocomplete-options").height(sz).css("overflow-y","hidden");m++;q()}}else a.choppedDetails[k].count=
-m};if(h){var l=h.count;if(l>0){h=2*h.length-l-b.length-2;b.filter(":lt("+(b.length-1)+")").filter(":gt("+h+")").remove();b=jQuery(".ui-ncbiautocomplete-options li");sz=c*b.length;b.closest(".ui-ncbiautocomplete-holder").height(sz).css("min-height",sz+"px");b.closest(".ui-ncbiautocomplete-options").height(sz).css("overflow-y","hidden")}m=l}else this.choppedDetails[k]={count:0,length:b.length};q()}else{l=Math.floor((d-f)/c)*c;h=b.length*c;if(l>h)l=h;b.closest(".ui-ncbiautocomplete-holder").height(l).css("min-height",
-l+"px");b.closest(".ui-ncbiautocomplete-options").height(l).css("overflow-y","auto")}}},isValid:function(){return this.isInDictionary(this.element.val())},isInDictionary:function(a){var b=false;if(a&&a.length>=this.options.minLength&&this.options.dictionary&&this.options.dictionary.length>0&&this.options.isEnabled){var c=false,e="l"+(this.options.maxListLimit||"n"),d=a.toLowerCase();if(this._localCache[this.options.dictionary]&&this._localCache[this.options.dictionary][e]){e=this._localCache[this.options.dictionary][e];
-c=true;if(e[d])b=this._isValidCheck(d,e[d].matches);else for(var f in e)if(b=this._isValidCheck(d,e[f].matches))break}if(!b&&!c)b=this._validSeverCall(a)}return b},_isValidCheck:function(a,b){var c=false;if(b){c=jQuery.inArray(a.toLowerCase(),b)>-1;if(!c){var e=new RegExp("(^|@)("+a.toLowerCase()+")(@|$)","i");jQuery.each(b,function(d,f){if(f.match(e)){c=true;return false}})}}return c},_customFormat:function(a){if(typeof this.options.responseProcessor==="string")this.options.responseProcessor=jQuery.ui.jig._getFncFromStr(this.options.responseProcessor);
-this._displayOptions({matchedText:this._lastEnteredTerm,matches:this.options.responseProcessor.call(this,a),isCompleteList:0})}});jQuery.ui.ncbiautocomplete._globalOptionsList=null;
--- a/Blast output page example_files/jquery_005.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-a.ui-ncbitoggler{color:#22c;}a.ui-ncbitoggler,a.ui-ncbitoggler-open{padding-left:16px;position:relative;display:block;}a.ui-ncbitoggler-no-icon{padding-left:0;}a.ui-ncbitoggler span.ui-icon-plus-minus-big,a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open{background-color:transparent;background-image:url(../img/ncbitoggler-plus-minus-big.gif);background-repeat:no-repeat;top:.2em;margin-left:-0.1em;}a.ui-ncbitoggler span.ui-icon-plus-minus-big{background-position:left -30px;}a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open{background-position:left 0;}.ui-ncbitoggler-slave,.ui-ncbitoggler-slave-open{margin:.2em 0 0 16px;}.ui-ncbitoggler-slave{display:none;}.ui-ncbitoggler-slave-open{display:block;}a.ui-ncbitoggler span.ui-icon,a.ui-ncbitoggler-open span.ui-icon{display:inline;position:absolute;left:0;_left:-1em;}a.ui-ncbitoggler-disabled{outline:none;}a.ui-ncbitoggler-disabled:active{outline:none;color:#551A8B;}
\ No newline at end of file
--- a/Blast output page example_files/jquery_005.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-(function(){var d=jQuery.ui.button.prototype._create;jQuery.ui.button.prototype.options.color="ui-ncbibutton-gray";jQuery.ui.button.validColors=["ui-ncbibutton-gray","ui-ncbibutton-copper","ui-ncbibutton-blue"];jQuery.ui.button.classColors=["jig-ncbibutton-gray","jig-ncbibutton-copper","jig-ncbibutton-blue"];var e=function(){d.apply(this,arguments);this._addClasses()};jQuery.widget("ui.ncbibutton",jQuery.ui.button,{_create:function(){e.apply(this,arguments)},_getColor:function(){for(var a=this.options.color,
-f=this.element[0].className,c=jQuery.ui.button.classColors,b=0;b<c.length;b++)if(f.indexOf(c[b])!==-1){a=jQuery.ui.button.validColors[b];break}if(a.indexOf("ui-ncbibutton-")!==0)a="ui-ncbibutton-"+a;if(jQuery.inArray(a,jQuery.ui.button.validColors)===-1){typeof console!=="undefined"&&console.warn&&console.warn("The color you picked: "+this.options.color+" is not a valid color choice.\n Valid colors: "+jQuery.ui.button.validColors.join(", "));a=jQuery.ui.button.validColors[0]}return a},_addClasses:function(){this.buttonElement.addClass("ui-ncbibutton").addClass(this._getColor()).removeClass("ui-button ui-widget")}})})();
--- a/Blast output page example_files/jquery_006.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-.ui-ncbipopper-wrapper{position:fixed;top:0;left:0;z-index:11;display:none;}.ui-ncbipopper-wrapper-relative-parent{position:fixed!important;}.ui-ncbipopper-basic{border:3px solid #3e72a6;background-color:#fff;color:#303030;padding:1em;text-align:left;-moz-border-radius:6px;-webkit-border-radius:6px;border-radius:6px;}button.ui-ncbipopper-close-button-generated{display:block;float:right;margin:-1.25em -1.3em 0 0;font-size:small;width:1.7em;text-align:center;padding:0;border:0;}button.ui-ncbipopper-close-button-generated,button.ui-ncbipopper-close-button-generated:active{margin:-0.615em;height:14px;width:13px;background-image:url(../img/ui-popper-closebutton.png);background-color:transparent;background-repeat:no-repeat;}button.ui-ncbipopper-close-button-generated .ui-button-text{color:transparent;text-shadow:none;}div.ui-ncbipopper-arrow-image{position:absolute;top:100px;left:100px;width:7px;height:7px;z-index:11;display:none;background-image:url(../img/ncbipopper-arrow.png);background-repeat:no-repeat;}div.ui-ncbipopper-arrow-left{background-position:center left;height:28px;}div.ui-ncbipopper-arrow-right{background-position:center right;height:28px;}div.ui-ncbipopper-arrow-top{background-position:top center;width:28px;}div.ui-ncbipopper-arrow-bottom{background-position:bottom center;width:28px;}.brieflinkpopdesc{font-size:.846em;margin-top:.4em;}.portlet .brieflinkpop{width:350px;}.portlet .brieflinkpop a{font-size:1em;}.portlet .brieflinkpopperctrl{display:inline-block;}
\ No newline at end of file
--- a/Blast output page example_files/jquery_006.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-jQuery.widget("ui.ncbigrid",{options:{isScrollable:false,height:"10em",hortScrollbarEnabled:false,width:null,isPageable:false,currentPage:1,isPageToolbarHideable:true,pageSize:10,isSortable:false,columnTypes:[],sortFunctions:[],isPresorted:false,sortColumn:-1,sortColumnDir:1,sortRowIndex:0,titleAscending:"sort ascending",titleDescending:"sort descending",ariaLabelAscending:"activate to sort column ascending",ariaLabelDescending:"activate to sort column descending",regExp:false,checkboxToolbarEnabled:false,
-filterToolbarEnabled:false,filterToolbarIsCaseInsensitive:null,filterToolbarColumnIndex:null,filterToolbarIsInverse:null,isLoadingMessageShown:true,loadingText:"Loading",collapseRowsEnabled:false,addCommas:false},_init:function(){},_create:function(){this._isStartPageOne=this.options.currentPage===1;this._wrapTable();this._addBasicStyles();this._checkIfCSSIsScrollable();this._attachLoadingMessageListener();if(this.options.isScrollable||this.options.isSortable||this.options.isPageable||this.options.checkboxToolbarEnabled||
-this.options.filterToolbarEnabled)this._addAriaRolesAndStates();this._addRowClickWatcher();this.options.isScrollable&&this._createScrollable();if(this.options.isPageable||this.options.isPagable){this.options.isPageable=true;this._createPageGrid()}if(this.options.isSortable){this._createSortGrid();this.updateAriaTH()}else this._enableCollapseTbodyRows();this.options.checkboxToolbarEnabled&&this._createCheckboxSelectors();this.options.filterToolbarEnabled&&this._createFilterBarControl();this._addRowHoverEvent();
-this._addContentsAdjustmentEvent();this._adjustContents()},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);this.options.isScrollable&&this._destroyScrollable();if(this.options.isPageable||this.options.isPagable)this._destroyPageGrid();this._destroyRowHoverEvent()},_addBasicStyles:function(){this.element.addClass("ui-ncbigrid").attr("cellpadding","0").attr("cellspacing","0")},_checkIfCSSIsScrollable:function(){if(this.element.hasClass("jig-ncbigrid-scroll"))this.options.isScrollable=
-true},_wrapTable:function(){var a=this.element.parent().parent();if(!a.hasClass("ui-ncbigrid-outer-div")){this.element.wrap('<div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"></div></div>');a=this.element.parent().parent()}this.element.find("caption").length>0&&a.addClass("caption-exists");var b=this.options.width;b&&a.css("width",b)},_addRowHoverEvent:function(){jQuery(this.element).on("mouseenter","tbody > tr",function(){var a=jQuery(this);a.hasClass("ignoreHoverHighlight")||
-a.addClass("ui-ncbigrid-row-hover")}).on("mouseleave","tbody > tr",function(){jQuery(this).removeClass("ui-ncbigrid-row-hover")})},_destroyRowHoverEvent:function(){jQuery(this.element).off("mouseenter mouseleave","tr")},_addContentsAdjustmentEvent:function(){var a=this;this.element.on("ncbigridupdated",function(){a._adjustContents()})},_getNumCommaIndices:function(){var a=this.options.columnTypes;if(!a)return[];for(var b=[],c=0;c<a.length;c++)if(a[c]=="numComma"||a[c]=="numberComma")b.push(c);return b},
-_getCommaSeparatedValue:function(a){var b=parseInt(a);if(isNaN(b))return a;else{a=a.split(".");b=a[0].replace(/(\d)(?=(\d\d\d)+(?!\d))/g,"$1,");return a[1]?b+"."+a[1]:b}},_adjustContentsForCommas:function(){var a=this._getNumCommaIndices();if(a.length){var b=this;jQuery(this.element).find("tbody td").each(function(){var c=jQuery(this),d=c.parent().find("td").index(c);jQuery.inArray(d,a)!=-1&&c.html(b._getCommaSeparatedValue(c.html()))})}},_adjustContents:function(){this.options.addCommas&&this._adjustContentsForCommas()},
-_addAriaRolesAndStates:function(){var a=this.element;a.attr("id")||a.attr("id",jQuery.ui.jig._generateId(this.widgetName));a.parent().parent().attr("role","grid").attr("tabindex","0");a.children("thead").children("tr").attr("role","row").children("th").attr({"aria-controls":a.attr("id"),role:"columnheader",tabindex:"0"});a.children("tbody").attr({role:"alert","aria-live":"polite","aria-relevant":"text"})},updateAriaTH:function(){if(this.options.isSortable){var a=this;this.element.parent().parent().find("div, table").attr("tabindex",
-"0").end().find("thead").find("th").each(function(b,c){b="";var d=a.options.ariaLabelAscending;if(jQuery(c).is(".sortDsc")){b="descending";d=a.options.ariaLabelAscending}else if(jQuery(c).is(".sortAsc")){b="ascending";d=a.options.ariaLabelDescending}c=jQuery(c).children("a");jQuery(c).attr("aria-label",jQuery(c).text()+": "+d);b==""?jQuery(c).removeAttr("aria-sort"):jQuery(c).attr("aria-sort",b)})}},_createScrollable:function(){this._storeRefs();this._addScrollClasses();this._copyCaptionHeader();
-this._setWidthHeight();this._setWidths();this._registerScrollableListeners()},_destroyScrollable:function(){this._removeScrollClasses();if(this.parts){this.parts.scrollWrapper.removeClass("ui-ncbigrid-scroll");this.parts.headerWrapper.remove();for(var a in this.parts)this.parts[a]=null;this.parts=null}this._windowResize&&jQuery(window).unbind("resize",this._windowResize)},_storeRefs:function(){var a=this.element;this.parts={table:a,ths:a.find("> thead th")}},_addScrollClasses:function(){var a=this.element,
-b=a.parent().addClass("ui-ncbigrid-scroll");this.parts.scrollWrapper=b;if(jQuery.browser.webkit){var c=navigator.userAgent;c.indexOf("AppleWebKit")>0&&c.indexOf("Chrome")==-1&&a.addClass("safari")}this.options.hortScrollbarEnabled&&b.addClass("ui-ncbigrid-hort-scroll")},_removeScrollClasses:function(){this.element.removeClass("ui-ncbigrid").removeClass("safari").parent().removeClass("ui-ncbigrid-scroll")},_copyCaptionHeader:function(){var a=this.element,b=a.parent();b.parent();var c=a.find("caption").clone();
-a=a.find("> thead").clone();c=jQuery("<div class='ui-ncbigrid-header-wrapper'></div>").append("<table cellpadding='0' cellspacing='0' class='ui-ncbigrid ui-ncbigrid-header'></table>").find("table").append(c).append(a).end();c.insertBefore(b);b=c.find("caption");b.wrapInner("<div></div>");this.parts.captionDiv=b.find("div");this.parts.headerWrapper=c;this.parts.headerThs=c.find("thead th")},_setWidthHeight:function(){this.options.height!==null&&this.parts.scrollWrapper.height(this.options.height)},
-_setWidths:function(){function a(j){jQuery(this).width(h[j])}var b=this.parts,c=b.table,d=b.ths,e=b.scrollWrapper,g=b.headerWrapper;b=b.headerThs;var f=jQuery.browser.msie;if(!this.options.hortScrollbarEnabled&&c.data("isMinSet")!==true&&this.element.is(":visible")){var i=c.outerWidth();if(c.width()>e.width()){e.css("min-width",i+16);c.data("isMinSet",true)}}var h=[];d.each(function(){var j=0;if(jQuery(this).is(":visible"))j=jQuery(this).width()+0;h.push(j)});d=c.height()>e.height()?16:0;f=this.options.isSortable&&
-f&&parseInt(jQuery.browser.version,10)<8?d:0;c.parent().parent().find("table.ui-ncbigrid-header").width(c.width()+2-f);c=e.width()-d;g.width(c);this.parts.captionDiv&&this.parts.captionDiv.width(c);b.each(a)},_handleScroll:function(a,b,c){function d(){g._handleScroll(a,b,true)}var e=a.scrollLeft;b.scrollLeft=e;this.parts.captionDiv&&this.parts.captionDiv.css("margin-left",e+"px");var g=this;if(!c){window.setTimeout(d,1);window.setTimeout(d,5)}},_registerScrollableListeners:function(){var a=this;this._windowResize=
-function(){a._setWidths()};jQuery(window).resize(this._windowResize);var b=this.element.parent().parent().find(".ui-ncbigrid-header-wrapper")[0];this.element.parent().scroll(function(){a._handleScroll(this,b)});this.element.bind("ncbigridupdated",function(){a._setWidths()});this.element.bind("resetScroll",function(){a._resetScrollToTop()})},_resetScrollToTop:function(){this.parts.scrollWrapper.scrollTop(0)},_createPageGrid:function(){this._createPageBars();this._addPagingEvents();this._gotoPage(this.options.currentPage)},
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-_createPageBars:function(){this._pageToolBar_top=jQuery(this._pagingControlsHTML).addClass("ui-ncbigrid-paged-toolbar-top");this._pageToolBar_bottom=jQuery(this._pagingControlsHTML).addClass("ui-ncbigrid-paged-toolbar-bottom");var a=this.element,b=a.parent().parent();b.prepend(this._pageToolBar_top);b.append(this._pageToolBar_bottom);b.children(".ui-ncbigrid-paged-toolbar-top").children(".ui-ncbigrid-paged-countItems").attr("id",jQuery.ui.jig._generateId("ui-ncbigrid-paged-countItems"));a.attr("aria-describedby",
-this._pageToolBar_top.children(".ui-ncbigrid-paged-countItems").attr("id"));this._pageBars=this._pageToolBar_top.add(this._pageToolBar_bottom);this._pageBars.find(":input").each(function(c,d){jQuery(d).attr("id",jQuery.ui.jig._generateId("ui-ncbigrid-paged-current-page")).prev().attr("for",jQuery(d).attr("id"))})},_removePageBars:function(){this._pageToolBar_top.remove();this._pageToolBar_top=null;this._pageToolBar_bottom.remove();this._pageBars=this._pageToolBar_bottom=null;this.element.removeAttr("aria-describedby")},
-_addPagingEvents:function(){var a=this,b=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-first"),c=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-previous"),d=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-next"),e=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-last"),g=this._pageBars.find("input");b.click(function(f){a.gotoFirstPage();f.preventDefault()});c.click(function(f){a.gotoPrevPage();f.preventDefault()});d.click(function(f){a.gotoNextPage();f.preventDefault()});e.click(function(f){a.gotoLastPage();
-f.preventDefault()});g.keypress(function(f){if(f.keyCode===13){a.gotoPage(this.value.replace(/,/g,""));f.preventDefault()}})},_removePagingEvents:function(){this._pageBars.find("a").unbind("click").end().find("input").unbind("keypress")},_showHidePageToolbar:function(){if(this._pageBars)if(this.options.isPageToolbarHideable)parseInt(this.getRowCount())<=parseInt(this.options.pageSize)?this._pageBars.hide():this._pageBars.show()},_setPage:function(){this.element.trigger("resetScroll");this.element.trigger("pagechanged");
-var a=this._getCurrentPage(),b=this.getMaxPage();this._showHidePageToolbar();this._updateRows(a,b);this._updateButtons(a,b);this._updatePagingText(a,b);this._updateGoto(a,b);this._updateItemRange(a,b);this._pageBars.find(".ui-ncbigrid-paged-pageControl").attr({"aria-valuemin":"1","aria-controls":this.element.attr("id"),"aria-valuemax":b,"aria-valuenow":a});this._notifyGridUpdated()},_updateRows:function(a){var b=this.options.pageSize,c=this.getRowCount();a=(a-1)*b;var d=a+b;b=this.element.find("> tbody > tr:not(.ncbigrid-row-filtered)");
-var e=this.element.find("> tbody").length>1,g=0;if(e&&a>0)g=b.filter(":lt("+a+")").filter(":has(th)").length;var f="";if(d<c)f+=":lt("+(d+g)+")";if(a>0)f+=":gt("+(a-1+g)+")";c=b;if(f.length>0){b.not(".ui-ncbigrid-rowHidden").addClass("ui-ncbigrid-rowHidden");c=b.filter(f)}c.removeClass("ui-ncbigrid-rowHidden");if(e){a=c.filter(":has(th)").length;if(a>0){b=0;for(c=c.last().next();b<a&&c.length===1;){if(!c.hasClass("ncbigrid-row-filtered")){c.has("th")||b++;c.removeClass("ui-ncbigrid-rowHidden")}c=
-c.next()}}}this._notifyGridUpdated()},_updateButtons:function(a,b){var c=b===2,d=a===1,e=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-previous,a.ui-ncbigrid-paged-pageControl-first").css("display",d?"none":"inline").filter("a.ui-ncbigrid-paged-pageControl-first");d=this._pageBars.find("span.ui-ncbigrid-paged-pageControl-previous,span.ui-ncbigrid-paged-pageControl-first").css("display",d?"inline":"none").filter("span.ui-ncbigrid-paged-pageControl-first");b=a===b||b==0;a=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-next,a.ui-ncbigrid-paged-pageControl-last").css("display",
-b?"none":"inline").filter("a.ui-ncbigrid-paged-pageControl-last");b=this._pageBars.find("span.ui-ncbigrid-paged-pageControl-next,span.ui-ncbigrid-paged-pageControl-last").css("display",b?"inline":"none").filter("span.ui-ncbigrid-paged-pageControl-last");c&&e.add(d).add(a).add(b).css("display","none")},_updatePagingText:function(a,b){if(b<1)b=1;if(this.options.addCommas)b=this._getCommaSeparatedValue(""+b);this._pageBars.find("div.ui-ncbigrid-paged-pageControl").find("span.ui-ncbigrid-paged-endPage").html(b)},
-_updateGoto:function(a){if(this.options.addCommas)a=this._getCommaSeparatedValue(""+a);this._pageBars.find("input").val(a)},_updateItemRange:function(a){var b=parseInt(this.options.pageSize,10),c=this.getRowCount();a=(a-1)*b+1;b=a+b-1;if(b>c)b=c;if(c==0)a=0;if(this.options.addCommas){c=this._getCommaSeparatedValue(""+c);a=this._getCommaSeparatedValue(""+a);b=this._getCommaSeparatedValue(""+b)}var d=this._pageBars.find("div.ui-ncbigrid-paged-countItems");d.find("span.ui-ncbigrid-paged-startRow").html(a);
-d.find("span.ui-ncbigrid-paged-endRow").html(b);d.find("span.ui-ncbigrid-paged-totalRows").html(c)},_getCurrentPage:function(){return this.options.currentPage},getCurrentPage:function(){return this._getCurrentPage()},getMaxPage:function(){return Math.ceil(this.getRowCount()/this.options.pageSize)},getRowCount:function(){return jQuery(this.element).find("> tbody > tr:not(.ncbigrid-row-filtered):not(:has(> th))").length},getHeaderRowCount:function(){return jQuery(this.element).find("tbody > tr:has(th)").length},
-gotoFirstPage:function(){this._gotoPage(1)},gotoLastPage:function(){this._gotoPage(this.getMaxPage())},gotoNextPage:function(){this._gotoPage(this._getCurrentPage()+1)},gotoPrevPage:function(){this._gotoPage(this._getCurrentPage()-1)},gotoPage:function(a){this._gotoPage(parseInt(a,10))},_gotoPage:function(a){if(isNaN(a)||a<1)a=1;else if(a>this.getMaxPage()){a=this.getMaxPage();if(a<1)a=1}this.options.currentPage=a;this._pagingSelectAllQuestions&&this._pagingSelectAllQuestions.hide();this._setPage()},
-_createSortGrid:function(){var a=this.options.sortColumn;if(this.options.sortColumn!==-1){a=a-1;this.options.sortColumn=a!==-1?a:0}this._indexGrid();this._addSortEvents();this._setSortHeaders();this._checkInitialState();this._notifyGridUpdated()},_destroySortGrid:function(){},reindex:function(){for(var a=0;a<this.element.find("tbody tr:eq(0) td").length;a++)this.element.data("sort_order_col_"+a,null);this.element.data("rows",null);this._indexGrid()},_indexGrid:function(){var a=this,b=this.element.find("> tbody");
-if(b.length===0)this._isIndexed=false;else for(var c=0;c<b.length;c++)(function(d,e){function g(){for(var o=0;o<50&&k<m;o++){var p=l[k],q=a.getRowValues_DOM(p);if(q.length==0){a._enableCollapseTbodyRows(p);i.push(p);j++}else{q.unshift(k-j,p);f.push(q);h.push(q)}k++}if(k<m)window.setTimeout(g,0);else{a.element.data("tbody"+e+"-rows",h);a.element.data("tbody"+e+"-header",i);a._presort(f,e)}}var f=[],i=[],h=[],j=0,l=jQuery(d).find("> tr"),k=0,m=l.length;if(m===0)a._isIndexed=false;else{a._isIndexed=
-true;g()}})(b[c],c)},_presort:function(a,b){function c(h){var j=g.options.sortFunctions[h-2];j||(j=g.element.find("> thead th:eq("+(h-2)+")").data("sortfunc"));if(j)if(typeof j==="function")return j;else if(j.indexOf("fnc:")===0){j=j.substr(4,j.length).split(".");for(var l=window[j[0]],k=1;k<j.length;k++)l=l[j[k]];return g.options.sortFunctions[h]=l}return null}function d(h,j,l){function k(n){if(n.length<2)return n;var r=parseInt(n.length/2),s=n.slice(0,r);n=n.slice(r,n.length);return m(k(s),k(n))}
-function m(n,r){for(var s=[];n.length&&r.length;){var u=false;(u=o?-g.options.sortColumnDir==o.call(g,{data:n[0][j],row:jQuery(n[0][1])},{data:r[0][j],row:jQuery(r[0][1])}):n[0][j]<=r[0][j])?s.push(n.shift()):s.push(r.shift())}for(;n.length;)s.push(n.shift());for(;r.length;)s.push(r.shift());return s}var o=c(j),p=jQuery.browser.msie?100:1E3,q=0,t=[];(function(){for(var n=0;n<p&&q<h.length;n++){t.push(h[q]);q++}q<h.length?setTimeout(arguments.callee,0):l(k(t),j)})()}function e(h,j){var l=0,k=[];(function(){for(var m=
-0;m<50&&l<h.length;m++){k.push(h[l][0]);l++}l<h.length?setTimeout(arguments.callee,0):g.element.data("tbody"+b+"-sort_order_col_"+(j-2),k)})()}for(var g=this,f=a[0].length,i=2;i<f;i++)this._getColumnType(i-2)!=="none"&&d(a,i,e)},_getColumnType:function(a){var b=this.options.columnTypes[a];b||(b=this.element.find("> thead th:eq("+a+")").data("columntype"));return b||"str"},getColumnType:function(a){return this._getColumnType(a-1)},getRowValues:function(a){if(typeof a==="number")a=this.element.find("tbody tr:eq("+
-a+")");var b=[];a=a[0].getElementsByTagName("td");for(var c=a.length,d=0;d<c;d++)b.push(this._getCellValueHelper(a[d].innerHTML,d));return b},getRowValues_DOM:function(a){var b=[];a=jQuery(a).children("td");for(var c=a.length,d=0;d<c;d++)b.push(this._getCellValueHelper(a[d].textContent||a[d].innerText||"",d));return b},_getCellValue:function(a,b){return this._getCellValueHelper(a.html(),b)},_getCellValueHelper:function(a,b){var c=this._getColumnType(b);switch(c){case "num":case "number":case "float":return a!==
-undefined&&a.length>0?parseFloat(a):Number.POSITIVE_INFINITY;case "int":return a!==undefined&&a.length>0?parseInt(a,10):Number.POSITIVE_INFINITY;case "numberComma":case "numComma":a=(a||"").replace(/[, ]/g,"");return a.length>0?parseFloat(a):Number.POSITIVE_INFINITY;case "date":return new Date(a);case "str-insensitive":return a.toLowerCase();case "str":default:if(typeof c==="function")return c(a);else if(c.indexOf("fnc:")===0){c=c.substr(4,c.length).split(".");for(var d=window[c[0]],e=1;e<c.length;e++)d=
-d[c[e]];this.options.columnTypes[b]=d;return d(a)}else return a||""}},getCellValue:function(a,b){if(typeof a==="number")a=this.element.find("tbody tr:eq("+a+")");return this._getCellValue(a.find("td:eq("+b+")"),b)},_addSortEvents:function(){function a(e){b._getColumnType(e)!=="none"&&jQuery(this).wrapInner(d).find("a").data("index",e)}var b=this,c=this.element.find("> thead tr:eq("+this.options.sortRowIndex+") th");this.element.bind("ncbigridcontentchanged",function(){b.reindex()});var d="<a href='#' title='"+
-this.options.titleAscending+"'></a>";c.each(a);c=c;if(this.parts&&this.parts.headerThs){this.parts.headerThs.each(a);c=c.add(this.parts.headerThs)}c.find("a").click(function(e){b._sort(jQuery(this).data("index"));e.preventDefault()})},sort:function(a,b){this._sort(a-1,b)},_sort:function(a,b){if(this._isIndexed){this.options.isPageable&&this.element.trigger("resetCheckboxes");var c=b;if(b===undefined)c=this.options.sortColumn!==a?1:-1*this.options.sortColumnDir;this.options.sortColumn=a;this.options.sortColumnDir=
-c;this.element.trigger("ncbigridshowloadingbar");this._setSortHeaders();this._waitForCache()}},_setSortHeaders:function(){var a=this.element.find("> thead tr:eq("+this.options.sortRowIndex+") th"),b=null;if(this.parts&&this.parts.headerThs)b=this.parts.headerThs;a.add(b).removeClass("sortAsc sortDsc").addClass("sortNone").find("a").attr("title",this.options.titleAscending);var c=this.options.sortColumn;if(this.options.sortColumn!==-1){var d=this.options.sortColumnDir===1?"sortAsc":"sortDsc",e=this.options.sortColumnDir===
-1?this.options.titleDescending:this.options.titleAscending;a.eq(c).addClass(d).removeClass("sortNone").find("a").attr("title",e);b&&b.eq(c).addClass(d).removeClass("sortNone").find("a").attr("title",e)}this.options.isSortable&&this.updateAriaTH()},_waitForCache:function(){for(var a=this,b=this.options.sortColumn,c=this.element.find("tbody"),d=0;d<c.length;d++)(function(e){var g=a.element.data("tbody"+e+"-sort_order_col_"+b);if(g)a._setTheRows(g,e);else{var f=arguments.callee;setTimeout(function(){f(e)},
-10)}})(d)},_setTheRows:function(a,b){var c=this.element.data("tbody"+b+"-header"),d=this.element.data("tbody"+b+"-rows");b=this.element.find("tbody:eq("+b+")");var e=jQuery("<tbody>"),g=c.length;if(g>0)for(var f=0;f<g;f++)e.append(c[f]);if(this.options.sortColumnDir==1)for(f=0;f<a.length;f++){c=d[a[f]][1];e.append(c)}else for(f=a.length-1;f>=0;f--){c=d[a[f]][1];e.append(c)}b.replaceWith(e);this.element.trigger("ncbigridhideloadingbar");if(this.options.isPageable)if(this._isStartPageOne)this.gotoFirstPage();
-else{this._gotoPage(this.options.currentPage);this._isStartPageOne=true}this.element.trigger("ncbigridcolumnsorted",[this.options.sortColumn+1,this.options.sortColumnDir])},_checkInitialState:function(){!this.options.isPresorted&&this.options.sortColumn!==-1&&this._sort(this.options.sortColumn,this.options.sortColumnDir)},_checkboxControlsHTML:'                                         <div class="ui-ncbigrid-checkbox-toolbar">                        \t\t\t\t\t\t<label>Select:</label>\t\t\t\t\t\t<a href="#" class="ui-ncbigrid-select-all">All</a>\t\t\t\t\t\t<a href="#" class="ui-ncbigrid-select-none">None</a>\t\t\t\t\t\t<label>Selected:</label>\t\t\t\t\t\t<span class="ui-ncbigrid-selected-text">0</span>                                            </div>',
-_pagingSelectAllQuestionHTML:'<div class="ui-ncbigrid-select-question">All <span class="ui-ncbigrid-select-row-count">10</span> items on this page are <span class="selectText1">selected</span>. <a href="#" class="ui-ncbigrid-select-question-all"><span class="selectText2">Select</span> all rows in table</a> <a href="#" class="ui-ncbigrid-select-question-cancel">Cancel</a></div>',_createCheckboxSelectors:function(){this._createCheckboxBar();this._addCheckboxEvents();this._updateCount()},_createCheckboxBar:function(){this._checkboxToolBar_top=
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-this.element.attr("id"));this._chekboxBars=this._checkboxToolBar_top.add(this._checkboxToolBar_bottom)},_addCheckboxEvents:function(){var a=this;this._chekboxBars.find("a.ui-ncbigrid-select-all").click(function(b){a.checkAll();a._askSelectAllQuestion();b.preventDefault()});this._chekboxBars.find("a.ui-ncbigrid-select-none").click(function(b){a.uncheckAll();a._askSelectAllQuestion(true);b.preventDefault()});jQuery(this.element).on("click","tbody",function(b){a._rowClicked(b)});this.element.bind("resetCheckboxes",
-function(){a.uncheckAll()});this._addSelectAllQuestionToolbarEvents()},_addSelectAllQuestionToolbar:function(){if(this.options.checkboxToolbarEnabled){this._pagingSelectAllQuestion_top=jQuery(this._pagingSelectAllQuestionHTML).addClass("ui-ncbigrid-select-question-header");this._pagingSelectAllQuestion_bottom=jQuery(this._pagingSelectAllQuestionHTML).addClass("ui-ncbigrid-select-question-footer");this._pagingSelectAllQuestion_top.insertAfter(this._pageToolBar_top);this._pagingSelectAllQuestion_bottom.insertAfter(this._pageToolBar_bottom);
-this._pagingSelectAllQuestions=this._pagingSelectAllQuestion_top.add(this._pagingSelectAllQuestion_bottom);this._pagingSelectAllQuestions.find(".ui-ncbigrid-select-question-all").attr("aria-controls",this.element.attr("id"))}},_addSelectAllQuestionToolbarEvents:function(){if(this.options.checkboxToolbarEnabled){var a=this;this._pagingSelectAllQuestions.find("a.ui-ncbigrid-select-question-all").click(function(b){a[a._askAllSelectionMode](true);a._pagingSelectAllQuestions.hide();b.preventDefault()});
-this._pagingSelectAllQuestions.find("a.ui-ncbigrid-select-question-cancel").click(function(b){a._pagingSelectAllQuestions.hide();b.preventDefault()});this.element.bind("ncbigridpagechanged checkboxrowclicked",function(){a._pagingSelectAllQuestions&&a._pagingSelectAllQuestions.hide()})}},_askSelectAllQuestion:function(a){this._askAllSelectionMode=a?"uncheckAll":"checkAll";if(this.options.isPageable)if(parseInt(this.getRowCount())>=parseInt(this.options.pageSize)){this._pagingSelectAllQuestions.show();
-this._updateSelectPageCount(a)}else this._pagingSelectAllQuestions.hide()},_updateSelectPageCount:function(a){var b=this.element.find("> tbody > tr > td > input[type=checkbox]:visible").length;this._pagingSelectAllQuestions.find(".ui-ncbigrid-select-row-count").html(b);this._pagingSelectAllQuestions.find(".selectText1").html(a?"deselected":"selected");this._pagingSelectAllQuestions.find(".selectText2").html(a?"Deselect":"Select")},_updateCount:function(){var a=this.element.find("tbody input[type=checkbox]");
-a=a.length>0?a.filter(":checked").length:this.element.find("tbody tr.ui-ncbigrid-row-selected").length;this._chekboxBars.find("span.ui-ncbigrid-selected-text").html(a)},_checkHelper:function(a,b){if(b){b=jQuery(this.element).find("> tbody > tr:not(.ncbigrid-row-filtered) > td > input[type=checkbox]");this._trigger(a?"checkall":"uncheckall",null,[a]);this._checkAllState=a}else b=a&&this.options.isPageable?this.element.find("> tbody > tr > td > input[type=checkbox]:visible"):this.element.find("> tbody > tr > td >  input[type=checkbox]");
-b.attr("checked",a);b=b.length===0?this.element.find("tbody tr").data("row-selected",a):b.closest("tr");a?b.addClass("ui-ncbigrid-row-selected"):b.removeClass("ui-ncbigrid-row-selected");this._updateCount()},checkAll:function(a){this._checkHelper(true,a);this._trigger("selectallclicked",null,[{acrossAllPages:a}])},uncheckAll:function(a){this._checkHelper(false,a);this._trigger("selectnoneclicked",null,[{acrossAllPages:a}])},_rowClicked:function(a){var b=jQuery(a.target||a.srcElement);a=null;if(b.is("input[type=checkbox]")){a=
-b;var c=a.is(":checked")}else if(!b.is("a")){a=b.closest("tr").find("input[type=checkbox]");c=!a.is(":checked");a.attr("checked",c)}b=b.closest("tr");if(a&&a.length===0){c=!b.data("row-selected");b.data("row-selected",c)}c?b.addClass("ui-ncbigrid-row-selected"):b.removeClass("ui-ncbigrid-row-selected");this.element.trigger("checkboxrowclicked");this._updateCount()},_filterBarControlsHTML:'                                         <div class="ui-ncbigrid-filter-toolbar">                        \t\t\t\t\t\t\t<label>Filter:</label>\t\t\t\t\t\t\t<input type="text" name="gridFilter" />                                            </div>',
-_createFilterBarControl:function(){this._createFilterBar();this._addFilterEvents()},_createFilterBar:function(){this._filterToolBar=jQuery(this._filterBarControlsHTML);var a=this.element.parent().parent();a.prepend(this._filterToolBar).children(".ui-ncbigrid-filter-toolbar").attr("aria-controls",this.element.attr("id"));a.addClass("filterToolbar-exists");var b=jQuery.ui.jig._generateId("gridFilter");a.children(".ui-ncbigrid-filter-toolbar").children(":input").attr("id",b).prev().attr("for",b)},_addFilterEvents:function(){var a=
-this;this._filterToolBar.find("input[type=text]").keyup(function(b){a._filterGrid(b,this)})},_filterGrid:function(a,b){if(!this._lastRunFilter)this._lastRunFilter="";a=b.value;b=this.options.filterToolbarIsCaseInsensitive||null;var c=this.options.filterToolbarColumnIndex||null,d=this.options.filterToolbarIsInverse||null;this._lastRunFilter.length>0&&a.indexOf(this._lastRunFilter)!==0&&this.removeFilterRows();this._lastRunFilter=a;if(this._lastRunFilter.length>0){var e=false;if(this.options.regExp)try{a=
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-f,i=0;i<a.length;i++){var h=a[i],j=h[0],l=h[2],k=h[3];h="";if(typeof l!="undefined"&&l!==null)h=":nth-child("+l+")";k=k?"not-":"";var m="",o=null;if(typeof j==="function"){m="-functionTest";o=this._custFilterCnt;this._custFilterCnt=o+1;o="filter_temp_"+o;jQuery.ui.jig[o]=j;j="jQuery.ui.jig."+o}else if(j.constructor&&j.constructor.toString().indexOf("RegExp")>0)m="-regexp";else if(b)m="-insensitive";f=l!==null?f.find("td"+h+":"+k+"contains"+m+"("+j+")").parent():f.filter(":"+k+"contains"+m+"("+j+")");
-if(o)jQuery.ui.jig[o]=null}var p=this;if(d){g=d.not(f);var q=g.length,t=0;(function(){for(;t<q;){g.eq(t).addClass("ncbigrid-row-filtered").attr("isfiltered","true");t++}e()})()}else e()}},removeFilterRows:function(a,b,c,d,e){function g(){if(l){jQuery.ui.jig[l]=null;a=j}m.options.isPageable&&m._gotoPage(0);m.element.trigger("ncbigridfilterremoved",[a,b,c]);m.options.isPageable?m._gotoPage(m.options.currentPage):m._notifyGridUpdated()}var f=null;if(typeof a!="undefined"&&a.length>0){if(typeof d==="undefined")d=
-true;var i="",h="";if(d||e){i=":not(";h=")"}var j=d="",l=null;if(typeof a==="function"){d="-functionTest";var k=this._custFilterCnt;this._custFilterCnt=k+1;l="filter_temp_"+k;j=jQuery.ui.jig[l]=a;a="jQuery.ui.jig."+l}else if(a.constructor&&a.constructor.toString().indexOf("RegExp")>0)d="-regexp";else if(b)d="-insensitive";e=e?"not-":"";if(typeof c!="undefined"&&c!==null){i="tbody tr[isfiltered='true'] td:nth-child("+c+")"+i+":"+e+"contains"+d+"("+a+")"+h;f=this.element.find(i).parent()}else{i="tbody tr[isfiltered='true']"+
-i+":contains"+d+"("+a+")"+h;f=this.element.find(i)}}else f=this.element.find("tr.ncbigrid-row-filtered");var m=this;if(f!==null){var o=f.length,p=0;(function(){for(;p<o;){f.eq(p).removeClass("ncbigrid-row-filtered").attr("isfiltered","false");p++}g()})()}else g()},showColumn:function(a){var b=this.element;if(this.options.isScrollable)b=b.add(this.parts.headerWrapper.find("table"));b.children().find(">tr>*:nth-child("+a+")").removeClass("ui-ncbigrid-column-hidden");this._setColumnHiddenData(a,false);
-this.element.trigger("showColumn",[a]);this._notifyGridUpdated()},hideColumn:function(a){var b=this.element;if(this.options.isScrollable)b=b.add(this.parts.headerWrapper.find(">table"));b.children().find(">tr>*:nth-child("+a+")").addClass("ui-ncbigrid-column-hidden");this._setColumnHiddenData(a,true);this.element.trigger("hideColumn",[a]);this._notifyGridUpdated()},_setColumnHiddenData:function(a,b){var c=this.element.data("dataHiddenCols");c||(c=[]);c[a]=b;this.element.data("dataHiddenCols",c)},
-getHiddenShownColumns:function(){var a=[],b=[],c=this.element.data("dataHiddenCols");if(c)for(var d in c)c[d]?a.push(d):b.push(d);return{hidden:a,shown:b}},_attachLoadingMessageListener:function(){var a=this;this.element.bind("ncbigridshowloadingbar",function(){a._showLoadingMessage()}).bind("ncbigridhideloadingbar",function(){a._hideLoadingMessage()})},_showLoadingMessage:function(){if(this.options.isLoadingMessageShown){if(!this.isPopperAttached){this.element.parent().parent().ncbipopper({triggerPosition:"top center",
-destPosition:"top center",hasArrow:false,closeEvent:"custom",openEvent:"custom",openAnimation:"none",closeAnimation:"none",destText:this.options.loadingText,isDestElementCloseClick:false,isDocumentElementCloseClick:false,isEscapeKeyClose:false,isTriggerElementCloseClick:false});this.isPopperAttached=true}this.element.parent().parent().ncbipopper("open")}},_hideLoadingMessage:function(){this.options.isLoadingMessageShown&&this.element.parent().parent().ncbipopper("close")},_addRowClickWatcher:function(){var a=
-this;jQuery(this.element).on("click","tbody",function(b){b=jQuery(b.srcElement||b.target).closest("td");if(b.length===1){var c=b.closest("tr");a.element.trigger("ncbigridrowclick",[{row:c,cell:b,rowIndex:c[0].rowIndex,cellIndex:b[0].cellIndex}])}})},_notifyGridUpdated:function(){this.element.trigger("ncbigridupdated")},_notifyGridContentChanged:function(){this.element.trigger("ncbigridcontentchanged")},addHTMLRowData:function(a,b,c,d){var e=this.getRowCount(),g="";if(typeof b=="undefined")g=":last-child";
-else{if(b>e)b=e;else if(b<0){b=1;c="before"}g=":nth-child("+b+")"}b=d!==undefined?":eq("+d+")":"";if(e===0)jQuery("tbody"+b+g,this.element).append(a);else c&&c.toLowerCase()==="before"?jQuery("tbody"+b+" tr"+g,this.element).before(a):jQuery("tbody"+b+" tr"+g,this.element).after(a);this.options.isPageable?this._gotoPage(this.options.currentPage):this._notifyGridUpdated();this._notifyGridContentChanged()},_deleteRowHelper:function(a,b){b=b!==undefined?":eq("+b+")":"";a?this.element.find("tbody"+b+" tr"+
-a).remove():this.element.find("tbody"+b).empty()},deleteAllRows:function(){this._deleteRowHelper();this.options.isPageable&&this._gotoPage(0);this._notifyGridUpdated();this._notifyGridContentChanged()},deleteRow:function(a,b){if(typeof a!="undefined"){a=jQuery.isArray(a)?a.sort():[a];for(var c=a.length-1;c>=0;c--)this._deleteRowHelper(":nth-child("+a[c]+")",b);this.options.isPageable&&this._gotoPage(this.options.currentPage);this._notifyGridUpdated();this._notifyGridContentChanged()}},getCellData:function(a,
-b,c){if(!(typeof a=="undefined"||typeof b=="undefined")){a=jQuery("tbody"+(c!==undefined?":eq("+c+")":"")+" tr:nth-child("+a+") td:nth-child("+b+")",this.element);if(a.length==0)return null;return this._getCellValue(a,b)}},getColumnCount:function(a){a=a===false?":visible":"";a=jQuery(this.element).find("tbody tr:not(.ui-ncbigrid-rowHidden):eq(0) td"+a).length;if(a===0)a=jQuery(this.element).find("> thead tr:last th").length;return a},getColumnData:function(a,b){if(typeof a==="undefined")return null;
-else if(jQuery.isArray(a)){for(var c=[],d=0;d<a.length;d++){if(a[d]<=0||a[d]>this.getColumnCount())c.push(null);c.push(this._getColumnDataHelper(a[d]),b)}return c}else{if(a<=0||a>this.getColumnCount())return null;return this._getColumnDataHelper(a,b)}},_getColumnDataHelper:function(a,b){var c=[],d=this,e=this._getColumnType(a-1);if(e==="str"||!e)e="str-sensitive";jQuery("tbody"+(b!==undefined?":eq("+b+")":"")+" tr td:nth-child("+a+")",this.element).each(function(g,f){c.push(d._csColumnTypeConversion(f,
-e,true))});if(c.length!==0)return c},getRowData:function(a,b){if(typeof a!=="undefined")if(jQuery.isArray(a)){for(var c=[],d=0;d<a.length;d++)c.push(this._getRowDataHelper(a[d]),b);return c}else return this._getRowDataHelper(a,b)},_getRowDataHelper:function(a,b){var c=[],d=this;jQuery("tbody"+(b!==undefined?":eq("+b+")":"")+" tr:nth-child("+a+") td",this.element).each(function(e){c.push(d._getCellValue(jQuery(this),e))});if(c.length!==0)return c},highlightRows:function(a,b,c,d){var e=jQuery.browser.msie&&
-parseFloat(jQuery.browser.version)<7;if(!(typeof a=="undefined"||a.length===0)){this.element.trigger("ncbigridshowloadingbar");var g=[],f=b?"-insensitive":"";d=d?"not-":"";if(a.constructor&&a.constructor.toString().indexOf("RegExp")>0){f="-regexp";d=""}typeof c!="undefined"?jQuery("tbody tr td"+(":nth-child("+c+")")+":"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).parent();h="ui-ncbigrid-high";if(e)h=i.hasClass("ui-ncbigrid-row-even")?"ui-ncbigrid-row-even-high-IE6":"ui-ncbigrid-row-odd-high-IE6";
-i.addClass(h);jQuery.inArray(i,g)===-1&&g.push(i)}):jQuery("tbody tr:"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h);h="ui-ncbigrid-high";if(e)h=i.hasClass("ui-ncbigrid-row-even")?"ui-ncbigrid-row-even-high-IE6":"ui-ncbigrid-row-odd-high-IE6";i.addClass(h);g.push(i)});this.element.trigger("ncbigridhighlightapplied",[a,b,c,g]).trigger("ncbigridhideloadingbar");return{highlightedRows:g}}},removeHighlightRows:function(a,b,c,d){var e=jQuery.browser.msie&&parseFloat(jQuery.browser.version)<
-7;if(typeof a!="undefined"&&a.length>0){var g=[],f=b?"-insensitive":"";d=d?"not-":"";if(a.constructor&&a.constructor.toString().indexOf("RegExp")>0){f="-regexp";d=""}typeof c!="undefined"?jQuery("tbody tr td"+(":nth-child("+c+")")+":"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).parent().removeClass("ui-ncbigrid-high");e&&i.removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6");jQuery.inArray(i,g)===-1&&g.push(i)}):jQuery("tbody tr:"+d+"contains"+
-f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).removeClass("ui-ncbigrid-high");e&&i.removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6");g.push(i)})}else{jQuery(".ui-ncbigrid-high",this.element).removeClass("ui-ncbigrid-high");e&&jQuery(".ui-ncbigrid-row-odd-high-IE6, .ui-ncbigrid-row-even-high-IE6",this.element).removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6")}this.element.trigger("ncbigridhighlightremoved",[a,
-b,c])},setCellData:function(a,b,c,d){jQuery("tbody"+(d!==undefined?":eq("+d+")":"")+" tr:nth-child("+a+") td:nth-child("+b+")",this.element).text(c);this.element.trigger("ncbigridcellchange",[a,b,this.getCellData(a,b)]);this._notifyGridUpdated();this._notifyGridContentChanged()},setRowData:function(a,b,c){jQuery("tbody"+(c!==undefined?":eq("+c+")":"")+" tr:nth-child("+a+") td",this.element).each(function(d,e){jQuery(e).text(b[d])});this.element.trigger("ncbigridrowchange",[a,this.getRowData(a,c)]);
-this._notifyGridUpdated();this._notifyGridContentChanged()},_enableCollapseTbodyRows:function(a){if(this.options.collapseRowsEnabled){a||(a=jQuery(this.element).find("tbody tr:has(th)"));var b=this;jQuery(a).each(function(){jQuery(this).addClass("ui-ncbigrid-collapsable").find("th").eq(0).prepend('<span class="collapsableTbodyIcon ui-icon ui-icon-plus-minus-big-open"></span>').find("span").click(function(c){c.stopPropagation();b._collapseTbodyRows(this.parentNode.parentNode)}).end().end().not(".ignoreCollapse").click(function(){b._collapseTbodyRows(this.parentNode)})})}},
-_collapseTbodyRows:function(a){jQuery(a).find("th span.collapsableTbodyIcon").toggleClass("ui-icon-plus-minus-big").toggleClass("ui-icon-plus-minus-big-open").end().siblings().toggleClass("collapsed")}});jQuery.extend(jQuery.expr[":"],{"contains-insensitive":function(a,b,c){return(a.textContent||a.innerText||"").toLowerCase().indexOf((c[3]||"").toLowerCase())>=0}});
-jQuery.extend(jQuery.expr[":"],{"contains-regexp":function(a,b,c){a=jQuery.trim(a.textContent||a.innerText||"");c=c[3];b=c.match(/\/([gi]+)$/);b=b!==null?b[1]:"";c=c.replace(/\/[gi]?$/,"").replace(/^\//,"");return a.match(new RegExp(c,b))!==null}});jQuery.extend(jQuery.expr[":"],{"contains-functionTest":function(a,b,c){a=a.textContent||a.innerText||"";return jQuery.ui.jig._getFncFromStr(c[3])(a)}});
-jQuery.extend(jQuery.expr[":"],{"not-contains":function(a,b,c){return(a.textContent||a.innerText||"").indexOf(c[3]||"")===-1}});jQuery.extend(jQuery.expr[":"],{"not-contains-insensitive":function(a,b,c){return(a.textContent||a.innerText||"").toLowerCase().indexOf((c[3]||"").toLowerCase())===-1}});
--- a/Blast output page example_files/jquery_007.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-html .ui-ncbimenu>li>a{color:#fff;}.jig-ncbimenu li.offscreen_noflow{position:absolute;left:-1000px;}.jig-ncbimenu{clear:both;}.jig-ncbimenu ul{display:none;}.jig-ncbimenu>li{display:inline;float:left;}ul.ui-ncbibasicmenu li{display:block;margin:0;}.ui-ncbimenu li>a{background-color:transparent;border:0;}.ui-ncbimenu ul{-moz-border-radius:6px;-webkit-border-radius:6px;border-radius:6px;border:1px solid #CCC;-webkit-box-shadow:.4em .4em .5em rgba(0,0,0,.3);-moz-box-shadow:.4em .4em .5em rgba(0,0,0,.3);box-shadow:.4em .4em .5em rgba(0,0,0,.3);}.ui-ncbimenu li.active a{background-color:#4c96df;}.ui-ncbimenu>li a:focus{outline:0;}.ui-ncbimenu li a.expandDown{padding-right:20px;background:url("../img/arrow-sprite.png") no-repeat scroll 96% -6% #FFF;}.ui-ncbimenu li a.expandRight{background:url("../img/arrow-sprite.png") no-repeat scroll 96% 106% #FFF;}.ui-ncbimenu>li>a.expandDown,.ui-ncbimenu>li>a.expandRight{background-color:transparent;}.ui-ncbimenu li>a:hover.expandRight{background:url("../img/arrow-sprite.png") no-repeat scroll 96% 106% #4C96DF;}.ui-ncbimenu li.ui-ncbimenu-item-no-hlt>a:hover.expandRight,.ui-ncbimenu li.ui-ncbimenu-item-skip>a:hover.expandRight{background-color:transparent;}.ui-ncbimenu li ul{display:none;z-index:200;}ul.ui-ncbimenu li ul li a{background-color:#fff;}.ui-ncbimenu ul{position:absolute;display:none;}.ui-ncbimenu>li a:hover,.ui-ncbimenu li.selected>a{background-color:#4C96DF;color:#fff;}.ui-ncbimenu li ul.ncbibasicmenu li.ui-ncbimenu-item-no-hlt,.ui-ncbimenu li ul.ncbibasicmenu li.ui-ncbimenu-item-skip{background-color:#FFF;}.ui-ncbimenu li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu li.selected.ui-ncbimenu-item-no-hlt>a,.ui-ncbimenu li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu li.selected.ui-ncbimenu-item-skip>a{color:#fff;}.ui-ncbimenu li ul li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu li ul li.selected.ui-ncbimenu-item-no-hlt>a,.ui-ncbimenu li ul li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu li ul li.selected.ui-ncbimenu-item-skip>a{color:#14376C;background-color:transparent;}.ui-ncbimenu .oneLevel li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu.ui-ncbibasicmenu>li.ui-ncbimenu-item-no-hlt>a:hover,.ui-ncbimenu .oneLevel li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu.ui-ncbibasicmenu>li.ui-ncbimenu-item-skip>a:hover{background-color:transparent;}.ui-ncbimenu .ui-ncbimenu-item-leaf{margin:0 .75em 0 0;}.ui-ncbimenu .ui-ncbimenu-item-leaf>a:hover{background-color:transparent;}.ui-ncbimenu:before,.ui-ncbimenu:after{content:"";display:table;}.ui-ncbimenu{*zoom:1;}
\ No newline at end of file
--- a/Blast output page example_files/jquery_007.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-jQuery.widget("ui.ncbibasicmenu",{options:{defaultSelection:-1,allowMultipleSelections:false,orientation:"vertical",preventDefaultCheck:true,stopPropagationCheck:true,normalizeSubsToOneLevel:false,disableSelect:false},styles:{itemNoHilite:"ui-ncbimenu-item-no-hlt",itemSkip:"ui-ncbimenu-item-skip"},_init:function(){this._loadedOnce&&this.rescan();this._loadedOnce=true},_create:function(){this._setSelectorString();this._addClasses();this._formatList();this._addEvents();this._setUpDefaults();this._setTabIndex();
-this._addAria()},rescan:function(){this._addClasses();this._setTabIndex();this._addAria();this._destroyFocusEvents();this._setUpFocusEvents()},destroy:function(){this._destroyTabIndex();this._destroyClasses();this._destroyEvents();this._destroyAria();this._destroyFormatList()},_setSelectorString:function(){var a=">";if(this.options.normalizeSubsToOneLevel){a="";this.element.addClass("oneLevel")}this._liSelector=a+"li:not(.ui-ncbimenu-item-skip)"},_addClasses:function(){this.isVert=this.options.orientation===
-"vertical";var a="ui-ncbibasicmenu";this.isVert||(a+=" orientation_hort");this.element.addClass(a)},_destroyClasses:function(){this.element.removeClass("ui-ncbibasicmenu")},_setUpDefaults:function(){this.selectedOption=this.options.defaultSelection;if(this.selectedOption!==-1){var a=this.element.find(this._liSelector+">a");if(this.options.allowMultipleSelections)for(var b=0;b<this.selectedOption.length;b++)this._makeSelection(a.eq(this.selectedOption[b]),"load");else this._makeSelection(a.eq(this.selectedOption),
-"load")}},_formatList:function(){},_destroyFormatList:function(){},_setTabIndex:function(){var a=this.element.find(this._liSelector+">a").attr("tabindex","-1"),b=this.element.find(this._liSelector+".selected>a");if(b.length>0)b=b.eq(0);else{var c=0;for(b=a.eq(0);b.is("."+this.styles.itemSkip+" a")&&c<a.length-1;){c+=1;b=a.eq(c)}}this.options.nested||b.removeAttr("tabindex")},_destroyTabIndex:function(){this.element.find(this._liSelector+">a").removeAttr("tabindex")},_addEvents:function(){this._setUpKeyListener();
-this._setUpClickEvents();this._setUpFocusEvents();this._setUpHoverEvents()},_destroyEvents:function(){this._destroyKeyListener();this._destroyClickEvents();this._destroyFocusEvents();this._destroyHoverEvents()},_setUpKeyListener:function(){if(!this._menuKeyListener){var a=this;this._menuKeyListener=function(b){if(a.element.is(":visible"))if(a._keyPressDetected(b.keyCode)){b.preventDefault();a.options.stopPropagationCheck&&b.stopPropagation()}};jQuery(document).keydown(this._menuKeyListener)}},_destroyKeyListener:function(){if(this._menuKeyListener){jQuery(window).unbind("keydown",
-this._menuKeyListener);this._menuKeyListener=null}},_setUpClickEvents:function(){var a=this;this._ulClickEvent=function(b){var c=b.srcElement||b.target;if(c){a.options.disableSelect||a._makeSelection(jQuery(c),"click");a.options.stopPropagationCheck&&b.stopPropagation();a.options.preventDefaultCheck&&jQuery(c).siblings("ul").length===1&&b.preventDefault()}};this.element.on("click.ncbibasicmenu",this._ulClickEvent)},_destroyClickEvents:function(){this.element.off("click",this._ulClickEvent)},_setUpFocusEvents:function(){var a=
-this;this._focusFnc=function(){a._menuFocused(this)};this._blurFnc=function(){a._menuBlured(this)};this.element.find(this._liSelector+">a").on("blur",this._blurFnc).on("focus",this._focusFnc)},_destroyFocusEvents:function(){this.element.find(this._liSelector+">a").off("blur",this._blurFnc).off("focus",this._focusFnc)},focus:function(){this._menuFocused(null)},_menuFocused:function(a){this._lastAnchor=a;this._isFocused=true},_menuBlured:function(a){if(this._lastAnchor==a)this._isFocused=false},removeFocus:function(){this._menuBlured()},
-_setUpHoverEvents:function(){var a=this;this._mouseEnterFnc=function(b){b=jQuery(b.target).closest("li");!b.hasClass(a.styles.itemNoHilite)&&!b.hasClass(a.styles.itemSkip)&&b.addClass("hover")};this.mouseLeaveFnc=function(){jQuery(this).removeClass("hover")};this.element.on("mouseenter","li",this._mouseEnterFnc).on("mouseleave","li",this.mouseLeaveFnc)},_destroyHoverEvents:function(){this.element.off("mouseenter",this._mouseEnterFnc).off("mouseleave",this.mouseLeaveFnc);this.mouseLeaveFnc=this._mouseEnterFnc=
-null},_makeSelection:function(a,b){var c=a.parent("li");if(c.length===1){var d=c.hasClass("selected");this.options.allowMultipleSelections||this._removeAllSelections();if(!c.hasClass(this.styles.itemSkip)){c.hasClass(this.styles.itemNoHilite)||c[d?"removeClass":"addClass"]("selected");var e=d?"unselected":"selected";b!=="menunav"&&this._trigger(e,"x",[a,c,b]);if(b==="click"||b==="load")this.selectedOption=this.element.find(this._liSelector+".selected").index();else d||c.find(">a").focus()}}this._setTabIndex()},
-_keys:{up:38,down:40,left:37,right:39,enter:13,escape:27,tab:9},_keyPressDetected:function(a){var b=this._keys,c=false;if(this._isFocused&&this.element.has(this._liSelector+">a:focus"))switch(a){case b.up:this._upDownPressed(-1);c=true;break;case b.down:this._upDownPressed(1);c=true;break;case b.left:this._leftRightPressed(-1);c=true;break;case b.right:this._leftRightPressed(1);c=true;break;case b.enter:this._enterSelected();c=false;break;case b.escape:this._escapeTyped();c=false;break;case b.tab:this._trigger("tab");
-default:c=false}return c},_upDownPressed:function(a){this.isVert?this._moveSelection(a):this._trigger(a===1?"actiondown":"actionup","x",this.focusedElement())},_leftRightPressed:function(a){this.isVert?this._trigger(a===1?"actionright":"actionleft","x",this.focusedElement()):this._moveSelection(a)},focusedElement:function(){return this.selectedOption!==-1?this.element.find(this._liSelector).eq(this.selectedOption):this.element.find(this._liSelector+":has(>a:focus)")},moveSelection:function(a){this._moveSelection(a)},
-_getNextIndex:function(a,b,c){a=a+b;if(a<0)a=c-1;else if(a>c-1)a=0;return a},_moveSelection:function(a){for(var b=this.element.find(this._liSelector+">a"),c=this._getNextIndex(this.selectedOption,a,b.length);b.eq(c).closest("li").hasClass(this.styles.itemSkip);)c=this._getNextIndex(c,a,b.length);this.selectedOption=c;this._makeSelection(b.eq(c),"keyboard")},removeAllSelections:function(){this.selectedOption=-1;this._removeAllSelections();this._setTabIndex()},_removeAllSelections:function(){this.element.find(this._liSelector).removeClass("selected")},
-_enterSelected:function(){this._trigger("enter")},_escapeTyped:function(){this._trigger("escape","x",this.focusedElement())},_addAria:function(){var a=this.element.parents('[role="menubar"]'),b=this.element.find(this._liSelector),c=b.find(">a");this.element.attr("role",a.length===0?"menubar":"menu");b.attr("role","presentation");c.attr("role","menuitem")},_destroyAria:function(){var a=this.element.find(this._liSelector),b=a.find(">a");this.element.removeAttr("role");a.removeAttr("role");b.removeAttr("role")},
-selectFirstItem:function(){this.selectedOption=0;this._moveSelection(0)}});
--- a/Blast output page example_files/jquery_008.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-ul.jig-ncbilocalnav,ul.ui-ncbilocalnav{list-style:none;margin:0;padding:0;width:100%;}ul.jig-ncbilocalnav:after,ul.ui-ncbilocalnav:after{content:".";display:block;height:0;clear:both;visibility:hidden;*zoom:1;*display:block;}ul.jig-ncbilocalnav li,ul.ui-ncbilocalnav li{float:left;position:relative;list-style:none;display:block;}ul.jig-ncbilocalnav li a,ul.ui-ncbilocalnav li a{color:#444;text-decoration:none;display:block;padding:.15em 1em .15em 1em;zoom:1;}ul.jig-ncbilocalnav ul{display:none;}ul.ui-ncbilocalnav ul{margin:0;margin-left:0!important;display:none;border-width:1px 0 0 1px;width:200px;padding-left:0;-moz-box-shadow:.4em .4em .5em #999;-webkit-box-shadow:.4em .4em .5em #999;box-shadow:.4em .4em .5em #999;_margin-top:1px;}ul.ui-ncbilocalnav li.open ul{display:block;position:absolute;left:-1px;}ul.ui-ncbilocalnav li:first-child{margin-left:1.333em;}ul.ui-ncbilocalnav ul li:first-child{margin-left:0;}ul.ui-ncbilocalnav ul li{float:none;display:block;position:relative;*line-height:125%;zoom:1;}ul.ui-ncbilocalnav li.has-child ul{z-index:1003;}ul.ui-ncbilocalnav li:first-child{border-left:1px solid #b0b0b0;}ul.ui-ncbilocalnav ul li:first-child{border-left:0;}ul.ui-ncbilocalnav{border-top:1px solid #c4c4c4;border-bottom:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul{border-left:1px solid #b0b0b0;}ul.ui-ncbilocalnav li{border-right:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul li{border-bottom:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul li:first-child{border-top:1px solid #b0b0b0;}ul.ui-ncbilocalnav li.active{border-right:1px solid #c4c4c4;*z-index:1005;}ul.ui-ncbilocalnav li.active ul li{*z-index:1006;}ul.ui-ncbilocalnav li.active,ul.ui-ncbilocalnav li.active ul li,ul.ui-ncbilocalnav li.hover,ul.ui-ncbilocalnav li.hover ul li{*z-index:1006;}ul.ui-ncbilocalnav li.selected>ul>li a{margin:0 .75em;padding:.15em 1.5em .15em .25em;}ul.ui-ncbilocalnav li.selected a{color:#444!important;background-color:transparent!important;}ul.ui-ncbilocalnav li.hover>a,ul.ui-ncbilocalnav li.hover.selected>a,ul.ui-ncbilocalnav li.selected>a{background-color:transparent!important;color:#444!important;}ul.ui-ncbilocalnav,ul.ui-ncbilocalnav li{background-color:#F4F4F4;background-image:-webkit-gradient(linear,left top,left bottom,from(#fff),to(#F4F4F4));background-image:-webkit-linear-gradient(top,#fff,#F4F4F4);background-image:-moz-linear-gradient(top,#fff,#F4F4F4);background-image:-ms-linear-gradient(top,#fff,#F4F4F4);background-image:-o-linear-gradient(top,#fff,#F4F4F4);background-image:linear-gradient(top,#fff,#F4F4F4);}ul.ui-ncbilocalnav li.hover,ul.ui-ncbilocalnav li.selected{background-color:#E0E0E0;background-image:-webkit-gradient(linear,left top,left bottom,from(#F2F2F2),to(#E0E0E0));background-image:-webkit-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-moz-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-ms-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-o-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:linear-gradient(top,#F2F2F2,#E0E0E0);}ul.ui-ncbilocalnav li li.hover{background-color:#EDEDED;background-image:-webkit-gradient(linear,left top,left bottom,from(#DEDEDE),to(#EDEDED));background-image:-webkit-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-moz-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-ms-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-o-linear-gradient(top,#DEDEDE,#EDEDED);background-image:linear-gradient(top,#DEDEDE,#EDEDED);}.ui-ncbilocalnav>li>a.expandDown{background:url(../img/ncbilocalnav-arrow.png) no-repeat right 8px!important;_background-position:right 11px!important;padding:.15em 1.5em .15em .25em;margin:0 .75em;color:#444;}ul.ui-ncbilocalnav li.selected ul li a{background-image:none!important;zoom:1;}
\ No newline at end of file
--- a/Blast output page example_files/jquery_008.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-(function(b){var h,i,j,g,l=function(){var a=b(this).find(":ui-button");setTimeout(function(){a.button("refresh")},1)},k=function(a){var c=a.name,e=a.form,f=b([]);if(c)f=e?b(e).find("[name='"+c+"']"):b("[name='"+c+"']",a.ownerDocument).filter(function(){return!this.form});return f};b.widget("ui.button",{options:{disabled:null,text:true,label:null,icons:{primary:null,secondary:null}},_create:function(){this.element.closest("form").unbind("reset.button").bind("reset.button",l);if(typeof this.options.disabled!==
-"boolean")this.options.disabled=this.element.propAttr("disabled");this._determineButtonType();this.hasTitle=!!this.buttonElement.attr("title");var a=this,c=this.options,e=this.type==="checkbox"||this.type==="radio",f="ui-state-hover"+(!e?" ui-state-active":"");if(c.label===null)c.label=this.buttonElement.html();if(this.element.is(":disabled"))c.disabled=true;this.buttonElement.addClass("ui-button ui-widget ui-state-default ui-corner-all").attr("role","button").bind("mouseenter.button",function(){if(!c.disabled){b(this).addClass("ui-state-hover");
-this===h&&b(this).addClass("ui-state-active")}}).bind("mouseleave.button",function(){c.disabled||b(this).removeClass(f)}).bind("click.button",function(d){if(c.disabled){d.preventDefault();d.stopImmediatePropagation()}});this.element.bind("focus.button",function(){a.buttonElement.addClass("ui-state-focus")}).bind("blur.button",function(){a.buttonElement.removeClass("ui-state-focus")});if(e){this.element.bind("change.button",function(){g||a.refresh()});this.buttonElement.bind("mousedown.button",function(d){if(!c.disabled){g=
-false;i=d.pageX;j=d.pageY}}).bind("mouseup.button",function(d){if(!c.disabled)if(i!==d.pageX||j!==d.pageY)g=true})}if(this.type==="checkbox")this.buttonElement.bind("click.button",function(){if(c.disabled||g)return false;b(this).toggleClass("ui-state-active");a.buttonElement.attr("aria-pressed",a.element[0].checked)});else if(this.type==="radio")this.buttonElement.bind("click.button",function(){if(c.disabled||g)return false;b(this).addClass("ui-state-active");a.buttonElement.attr("aria-pressed","true");
-var d=a.element[0];k(d).not(d).map(function(){return b(this).button("widget")[0]}).removeClass("ui-state-active").attr("aria-pressed","false")});else{this.buttonElement.bind("mousedown.button",function(){if(c.disabled)return false;b(this).addClass("ui-state-active");h=this;b(document).one("mouseup",function(){h=null})}).bind("mouseup.button",function(){if(c.disabled)return false;b(this).removeClass("ui-state-active")}).bind("keydown.button",function(d){if(c.disabled)return false;if(d.keyCode==b.ui.keyCode.SPACE||
-d.keyCode==b.ui.keyCode.ENTER)b(this).addClass("ui-state-active")}).bind("keyup.button",function(){b(this).removeClass("ui-state-active")});this.buttonElement.is("a")&&this.buttonElement.keyup(function(d){d.keyCode===b.ui.keyCode.SPACE&&b(this).click()})}this._setOption("disabled",c.disabled);this._resetButton()},_determineButtonType:function(){this.type=this.element.is(":checkbox")?"checkbox":this.element.is(":radio")?"radio":this.element.is("input")?"input":"button";if(this.type==="checkbox"||this.type===
-"radio"){var a=this.element.parents().filter(":last"),c="label[for='"+this.element.attr("id")+"']";this.buttonElement=a.find(c);if(!this.buttonElement.length){a=a.length?a.siblings():this.element.siblings();this.buttonElement=a.filter(c);if(!this.buttonElement.length)this.buttonElement=a.find(c)}this.element.addClass("ui-helper-hidden-accessible");(a=this.element.is(":checked"))&&this.buttonElement.addClass("ui-state-active");this.buttonElement.attr("aria-pressed",a)}else this.buttonElement=this.element},
-widget:function(){return this.buttonElement},destroy:function(){this.element.removeClass("ui-helper-hidden-accessible");this.buttonElement.removeClass("ui-button ui-widget ui-state-default ui-corner-all ui-state-hover ui-state-active  ui-button-icons-only ui-button-icon-only ui-button-text-icons ui-button-text-icon-primary ui-button-text-icon-secondary ui-button-text-only").removeAttr("role").removeAttr("aria-pressed").html(this.buttonElement.find(".ui-button-text").html());this.hasTitle||this.buttonElement.removeAttr("title");
-b.Widget.prototype.destroy.call(this)},_setOption:function(a,c){b.Widget.prototype._setOption.apply(this,arguments);if(a==="disabled")c?this.element.propAttr("disabled",true):this.element.propAttr("disabled",false);else this._resetButton()},refresh:function(){var a=this.element.is(":disabled");a!==this.options.disabled&&this._setOption("disabled",a);if(this.type==="radio")k(this.element[0]).each(function(){b(this).is(":checked")?b(this).button("widget").addClass("ui-state-active").attr("aria-pressed",
-"true"):b(this).button("widget").removeClass("ui-state-active").attr("aria-pressed","false")});else if(this.type==="checkbox")this.element.is(":checked")?this.buttonElement.addClass("ui-state-active").attr("aria-pressed","true"):this.buttonElement.removeClass("ui-state-active").attr("aria-pressed","false")},_resetButton:function(){if(this.type==="input")this.options.label&&this.element.val(this.options.label);else{var a=this.buttonElement.removeClass("ui-button-icons-only ui-button-icon-only ui-button-text-icons ui-button-text-icon-primary ui-button-text-icon-secondary ui-button-text-only"),
-c=b("<span></span>",this.element[0].ownerDocument).addClass("ui-button-text").html(this.options.label).appendTo(a.empty()).text(),e=this.options.icons,f=e.primary&&e.secondary,d=[];if(e.primary||e.secondary){if(this.options.text)d.push("ui-button-text-icon"+(f?"s":e.primary?"-primary":"-secondary"));e.primary&&a.prepend("<span class='ui-button-icon-primary ui-icon "+e.primary+"'></span>");e.secondary&&a.append("<span class='ui-button-icon-secondary ui-icon "+e.secondary+"'></span>");if(!this.options.text){d.push(f?
-"ui-button-icons-only":"ui-button-icon-only");this.hasTitle||a.attr("title",c)}}else d.push("ui-button-text-only");a.addClass(d.join(" "))}}});b.widget("ui.buttonset",{options:{items:":button, :submit, :reset, :checkbox, :radio, a, :data(button)"},_create:function(){this.element.addClass("ui-buttonset")},_init:function(){this.refresh()},_setOption:function(a,c){a==="disabled"&&this.buttons.button("option",a,c);b.Widget.prototype._setOption.apply(this,arguments)},refresh:function(){var a=this.element.css("direction")===
-"rtl";this.buttons=this.element.find(this.options.items).filter(":ui-button").button("refresh").end().not(":ui-button").button().end().map(function(){return b(this).button("widget")[0]}).removeClass("ui-corner-all ui-corner-left ui-corner-right").filter(":first").addClass(a?"ui-corner-right":"ui-corner-left").end().filter(":last").addClass(a?"ui-corner-left":"ui-corner-right").end().end()},destroy:function(){this.element.removeClass("ui-buttonset");this.buttons.map(function(){return b(this).button("widget")[0]}).removeClass("ui-corner-left ui-corner-right").end().button("destroy");
-b.Widget.prototype.destroy.call(this)}})})(jQuery);
--- a/Blast output page example_files/jquery_009.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-document.times=0;
-jQuery.widget("ui.ncbipopper",{destTextCallbackCalledCount:0,options:{openMethod:"",openEvent:"mouseover",openAnimation:"slideDown",openAnimationTime:290,closeMethod:"",closeEvent:"mouseout",closeAnimation:"slideUp",closeAnimationTime:150,isEscapeKeyClose:true,isSourceElementCloseClick:false,isTriggerElementCloseClick:true,isTargetElementCloseClick:false,isDestElementCloseClick:false,isDocumentCloseClick:true,addCloseButton:false,adjustFit:"autoAdjust",delayTimeout:300,sourcePosition:"",destPosition:"top left",
-sourceSelector:"",destSelector:"",targetPosition:"",triggerPosition:"bottom right",sourceText:null,destText:null,multipleHandlesSelector:"",openAtTarget:false,hasArrow:false,arrowDirection:"left",groupName:null,width:null,height:null,cssClass:null,excludeBasicCssStyles:false,wrapElement:false,loadingText:"loading...",showLoadingMessage:true,isDestTextCacheable:true,resizable:false,openAtMousePosition:false},_create:function(){this._setUpDestElem();this._addEventHandlers();this._addEscapeListener();
-this._addDocumentClickListener();this._addResizeListener();this._addCloseButton();this._addSharingDetails();this._addPopperHover();this.addTriggerAria()},updateTriggers:function(){this._addEventHandlers();this._addDocumentClickListener();this.addTriggerAria()},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);var a=this.isPopperShared();this._destroyDestAria();this._destroyTriggerAria();this._removeSharingDetails();this._destroyCloseButton(a);this._destroyResizeListener();this._destroyDocumentClickListener();
-this._destroyEscapeListener();this._removeEventHandlers();this._destroyDestElem(a)},getDestElement:function(a){var b=this.destElem;if(!this.origDestElem)this.origDestElem=b;if(b){if(a&&this._isWaitingToBeAddedToDom){a=jQuery("div.grid");a=a.length===1?a:jQuery(document.body);b.appendTo(a);this._isWaitingToBeAddedToDom=true;this._getActualText(b)}}else{b=this.options.destSelector||this.options.sourceSelector||this.element.prop("hash");a=this.options.destText||this.options.sourceText;if(b){b=jQuery(b);
-if(b.length===0)b=this._createTextHolder()}else if(a)b=this._createTextHolder();else throw"The popper can not find the popper element or text to display";if(this.options.wrapElement){if(!b.parent().hasClass("ui-ncbipopper-wrapper")){b.wrap('<div style="display:none"></div>');b.show()}if(!this.origDestElem)this.origDestElem=b;b=b.parent()}this.destElem=b;this._addDestAria()}if(!this.origDestElem)this.origDestElem=this.destElem;return b},_createTextHolder:function(){var a=jQuery('<div><div class="ui-ncbipopper-content"></div></div>');
-this._isWaitingToBeAddedToDom=true;return a},_getActualText:function(a){if(!this.isFunctionResultCached){var b=this.options.destText||this.options.sourceText,c=this._getFunction(b);if(typeof c==="function")b=this._getText(c);a.css("display","none").attr("generated","true").find(".ui-ncbipopper-content").html(b)}},_getFunction:function(a){var b=null;if(jQuery.ui.jig&&jQuery.ui.jig._getFncFromStr)b=jQuery.ui.jig._getFncFromStr(a);else if(typeof a==="function")b=a;return b},getDestTextCallbackCalledCount:function(){return this.destTextCallbackCalledCount},
-_getText:function(a){if(!(this.options.isDestTextCacheable&&this.getTextCalled||this.callbackInProgress)){this.getTextCalled=true;a||(a=this._getFunction(this.options.destText||this.options.sourceText));var b=this;this.callbackInProgress=true;a=a.call(this.element[0],function(c){b._setHTML(c);b.destTextCallbackCalledCount++;b.callbackInProgress=false})||this.options.loadingText;if(a!==this.options.loadingText)this.isFunctionResultCached=this.options.isDestTextCacheable;return a}},reloadContent:function(){var a=
-this._getText(),b=this.getDestElement().find(".ui-ncbipopper-content");b&&b.html(a);return this.element},_setHTML:function(a){var b=this.getDestElement().find(".ui-ncbipopper-content");if(b){b.html(a);this.isFunctionResultCached=this.options.isDestTextCacheable;!this.options.showLoadingMessage&&!this.isPopperDisplayed&&this._openAnimation()}},_setUpDestElem:function(){var a=this.getDestElement().addClass("ui-ncbipopper-wrapper");this.options.excludeBasicCssStyles||a.addClass("ui-ncbipopper-basic");
-this.options.resizable&&a.resizable();var b=this.options.cssClass;b&&a.addClass(b);this.options.width!==null&&a.width(this.options.width);this.options.height!==null&&a.height(this.options.height);this._resetElementPosition(a);a.removeClass("offscreen_noflow").hide();a.data("isOpen",false)},_setArrowDirection:function(){if(this.options.hasArrow){var a=this.options.arrowDirection;this._arrow&&this._arrow.removeClass("ui-ncbipopper-arrow-top ui-ncbipopper-arrow-bottom  ui-ncbipopper-arrow-left  ui-ncbipopper-arrow-right").addClass("ui-ncbipopper-arrow-"+
-a)}},_setUpArrow:function(a,b,c){if(this.options.hasArrow){var d=this.options.arrowDirection;if(this._arrow)this._arrow.removeClass("ui-ncbipopper-arrow-top ui-ncbipopper-arrow-bottom  ui-ncbipopper-arrow-left  ui-ncbipopper-arrow-right").addClass("ui-ncbipopper-arrow-"+d);else this._arrow=jQuery('<div class="ui-ncbipopper-arrow-image ui-ncbipopper-arrow-'+d+'">&nbsp;</div>').appendTo(document.body);a=this._getPositionSettings(a,"arrow",c);this._arrow.show().position({my:a.dest,of:this._activeTrigger||
-a.triggerElement||this.element,at:a.trigger,offset:a.offset,collision:"none"});if(b||this._arrowOverlapsPopper())this._arrow.hide()}},_destroyDestElem:function(a){a||this.getDestElement().removeClass("ui-ncbipopper-wrapper ui-ncbipopper-basic ui-ncbipopper-wrapper-relative-parent").attr("style","").show();this.options.wrapElement&&this.origDestElem.unwrap();this.destElem=null},_addEventHandlers:function(){var a=this,b=this.element,c=this.options.multipleHandlesSelector;if(c&&c.length>0)b=b.add(c);
-var d=this.options.openMethod||this.options.openEvent,e=this.options.closeMethod||this.options.closeEvent;if(d===e&&e==="click"){this._openFunction=function(f){a._toggle(f,f.currentTarget);f.preventDefault()};b.on("click",this._openFunction)}else{c={timeout:this.options.delayTimeout};if(d==="mouseover")c.over=function(f){a._isOverTrigger=true;a.open(f,this)};else{c.over=function(){a._isOverTrigger=true};this._openFunction=function(f){if(d==="click")if(a.option.isTriggerElementCloseClick){a._toggle(f,
-this);f.preventDefault()}else{a.isOpen(this)||f.preventDefault();a.open(f,this)}else a.open(f,this)};b.on(d,this._openFunction)}if(e==="mouseout")c.out=function(){a._isOverTrigger=false;a.isOpen(this)&&!a._isOverPopper&&a.close()};else{c.out=function(){};this._closeFunction=function(f){a.close();e==="click"&&f.preventDefault()};b.on(e,this._closeFunction)}if(d==="mouseover"||e==="mouseout")b.hoverIntent(c);if(this.options.isTriggerElementCloseClick&&e!=="click"&&d!=="click"){this._closeFunction2=
-function(f){a.isOpen(b)&&a.close();f.preventDefault()};b.on("click",this._closeFunction2)}}if(this.options.isDestElementCloseClick){this._closeFunctionPopper=function(f){a.isOpen(b)&&a.close();f.preventDefault()};this.getDestElement().on("click",this._closeFunctionPopper)}},_removeEventHandlers:function(){var a=this.element,b=this.getDestElement(),c=this.options.multipleHandlesSelector;if(c&&c.length>0)a=a.add(c);a.off("mouseover mouseout");if(this._openFunction){a.off(this.options.openMethod||this.options.openEvent,
-this._openFunction);this._openFunction=null}if(this._closeFunction){a.off(this.options.closeMethod||this.options.closeEvent,this._closeFunction);this._closeFunction=null}if(this._closeFunction2){a.off("click",this._closeFunction2);this._closeFunction2=null}if(this._closeFunctionPopper){b.off("click",this._closeFunctionPopper);this._closeFunctionPopper=null}},_toggle:function(a,b){this.isOpen(b)?this.close():this.open(a,b);a&&a.preventDefault&&a.preventDefault();return this.element},_arrowOverlapsPopper:function(){var a=
-this.getDestElement(),b=Math.floor(a.position().top),c=Math.floor(a.position().left),d=Math.floor(c+a.outerWidth());a=Math.floor(b+a.height());var e=this._arrow,f=Math.floor(e.position().top),g=Math.floor(e.position().left);Math.floor(g+e.width());var h=Math.floor(f+e.height());c=g>c&&g<d||g+e.css("width")>c&&g+e.css("width")<d;b=f>b&&f<a||f+e.css("height")>b&&h+e.css("height")<a;return c&&b?true:false},_openAnimation:function(a){function b(){var k=d.outerHeight(),l=jQuery(window).height();k>l&&d.css({"max-height":l-
-45+"px",overflow:"auto"});jQuery(window).trigger("resize")}var c=this,d=this.getDestElement().data("isOpening",this.element).stop(true,true),e=this._arrow,f=this.options.openAnimation,g=function(){c._trigger("opencomplete");c.getDestElement().data("isOpening",null);jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<=7&&c._positionPopper(a,false,true);b()},h=function(k){e.fadeTo(0,0);window.setTimeout(function(){e.stop(true,true).show();c._arrowOverlapsPopper()||e.css("opacity",1)},k)};if(f===
-"none"||this.isOpen()){d.show();e&&h(0);g()}else{var j=this.options.openAnimationTime;if(e){var i=0;if(e==="top")i=0;else if(e==="bottom")i=j;else{i=parseInt(e.css("top"),10)-parseInt(d.css("top"),10);var m=d.height()||i;i=i/m*j;if(i>j)i=j}h(i)}d[f](j,g)}},open:function(a,b){if(!b)b=this.element;if(this.options.openAtTarget){if(this._activeTrigger!==b){this.getDestElement().hide();this.getDestElement().data("isOpen",false)}this._activeTrigger=b}else this._activeTrigger=this.element;b=this.getDestElement();
-var c=b.data("isOpening");if(c&&c[0]!==this.element[0])(b.data("closeFnc")||function(){})(true);this._handleSharedPoppersOpen();this._handleGroupsOpen();b.data("isOpening",this.element);this._setUpArrow(a,true,true);jQuery.browser.msie&&this._positionPopper(a,true,true);this._setParentsZIndex(11);this._positionPopper(a,true,true);this._trigger("open");this.options.destText&&!this.options.showLoadingMessage&&!this.isFunctionResultCached||this._openAnimation(a);this._setAriaState(true);this.getDestElement().data("isOpen",
-true);return this.element},_handleGroupsOpen:function(){var a=this.options.groupName;if(a){this.closeGroup(a);jQuery.ui.ncbipopper.openGroups[a]=this.element}},_closeAnimation:function(a){var b=this,c=function(){b._setParentsZIndex(1);b._trigger("closecomplete")},d=this.getDestElement().data("isOpening");if(d&&this.element[0]!=d[0])c();else{d=this.getDestElement().stop(true,true);var e=this.options.closeAnimation;if(e==="none"||a){d.hide();this._resetElementPosition(d);c()}else{var f=d;d[e](this.options.closeAnimationTime,
-function(){b._resetElementPosition(f);c()})}}a=this.getDestElement().data("popperTriggers");for(e=0;e<a.length;e++){d=jQuery.ui.jig.getElementWidgets(a[e],"ncbipopper")[0];var g=d._arrow;if(g){g.stop(true,true).hide();d._resetElementPosition(g)}}},close:function(a){if(this.isOpen(this._activeTrigger)){this._handleGroupsClose(a);this._trigger("close");this._activeTrigger=null;this._closeAnimation(a);this._setAriaState(false);this.getDestElement().data("isOpen",false);return this.element}},closeGroup:function(a){if(a=
-a||this.options.groupName)(a=jQuery.ui.ncbipopper.openGroups[a])&&jQuery.ui.jig.getElementWidgets(a,"ncbipopper")[0].close(true);return this.element},_handleGroupsClose:function(a){var b=this.options.groupName;if(!a&&b)jQuery.ui.ncbipopper.openGroups[b]=null},_determineAutoPosition:function(a){var b=jQuery(this._activeTrigger||this.element),c=b.offset(),d=this.getDestElement(true),e=jQuery(window);if(a){a=e.width();d=d.outerWidth();b=b.width();e=e.scrollLeft();if(d+b+c.left<a+e){c="right";b=e="left"}else{c=
-"left";b=e="right"}}else{a=e.height();d=d.outerHeight();b=b.height();e=e.scrollTop();if(d+b+c.top<a+e){c="bottom";b=e="top"}else{c="top";b=e="bottom"}}return{posT:c,posP:e,arrow:b}},_getPositionSettings:function(a,b,c){var d=this.options.sourcePosition||this.options.destPosition,e=this.options.targetPosition||this.options.triggerPosition;d=d.split(/\s/);e=e.split(/\s/);if(d[0]==="middle")d[0]="center";if(d[1]==="middle")d[1]="center";if(e[0]==="middle")e[0]="center";if(e[1]==="middle")e[1]="center";
-this.options.sourcePosition=null;this.options.destPosition=d.join(" ");this.options.targetPosition=null;this.options.triggerPosition=e.join(" ");var f;if(d[0]==="auto"){f=this._determineAutoPosition(false);d[0]=f.posP;e[0]=f.posT;this.options.arrowDirection=f.arrow;this._setArrowDirection(f.arrow)}if(d[1]==="auto"){f=this._determineAutoPosition(true);d[1]=f.posP;e[1]=f.posT;this.options.arrowDirection=f.arrow;this._setArrowDirection(f.arrow)}f=d[1]+" "+d[0];var g=e[1]+" "+e[0],h="0px 0px";if(this.options.hasArrow)h=
-b==="popper"?this._getPopperOffsets(d[0],d[1]):this._getArrowOffsets(d[0],d[1]);if(this.options.openAtMousePosition&&c){h.xOffset=a.pageX-jQuery(a.target).offset().left+(h.xOffset-0)+1;h.yOffset=a.pageY-jQuery(a.target).offset().top+(h.yOffset-0)}if(this._isArea===undefined)this._isArea=((this._activeTrigger?this._activeTrigger[0]:false)||this.element[0]).nodeName.toUpperCase()==="AREA";if(this._isArea){a=this._areaElementAdjustment(h,e);triggerElement=a.positionElement;h=a.offset;g="left top"}else triggerElement=
-null;if(this.options.openAtMousePosition&&c)g="left top";return{dest:f,trigger:g,offset:typeof h=="string"?h:h.xOffset+"px "+h.yOffset+"px",triggerElement:triggerElement}},_getArrowOffsets:function(a,b){var c="0",d="0";switch(this.options.arrowDirection){case "left":case "right":switch(a){case "top":d="-13";break;case "center":d="0";break;case "bottom":d="13";break;default:d="0";break}break;case "top":case "bottom":switch(b){case "left":c="-13";break;case "center":c="0";break;case "right":c="13";
-break;default:c="0";break}break;default:throw"Valid arrow directions are top, bottom, left, right";}return{xOffset:c,yOffset:d}},_getPopperOffsets:function(a,b){var c="0",d="0";c=this.options.arrowDirection;switch(c){case "left":case "right":c=c==="left"?"7":"-7";switch(a){case "top":d="-13";break;case "center":d="0";break;case "bottom":d="13";break;default:d="0";break}break;case "top":case "bottom":d=c==="top"?"7":"-7";switch(b){case "left":c="-13";break;case "center":c="0";break;case "right":c=
-"13";break;default:c="0";break}break;default:throw"Valid arrow directions are top, bottom, left, right";}return{xOffset:c,yOffset:d}},_areaElementAdjustment:function(a,b){a=typeof a=="string"?a.split(" "):[a.xOffset,a.yOffset];var c=parseInt(a[0],10);a=parseInt(a[1],10);var d=jQuery(this._activeTrigger||this.element).parent(),e=jQuery(this._activeTrigger||this.element[0])[0];d=jQuery("img[usemap='#"+(d[0].name||d[0].id)+"']");var f=e.shape||"rect";e=(e.coords||"").split(/\s?,\s?/g);d=d;var g=0,h=
-0;if(f==="circle"){if(b[0]=="top")h=parseFloat(e[1])-parseFloat(e[2]);else if(b[0]=="bottom")h=e[3]+parseFloat(e[2]);else if(b[0]=="center")h=parseFloat(e[1]);if(b[1]==="left")g=e[0]-parseFloat(e[2]);else if(b[1]==="right")g=e[2]+parseFloat(e[2]);else if(b[1]==="center")g=parseFloat(e[0])}else{if(b[0]=="top")h=parseFloat(e[1]);else if(b[0]=="bottom")h=parseFloat(e[3]);else if(b[0]=="center")h=(parseFloat(e[1])+parseFloat(e[3]))/2;if(b[1]==="left")g=parseFloat(e[0]);else if(b[1]==="right")g=parseFloat(e[2]);
-else if(b[1]==="center")g=(parseFloat(e[0])+parseFloat(e[2]))/2}g+=c;h+=a;return{positionElement:d,offset:g+"px "+h+"px"}},_getCollisionSetting:function(){var a=this.options.adjustFit;return a=a==="autoAdjust"||a==="slide"?"fit":"none"},_resetElementPosition:function(a){a.css("top","-100px").css("left","-100px")},_positionPopper:function(a,b,c){a=this._getPositionSettings(a,"popper",c);c=this._getCollisionSetting();var d=a.triggerElement||this.options.openAtTarget&&this._activeTrigger||this.element;
-a=this.getDestElement(true).stop().show().position({my:a.dest,of:d,at:a.trigger,offset:a.offset,collision:c}).data("attached-to",d);b&&a.hide();document.times++},_addEscapeListener:function(){if(this.options.isEscapeKeyClose){this._registerGlobalEscapeListener();var a=this;this._ncbipopperescapepressedFunction=function(){a.close()};jQuery(document).bind("ncbipopperescapepressed",this._ncbipopperescapepressedFunction)}},_destroyEscapeListener:function(){if(this._ncbipopperescapepressedFunction){jQuery(document).unbind("ncbipopperescapepressed",
-this._ncbipopperescapepressedFunction);this._ncbipopperescapepressedFunction=null}},_registerGlobalEscapeListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalEscapeRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalEscapeRegistered=true;var a=document,b="keypress";if(!jQuery.browser.msie&&!jQuery.browser.mozilla){a=window;b="keydown"}jQuery(a)[b](function(c){c.keyCode===27&&jQuery(document).trigger("ncbipopperescapepressed")})}},_addDocumentClickListener:function(){if(this.options.isDocumentCloseClick){this._registerGlobalClickListener();
-var a=this;this._ncbipopperdocumentclickFunction=function(b,c){a._checkDocumentClick(b,c)};jQuery(document).bind("ncbipopperdocumentclick",this._ncbipopperdocumentclickFunction)}},_destroyDocumentClickListener:function(){this._ncbipopperdocumentclickFunction&&jQuery(document).unbind("ncbipopperdocumentclick",this._ncbipopperdocumentclickFunction)},_registerGlobalClickListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalClickRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalClickRegistered=
-true;jQuery(document).click(function(a){jQuery(document).trigger("ncbipopperdocumentclick",[a.srcElement||a.target])})}},_checkDocumentClick:function(a,b){if(b&&this.isOpen()){b=jQuery(b);if(!(this._isSameElementOrChild(jQuery(this.element),b)||this._isSameElementOrChild(this.getDestElement(),b)))if(!(jQuery.ui.jig.getElementWidgets(jQuery(b),"ncbipopper")[0]&&this.getDestElement()[0]==jQuery.ui.jig.getElementWidgets(jQuery(b),"ncbipopper")[0].getDestElement()[0])){if(a=this.options.multipleHandlesSelector){var c=
-false,d=this;jQuery(a).each(function(){if(d._isSameElementOrChild(jQuery(this),b))c=true});if(c)return}this.close()}}},_isSameElementOrChild:function(a,b){return a[0]==b[0]||jQuery(a).has(b).length===1},_addResizeListener:function(){this._registerGlobalResizeListener();var a=this;this.ncbipopperdocumentresizeFunction=function(b){a._pageResized(b)};jQuery(window).bind("ncbipopperdocumentresize",this.ncbipopperdocumentresizeFunction)},_destroyResizeListener:function(){if(this.ncbipopperdocumentresizeFunction){jQuery(window).unbind("ncbipopperdocumentresize",
-this.ncbipopperdocumentresizeFunction);this.ncbipopperdocumentresizeFunction=null}},_registerGlobalResizeListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalResizeRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalResizeRegistered=true;jQuery(window).on("resize scroll",function(){jQuery(window).trigger("ncbipopperdocumentresize")})}},_pageResized:function(a){if(this.isOpen()){this._positionPopper(a);this._setUpArrow(a)}},_addCloseButton:function(){if(this.options.addCloseButton){var a=
-this.getDestElement(),b=a.find(".ui-ncbipopper-close-button, .ncbipopper-close-button");if(b.length===0){b=jQuery("<button class='ui-ncbipopper-close-button ui-ncbipopper-close-button-generated'>x</button>").attr("generated","true").prependTo(a);b.ncbibutton({color:"blue"})}if(b){var c=this;this._closeButtonFunction=function(d){c.close();d.preventDefault()};b.on("click",this._closeButtonFunction)}}},_destroyCloseButton:function(a){this._closeButtonFunction&&this.getDestElement().find(".ui-ncbipopper-close-button, .ncbipopper-close-button").off("click",
-this._closeButtonFunction).filter(function(){return!a}).filter(".ui-ncbipopper-close-button-generated").ncbibutton("destroy").remove()},isPopperShared:function(){return(this.getDestElement().data("popperTriggers")||[]).length>1},_addSharingDetails:function(){var a=this.getDestElement(),b=a.data("popperTriggers")||[];b.push(this.element);a.data("popperTriggers",b)},_removeSharingDetails:function(){for(var a=this.getDestElement(),b=a.data("popperTriggers"),c=this.element[0],d=0;d<b.length;d++)if(b[d][0]==
-c){b.slice(d,1);break}b.length===0?a.removeData("popperTriggers"):a.data("popperTriggers",b)},_handleSharedPoppersOpen:function(){if(this.isPopperShared())for(var a=this.getDestElement().data("popperTriggers"),b=this.element[0],c=0;c<a.length;c++)if(a[c][0]!=b&&jQuery.ui.jig.getElementWidgets(a[c],"ncbipopper")[0].isOpen()){jQuery.ui.jig.getElementWidgets(a[c],"ncbipopper")[0].close(true);break}},_addPopperHover:function(){if((this.options.closeMethod||this.options.closeEvent)==="mouseout"){var a=
-this.getDestElement();if(this._arrow)a=a.add(this._arrow);var b=this,c={timeout:this.options.delayTimeout,over:function(){},out:function(){b._overPopper(false)}};jQuery(a).hoverIntent(c);jQuery(a).mouseenter(function(){b._overPopper(true);b._lastOver=new Date});jQuery(a).mouseleave(function(){new Date-b._lastOver<b.options.delayTimeout&&b._overPopper(false)}).mouseout(function(d){var e=jQuery(d.target||d.srcElement);if(e.hasClass("ui-ncbipopper-wrapper")||e.hasClass("ui-ncbipopper-arrow-image"))if(e.find(d.relatedTarget).length===
-0){b._isOverPopper=false;b._outTimer=window.setTimeout(function(){b._overPopper(false)},200)}})}},_destroyPopperHover:function(){var a=jQuery(this.getDestElement());a.unbind("mouseenter").unbind("mouseleave");a.removeProp("hoverIntent_t");a.removeProp("hoverIntent_s")},_overPopper:function(a){this._outTimer&&window.clearInterval(this._outTimer);if(a)this._pTimer=new Date;this._isOverPopper=a;if(!a)if(this._isOverTrigger){var b=this;window.setTimeout(function(){!b._isOverPopper&&!b._isOverTrigger&&
-b._overPopper(false)},300)}else this.close()},isOpen:function(a){if(!a)a=this._activeTrigger;a=jQuery(a);var b=jQuery(this._activeTrigger),c=this.getDestElement().data("popperTriggers");a=this.options.openAtTarget||c.length>1?a&&a.length&&b&&b.length&&b[0]===a[0]:true;return this.getDestElement().data("isOpen")&&a?true:false},_setParentsZIndex:function(a){if(jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<=7){var b=this.getDestElement().parents(),c=0;if(b.length>1){b.each(function(e){if(jQuery(this).css("position")===
-"relative"){c=e===0?0:e+1;return false}});b=b.eq(c);var d=b.css("position");b.data("orgPosition")||b.data("orgPosition",d);if(d==="static"||d==="relative"){d=a===1?b.data("orgPosition"):"relative";b.css({position:d,"z-index":a})}}}},addTriggerAria:function(a){var b=a;if(!a){b=this.element;if((a=this.options.multipleHandlesSelector)&&a.length>0)b=b.add(a)}b.attr("role","button").attr("aria-expanded",false).attr("aria-haspopup",true)},_destroyTriggerAria:function(){var a=this.element,b=this.options.multipleHandlesSelector;
-if(b&&b.length>0)a=a.add(b);a.removeAttr("role aria-expanded aria-haspopup")},_addDestAria:function(){this.getDestElement().attr("aria-live","assertive").attr("aria-hidden",true).addClass("ui-helper-reset")},_destroyDestAria:function(){this.getDestElement().removeAttr("aria-live aria-hidden").removeClass("ui-helper-reset")},_setAriaState:function(a,b,c){b=b?b:this.element;c=c?c:this.getDestElement();b.attr("aria-expanded",a);c.attr("aria-hidden",!a)}});jQuery.ui.ncbipopper.openGroups={};
-jQuery.ui.ncbipopper.globalEvents={isGlobalEscapeRegistered:false,isGlobalClickRegistered:false,isGlobalResizeRegistered:false};
--- a/Blast output page example_files/main.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,337 +0,0 @@
-/*
-LEGAL
-=====
-Copyright: Daemon Pty Limited 1995-2006, http://www.daemon.com.au & http://www.mollio.org/
-License: Released Under the "Common Public License 1.0", http://www.opensource.org/licenses/cpl.php
-Version: 010306
-*/
-body {padding: 0 0 10px;background: #fff url("images/body_bg-ncbi.gif") repeat-x 0 100%;color:#333;font:83%/1.5 arial,tahoma,verdana,sans-serif;}
-body { margin: 0; padding: 0; }
-/* LINKS */
-a,a:link,a:link,a:link,a:hover {text-decoration:underline;cursor:pointer}
-a:link {color:#369}
-/* Original: a:visited {color:#999} */
-a:visited {color:#664E99;}
-a:hover,a:active {color:#069}
-/* FORMS */
-form {margin: 0 0 1.5em}
-input {font-family: arial,tahoma,verdana,sans-serif;margin: 2px 0 0}
-label {display:block;padding: 5px 0}
-label br {clear:left}
-#desc {font-weight: bold;margin-bottom: 5px;}
-#desc a {font-weight: normal;}
-#logolink, #logolink img {float: left;border: 0;margin: 0;}
-
-/* TYPOGRAPHY */
-p, ul, ol {margin: 0 0 1.5em}
-/* Original: h1, h2, h3, h4, h5, h6 {letter-spacing: -1px;font-family: arial,verdana,sans-serif;margin: 1.2em 0 .3em;color:#000;border-bottom: 1px solid #eee;padding-bottom: .1em}*/
-h1, h2, h3, h4, h5, h6 { letter-spacing: -1px;font-family: arial,verdana,sans-serif;margin: 1.2em 0 .3em;color:#2A6979;border-bottom: 1px solid #ccc;padding-bottom: .1em}
-h1 {font-size: 196%;margin-top:.6em}
-h2 {font-size: 136%}
-h3 {font-size: 126%}
-h4 {font-size: 116%}
-h5 {font-size: 106%}
-h6 {font-size: 96%}
-.highlight {color:#4E8999; padding: 3px; border: solid 1px #ccc;}
-.featured { background-color: #ffc; padding: 0.25em 0.5em;margin:0; }
-.subdued {color:#999}
-
-small {font-size:11px}
-
-/* LISTS */
-ul {margin: .3em 0 1.5em 0;list-style-type:none}
-ul.related {margin-top: -1em}
-ol {margin: .5em .5em 1.5em}
-ol li {margin-left: 1.4em;padding-left: 0;background: none; list-style-type: decimal}
-.section li {line-height: 1.4em;padding-left: 25px;background: transparent url("images/sprites-ncbi.gif") no-repeat 0 0}*/
-li.doc {background-position: 3px -500px}
-ul.nomarker li {background:none;padding-left:0}
-dl {margin: 0 0 1em 0}
-dt {font-weight:bold;margin-top: 1.3em}
-dl dl {margin: 0 0 1.5em 30px}
-
-/* GENERAL */
-/*img {border:none} */
-hr {margin: 1em 0;background:#f2f2f2;height:1px;color:#f2f2f2;border:none;clear:both}
-.clear {clear:both;position:relative;font-size:0px;height:0px;line-height:0px}
-/* LAYOUT - HEADER */
-#header {background: #204174  url("images/sprites-ncbi.gif") repeat-x 0 100%;margin: 0 0 3px;padding: 0 0 8px;white-space:nowrap;}
-#header #site-name {font: 120% arial;letter-spacing: -.05em;margin: 0 ;padding:3px 0; color:#ffffff;font-weight: bold;}
-#header #site-name h1 {font-style: italic; letter-spacing: 0; color: #68a; margin:0 0 0 5em; position: relative; left: 200px;font-size:85%;border:none;padding-bottom:0;display:inline;}
-#header {min-width:770px;position:relative;}
-/* NAV - top horizontal nav */
-#nav, #nav ul {padding: 0;margin: 0;list-style: none}
-#nav {font-weight:bold;height:2.09em;font: bold 95% arial;margin: 0 105px 0 40px; width: 430px;}
-#nav li {background: #999;float: left;width: auto;display:block;margin: 0;border-bottom: 3px solid #666;border-right: 3px solid #252525;padding:0}
-#nav a, #nav a:link, #nav a:visited, #nav a:hover, #nav a:active {text-decoration:none;cursor:pointer;color:#fff;display: block;padding: 4px 10px 2px}
-#nav a:hover {color:#000}
-#nav li ul {border-left: 1px solid #ccc;background: #eee;width:22.8em;font-size:90%;margin-top:3px;position: absolute;font-weight:normal;left: -999em}
-#nav li:hover ul, #nav li.sfhover ul {left: 0;z-index:99999;}
-#nav li li {background:none;float:none;border:none;border: 1px solid #999;border-top:1px solid #fff;border-right:solid 1px #ccc;border-left:none;padding-left:0}
-#nav li li.last {border-bottom:solid 1px #ccc;}
-#nav li li a, #nav li li a:link, #nav li li a:visited, #nav li li a:hover {color:#000;padding: 3px 10px 2px;width:21em}
-#nav li li a:hover {color:#fff;background:#4E8999}
-#nav li.active {background: #4E8999;border-bottom: 3px solid #4E8999}
-#nav li.active a:link, #nav li.active a:visited, #nav li.active a:hover, #nav li.active a:active {}
-#nav li.active a:hover {color:#000}
-#nav li.active li {border:none;border-top: 1px solid #ccc;border-bottom: 1px solid #ccc;}
-#nav li.active li {border: solid 1px #ccc;border-right: solid 1px #4E8999;border-left: solid 1px #4E8999;}
-#nav li.active li.last {border-bottom: solid 1px #4E8999;}
-#nav li.active li a:link, #nav li.active li a:visited, #nav li.active li a:hover, #nav li.active li a:active {color:#000}
-#nav li.active li a:hover {background: #666 url("images/sprites-ncbi.gif") repeat-x 0 99%;color:#fff; filter:progid:DXImageTransform.Microsoft.AlphaImageLoader (src='images/sprites-ncbi.gif', sizingMethod='crop');}
-#nav li.active li.active a:link, #nav li.active li.active a:visited, #nav li.active li.active a:hover, #nav li.active li.active a:active {color:#fff;font-weight:bold;background: #666 url("images/sprites-ncbi.gif") repeat-x 0 99%; filter:progid:DXImageTransform.Microsoft.AlphaImageLoader (src='images/sprites-ncbi.gif', sizingMethod='crop');}
-
-/* hide from IE mac \*/
-#nav li {width:auto}
-/* end hiding from IE5 mac */
-
-/* SEARCH */
-#search {color:#fff;font-weight:bold;position:absolute;top:10px;right:4em}
-#search form {margin:0}
-#search input {width:8em;margin: 0 0 -1px;height:1.2em}
-#search label {padding:5px 0 0;display:inline}
-#search input.f-submit {width:auto;font-size:81%;margin:0 0 -.15em;height:1.95em}
-#content {margin: 0;}
-#type-d #content {margin: 0 0 0 40px;}
-#breadcrumb {margin-top:-5px;font-size:93%;font-weight:bold; margin-left: 1em; margin-bottom: 0; padding: 0 6px 0 12px;; background: url("images/right-arrow.gif") no-repeat center left;display:inline;}
-#breadcrumb strong{font-weight:bold;}
-#breadcrumb a:link, #breadcrumb a:visited {text-decoration:none}
-#breadcrumb a:hover, #breadcrumb a:active {text-decoration:underline}
-/* CODE - formatting for code inserted into body - more here: http://dizque.lacalabaza.net/temp/lipt/ */
-ol.code {font-family: monospace;position:relative}
-ol.code li {color: #666;margin-bottom: 1px}
-ol.code code {color: #000;display: block}
-ol.code .cmt {color: #4077d2}
-li.tab0 code {padding-left: 4em}
-li.tab1 code {padding-left: 8em}
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-{
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-{
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-a.errorHelp
-{
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-margin-right:2em;
-margin-top:-2em;*/
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-}
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-{
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-}
-
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-{
-    color:Red;
-}
-.orgHint
-{
-    color:#AAAAAA;
-}
-
-
-span.acPromt,.skp
-{
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-}
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-
-
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-{
-    margin-left:35em;
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-{
-    vertical-align:super;
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-}
-
-.print-log-res { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }
-.print-log-res li { list-style-image: none; }
-
-/* jig toggler adjustments */
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-{
-    font-size:100%;
-}
-
-.helplink.ui-widget
-{
-  display:inline;
-}
-
-
-#content a.ui-ncbitoggler.ui-widget, #content a.ui-ncbitoggler-open
-{
-color:#336699;
-}
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-#moreHelp span
-{
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-}
-
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-#content #moreHelp.ui-ncbitoggler, #content #moreHelp.ui-ncbitoggler-open
-{
-    font-size:80%;
-}
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-#content  .ui-ncbitoggler-slave-open
-{
-    line-height:1.4em;
-}
-
-div.ui-ncbiautocomplete-holder {
-  font-size: 80%;
-}
-ul.ui-ncbiautocomplete-options li span{ color: red;}
-.ytb,.section a.ytb
-{
-    margin-bottom:-5px;
-    background: url("/core/assets/guide/images/YouTube.png") no-repeat scroll left center transparent !important;
-    height:22px;
-    padding-left:55px;
-    font-weight:normal;
-}
\ No newline at end of file
Binary file Blast output page example_files/myncbihelpicon.gif has changed
--- a/Blast output page example_files/plinkcgi.html	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-<html xmlns:xs="http://www.w3.org/2001/XMLSchema"><head>
-<meta http-equiv="content-type" content="text/html; charset=UTF-8">
-  </head><body>
-    <p class="featured" id="prlink">
-      <a href="http://www.ncbi.nlm.nih.gov/projects/primer-blast/index.cgi?LINK_LOC=BlastDescAd" target="pr_win">
-        <img src="plinkcgi_data/primerAd.png" alt="New" border="0">
-      </a>
-    </p>
-
-
-</body></html>
\ No newline at end of file
--- a/Blast output page example_files/plinkcgi_002.html	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-<html xmlns:xs="http://www.w3.org/2001/XMLSchema"><head>
-<meta http-equiv="content-type" content="text/html; charset=UTF-8">
-  </head><body>
-    <p class="featured" id="prlink">
-      <a href="http://www.ncbi.nlm.nih.gov/projects/primer-blast/index.cgi?LINK_LOC=BlastAlnAd" target="pr_win">
-        <img src="plinkcgi_data/primerAd.png" alt="New" border="0">
-      </a>
-    </p>
-
-
-</body></html>
\ No newline at end of file
Binary file Blast output page example_files/plinkcgi_data/primerAd.png has changed
--- a/Blast output page example_files/print.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,305 +0,0 @@
-/*
-LEGAL
-=====
-Copyright: Daemon Pty Limited 1995-2006, http://www.daemon.com.au & http://www.mollio.org/
-License: Released Under the "Common Public License 1.0", http://www.opensource.org/licenses/cpl.php
-Version: 010306
-*/
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-
-body {font: 10pt arial,tahoma,verdana,sans-serif}
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-
-* {float:none;position:static;background:#fff}
-p {margin: 0 0 1em}
-dt {font-weight:bold}
-
-#nav, #search, #nav-secondary,  #poweredby {display:none}
-
-/* =LINKS */
-a {border:none}
-a,a:link,a:link,a:link,a:hover {background:transparent;text-decoration:underline;cursor:pointer}
-a:link {color:#5291c4}
-a:visited {color:#666}
-a:hover {color:#ff9900;border:none}
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-margin-top:0.25em;;
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-margin-bottom: 2em;;
-font-size: 110%;;
-padding-bottoM:0.5em;;
-}
-
-/* TABLES */
-table {font-size: 9pt;margin: 0 0 1em;border-collapse:collapse;}
-
-	table th {border-bottom: 3px solid #000;vertical-align:top;padding: 1.5em 3px 3px;line-height:1.1;font: bold 145% arial;letter-spacing:0;text-align:left}
-	.table1 th.time {border-bottom: none;font: bold 89% verdana;color:#ff9c00;vertical-align:top;padding: 3px}
-	.table1 td {border: 1px solid #ddd;font-size: 9pt;padding: 3px;vertical-align:top}
-	.table1 td a {display:block;width:auto;font-weight:bold}
-	.table1 td a:link, .table1 td a:visited, .table1 td a:hover, .table1 td a:active {border:none;text-decoration:none}
-	.table1 th.sub {background: #aaa}
-	.table1 th.sub2 {background: #bbb;color:#000}
-	.table1 td ul li {background: #fff}
-
-
-#logolink img {
-display: none;
-}
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-#site-name {
-font-size: 140%;
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-margin : 0 0.25in;
-}
-
-#blHeader pre, #query pre {
-white-space: normal;
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-
-#blHeader pre p {
-display: none; /* Get rid of pointer to BLAST FAQs */
-}
-
-#graphic input {
-display: none;
-}
-
-#descs td { vertical-align: top; }
-td.lim { white-space: normal; padding-bottom: 0.5em;}
-#descs td { vertical-align: top; border-bottom: solid 1px #888; border-collapse: collapse; padding-top: 0;}
-
-#descs a {
-text-decoration: none;
-color: black;
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-#graphic {page-break-after: always; }
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-td.l a { padding: 0; margin-right: 1em !important; font-weight:bold;}
-#descs td {color: black;}
-
-/* Get rid of stupid long headers */
-#desctbl { margin-top: 1em; border-top: solid 1px #ccc; page-break-after: always;}
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-#desctbl table tr td { width: 4em; }
-#desctbl table td.lim { width: 40em; }
-
-#alignments { line-height: 0.9em; }
-#alignments center b {
- display: block; z-index: 100; position: relative;
-}
-#alignments center b font { color: black; display: block; text-align: left; font-size: 120%; padding: 0 0 3px; border-bottom: solid 2px #444; margin-left: -1.5em; }
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-#footer {
-display: none;
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-h1
-{
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-font-weight:bold;
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-{
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-{
-   display:none;
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-{
-    display:none;
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-{
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-{
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-{
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-}
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-{
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-{
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-.print-log-res { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }
-.print-log-res li { list-style-image: url("images/img_blast_results_gif"); }
-
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-{
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-{
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-{
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-}
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-{
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-span.r label
-{
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-{
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-{
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-{
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-{
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Binary file Blast output page example_files/query_no_scale.gif has changed
Binary file Blast output page example_files/reformat.jpg has changed
--- a/Blast output page example_files/remote_data_provider.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-//=========================================================================================================
-function RemoteDataProvider(sUrl) {
-    this.iActiveRequests = 0;
-    this.sUrl = sUrl;
-}
-
-//-------------------------------------------------------------------------------------------------------------
-RemoteDataProvider.prototype.GetHttpObj = function() {
-    var oHttpObj = null;
-    try {
-        oHttpObj = new ActiveXObject("Msxml2.XMLHTTP");
-    } catch(e) {
-        try {
-            oHttpObj = new ActiveXObject("Microsoft.XMLHTTP")
-        } catch(oc) {
-            oHttpObj = null;
-        }
-    }
-    if (!oHttpObj && typeof XMLHttpRequest != "undefined") {
-        oHttpObj = new XMLHttpRequest();
-    }
-    return oHttpObj;
-}
-
-//-------------------------------------------------------------------------------------------------------------
-RemoteDataProvider.prototype.Request = function(sRequest, method) {
-    var oHttpObj = this.GetHttpObj();
-    if (null == oHttpObj) return;
-
-    method = (!method) ? "GET" : "POST";
-    var sURL = (method == "GET") ? this.sUrl + "?" + sRequest : this.sUrl;        //alert(sURL);
-    this.iActiveRequests++;
-    var oThis = this;
-    oHttpObj.onreadystatechange = function () {
-        if (oHttpObj.readyState == 4 && oHttpObj.status == 200) {
-            oThis.onSuccess(oHttpObj);
-            oThis.iActiveRequests--;
-            oThis.onStop();
-        } else if(oHttpObj.readyState == 4 && oHttpObj.status != 200) {
-            oThis.onError(oHttpObj);
-            oThis.iActiveRequests--;
-            oThis.onStop();
-        }
-    };
-
-    if (oHttpObj.readyState != 0) oHttpObj.abort();
-    this.onStart();
-    oHttpObj.open(method, sURL, true);
-//    oHttpObj.setRequestHeader('Cache-Control', 'no-cache');
-    var params = (method == "GET") ? null : sRequest;
-    if (params) {
-        oHttpObj.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
-        oHttpObj.setRequestHeader("Content-length", params.length);
-        oHttpObj.setRequestHeader("Connection", "close");
-    }
-    oHttpObj.send(params);
-}
-
-//-------------------------------------------------------------------------------------------------------------
-RemoteDataProvider.prototype.onSuccess = function(obj) {
-    alert(["success:", this.iActiveRequests, obj.responseText]);
-}
-
-//-------------------------------------------------------------------------------------------------------------
-RemoteDataProvider.prototype.onStart = function() {
-//    alert(["start:", this.iActiveRequests]);
-}
-
-//-------------------------------------------------------------------------------------------------------------
-RemoteDataProvider.prototype.onStop = function() {
-//    alert(["start:", this.iActiveRequests]);
-}
-
-//-------------------------------------------------------------------------------------------------------------
-RemoteDataProvider.prototype.onError = function(obj) {
-    //alert(["error:", this.iActiveRequests, obj.status]);
-}
-
-
--- a/Blast output page example_files/results.css	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1224 +0,0 @@
-#summary {
-font-size:1.2em;
-}
-#summary {
-margin-top:0pt;
-padding-bottom:1em;
-padding-top:0.5em;
-font-family:Verdana,Arial,Sans-Serif;
-font-size:90%;
-
-}
-#summarylists {
-margin:1em 0pt 0pt;
-overflow:hidden;
-}
-#seealso {
-margin-left:2em;
-}
-#querysummary {
-float:left;
-padding:0pt;
-width:49%;
-}
-#dbsummary {
-margin-left:51%;
-padding:0pt;
-}
-#summary dl {
-margin:0pt 0pt 0.5em;
-padding:0pt;
-}
-#summary dt, #summary dd {
-line-height:1.4em;
-}
-#summary dt {
-float:left;
-font-weight:bold;
-text-align:right;
-width:10em;
-margin-top:0;
-}
-#summary dd {
-margin-left:11em;
-white-space:normal !important;
-overflow:hidden;
-}
-#summary h3 {
-color:#444444;
-font-style:italic;
-margin-bottom:-0.5em;
-margin-top:0pt;
-text-align:center;
-}
-
-#multipleSeqs {
-font-weight: bold;
-}
-#multipleSeqs a {
-font-size:80%;
-font-weight:normal;
-}
-#breadcrumb {
-background:transparent url(images/right-arrow.gif) no-repeat scroll left center;
-font-size:93%;
-font-weight:bold;
-margin-top:-5px;
-padding:0pt 6px 0pt 12px;
-}
-#breadcrumb a {
-color:#336699;
-}
-
-#jobTitle
-{
-color:#669;
-/*color:#2A6980;*/
-font-weight:bold;
-margin-bottom:-0.5em;
-}
-
-#type-a #content-wrap {white-space:normal; padding-bottom:2em;}
-
-#statInfo
-{
-    font-size:100%;
-}
-
-
-#resMsg
-{
-background-color:#FFFFCC;
-font-size:110%;
-/*margin-top:4em;
-padding-left:0.5em;*/
-text-align:center;
-}
-
-#seealso label
-{
-    display:inline;
-}
-
-#seealso a
-{
-    padding: 0,4px;
-}
-
-a.shown
-{
-    display:inline;
-}
-
-
-table.dbInfo
-{
-    width:50%;
-    border:solid 1px gray;
-    font-size:100%;
-    border-collapse:collapse;
-    margin-top:1em;
-}
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-table.dbInfo caption
-{
-   border:solid 1px gray;
-   padding: 1px 4px;
-}
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-    background-color:#acf;
-    text-align:center;
-    border-bottom:none;
-    margin-bottom:-0.2em;
-    font-weight:bold;
-    margin-top:1em;
-}
-#resStat, #dbDetails
-{
-    padding-left:25%;
-}
-
-table.dbInfo td
-{
-    text-align:left;
-}
-
-table.dbInfo th {
-visibility:hidden;
-/*padding:0;*/
-}
-
-
-table.dbInfo th div {
-height:0;
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-{
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-{
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-#nextDbSet,#lastDbSet {
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--- a/Blast output page example_files/results.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,649 +0,0 @@
-// JScript source code
-
-//Display Reformat page button only after the whole page is loaded
-
-function ReformatPageEvent()
-{
-	var refPageLink = document.getElementById("refPage");
-
-	//alert(refPageLink);
-	//alert(refPageLink.getAttribute("submitForm"));
-	var submitForm = refPageLink.getAttribute("submitForm");
-	alert(submitForm);
-	if(refPageLink && submitForm) {
-		utils.addEvent(refPageLink,
-					   "click",
-					   function() {
-							document.getElementById(submitForm).submit();
-						},
-						false);
-	}
-}
-
-
-function SubmitEvent(linkID)
-{
-
-	var link = document.getElementById(linkID);
-	//alert(link.getAttribute("submitForm"));
-	var submitForm = link.getAttribute("submitForm");
-	if(link && submitForm) {
-		utils.addEvent(link,
-					   "click",
-					   function() {
-							document.getElementById(submitForm).submit();
-						},
-						false);
-	}
-}
-
-
-function SubmitEventSave(linkID)
-{
-
-	var link = document.getElementById(linkID);
-	//alert(link.getAttribute("submitForm"));
-	var submitForm = link.getAttribute("submitForm");
-	if(link && submitForm) {
-		utils.addEvent(link,
-					   "click",
-					   function() {
-							//$(submitForm).CMD.value = "GetSaved";
-							document.getElementById(submitForm).submit();
-						},
-						false);
-	}
-}
-
-
-
-
-//This function creates submit form event on click
-//form submitted is defined in submitForm attribute
-//It also copies params from forms[0] (search paramateres) created by formatter
-function SubmitEventNew(linkID)
-{
-
-	var link = document.getElementById(linkID);
-	//alert(link.getAttribute("submitForm"));
-	if(!link) return;
-	var submitForm = link.getAttribute("submitForm");
-	if(link && submitForm) {
-		utils.addEvent(link,
-					   "click",
-					   function() {
-							document.forms[0].CMD.value = "";
-							if(document.forms[0].PAGE_TYPE) {
-								document.forms[0].PAGE_TYPE.value = "";
-							}
-							var s = document.forms[0].innerHTML;
-							var form = $(submitForm);
-							form.innerHTML = s + form.innerHTML;
-							form.submit();
-						},
-						false);
-	}
-}
-
-function GetResults()
-{
-    form = $("results");
-    form.QUERY_INDEX.value = $("queryList")[$("queryList").selectedIndex].value;
-    form.submit();
-}
-
-function isIdIn(id, idArray){
-  var idSeen=false;
-
-  for(i=0; i<idArray.length; i++){
-    if(id==idArray[i]){
-      idSeen=true;
-      break;
-    }
-  }
-  return idSeen;
-}
-
-function GetSelectedSeqString(formName)
-{
-    var selSeqs = "";
-    var idArray=new Array();
-    forms = document.getElementsByName(formName);
-    for(var j=0; j < forms.length; j++){
-      for(var i=0; i < forms[j].elements.length; i++){
-        var theElem=forms[j].elements[i];
-        if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"&&theElem.checked){
-          if(!isIdIn(theElem.value, idArray)){
-            idArray[idArray.length]=theElem.value;
-          }
-        }
-      }
-    }
-    selSeqs = idArray.join();
-    return selSeqs;
-}
-
-function ViewSelectedSeqs(e)
-{
-    var submitForm = $("submitterTop");
-    var targetForm = submitForm.getAttribute("seqsForm");
-    $("selSeqs").value = GetSelectedSeqString(targetForm);
-    submitForm.submit();
-    utils.preventDefault(e);
-}
-
-
-function ViewSelectedSeqTree()
-{
-    var submitForm = $("treesubmitterTop");
-    var targetForm = submitForm.getAttribute("seqsForm");
-    $("seqSet").value = GetSelectedSeqString(targetForm);
-    $("scrWidth").value = screen.width;
-    $("scrHeight").value = screen.height;
-    submitForm.submit();
-}
-
-function ViewTree(linkID) {
-    link = document.getElementById(linkID);
-    var target = link.target;
-    winRef = window.open(link.href + "&screenWidth=" + screen.width + "&screenHeight=" + screen.height, target);
-}
-
-function ViewSelectedSeqMultiAlign()
-{
-    var submitForm = $("multisubmitterTop");
-    var targetForm = submitForm.getAttribute("seqsForm");
-    $("seqSetM").value = GetSelectedSeqString(targetForm);
-    submitForm.submit();
-}
-
-
-
-function selectAllSeqs()
-{
-    var formName = this.getAttribute("seqsForm");
-    forms = document.getElementsByName(formName);
-    for(var j=0; j < forms.length; j++){
-        for(var i=0; i < forms[j].elements.length; i++){
-    //for(var i=0; i < document.forms[formName].elements.length; i++){
-            var theElem=forms[j].elements[i];
-            if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"){
-                theElem.checked=this.checked;
-            }
-        }
-    }
-    links = document.getElementsByName("selectAll");
-    for(var i=0; i < links.length;i++) {
-        if(links[i] != this)  links[i].checked = this.checked;
-    }
-}
-
-
-function InitSeqAlignLinks()
-{
-    var links = document.getElementsByName("getSeqs");
-    for(var i=0; i < links.length;i++) {
-        utils.addEvent(links[i],"click",ViewSelectedSeqs,false);
-    }
-    links = document.getElementsByName("treeView");
-    for(var i=0; i < links.length;i++) {
-        utils.addEvent(links[i],"click",ViewSelectedSeqTree,false);
-    }
-    links = document.getElementsByName("mltiAln");
-    for(var i=0; i < links.length;i++) {
-        utils.addEvent(links[i],"click",ViewSelectedSeqMultiAlign,false);
-    }
-    links = document.getElementsByName("selectAll");
-    for(var i=0; i < links.length;i++) {
-        utils.addEvent(links[i],"click",selectAllSeqs,false);
-    }
-
-    if($("showAlign"))
-        utils.addEvent($("showAlign"),"click",showHideLinks,false);
-}
-
-function InitDownLoad()
-{
-    var deltaBlast = ($("diThresh") && $("diThresh").value != "") ? true : false;
-    if (!deltaBlast && ($("stepNumber").value == "" || $("stepNumber").value < 2)) {
-        utils.addClass($("dnPSSMPar"),"hidden");
-    }
-}
-function Reformat()
-{
-    if(utils.hasClass($("FormatForm").FORMAT_ORGANISM,"orgHint"))  $("FormatForm").FORMAT_ORGANISM.value = "";
-
-    $("FormatForm").submit();
-}
-function InitCustomButton(bn)
-{
-  utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
-  utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
-  utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
-  utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);
-}
-
-function InitAllCustomButtons()
-{
-    if($("go")) InitCustomButton($("go"));
-    if($("dn")) InitCustomButton($("dn"));
-    if($("onPageReformat")) InitCustomButton($("onPageReformat"));
-}
-function showHideLinks()
-{
-    var links = document.getElementsByName("selectAll");
-    for(var i=0; i < links.length;i++) {
-        //This is done since IE does not recognize getElementsByName for span elem
-        var allLinks = utils.getParent(links[i]);
-        var removeClass,addClass;
-        if(utils.hasClass(allLinks,"shownInl")) {
-            removeClass="shownInl";
-            addClass="hidden";
-        }
-        else {
-            removeClass="hidden";
-            addClass="shownInl";
-        }
-        utils.removeClass(allLinks,removeClass);
-        utils.addClass(allLinks,addClass);
-    }
-}
-/*remove this function */
-function InitHelpLinks()
-{
-    for(var i=1; i <= 11;i++) {
-        InitToggleEvent($("hlp" + i));
-    }
-}
-//This function is used for collapsible deflines onmouseover="showInfo(this)"
-//Initialized in showdefline.cpp
-function showInfo(elem)
-{
-    var targetElem = $("info_" + elem.id);
-    if(!targetElem) return;
-    if(elem.getAttribute("init") == "on") return;
-
-    Toggle.addTarget(elem, targetElem);
-    elem.setAttribute("init","on");
-}
-
-function InitPsiBlast()
-{
-    //utils.addEvent($("ttt"),"keyup",SetHitlistSize,false);
-    var hts = document.getElementsByName("HITLIST_SIZE");
-    for(var i=0; i < hts.length;i++) {
-        utils.addEvent(hts[i],"keyup",SetHitlistSize,false);
-    }
-    if($("psiInp")) {
-        var numSubsets = $("psiInp").getAttribute("numSubsets");
-        for(var i=1; i <= numSubsets;i++) {
-            if ($("alnPos" + i)) InitToggleEvent($("alnPos" + i));
-            if ($("deflnG" + i)) InitToggleEvent($("deflnG" + i));
-            if ($("deflnB" + i)) InitToggleEvent($("deflnB" + i));
-        }
-    }
-}
-
-function SetHitlistSize()
-{
-    var hts = document.getElementsByName("HITLIST_SIZE");
-    for(var i=0; i < hts.length;i++) {
-        if(this != hts[i]) {
-            hts[i].value = this.value;
-        }
-    }
-}
-function InitToggleEvent(toggleNode)
-{
-    if(toggleNode) {
-        var srcid = toggleNode.getAttribute("toggle");
-        if(srcid) Toggle.addTarget(srcid, toggleNode);
-    }
-}
-
-function InitIFrameLinks()
-{
-    CheckIframe($("RSIFrameNoRes"),"prlink");
-    CheckIframe($("RSIFrameDesc"),"prlink");
-    CheckIframe($("RSIFrameAln"),"prlink");
-}
-
-function CheckIframe(iframe,contentElemID)
-{
-    if(!iframe) return;
-
-    var iframeDoc;
-
-    if(iframe.contentDocument) {//Firefox
-        iframeDoc = iframe.contentDocument;
-    }
-    else if (iframe.contentWindow) {//IE
-        iframeDoc = iframe.contentWindow.document;
-    }
-    else if(iframe.document) {
-        iframeDoc = iframe.document;
-    }
-    if(iframeDoc){
-        if(iframeDoc.getElementById(contentElemID)) {
-            utils.addClass(iframe,"shown");
-            utils.removeClass(iframe,"hidden");
-        }
-     }
-}
-
-
-function InitHitMatrix()
-{
-    if($("bl2seImg")) {
-
-        utils.addEvent($("hitmtImg"),"load",
-                        function() {
-						    utils.addClass($("bl2seImg"),"shown");
-                            utils.removeClass($("bl2seImg"),"hidden");
-
-						},
-						false);
-        utils.addEvent($("showHitMatrix"),"click",
-                        function() {
-                            $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
-                            if(utils.hasClass($("htmb"),"shown")) {
-							    utils.addClass($("htmb"),"hidden");
-                                utils.removeClass($("htmb"),"shown");
-                            }
-                            else {
-                                utils.addClass($("htmb"),"shown");
-                                utils.removeClass($("htmb"),"hidden");
-                            }
-						},
-						false);
-
-        if($("blastSpec") && $("blastSpec").value=="GlobalAln") {
-            $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
-        }
-    }
-}
-
-
-
-
-
-function SetFormSubmitEvent()
-{
-    var el = $("refPage");
-    if(el) {
-	    SubmitEventNew("refPage");
-	}
-	SubmitEventNew("frmPage");
-	el = $("searchOptions");
-	if(el) {
-	    SubmitEventNew("searchOptions");
-	}
-	el = $("saveSearchOptions");
-	if(el) {
-	    SubmitEventNew("saveSearchOptions");
-	}
-	//SubmitEventNew("breadCrSearchOptions");
-	list = $("queryList");
-	if(list) {
-        utils.addEvent(list,"change",GetResults,false);
-    }
-
-    list = $("go");
-	if(list) {
-        utils.addEvent(list,"click",GetResults,false);
-    }
-
-
-    list= $("onPageReformat");
-    if(list) {
-        utils.addEvent(list,"click",Reformat,false);
-    }
-
-    if ($("cddResults") && $("statInfo")) {
-        jQuery($("cddResults")).ncbitoggler('toggle');
-    }
-    //New design still uses toggle
-    if ($("showCDD")) {
-        InitToggleEvent($("cddInfo"));
-    }
-    InitToggleEvent($("refInfo"));
-    InitToggleEvent($("resStat"));
-    InitToggleEvent($("dbDetails"));
-    InitToggleEvent($("graphicInfo"));
-    InitToggleEvent($("descrInfo"));
-    InitToggleEvent($("alignInfo"));
-    InitToggleEvent($("ovrInfo"));
-    InitToggleEvent($("queryInfo"));
-    InitToggleEvent($("hitMatrixInfo"));
-    InitToggleEvent($("bl2ovrInfo"));
-    //Init only for PSI blastfse
-    if($("prevRID")) InitPsiBlast();
-    InitSeqAlignLinks();
-    InitAllCustomButtons();
-    if($("dnPSSMPar")) InitDownLoad();
-    InitHitMatrix();
-    if($("noRes")) {
-        if($("hitCvs")) utils.addClass($("hitCvs"),"hidden");
-        if($("hitText")) utils.addClass($("hitText"),"hidden");
-    }
-    InitIFrameLinks();
-    showDbDetails(); //fill behind the scene
-    if ($("showDetails") && utils.hasClass($("showDetails"), "shown")) {
-        utils.addEvent($("showDetails"), "click", showDbDetails, false);
-    }
-    initContentWidth();
-}
-
-function initContentWidth() {
-    var lineLengthElem = $("FormatForm").LINE_LENGTH;
-    if (lineLengthElem) {
-        var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
-        if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
-
-        var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
-        var minWidth = (lineLength + parseInt(17)) * charWidth;
-
-
-        var alignView = $("FormatForm").ALIGNMENT_VIEW;
-        var formatType = $("FormatForm").FORMAT_TYPE;
-        var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
-
-        var addWidth = ($("FormatForm").OLD_VIEW.checked || queryAnch) ? 250 : 350;
-
-        minWidth = minWidth + parseInt(addWidth) + "px";
-        jQuery($("content")).css("min-width", minWidth);
-    }
-
-}
-
-
-
-
-
-function ShowHideAlnDeflines(alnID, checkbx) {
-    var dflTableID = "dln_" + alnID;
-    if ($(dflTableID)) {
-        var rmClass, addClass;
-        if (checkbx.checked) {
-            rmClass = "hidden";
-            addClass = "shown";
-        }
-        else {
-            rmClass = "shown";
-            addClass = "hidden";
-        }
-        var elems = $C(rmClass, "class", $(dflTableID), "tr");
-        if (elems) {
-            //alert(elems.length);
-            for (var i = 0; i < elems.length; i++) {
-                utils.removeClass(elems[i], rmClass);
-                utils.addClass(elems[i], addClass);
-            }
-        }
-    }
-}
-
-function SortAln(e, sortLink, sortItem) {
-    var p = utils.getParent(sortLink);
-    var p = utils.getParent(p);
-    p_TD = utils.getParent(p);
-    p_TR = utils.getParent(p_TD);
-    if (utils.hasClass(p_TR, "dflnAln")) {
-        p_TD.innerHTML = "Reading seqaligns...";
-        var gi = p_TD.id.substr(2);
-        var rid = p_TD.getAttribute("rid");
-        getAlignSort(rid, gi, p_TD, sortItem);
-        e = e || window.event;
-        utils.preventDefault(e);
-        return;
-    }
-    var links = document.getElementsByName("alnSort");
-    if (links.length >= sortItem) {
-        var href = links[sortItem].href.replace(new RegExp("selectAllTop.*(&|$)"), "");
-        var hrefLn = sortLink.href.replace(new RegExp(".*#"), "");
-        sortLink.href = href + hrefLn;
-    }
-}
-
-
-
-var fullArr;
-var numDbs;
-function showDbDetails(e,dbSetIndex)
-{
-    if (!($("dbPlusSpecies"))) return; //No org display
-    if ($("dbPlusSpecies").getAttribute("init") == "on" && dbSetIndex == null) return;
-    $("dbPlusSpecies").setAttribute("init", "on");
-
-    dbInfoUrl = "getDBInfo.cgi";
-    var rp = new RemoteDataProvider(dbInfoUrl);
-    rp.minArr = 10;
-
-    if (!fullArr) {
-        var arr = $("results").DATABASE.value.split(" ");
-        numDbs = arr.length;
-        if (arr.length > rp.minArr) {
-            fullArr = new Array();
-            while (arr.length > 1) {
-                var arrNew = arr.splice(0, rp.minArr); //does not include stopindex
-                fullArr.push(arrNew);
-            }
-            if (!dbSetIndex) dbSetIndex = 0;
-        }
-    }
-
-    rp.onSuccess = function(obj) {
-        var navDB = document.createElement("div");
-        if (fullArr) {
-            var prevLink, nextLink, firstLink, lastLink;
-            if (this.currDbSetIndex >= 1) {
-                var firstStart = 1;
-                var firstEnd = firstStart + fullArr[0].length - 1;
-                firstLink = document.createElement("a");
-                jQuery(firstLink).attr("href", "#");
-                jQuery(firstLink).attr("id", "firstDbSet");
-                jQuery(firstLink).attr("onclick", "showDbDetails(event,0);");
-                jQuery(firstLink).attr("title", "Databases " + firstStart + "-" + firstEnd);
-                jQuery(firstLink).html("First " + this.minArr + " dbs");
-
-            }
-            if (this.currDbSetIndex >= 1) {
-                var prevStart = (this.currDbSetIndex - 1) * this.minArr + 1;
-                var prevEnd = prevStart + fullArr[this.currDbSetIndex - 1].length - 1;
-                prevLink = document.createElement("a");
-                jQuery(prevLink).attr("href", "#");
-                jQuery(prevLink).attr("id", "prevDbSet");
-                jQuery(prevLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex - 1) + ");");
-                jQuery(prevLink).attr("title", "Databases " + prevStart + "-" + prevEnd);
-                jQuery(prevLink).html("Prev " + this.minArr + " dbs");
-            }
-
-            if (this.currDbSetIndex < fullArr.length - 1) {
-                var nextStart = (this.currDbSetIndex + 1) * this.minArr + 1;
-                var nextEnd = nextStart + fullArr[this.currDbSetIndex + 1].length - 1;
-                nextLink = document.createElement("a");
-                jQuery(nextLink).attr("href", "#");
-                jQuery(nextLink).attr("id", "nextDbSet");
-                jQuery(nextLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex + 1) + ");");
-                jQuery(nextLink).attr("title", "Databases " + nextStart + "-" + nextEnd);
-                jQuery(nextLink).html("Next " + this.minArr + " dbs");
-            }
-            if (this.currDbSetIndex < fullArr.length - 1) {
-                var lastInd = fullArr.length - 1;
-                var lastStart = numDbs - fullArr[lastInd].length;
-                var lastEnd = numDbs;
-                lastLink = document.createElement("a");
-                jQuery(lastLink).attr("href", "#");
-                jQuery(lastLink).attr("id", "lastDbSet");
-                jQuery(lastLink).attr("onclick", "showDbDetails(event," + lastInd + ");");
-                jQuery(lastLink).attr("title", "Databases " + lastStart + "-" + lastEnd);
-                jQuery(lastLink).html("Last " + this.minArr + " dbs");
-            }
-
-
-            jQuery(navDB).attr("id", "addDbSet");
-            if (firstLink) jQuery(navDB).append(firstLink);
-            if (prevLink) jQuery(navDB).append(prevLink);
-            if (lastLink) jQuery(navDB).append(lastLink);
-            if (nextLink) jQuery(navDB).append(nextLink);
-        }
-
-        jQuery($("dbPlusSpecies")).html(navDB);
-        jQuery(navDB).after(obj.responseText);
-        if (fullArr) {
-            var cap = jQuery($("dbSpecies")).find("caption");
-            if (cap) {
-                var currStart = (this.currDbSetIndex) * this.minArr + 1;
-                var currEnd = currStart + fullArr[this.currDbSetIndex].length - 1;
-                var capText = cap.html() + "<div class=\"cpAdd\"> Databases " + currStart + "-" + currEnd;
-                cap.html(capText);
-            }
-        }
-    };
-    rp.onError = function(obj) {
-        $("dbPlusSpecies").innerHTML += "error, requests:" + this.iActiveRequests + " status:" + obj.status;
-    }
-    var dbs;
-    if (fullArr) {
-        rp.currDbSetIndex = dbSetIndex;
-        var currArr = fullArr[dbSetIndex];
-        dbs = currArr.join(",");
-    }
-    else {
-        dbs = $("results").DATABASE.value.replace(/ /g, ",");
-    }
-
-    rp.Request("CMD=getDBOrg&DATABASE=" + dbs, "POST");
-    if(e) utils.preventDefault(e);
-}
-
-function synchronizeCheck(id, formName, inputName, isChecked) {
-
-    for (var i = 0; i < document.forms[formName].elements.length; i++) {
-        var theElem = document.forms[formName].elements[i];
-        if (theElem.type == "checkbox" && theElem.name == inputName && id == theElem.value) {
-            theElem.checked = isChecked;
-
-        }
-    }
-
-}
-
-utils.addEvent(window,
-				"load", SetFormSubmitEvent,
-				false);
-
-
-/* If user agent has "safari" in it, include safari-specific stylesheet. */
-if (navigator.userAgent.match(/safari/i) || navigator.userAgent.match(/opera/i)) {
-document.write("<link rel='stylesheet' type='text/css' href='css/safari-descriptions.css'  media='screen'/>");
-}
-if (navigator.userAgent.match(/opera/i)) {
-document.write("<link rel='stylesheet' type='text/css' href='css/opera-descriptions.css'  media='screen'/>");
-}
-if (navigator.userAgent.match(/firefox/i) || navigator.userAgent.match(/safari/i)) {
-document.write("<link rel='stylesheet' type='text/css' href='css/firefox-descriptions.css'  media='screen'/>");
-}
-
-
-
Binary file Blast output page example_files/scale.gif has changed
Binary file Blast output page example_files/score.gif has changed
--- a/Blast output page example_files/toggle.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,174 +0,0 @@
-
-Toggle = function(node) {
-   this.init(node);
-}
-
-/**
-* @class Creates a  new Toggle class with "node" as src
-* @return Reutrns a new toggle instance
-*/
-Toggle.prototype = {
-
-   init: function(node) {
-
-      // Subclass instance?
-      if (typeof(arguments[0]) == 'undefined') return;
-
-      var oThis = this;
-      this.node = node;
-
-      // Initialize "showing" variable based on presence of "showing" or
-      // "hiding" class. If neither, then showing. Be sure class is
-      // set to reflect variable value
-      node.showing =
-         utils.hasClass(node, "showing") || !utils.hasClass(node, "hiding");
-      utils.addClass(node, node.showing ? "showing" : "hiding");
-
-      // Set notifier for node
-      utils.addEvent(node, "click", function(e) {
-         e = e || window.event;
-         utils.preventDefault(e);
-
-         var theNode = utils.getTargetObj(e);
-
-         // Send message to global notifier, if one exists
-         if (typeof(Notifier) != 'undefined') {
-            var notifier = Notifier.getInstance();
-            // Notify before change
-            notifier.Notify(oThis, "change:" + theNode.id, !this.showing);
-         }
-
-         // Hide or show based on current state
-         if (this.showing) {
-             oThis.hide();
-         } else {
-             oThis.show();
-         }
-
-      }, false);
-
-      utils.addEvent(node, "selectstart", function(e) { utils.preventDefault(e); }, true);
-      utils.addEvent(node, "drag", function(e) { utils.preventDefault(e); }, true);
-
-      // Cache "this" for ID lookup
-      if (!node.id) {
-          node.id = utils.createNewId();
-      }
-      var m = Toggle.getSrcs();
-      m[node.id] = this;
-   },
-
-   // Hide targets, and set self to hiding.
-   hide: function() {
-       var oThis = this;
-
-       oThis.setHiding();
-       if (oThis.listeners) {
-           forEach(oThis.listeners, function(l) {
-               oThis.hideTarget(l);
-           });
-       }
-   },
-
-   // Show targets, and set self to showing.
-   show: function() {
-       var oThis = this;
-
-       oThis.setShowing();
-       if (oThis.listeners) {
-           forEach(oThis.listeners, function(l) {
-               oThis.showTarget(l);
-           });
-       }
-   },
-
-   // Set own presentation to "showing"
-   setShowing: function() {
-       utils.addClass(this.node, "showing");
-       utils.removeClass(this.node, "hiding");
-       this.node.showing = true;
-   },
-
-   // Set own presentation to "hiding"
-   setHiding: function() {
-       utils.addClass(this.node, "hiding");
-       utils.removeClass(this.node, "showing");
-       this.node.showing = false;
-   },
-
-   // Show a target
-   showTarget: function(l) {
-       utils.addClass(l, "shown");
-       utils.removeClass(l, "hidden");
-   },
-
-   // Hide a target
-   hideTarget: function(l) {
-      utils.addClass(l, "hidden");
-      utils.removeClass(l, "shown");
-   },
-
-   // Add a target to this toggle.
-   add: function(target) {
-      if (!this.listeners) {
-          this.listeners = new Array();
-      }
-      this.listeners[this.listeners.length] = target;
-
-      if (utils.hasClass(target, "hidden")) {
-        this.setHiding();
-        this.node.showing = false;
-      } else {
-        this.setShowing();
-        this.node.showing = true;
-      }
-   }
-}
-
-// Show/hide a "target" (a node controlled by the node with the given ID)
-Toggle.addTarget = function(srcid, target) {
-   var tn = Toggle.findOrMake(srcid);
-   tn.add(target);
-}
-
-// Assoc array of srcs indexed by their ids
-Toggle.getSrcs = function() {
-   if (!Toggle.srcs) {
-      Toggle.srcs = new Object();
-   }
-   return Toggle.srcs;
-}
-
-// Find or make toggle for given id
-Toggle.findOrMake = function(srcid) {
-   var ts = Toggle.getSrcs();
-   var tn = ts[srcid];
-   if (!tn) {
-      tn = new Toggle($(srcid));
-   }
-   return tn;
-}
-
-// This dispatches the call to Toggle.onload, which may be
-// overridden by instances (subclasses)
-Toggle._onload = function() {
-   Toggle.onload();
-}
-
-// A toggle source node controls other nodes that reference it by id using
-// their toggle= attribute. A node may be both a toggle source and destination.
-Toggle.onload = function() {
-//alert("toggle start");
-   if(utils.hasClass(document.body,"noToggleCheck")) return;
-
-   shnodes = jQuery("[toggle]");
-   // Now hook up dst nodes
-   forEach(shnodes, function(node) {
-      // Link toggle node to its source
-      var srcid = node.getAttribute("toggle");
-      Toggle.addTarget(srcid, node);
-   });
-    //alert("toggle 2 end");
-}
-
-utils.addEvent(window, 'load', Toggle._onload, false);
--- a/Blast output page example_files/utils.js	Thu May 15 16:53:04 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,633 +0,0 @@
-// $Id: utils.js,v 1.4 2014/02/26 14:47:32 zaretska Exp $
-
-utils = {
-
-KeyCode_TAB: 9,
-KeyCode_DELETE: 46,
-KeyCode_BACKSPACE: 8,
-KeyCode_LEFT_ARROW: 37,
-KeyCode_RIGHT_ARROW: 39,
-KeyCode_HOME: 36,
-KeyCode_END: 35,
-KeyCode_PAGE_UP: 33,
-KeyCode_PAGE_DOWN: 34,
-KeyCode_UP_ARROW: 38,
-KeyCode_DOWN_ARROW: 40,
-KeyCode_ESC: 27,
-KeyCode_ENTER: 13,
-KeyCode_SPACE: 32,
-KeyCode_SHIFT_KEY: 16,
-KeyCode_CTRL_KEY: 17,
-KeyCode_ALT_KEY: 18,
-KeyCode_LEFT_MS_WINDOWS_KEY: 91,
-KeyCode_RIGHT_MS_WINDOWS_KEY: 92,
-KeyCode_MS_MENU_KEY: 93,
-
-isObject: function(a) { return (a && typeof a == 'object'); },
-
-isArray: function(a) { return this.isObject(a) && a.constructor == Array; },
-
-insertInHtml: function(text, obj) {
-	if (document.all) {
-		obj.innerHTML += text;
-	} else {
-		var range = document.createRange();
-		range.setStartAfter(obj);
-		var docFrag = range.createContextualFragment(text);
-		obj.appendChild(docFrag);
-	}
-
-},
-
-replaceInHtml: function(text, obj) {
-	if (document.all) {
-		obj.innerHTML = text;
-	} else {
-		while (obj.hasChildNodes()) obj.removeChild(obj.firstChild);
-		var range = document.createRange();
-		range.setStartAfter(obj);
-		var docFrag = range.createContextualFragment(text);
-		obj.appendChild(docFrag);
-	}
-},
-
-
-getTargetObj: function(eEvent) {
-    var oTarget;
-    var e = eEvent || window.event;
-    if (e == null) return null;
-    if (e.srcElement == null)  {
-        oTarget = e.target;
-    } else {
-        oTarget = e.srcElement;
-    }
-    while ( oTarget && oTarget.nodeType != 1 ) oTarget = oTarget.parentNode;
-    return oTarget;
-},
-
-
-
-
-getParent: function(obj) {
-     if (obj) {
-         var result = obj.parentNode;
-         while (result && result.nodeType != 1) result = result.nextSibling;
-         if (result) return result;
-     }
-     return null;
-},
-
-getFirstChild: function(obj) {
-     if (obj) {
-         var result = obj.firstChild;
-         while (result && result.nodeType != 1) result = result.nextSibling;
-         if (result) return result;
-     }
-     return null;
-},
-
-getNextSibling: function(obj, tagName) {
-    if (obj) {
-        var result = obj.nextSibling;
-        if (tagName) {
-            var tn = tagName.toUpperCase();
-            while (result && result.tagName != tn) result = result.nextSibling;
-        } else {
-            while (result && result.nodeType != 1) result = result.nextSibling;
-        }
-        return result;
-    }
-    return null;
-},
-
-getPreviousSibling: function(obj, tagName) {
-     if (obj) {
-         var result = obj.previousSibling;
-         if (tagName) {
-             var tn = tagName.toUpperCase();
-             while (result && result.tagName != tn) result = result.previousSibling;
-         } else {
-             while (result && result.nodeType != 1) result = result.previousSibling;
-         }
-         return result;
-     }
-     return null;
-},
-
-removeChildren: function(oObj) {
-     if (!oObj || typeof oObj != "object") return;
-     while(oObj.hasChildNodes()) oObj.removeChild(oObj.firstChild)
-},
-
-insertAfter: function(parent, node, referenceNode) {
-	parent.insertBefore(node, referenceNode.nextSibling);
-},
-
-nextItem: function(item, nodeName) {
-    if (item == null) return;
-    var next = item.nextSibling;
-    while (next != null) {
-        if (next.nodeName == nodeName) return next;
-        next = next.nextSibling;
-    }
-    return null;
-},
-
-previousItem: function(item, nodeName) {
-    var previous = item.previousSibling;
-    while (previous != null) {
-        if (previous.nodeName == nodeName) return previous;
-        previous = previous.previousSibling;
-    }
-    return null
-},
-
-moveBefore: function(item1, item2) {
-    var parent = item1.parentNode;
-    parent.removeChild(item1);
-    parent.insertBefore(item1, item2);
-},
-
-moveAfter: function(item1, item2) {
-    var parent = item1.parentNode;
-    parent.removeChild(item1);
-    parent.insertBefore(item1, item2 ? item2.nextSibling : null);
-},
-
-
-
-
-createCookie: function(name, value, days) {
-    if (days) {
-        var date = new Date();
-        date.setTime(date.getTime() + (days * 24 * 60 * 60 * 1000));
-        var expires = '; expires=' + date.toGMTString();
-    } else expires = '';
-    document.cookie = name + '=' + value + expires + '; path=/';
-},
-
-readCookie: function(name) {
-    var nameEQ = name + '=';
-    var ca = document.cookie.split(';');
-    for (var i = 0; i < ca.length; i++) {
-        var c = ca[i];
-        while (c.charAt(0)==' ') c = c.substring(1, c.length);
-        if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length, c.length);
-    }
-    return "";
-},
-
-eraseCookie: function(name) {
-	document.cookie = name + "=null; expires=Thu, 01-Jan-1970 00:00:01 GMT; domain=nih.gov; path=/";
-	document.cookie = name + "; expires=Thu, 01-Jan-1970 00:00:01 GMT; domain=nih.gov; path=/";
-},
-
-addClass: function(element, className) {
-    if (!this.hasClass(element, className)) {
-        if (element.className) element.className += " " + className;
-        else element.className = className;
-    }
-},
-
-removeClass: function(element, className) {
-    var regexp = new RegExp("(^|\\s)" + className + "(\\s|$)");
-    element.className = element.className.replace(regexp, "$2");
-},
-
-hasClass: function(element, className) {
-    var regexp = new RegExp("(^|\\s)" + className + "(\\s|$)");
-    return regexp.test(element.className);
-},
-
-
-getXY: function (obj){
-     /*
-     +------------- w ----
-     | (x,y)
-     |
-     h
-     |
-     */
-     var b={x:0, y:0, w:obj.offsetWidth, h:obj.offsetHeight};
-
-     if (obj.offsetParent) {
-         while(obj) {
-             b.x += obj.offsetLeft;
-             b.y += obj.offsetTop;
-             obj = obj.offsetParent;
-         }
-     } else if (obj.x) {
-         b.x = obj.x;
-         b.y = obj.y;
-     }
-     return b;
-},
-
-/* Based on ppk (untested) */
-getEventXY: function(e) {
-    var xpos = 0;
-    var ypos = 0;
-    e = e || window.event;
-    xpos = e.pageX || (e.clientX + document.body.scrollLeft +
-                    document.documentElement.scrollLeft);
-    ypos = e.pageY || (e.clientY + document.body.scrollTop +
-                    document.documentElement.scrollTop);
-    return {x: xpos, y: ypos};
-},
-
-drawText: function (sText, sId, add) {
-    if (!sId) sId = "debug";
-    var obj = document.getElementById(sId);
-    if (obj) {
-        if (add)
-            this.insertInHtml("<br/>" + sText, obj);
-        else
-            this.replaceInHtml(sText, obj);
-    }
-},
-
-
-selectRange: function (oObj /*:object*/, iStart /*:int*/, iLength /*:int*/) {
-    if (!(oObj && oObj.value)) return;
-
-    if (oObj.createTextRange) {
-        //use text ranges for Internet Explorer
-        var oRange = oObj.createTextRange();
-        oRange.moveStart("character", iStart);
-        oRange.moveEnd("character", iLength - oObj.value.length);
-        oRange.select();
-    } else if (oObj.setSelectionRange) {
-        //use setSelectionRange() for Mozilla
-        oObj.setSelectionRange(iStart, iLength);
-    }
-    //set focus back to the textbox
-    oObj.focus();
-},
-
-getSelection: function() {
-     var text = "";
-     if (window.getSelection) {
-         text += window.getSelection();
-     } else if (document.getSelection) {
-         text += document.getSelection();
-     } else if (document.selection){        //IE
-         text += document.selection.createRange().text;
-     }
-     return text;
-},
-
-
-
-
-// http://ejohn.org/apps/jselect/event.html
-addEvent: function(obj, type, fn, b) {
-    if (obj.attachEvent) {
-        var name = "" + type + fn;
-//        name = name.substring(0, name.indexOf("\n"));   // IE  This doesn't work
-        obj["e" + name] = fn;
-        obj[name] = function(){ obj["e" + name](window.event);}
-        obj.attachEvent("on" + type, obj[name]);
-    } else {
-        obj.addEventListener(type, fn, b);
-        return true;
-    }
-},
-
-
-removeEvent: function(obj, type, fn, b) {
-    if (obj.detachEvent) {
-        var name = "" + type + fn;
-//        name = name.substring(0, name.indexOf("\n"));   //IE This doesn't work
-        if ("function" == typeof obj[name]) {
-            obj.detachEvent("on" + type, obj[name]);
-            obj[name] = null;
-            obj["e" + name] = null;
-        }
-    } else {
-      obj.removeEventListener(type, fn, b);
-      return true;
-    }
-},
-
-noBubbleEvent: function(e) {
-	if (e && e.stopPropagation) e.stopPropagation();
-	else window.event.cancelBubble = true;
-},
-
-targetEvent: function(e) {
-     if (e.srcElement == null) {
-         return e.target;
-     } else {
-         return window.event.srcElement;
-     }
-},
-
-preventDefault: function(e) {
-     if (e.preventDefault) e.preventDefault();
-     else window.event.returnValue = false;
-},
-
-relatedTarget: function(e) {
-    if (!e) var e = window.event;
-	if (e.relatedTarget)    return e.relatedTarget;
-	else if (e.toElement)   return e.toElement;
-    else if (e.fromElement) return e.fromElement;
-},
-
-readStyle: function(element, property) {
-    if (element.style[property]) {
-        return element.style[property];
-    } else if (element.currentStyle) {
-        return element.currentStyle[property];
-    } else if (document.defaultView && document.defaultView.getComputedStyle) {
-        var style = document.defaultView.getComputedStyle(element, null);
-        if (style) return style.getPropertyValue(property);
-    }
-    return "";
-},
-
-
-printObj: function (oObj, iLevel) {
-     var s = "";
-     var sIdent = "";
-     if (!iLevel) iLevel = 0;
-     for (var i = 0; i < iLevel; i++) {
-         sIdent += "__";
-     }
-     for (var i in oObj) {
-         var ss = [];
-         if ("string" == typeof oObj[i]) {
-             ss = oObj[i].split("<");
-         }
-         s += sIdent + " " + i + " : [" + (typeof oObj[i]) + "] : " + ss.join("&lt;") + "<br/>";
- //        if (oObj[i] && "object" == typeof oObj[i] && iLevel < 2) {
- //            s+= "<br/>-----" + typeof oObj[i] + " --- " + iLevel + "</br>";
- //            s += this.printObj(oObj[i], iLevel + 1);
- //        }
-     }
-     return s;
-},
-
-jsLoader:  {
-    sBase: "", /* Base is this directory */
-    oLoaded: [],
-    load: function (aScripts) {
-
-       var oS = document.getElementsByTagName("script");
-       var k = 0;
-       for (var j = 0; j < oS.length; j++) {
-           if (oS[j].src == "") continue;
-           this.oLoaded[k++] = oS[j].src;
-       }
-
-        var oHead = document.getElementsByTagName("head")[0];
-
-        for (var i = 0; i < aScripts.length; i++) {
-            var sNewSrc = this.sBase + aScripts[i];
-            var oS = document.getElementsByTagName("script");
-            var b = true;
-            for (var j = 0; j < this.oLoaded.length; j++) {
-                if (sNewSrc == this.oLoaded[j]) {
-//                    alert(sNewSrc + " : already loaded");
-                    b = false;
-                }
-            }
-
-            if (b) {
-                var oScript = document.createElement("script");
-                oScript.src = sNewSrc;
-                oScript.setAttribute("type", "text/javascript");
-                oHead.appendChild(oScript);
-                this.oLoaded[this.oLoaded.length] = sNewSrc;
-            }
-        }
-    }
-},
-
-// Create an id that doesn't exist in this document
-createNewId: function()
-{
-   var newid = null
-
-   while (!newid || document.getElementById(newid)) {
-       newid = "XID" + Math.round(Math.random() * 65536).toString(16)
-   }
-   return newid
-}
-
-};
-
-
-String.prototype.trimSpaces = function(trimMode) {
-    // 0 = trim begin and end
-    // 1 = trim begin only
-    // 2 = trim after only
-
-    var targetString = this;
-    var iPos = 0;
-    if (!trimMode) trimMode = 0;
-
-    if (trimMode==0 || trimMode==1) {
-        if (targetString.charAt(iPos)==" ") {
-            while(targetString.charAt(iPos)==" ") iPos++;
-            targetString = targetString.substr(iPos);
-        }
-    }
-
-    iPos = targetString.length-1;
-    if (trimMode==0 || trimMode==2) {
-        if (targetString.charAt(iPos) == " ") {
-            while(targetString.charAt(iPos) == " ") iPos--;
-            targetString = targetString.substr(0, iPos + 1);
-        }
-    }
-    return targetString;
-}
-
-
-
-
-/* Shortcuts */
-
-// Get elements by Id's
-function $() {
-  var elements = new Array();
-
-  for (var i = 0; i < arguments.length; i++) {
-    var element = arguments[i];
-    if (typeof element == 'string')
-      element = document.getElementById(element);
-
-    if (arguments.length == 1)
-      return element;
-
-    elements.push(element);
-  }
-
-  return elements;
-}
-
-// Get elements by AttributeValue for Attributename
-// http://www.dustindiaz.com/top-ten-javascript/ (but has some errors)
-function $C(attrValue, attrName, node, tag) {
-    //alert([attrValue, attrName, node, tag])
-    if ("*" == attrValue) {
-        return $AN(attrName, node, tag);
-    }
-	var oElements = new Array();
-	if (!node) node = document;
-	if (!tag) tag = '*';
-	if (!attrName) attrName = 'class';
-
-	var els = node.getElementsByTagName(tag);
-	var elsLen = els.length;
-	var pattern = new RegExp("(^|\\s)" + attrValue + "(\\s|$)");
-    var j = 0;
-	for (i = 0; i < elsLen; i++) {
-		if (attrName == "class" && pattern.test(els[i].className)) {
-            // IE behavior
-//            oElements.push(els[i]);
-            oElements[j++] = els[i];
-		} else if (pattern.test(els[i].getAttribute(attrName))) {
-			oElements[j++] = els[i];
-//			oElements.push(els[i]);
-		}
-	}
-    return oElements;
-}
-
-
-function $AN(attrName, node, tag) {
-	var oElements = new Array();
-	if (node == null) node = document;
-	if (tag == null)tag = '*';
-	var els = node.getElementsByTagName(tag);
-	for (i = 0; i < els.length; i++) {
-		if (els[i].getAttribute(attrName) != null) {
-			oElements.push(els[i]);
-		}
-	}
-	return oElements;
-}
-
-function dump(aMessage) {
-  var consoleService = Components.classes["@mozilla.org/consoleservice;1"]
-                                 .getService(Components.interfaces.nsIConsoleService);
-  consoleService.logStringMessage(aMessage);
-}
-
-
-// forEach iterators from Dean Edwards: http://dean.edwards.name/weblog/2006/07/enum/
-// generic enumeration
-Function.prototype.forEach = function(object, block, context) {
-    for (var key in object) {
-        if (typeof this.prototype[key] == "undefined") {
-            block.call(context, object[key], key, object);
-        }
-    }
-};
-
-// globally resolve forEach enumeration
-var forEach = function(object, block, context) {
-    if (object) {
-        var resolve = Object; // default
-        if (object instanceof Function) {
-            // functions have a "length" property
-            resolve = Function;
-        } else if (object.forEach instanceof Function) {
-            // the object implements a custom forEach method so use that
-            object.forEach(block, context);
-            return;
-        } else if (typeof object.length == "number") {
-            // the object is array-like
-            resolve = Array;
-        }
-        resolve.forEach(object, block, context);
-    }
-};
-
-//
-// Update Array class to JS 1.5 if not yet there.
-//
-
-// array-like enumeration
-if (!Array.forEach) { // mozilla already supports this
-    Array.forEach = function(object, block, context) {
-        for (var i = 0; i < object.length; i++) {
-            block.call(context, object[i], i, object);
-        }
-    };
-}
-
-if (!Array.prototype.indexOf)
-	Array.prototype.indexOf = function(item, startIndex) {
-		var len = this.length;
-		if (startIndex == null)
-			startIndex = 0;
-		else if (startIndex < 0) {
-			startIndex += len;
-			if (startIndex < 0)
-				startIndex = 0;
-		}
-		for (var i = startIndex; i < len; i++) {
-			var val = this[i] || this.charAt && this.charAt(i);
-			if (val == item)
-				return i;
-		}
-		return -1;
-	};
-
-if (!Array.prototype.lastIndexOf)
-	Array.prototype.lastIndexOf = function(item, startIndex) {
-		var len = this.length;
-		if (startIndex == null || startIndex >= len)
-			startIndex = len - 1;
-		else if (startIndex < 0)
-			startIndex += len;
-		for (var i = startIndex; i >= 0; i--) {
-			var val = this[i] || this.charAt && this.charAt(i);
-			if (val == item)
-				return i;
-		}
-		return -1;
-	};
-
-if (!Array.prototype.map)
-	Array.prototype.map = function(func, thisVal) {
-		var len = this.length;
-		var ret = new Array(len);
-		for (var i = 0; i < len; i++)
-			ret[i] = func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this);
-		return ret;
-	};
-
-if (!Array.prototype.filter)
-	Array.prototype.filter = function(func, thisVal) {
-		var len = this.length;
-		var ret = new Array();
-		for (var i = 0; i < len; i++) {
-			var val = this[i] || this.charAt && this.charAt(i);
-			if(func.call(thisVal, val, i, this))
-				ret[ret.length] = val;
-		}
-		return ret;
-	};
-
-if (!Array.prototype.every)
-	Array.prototype.every = function(func, thisVal) {
-		var len = this.length;
-		for (var i = 0; i < len; i++)
-			if (!func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this))
-				return false;
-		return true;
-	};
-
-if (!Array.prototype.some)
-	Array.prototype.some = function(func, thisVal) {
-		var len = this.length;
-		for (var i = 0; i < len; i++)
-			if (func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this))
-				return true;
-		return false;
-	};
-
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example.html	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,2071 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"><head>
+
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
+<meta name="jig" content="ncbitoggler ncbiautocomplete ncbilocalnav ncbigrid ncbipopper">
+<meta name="ncbitoggler" content="animation:'none'">
+<meta name="ncbipopper" content="animation:'none',closeEvent: 'click',openEvent: 'click',destPosition: 'top right',triggerPosition: 'bottom right'">
+
+<meta name="ncbi_app" content="blast">
+<meta name="ncbi_pdid" content="blastresults">
+<meta name="ncbi_stat" content="false">
+<meta name="ncbi_sessionid" content="8A8E11EE2CABF371_0000SID">
+<meta name="ncbi_phid" content="5AAB74D7368F2C81000000000000C9C8">
+<script type="text/javascript"> var ncbi_startTime = new Date(); </script>
+<title>NCBI Blast:Nucleotide Sequence (16 letters)</title>
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jig.js"></script><link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/jig.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_002.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_005.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_004.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_004.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_007.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_003.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_007.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_003.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_008.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_008.js"></script><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_005.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_009.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_006.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_006.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_002.css">
+<script type="text/javascript">    jQuery.getScript("/core/alerts/alerts.js", function() {
+        galert(['div#header', 'body > *:nth-child(1)'])
+    });</script>
+<link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/main.css" media="screen">
+<link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/blastRes.css" media="screen">
+<!--[if IE]>
+<link rel="stylesheet" type="text/css" href="css/descriptionsIE.css" media="screen" />
+<![endif]-->
+<link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/print.css" media="print">
+<!--[if lte IE 6]>
+<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
+<![endif]-->
+<link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/blastReq.css" media="screen">
+<link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/results.css" media="screen">
+<link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/dynFormatRes.css" media="screen">
+
+<style media="print" type="text/css">.print-log { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }.print-log li { list-style-image: url('/stat?jsevent=print&ncbi_app=blast&ncbi_pdid=blastresults&ncbi_phid=5AAB74D7368F2C81000000000000C9C8'); }</style><style type="text/css">.print-log { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }</style></head>
+
+<body id="type-a" class="noToggleCheck ">
+<div id="wrap">
+			<div id="header">
+		<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov/" title="NCBI Home Page"><img src="NCBI%20Blast%20reference%20example_files/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page"></a>BLAST <span id="trdm"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
+		</div>
+		<div id="search">
+
+<div>
+<script language="JavaScript" type="text/javascript"><!--
+// --></script><table class="medium1" style="border:2px solid #336699;" id="myncbi_off" cellpadding="2" cellspacing="0"><tbody><tr><td align="left" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td align="right" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img src="NCBI%20Blast%20reference%20example_files/myncbihelpicon.gif" alt="My NCBI help" border="0"></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to sign in" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Sign In]</a> <a href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to register for an account" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Register]</a></td></tr></tbody></table></div>
+		</div>
+		<a class="skp" href="#content-wrap">Jump to Page Content</a>
+		<ul id="nav">
+                <li class="first "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
+                <li class="recent "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&amp;RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
+                <li class="saved "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
+                <li class="last documentation "> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>
+                </ul>
+    </div>
+
+        <div id="content-wrap">
+
+                <div id="breadcrumb" class="inlineDiv">
+                   <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
+                   <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome">BLAST</a>/
+                   <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&amp;PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=">blastn suite</a>/
+                   <strong>Formatting Results - PHWP1JNZ014</strong>
+                </div>
+                <div class="inlineDiv resHeader resPage">
+
+                </div>
+                <ul class="print-log-res"><li></li></ul>
+
+                <!-- CDD info for old design -->
+
+
+
+
+
+
+
+
+                <div id="content">
+
+                <!--<ul id="msg" class="msg"><li class="info"><p class=""></p><p class=""></p><p class=""></p></li></ul>-->
+                <ul id="msg" class="msg"><li class="info"><p class="info">Your search parameters were adjusted to search for a short input sequence.</p></li></ul>
+                <a href="#" class="resLink resPage" id="searchOptions" submitform="setSavedOptions">Edit and Resubmit</a>
+<a href="#" class="resLink resPage hidden" id="saveSearchOptions" submitform="saveOptions">Save Search Strategies</a>
+<span class="reslink  resPage">[Sign in above to save your search strategy]</span>
+<a aria-expanded="false" role="button" aria-disabled="false" id="showFormat" class="resLink resPage resArrowLinkB ui-ncbitoggler jig-ncbitoggler ui-widget" data-ncbitoggler-toggles="FormatForm" href="#">
+<span class="ui-ncbitoggler-master-text">Formatting options </span>
+<span class="ui-icon ui-icon-triangle-1-e"></span>
+</a>
+<a aria-expanded="false" role="button" aria-disabled="false" id="showDownload" class="resLink resPage resArrowLinkB jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="FormatDownload" href="#">
+<span class="ui-ncbitoggler-master-text">Download</span>
+<span class="ui-icon ui-icon-triangle-1-e"></span>
+</a>
+<span id="hnr">
+<a id="ytb" class="ytb " title="External link to YouTube" href="http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq" target="lnkPHWP1JNZ014">How to read this page</a>
+<a id="brFtp" class="" title="Blast report description" href="ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_NewBLAST.pdf" target="lnkPHWP1JNZ014">Blast report description</a>
+</span>
+                <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
+                <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden"><input name="ALIGNMENTS" value="100" type="hidden"><input name="ALIGNMENT_VIEW" value="Pairwise" type="hidden"><input name="BLAST_PROGRAMS" value="blastn" type="hidden"><input name="CLIENT" value="web" type="hidden"><input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden"><input name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden"><input name="DATABASE" value="pdb" type="hidden"><input name="DBTYPE" value="gc" type="hidden"><input name="DEFAULT_PROG" value="megaBlast" type="hidden"><input name="DESCRIPTIONS" value="100" type="hidden"><input name="DYNAMIC_FORMAT" value="on" type="hidden"><input name="EQ_OP" value="AND" type="hidden"><input name="EXPECT" value="1000" type="hidden"><input name="FORMAT_NUM_ORG" value="1" type="hidden"><input name="FORMAT_OBJECT" value="Alignment" type="hidden"><input name="FORMAT_TYPE" value="HTML" type="hidden"><input name="FULL_DBNAME" value="pdb" type="hidden"><input name="GAPCOSTS" value="5 2" type="hidden"><input name="GET_SEQUENCE" value="on" type="hidden"><input name="HSP_RANGE_MAX" value="0" type="hidden"><input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="LAYOUT" value="OneWindow" type="hidden"><input name="LINE_LENGTH" value="60" type="hidden"><input name="MASK_CHAR" value="2" type="hidden"><input name="MASK_COLOR" value="1" type="hidden"><input name="MATCH_SCORES" value="1,-3" type="hidden"><input name="MAX_NUM_SEQ" value="100" type="hidden"><input name="NUCL_PENALTY" value="-2" type="hidden"><input name="NUCL_REWARD" value="1" type="hidden"><input name="NUM_DIFFS" value="1" type="hidden"><input name="NUM_OPTS_DIFFS" value="0" type="hidden"><input name="NUM_ORG" value="1" type="hidden"><input name="NUM_OVERVIEW" value="100" type="hidden"><input name="OLD_BLAST" value="false" type="hidden"><input name="OLD_VIEW" value="false" type="hidden"><input name="PAGE" value="Nucleotides" type="hidden"><input name="PAGE_TYPE" value="BlastSearch" type="hidden"><input name="PROGRAM" value="blastn" type="hidden"><input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="QUERY_LENGTH" value="16" type="hidden"><input name="REPEATS" value="repeat_9606" type="hidden"><input name="RID" value="PHWP1JNZ014" type="hidden"><input name="RTOE" value="42" type="hidden"><input name="SEARCH_DB_STATUS" value="43" type="hidden"><input name="SELECTED_PROG_TYPE" value="megaBlast" type="hidden"><input name="SERVICE" value="plain" type="hidden"><input name="SHORT_QUERY_ADJUST" value="on" type="hidden"><input name="SHOW_LINKOUT" value="on" type="hidden"><input name="SHOW_OVERVIEW" value="on" type="hidden"><input name="USER_DEFAULT_MATCH_SCORES" value="0" type="hidden"><input name="USER_DEFAULT_PROG_TYPE" value="megaBlast" type="hidden"><input name="USER_TYPE" value="2" type="hidden"><input name="WORD_SIZE" value="7" type="hidden"><input name="_PGR" value="2" type="hidden"><input name="db" value="nucleotide" type="hidden"><input name="stype" value="nucleotide" type="hidden">
+                <input name="QUERY_INDEX" value="0" type="hidden">
+                <input name="_PGR" value="2" type="hidden">
+                <input id="seqViewUrl" value="http://www.ncbi.nlm.nih.gov/projects/sviewer" type="hidden">
+                <input name="CMD" value="Get" type="hidden">
+                </form>
+                <!-- Reformat and downlaod for new design -->
+                <div class="ui-helper-reset" aria-live="assertive">
+<form aria-hidden="true" action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="FormatForm" id="FormatForm" class="resbox ui-ncbitoggler-slave  ui-ncbitoggler">
+<table class="options blastn ">
+<tbody><tr>
+<td class="frh" colspan="2">
+<div class="fi">
+<div class="tb">Formatting options</div>
+<input id="onPageReformat" src="NCBI%20Blast%20reference%20example_files/reformat.jpg" class="blastbutton" alt="Reformat" mouseovimg="css/images/reformatOver.jpg" mouseoutimg="css/images/reformat.jpg" mousedownimg="css/images/reformatDown.jpg" mouseupimg="css/images/reformatOver.jpg" border="0" type="image">
+</div>
+</td></tr>
+<tr class="paramSet xgl">
+<td class="hd"><label for="FORMAT_OBJECT">Show</label></td>
+<td>
+<div class="fi">
+<input id="FORMAT_OBJECT" value="Alignment" name="FORMAT_OBJECT" type="hidden">
+<label for="FORMAT_TYPE" id="nft">Alignment as</label>
+<select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defval="HTML">
+<option value="HTML" selected="selected">HTML</option>
+<option value="Text">Plain text</option>
+
+</select>
+
+<span id="advView" class="">
+<span class=""><input name="OLD_VIEW" id="OLD_VIEW" class="cb reset" defval="unchecked" false="" type="checkbox">
+<label for="OLD_VIEW">Old View</label></span>
+</span>
+<a class="resetAll" id="resetAll">Reset form to defaults</a>
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments object formatting help" id="formatHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp1">
+These options control formatting of alignments in results pages. The
+default is HTML, but other formats (including plain text) are available.
+PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
+The Advanced view option allows the database descriptions to be sorted by various indices in a table.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+<tr class="odd paramSet">
+<td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td>
+<td>
+<div class="fi">
+<select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defval="Pairwise" class="reset">
+<option value="Pairwise" selected="selected">Pairwise</option>
+<option value="PairwiseWithIdentities">Pairwise with dots for identities</option>
+<option value="QueryAnchored">Query-anchored with dots for identities</option>
+<option value="QueryAnchoredNoIdentities">Query-anchored with letters for identities</option>
+<option value="FlatQueryAnchored">Flat query-anchored with dots for identities</option>
+<option value="FlatQueryAnchoredNoIdentities">Flat query-anchored with letters for identities</option>
+
+</select>
+
+
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments view options help" id="alnViewHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp2">
+Choose how to view alignments.
+The default "pairwise" view shows how each subject sequence aligns
+individually to the query sequence. The "query-anchored" view shows how
+all subject sequences align to the query sequence. For each view type,
+you can choose to show "identities" (matching residues) as letters or
+dots.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+<tr class="paramSet">
+<td class="hd"><label>Display</label></td>
+<td class="cb">
+<div class="fi">
+<input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" class="cb reset" defval="checked" checked="checked" type="checkbox">
+<label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label>
+
+<span class="hidden" id="shl">
+<input name="SHOW_LINKOUT" id="SHOW_LINKOUT" class="cb reset" defval="checked" checked="checked" type="checkbox">
+<label class="rb" for="SHOW_LINKOUT">Linkout</label>
+</span>
+<span class="hidden" id="gts">
+<input name="GET_SEQUENCE" id="GET_SEQUENCE" class="cb reset" defval="checked" checked="checked" type="checkbox">
+<label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label>
+</span>
+
+<input name="NCBI_GI" id="NCBI_GI" class="cb reset" defval="unchecked" type="checkbox">
+<label class="rb" for="NCBI_GI">NCBI-gi</label>
+<span id="scf">
+<input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" class="cb reset blastn" defval="unchecked" type="checkbox">
+<label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label>
+</span>
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments display options help" id="displayHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp3">
+<li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to  query.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a>
+</li>
+<li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin">more...</a>
+</li>
+<li>Sequence Retrieval: Show buttons to download matching sequences.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin">more...</a>
+</li>
+<li>NCBI-gi: Show NCBI gi identifiers.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin">more...</a>
+</li>
+<li>CDS feature: Show annotated coding region and translation.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin">more...</a>
+</li></ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+
+<tr class="paramSet odd xgl">
+<td class="hd"><label>Masking</label></td>
+<td>
+<div class="fi">
+<label for="MASK_CHAR"> Character: </label>
+<select name="MASK_CHAR" id="MASK_CHAR" class="reset" defval="2">
+<option value="0">X for protein, n for nucleotide</option>
+<option value="2" selected="selected">Lower Case</option>
+</select>
+<label for="MASK_COLOR"> Color:</label>
+<select name="MASK_COLOR" id="MASK_COLOR" class="reset" defval="1">
+<option value="0">Black
+</option>
+
+<option value="1" selected="selected">Grey
+</option>
+
+<option value="2">Red
+</option>
+
+</select>
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments masking help" id="maskingHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp4">
+<li>Masking Character: Display masked (filtered) sequence regions as
+lower-case or as specific letters (N for nucleotide, P for protein).
+</li>
+<li>Masking Color: Display masked sequence regions in the given color.</li>
+</ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+
+<tr id="lr" class="paramSet xgl">
+<td class="hd"><label>Limit results</label></td>
+<td>
+<div class="fi">
+<label for="FRM_DESCRIPTIONS">Descriptions:</label>
+<select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defval="100">
+
+<option value="10">10</option>
+<option value="50">50</option>
+<option value="100" selected="selected">100</option>
+
+
+
+
+
+
+</select>
+
+<label for="FRM_NUM_OVERVIEW">Graphical overview:</label>
+<select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defval="100">
+<option value="0">0</option>
+<option value="10">10</option>
+<option value="50">50</option>
+<option value="100" selected="selected">100</option>
+
+
+
+</select>
+<span class="hidden" id="frmAln">
+<label for="FRM_ALIGNMENTS">Alignments:</label>
+<select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defval="100">
+<option value="0">0</option>
+<option value="10">10</option>
+<option value="50">50</option>
+<option value="100" selected="selected">100</option>
+
+
+
+
+
+
+</select>
+</span>
+<label for="FRM_LINE_LENGTH">Line length:</label>
+<select name="LINE_LENGTH" id="FRM_LINE_LENGTH" class="reset" defval="60">
+<option value="60" selected="selected">60</option>
+<option value="90">90</option>
+<option value="120">120</option>
+<option value="150">150</option>
+</select>
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit number of descriptions/alignments help" id="numHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp5">
+<li>Descriptions: Show short descriptions for up to the given number of  sequences.</li>
+<li>Alignments:  Show alignments for up to the given number of sequences, in order of statistical significance.</li>
+<li>Line lenghth:  ....</li>
+</ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+<tr class="paramSet odd xgl ">
+<td class="hd"></td>
+<td>
+<div class="">
+<label for="qorganism">Organism</label>
+<span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br>
+<input role="textbox" aria-autocomplete="list" aria-haspopup="true" title="Use up and down arrows to choose an item from the autocomplete." name="FORMAT_ORGANISM" size="55" id="qorganism" value="Enter organism name or id--completions will be suggested" data-jigconfig="dictionary:'taxids_sg'" autocomplete="off" class="jig-ncbiautocomplete reset orgHint" type="text">
+<input name="FORMAT_ORG_EXCLUDE" class="oExclR cb" id="orgExcl" type="checkbox">
+<input value="1" name="FORMAT_NUM_ORG" id="numOrg" type="hidden">
+<label for="orgExcl" class="right">Exclude</label>
+<a href="#" title="Add organism" id="addOrg"><img src="NCBI%20Blast%20reference%20example_files/addOrg.jpg" id="addOrgIm" alt="Add organism" mouseovimg="css/images/addOrgOver.jpg" mouseoutimg="css/images/addOrg.jpg" mousedownimg="css/images/addOrgDown.jpg" mouseupimg="css/images/addOrgOver.jpg" border="0"></a>
+<div id="orgs">
+
+</div>
+<div class="fi">
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by organism help" id="organismHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp6">
+Show only sequences from the given organism.
+</p>
+</div><!-- ARIA -->
+</div>
+</div>
+</td>
+</tr>
+
+<tr class="paramSet xgl ">
+<td class="hd"></td>
+<td>
+<div class="fi">
+<label for="FORMAT_EQ_TEXT">Entrez query:</label>
+<input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" class="reset" type="text">
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by Entrez query help" id="entrezHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp7">
+Show only those sequences that match the given Entrez query.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#limit_result" target="helpWin" title="Additional limit results by Entrez query help">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+
+<tr class="paramSet odd xgl">
+<td class="hd"></td>
+<td>
+<div class="fi">
+<label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" class="reset" type="text">
+<label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" class="reset" type="text">
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by expect value range help" id="expectHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp8">
+Show only sequences with expect values in the given range.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect_range" target="helpWin" title="Additional limit results by expect value range help">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+<tr class="paramSet xgl">
+<td class="hd"></td>
+<td>
+ <div class="fi">
+<label for="PERC_IDENT_LOW">Percent Identity Min:</label> <input name="PERC_IDENT_LOW" id="PERC_IDENT_LOW" size="10" class="reset" type="text">
+<label for="PERC_IDENT_HIGH">Percent Identity Max:</label> <input name="PERC_IDENT_HIGH" id="PERC_IDENT_HIGH" size="10" class="reset" type="text">
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by percent identity range help" id="percIdentHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp10">
+ Show only sequences with percent identity values in the given range.
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+<tr class="psiBlast odd paramSet xgl">
+<td class="hd"><label>Format for</label></td>
+<td>
+<div class="fi">
+<input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" class="cb psiBlast" type="checkbox">
+<label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label>
+<label for="I_THRESH">with inclusion threshold:</label>
+<input name="I_THRESH" id="I_THRESH" size="10" defval="0.005" type="text">
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink  jig-ncbitoggler ui-ncbitoggler ui-widget" title="PSI BLAST formatting help" id="psiHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive">
+<ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp9">
+<li>Format for PSI-BLAST: The Position-Specific Iterated BLAST
+(PSI-BLAST) program performs iterative searches with a protein query,
+in which sequences found in one round of search are used to build a
+custom score model for the next round.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a>
+</li>
+<li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used
+by PSI-BLAST to create the PSSM on the next iteration.</li>
+</ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+</tbody></table>
+
+
+<input name="ViewReport" value="ViewReport" type="hidden">
+<input name="REFORMAT_REPORT" value="shown" type="hidden">
+<input name="RID" value="PHWP1JNZ014" type="hidden">
+<input name="CDD_RID" value="" type="hidden">
+<input name="CDD_SEARCH_STATE" value="" type="hidden">
+
+<input name="STEP_NUMBER" value="" id="stepNumber" type="hidden">
+<input name="CMD" value="Get" type="hidden">
+<input name="FORMAT_EQ_OP" value="AND" type="hidden">
+<input name="RESULTS_PAGE_TARGET" id="resPageTarget" value="" type="hidden">
+<!-- <input name="QUERY_INFO" type="hidden" value="Nucleotide Sequence (16 letters)" /> -->
+<!-- <input name="ENTREZ_QUERY" type="hidden" value="" /> -->
+<input name="QUERY_INDEX" value="0" type="hidden">
+<input name="NUM_QUERIES" value="1" type="hidden">
+<input name="PHI_PTTRN_INDEX" value="" type="hidden">
+<input id="cfcDsSave" name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden">
+<!-- Those params are set in the template (blastn.dat, blastp.dat etc. -->
+<input name="BLAST_PROGRAMS" value="blastn" type="hidden">
+<input name="PAGE" value="Nucleotides" type="hidden">
+<input name="PROGRAM" value="blastn" type="hidden">
+<input name="MEGABLAST" value="" type="hidden">
+<input name="RUN_PSIBLAST" value="" type="hidden">
+<input name="BLAST_SPEC" id="blastSpec" value="" type="hidden">
+
+
+<input name="QUERY" value="" type="hidden">
+<input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden">
+<input name="QUERY_TO" value="" type="hidden">
+<input name="QUERY_FROM" value="" type="hidden">
+<input name="EQ_TEXT" value="" type="hidden">
+<input name="ORGN" value="" type="hidden">
+<input name="EQ_MENU" value="" type="hidden">
+<input name="ORG_EXCLUDE" value="" type="hidden">
+<input name="PHI_PATTERN" value="" type="hidden">
+<input name="EXPECT" value="1000" type="hidden">
+<input name="DATABASE" value="pdb" type="hidden">
+<input name="DB_GROUP" value="" type="hidden">
+<input name="SUBGROUP_NAME" value="" type="hidden">
+
+<input name="GENETIC_CODE" value="" type="hidden">
+<input name="WORD_SIZE" value="7" type="hidden">
+<input name="MATCH_SCORES" value="1,-3" type="hidden">
+<input name="MATRIX_NAME" value="" type="hidden">
+<input name="GAPCOSTS" value="5 2" type="hidden">
+<input name="MAX_NUM_SEQ" id="maxNumSeq" value="100" type="hidden">
+<input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden">
+<input name="NEWWIN" value="" type="hidden">
+<input name="SHORT_QUERY_ADJUST" value="on" type="hidden">
+<input name="FILTER" value="" type="hidden">
+<input name="REPEATS" value="repeat_9606" type="hidden">
+<input name="ID_FOR_PSSM" value="" type="hidden">
+<input name="EXCLUDE_MODELS" value="" type="hidden">
+<input name="EXCLUDE_SEQ_UNCULT" value="" type="hidden">
+<input name="WP_PROTEINS" value="" type="hidden">
+<input name="SEQ_FROM_TYPE" value="" type="hidden">
+<input name="ENTREZ_QUERY_PRESET" value="" type="hidden">
+<input name="ENTREZ_QUERY_PRESET_EXCL" value="" type="hidden">
+<input name="NUM_ORG" value="1" type="hidden">
+
+<!-- PSSM -->
+<input name="LCASE_MASK" value="" type="hidden">
+<input name="TEMPLATE_TYPE" value="" type="hidden">
+<input name="TEMPLATE_LENGTH" value="" type="hidden">
+<input name="I_THRESH" value="" type="hidden">
+<input name="PSI_PSEUDOCOUNT" value="" type="hidden">
+<input name="DI_THRESH" id="diThresh" value="" type="hidden">
+<input name="HSP_RANGE_MAX" value="0" type="hidden">
+
+
+
+<input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden">
+<input name="MIXED_QUERIES" value="" type="hidden">
+<input name="MIXED_DATABASE" id="mixedDb" value="" type="hidden">
+<input name="BUILD_NAME" value="" type="hidden">
+<input name="ORG_DBS" value="" type="hidden">
+
+</form>
+</div> <!-- aria -->
+                <div class="ui-helper-reset" aria-live="assertive">
+<form aria-hidden="true" name="FormatDownload" id="FormatDownload" class="resbox ui-ncbitoggler-slave ui-ncbitoggler">
+<table class="options dwnl ">
+<tbody><tr><td class="frh" colspan="6"><div class="tb">Download</div></td></tr>
+<tr>
+<td id="tdal">
+<div class="dnHeader">Alignment</div>
+<div class="dnLinks">
+<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;DESCRIPTIONS=100&amp;ALIGNMENTS=100&amp;CMD=Get">Text</a>
+<a class="xgl" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=XML&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get">XML</a>
+<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get">ASN.1</a>
+<a id="hitText" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get">Hit Table(text)</a>
+<a id="hitCvs" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=CSV&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get">Hit Table(csv)</a>
+</div>
+</td>
+<td class="dnl xgl">
+<div class="dnHeader">Search Strategies</div>
+<div class="dnLinks">
+<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&amp;RECENT_RESULTS=on&amp;RID=PHWP1JNZ014&amp;DOWNLOAD_OPTIONS=true">ASN.1</a>
+</div>
+</td>
+<td class="dnl hidden" id="dnPSSMPar">
+<div class="dnHeader">PssmWithParameters</div>
+<div class="dnLinks">
+<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=PSSM_Scoremat&amp;CMD=Get">ASN.1</a>
+</div>
+</td>
+<td>
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Download help" data-ncbitoggler-toggles="hlp11" id="dnHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+</td>
+</tr>
+</tbody></table>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp11">
+  The Download link provides BLAST output that may be used as input to
+another program.
+  This includes parseable formats such as the tabular report or XML as
+well as the Search Strategy files read by the BLAST+ applications.
+  More details on the parseable (XML, tabular, and ASN.1) reports can be
+ found at
+  <a href="http://www.ncbi.nlm.nih.gov/books/NBK21097/" target="helpWin">http://www.ncbi.nlm.nih.gov/books/NBK21097/</a><br>
+  <br>
+  The following formats are offered under the Alignment section:<br>
+    1). "Text". Non-HTML standard BLAST report.<br>
+
+    2). "XML". XML report based upon the DTD at <a href="http://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd" target="helpWin">http://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd</a><br>
+
+    3). "ASN.1" Alignment. This is the alignment written out in Abstract Syntax Notation 1.<br>
+
+    4). "Hit Table(text)". The tabular report as text.<br>
+
+    5). "Hit Table(csv)". The tabular report ready for import into spread-sheet programs like Excel.<br>
+  <br>
+  The following report is offered under the Search Strategy section:<br>
+
+  1). "ASN.1" Search Strategy. A record of the parameters, query, and
+database used in the search. This file can be used to start a
+stand-alone BLAST search, see
+  <a href="http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra" target="helpWin">http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra</a>
+</p>
+</div><!-- ARIA -->
+</form>
+</div> <!-- aria -->
+                <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" name="overview0">
+                <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden"><input name="ALIGNMENTS" value="100" type="hidden"><input name="ALIGNMENT_VIEW" value="Pairwise" type="hidden"><input name="BLAST_PROGRAMS" value="blastn" type="hidden"><input name="CLIENT" value="web" type="hidden"><input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden"><input name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden"><input name="DATABASE" value="pdb" type="hidden"><input name="DBTYPE" value="gc" type="hidden"><input name="DEFAULT_PROG" value="megaBlast" type="hidden"><input name="DESCRIPTIONS" value="100" type="hidden"><input name="DYNAMIC_FORMAT" value="on" type="hidden"><input name="EQ_OP" value="AND" type="hidden"><input name="EXPECT" value="1000" type="hidden"><input name="FORMAT_NUM_ORG" value="1" type="hidden"><input name="FORMAT_OBJECT" value="Alignment" type="hidden"><input name="FORMAT_TYPE" value="HTML" type="hidden"><input name="FULL_DBNAME" value="pdb" type="hidden"><input name="GAPCOSTS" value="5 2" type="hidden"><input name="GET_SEQUENCE" value="on" type="hidden"><input name="HSP_RANGE_MAX" value="0" type="hidden"><input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="LAYOUT" value="OneWindow" type="hidden"><input name="LINE_LENGTH" value="60" type="hidden"><input name="MASK_CHAR" value="2" type="hidden"><input name="MASK_COLOR" value="1" type="hidden"><input name="MATCH_SCORES" value="1,-3" type="hidden"><input name="MAX_NUM_SEQ" value="100" type="hidden"><input name="NUCL_PENALTY" value="-2" type="hidden"><input name="NUCL_REWARD" value="1" type="hidden"><input name="NUM_DIFFS" value="1" type="hidden"><input name="NUM_OPTS_DIFFS" value="0" type="hidden"><input name="NUM_ORG" value="1" type="hidden"><input name="NUM_OVERVIEW" value="100" type="hidden"><input name="OLD_BLAST" value="false" type="hidden"><input name="OLD_VIEW" value="false" type="hidden"><input name="PAGE" value="Nucleotides" type="hidden"><input name="PAGE_TYPE" value="BlastSearch" type="hidden"><input name="PROGRAM" value="blastn" type="hidden"><input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="QUERY_LENGTH" value="16" type="hidden"><input name="REPEATS" value="repeat_9606" type="hidden"><input name="RID" value="PHWP1JNZ014" type="hidden"><input name="RTOE" value="42" type="hidden"><input name="SEARCH_DB_STATUS" value="43" type="hidden"><input name="SELECTED_PROG_TYPE" value="megaBlast" type="hidden"><input name="SERVICE" value="plain" type="hidden"><input name="SHORT_QUERY_ADJUST" value="on" type="hidden"><input name="SHOW_LINKOUT" value="on" type="hidden"><input name="SHOW_OVERVIEW" value="on" type="hidden"><input name="USER_DEFAULT_MATCH_SCORES" value="0" type="hidden"><input name="USER_DEFAULT_PROG_TYPE" value="megaBlast" type="hidden"><input name="USER_TYPE" value="2" type="hidden"><input name="WORD_SIZE" value="7" type="hidden"><input name="_PGR" value="2" type="hidden"><input name="db" value="nucleotide" type="hidden"><input name="stype" value="nucleotide" type="hidden">
+                <input name="CMD" value="Get" type="hidden">
+                <p id="qb"><!--
+QBlastInfoBegin
+	Status=READY
+QBlastInfoEnd
+--></p>
+<div id="page">
+
+<div id="summary" class="">
+<div id="ht"></div>
+<h1>Nucleotide Sequence (16 letters) <span id="hdTitle" class="shownInl"></span></h1>
+<div>
+<div id="multipleSeqs" class="hidden">
+<label for="queryList">Results for:</label>
+<select id="queryList" name="queryList">
+<option value="0" selected="selected" class="">lcl|59987 None(16bp)</option>
+</select>
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="queryInfo" title="Multiple quries help" id="queryHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+</div><!--/#multipleSeqs"-->
+
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" id="queryInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
+Your BLAST job specified more than one input sequence.
+This box lets you choose which input sequence to show BLAST results for.
+</p>
+</div><!-- ARIA -->
+</div>
+<div id="summarylists">
+<dl>
+<dt>RID</dt>
+<dd>
+<a title="BLAST search request ID" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014">PHWP1JNZ014</a> (Expires on 05-07 22:33 pm)
+</dd>
+</dl>
+<div id="querysummary">
+<dl>
+<dt>Query ID</dt>
+<dd class="hidden">
+<a title="Find query in Entrez" href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&amp;db=nucleotide&amp;term=59987&amp;dopt=GenBank" target="lnkPHWP1JNZ014">lcl|59987</a>
+</dd>
+<dd class="">lcl|59987</dd>
+<dt>Description</dt>
+<dd>None</dd>
+<dt>Molecule type</dt>
+<dd>nucleic acid</dd>
+<dt>Query Length</dt>
+<dd>16</dd>
+</dl>
+</div><!--/#querysummary-->
+
+<div id="dbsummary">
+<dl>
+<dt>   </dt><dd>   </dd>
+<dt>Database Name</dt>
+<dd>pdb</dd>
+<dt>Description</dt>
+<dd>PDB nucleotide database <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="See multiple databases detailed information" class="jtg resArrowLinkB hidden  jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="dbDetails" id="showDetails"><span class="ui-ncbitoggler-master-text">See details</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd> <!-- -- Database or subject info ---->
+<dt class="xgl">Program</dt>
+<dd class="xgl">BLASTN 2.2.29+ <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="How to cite BLAST in publications" class="resArrowLinkB hidden shown jig-ncbitoggler ui-ncbitoggler jtg ui-widget" data-ncbitoggler-toggles="refInfo" id="showRefs"><span class="ui-ncbitoggler-master-text">Citation</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd>
+</dl>
+</div><!--/#dbsummary-->
+</div><!--/#summarylists -->
+<br>
+<div class="ui-helper-reset" aria-live="assertive">
+<div aria-hidden="true" id="dbDetails" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
+ <!-- multiple databases or subjects table -->
+</div>
+</div> <!-- aria end -->
+<div class="ui-helper-reset" aria-live="assertive">
+<div aria-hidden="true" id="refInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
+<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Retrieve&amp;list_uids=9254694&amp;dopt=Citation">Reference </a>
+<div>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer,
+Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
+"Gapped BLAST and PSI-BLAST: a new generation of protein database search
+ programs", Nucleic Acids Res. 25:3389-3402.</div>
+ </div>  <!-- refInfo -->
+</div> <!-- aria end -->
+
+<div id="seealso">
+<label>Other reports:</label>
+ <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="Show statistics" class="resArrowLinkB jtg jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="resStat" id="showStat"><span class="ui-ncbitoggler-master-text">Search Summary</span><span class="ui-icon ui-icon-triangle-1-e"></span></a>
+ <span class="xgl">
+ <a id="tax" class="hidden shown" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=PHWP1JNZ014&amp;FORMAT_OBJECT=TaxBlast&amp;NCBI_GI=off&amp;DESCRIPTIONS=100&amp;ALIGNMENTS=100&amp;FORMAT_BLOCK_ON_RESPAGE=Top&amp;MASK_COLOR=1&amp;MASK_CHAR=2" target="lnkPHWP1JNZ014" title="See results arranged by taxonomy">[Taxonomy reports]</a>
+ <a href="http://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl%7C59987&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;ns=100" class="" id="TreeViewlcl|59987" onclick="ViewTree('TreeViewlcl|59987');return false;" target="lnkPHWP1JNZ014" title="See a distance tree of these pairwise comparisons">[Distance tree of results]</a>
+
+
+
+ </span>
+</div> <!-- seealso -->
+
+<div class="ui-helper-reset" aria-live="assertive">
+<div aria-hidden="true" id="resStat" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
+ <table id="params" class="dbInfo">
+ <caption>Search Parameters</caption>
+ <tbody><tr><th><div>Search parameter name</div></th><th><div>Search parameter value</div></th></tr>
+ <tr><td>Program</td><td>blastn</td></tr><tr><td>Word size</td><td>7</td></tr><tr><td>Expect value</td><td>1000</td></tr><tr><td>Hitlist size</td><td>100</td></tr><tr><td>Match/Mismatch scores</td><td>1,-3</td></tr><tr><td>Gapcosts</td><td>5,2</td></tr><tr><td>Filter string </td><td>F</td></tr><tr><td>Genetic Code</td><td>1</td></tr>
+ </tbody></table>
+  <table id="dbStat" class="dbInfo">
+ <caption>Database</caption>
+ <tbody><tr><th><div>Database parameter name</div></th><th><div>Database parameter value</div></th></tr>
+ <tr><td>Posted date</td><td>Apr 29, 2014  3:14 AM</td></tr>
+ <tr><td>Number of letters</td><td>885,284</td></tr>
+ <tr><td>Number of sequences</td><td>8,975</td></tr>
+ <tr><td>Entrez query</td><td>none</td></tr>
+ </tbody></table>
+
+ <table id="Kappa" class="dbInfo show xgl">
+<caption>Karlin-Altschul statistics</caption>
+ <tbody><tr><th><div>Params</div></th><th><div>Ungapped</div></th><th><div>Gapped</div></th></tr>
+ <tr><td>Lambda</td><td>1.37406</td><td>1.37406</td></tr>
+ <tr><td>K</td><td>0.710603</td><td>0.710603</td></tr>
+ <tr><td>H</td><td>1.30725</td><td>1.30725</td></tr>
+
+ </tbody></table>
+
+
+ <table class="dbInfo show">
+ <caption>Results Statistics</caption>
+ <tbody><tr><th><div>Results Statistics parameter name</div></th><th><div>Results Statistics parameter value</div></th></tr>
+ <tr><td>Length adjustment</td><td> 11</td></tr><tr><td>Effective length of query</td><td> 5</td></tr><tr><td>Effective length of database</td><td> 786559</td></tr><tr><td>Effective search space</td><td> 3932795</td></tr><tr><td>Effective search space used</td><td> 3932795</td></tr>
+ </tbody></table>
+ <!-- Results statistics -->
+ </div>  <!-- resStat -->
+ </div> <!-- aria end -->
+</div><!--/#summary-->
+</div><!--/#page-->
+<iframe id="RSIFrameDesc" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="NCBI%20Blast%20reference%20example_files/plinkcgi.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe>
+
+<div id="grView" class="hidden shown">
+<h2 class="resArr">
+<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showGraphic" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="graphicInfo" title="Show/hide Graphic Summary">
+<span class="ui-ncbitoggler-master-text">Graphic Summary</span>
+<span class="ui-icon ui-icon-plus-minus-big-open"></span>
+</a>
+</h2>
+<div class="ui-helper-reset" aria-live="assertive">
+<div aria-hidden="false" id="graphicInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
+
+
+<div id="graphic" class="hidden shown">
+<h3>Distribution of 45 Blast Hits on the Query Sequence
+<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Graphic summary help" id="grHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a></h3>
+<div class="ui-helper-reset" aria-live="assertive">
+<p aria-hidden="true" id="ovrInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
+An overview of the database sequences aligned to the query sequence is
+shown. The score of each alignment is indicated by one of five
+different colors, which divides the range of scores into five groups.
+Multiple alignments on the same database sequence are connected
+by a striped line. <span class="hl">Mousing over</span> a hit sequence causes the definition and score to be shown in the window at the top,
+<span class="hl">clicking</span> on a hit sequence takes the user to the associated alignments.
+New:
+This graphic is an overview of database sequences aligned to the query sequence.
+Alignments are color-coded by score, within one of five score ranges.
+Multiple alignments on the same database sequence are connected by a dashed line.
+<span class="hl">Mousing</span> over an alignment shows the alignment definition and score in the box at the top.
+<span class="hl">Clicking</span> an alignment displays the alignment detail.
+</p>
+</div><!-- ARIA -->
+<center><input name="defline" size="85" value="Mouse-over to show defline and scores, click to show alignments" type="text"><table bordercolordark="#0000FF" bordercolorlight="#0000FF" border="1" cellpadding="10" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/score.gif" height="40" width="500"></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/query_no_scale.gif" height="10" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="51"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/3.gif" height="13" width="10"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/6.gif" height="13" width="10"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/9.gif" height="13" width="10"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="73"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/2.gif" height="13" width="10"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="73"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/5.gif" height="13" width="10"></td>
+</tr></tbody></table>
+<br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804451" onclick='DisplayAlignFromGraphics("557804451",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J5A_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804395" onclick='DisplayAlignFromGraphics("557804395",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J58_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804339" onclick='DisplayAlignFromGraphics("557804339",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J56_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804283" onclick='DisplayAlignFromGraphics("557804283",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J54_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804227" onclick='DisplayAlignFromGraphics("557804227",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J52_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804195" onclick='DisplayAlignFromGraphics("557804195",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J51_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804163" onclick='DisplayAlignFromGraphics("557804163",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J50_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#557804083" onclick='DisplayAlignFromGraphics("557804083",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J4X_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="250"></a></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
+<td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
+<td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 14" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=14 E=1.9e+02'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="219"></a></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
+<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="155"></a></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
+<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
+<td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="94"></td>
+<td align="LEFT" valign="CENTER"><a href="#357380483" onclick='DisplayAlignFromGraphics("357380483",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J0O_8 Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex .. S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="281"></a></td>
+</tr></tbody></table>
+<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
+</td></tr></tbody></table>
+</center><hr>
+</div><!--/#graphic-->
+</div><!-- graphicInfo -->
+</div><!-- ARIA -->
+</div>
+<!--HITMATRIX_VIEW - only for bl2seq -->
+
+<div id="dscrView" class="hidden shown">
+<h2 class="resArr">
+<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showDescr" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="descrInfo" title="Show/hide Descriptions">
+<span class="ui-ncbitoggler-master-text">Descriptions</span>
+<span class="ui-icon ui-icon-plus-minus-big-open"></span>
+</a>
+</h2>
+<div class="ui-helper-reset" aria-live="assertive">
+<div aria-hidden="false" id="descrInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
+ <!-- legend to links to other resources -->
+<a name="sort_mark"></a>
+
+
+<div id="debug">, Reading indexes 1-5, displaying indexes 1-5</div>
+<input id="Rid" value="PHWP1JNZ014" type="hidden">
+<input id="useAlignDB" name="useAlignDB" value="" type="hidden">
+<input id="dbType" value="GenBank" type="hidden"><!-- Indicates genbank, etc -->
+<input id="serviceType" value="plain" type="hidden">
+<input id="clientType" value="web" type="hidden">
+<input id="currQuery" value="" type="hidden">
+<input id="minDispAlnLen" value="2000" type="hidden">
+<input id="maxDispAlnLen" value="20000" type="hidden">
+<div class="hidden" id="dynHspTmpl"><div class="alnParLinks moreHsps" id="@moreHspsID@"><a class="gbd toolsCtr navNext" title="Load matches @segs@ out of @totalHSP@ for @accs@" onmouseover="scan(this)" ref="range=@segs@&amp;currseq=@alnSeqGi@" onclick="ReadNextHSPSet(@argstring@);"><span>Load next set</span></a><a class="gbd toolsCtr navPrev" title="Go to previous match #@aln_prev_num@ for @accs@" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a></div></div>
+<div id="descriptions" class="blRes">
+<!--<pre> -->
+<div class="cap">Sequences producing significant alignments:</div>
+<a id="shcl" href="#" onclick="showAllCol(event,this)" class="shcl hidden">
+Show all columns <span class="accsb"> of the table presenting sequences producing significant alignments </span>
+</a>
+<span id="cntDesc">
+<span>Select:<a href="#" id="cntSelA" sel="all">All</a><a href="#" id="cntSelN" sel="n">None</a></span>
+<span>Selected:<span id="slcNum">0</span></span>
+</span>
+
+<div id="descTblCtrl" class="cnf">
+<a href="#alignInfo" id="alnNav" class="toolsCtr alnNav" title="Go to alignments"><span>Alignments</span></a>
+<a aria-haspopup="true" aria-expanded="false" role="button" href="#dsDownload" minslct="1" class="jig-ncbipopper toolsCtr dnld dialog " data-jigconfig="hasArrow:'true',arrowDirection:'top'" id="dscDwnld" disabled="disabled" title="Download information for selected sequences"><span>Download</span></a>
+
+<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsDownload" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
+<div class=""><input name="dwn" checked="checked" id="dwFST" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST">FASTA (complete sequence)</label></div>
+<div class=""><input name="dwn" id="dwFSTAl" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl">FASTA (aligned sequences)</label></div>
+<div class=""><input name="dwn" id="dwGenBank" getgi="on" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class=" shownInl" for="dwGenBank">GenBank (complete sequence)</label></div>
+<div><input name="dwn" id="dwHitText" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get" type="radio"><label class="shownInl" for="dwHitText">Hit Table (text)</label></div>
+<div><input name="dwn" id="dwHitCsv" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=CSV&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get" type="radio"><label class="shownInl" for="dwHitCsv">Hit Table (CSV)</label></div>
+<div><input name="dwn" id="dwText" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get" type="radio"><label class="shownInl" for="dwText">Text</label></div>
+<div><input name="dwn" id="dwXML" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=XML&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get" type="radio"><label class="shownInl" for="dwXML">XML</label></div>
+<div><input name="dwn" id="dwASN" url="Blast.cgi?RESULTS_FILE=on&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get" type="radio"><label class="shownInl" for="dwASN">ASN.1</label></div>
+<div>
+<button class="cfg" id="dw_cont">Continue</button>
+<button class="cfg cnc">Cancel</button>
+</div>
+</div> <!-- dsDownload -->
+
+
+
+
+
+<a href="#" class="toolsCtr" minslct="1" view="dflt" frm="submitterTop" seqlist="selSeqs" title="See genbank report for selected sequences" disabled="disabled">GenBank</a> <!-- genbank or Traces -->
+<a href="#" class="toolsCtr " minslct="1" view="graph" title="See graphic representation for selected sequences" disabled="disabled">Graphics</a>
+<a href="#" class="toolsCtr hidden shown" view="tree" minslct="1" frm="sbmtTreeView" seqlist="selSeqsTr" disabled="disabled" title="See a distance tree of pairwise comparisons for the selected sequences">Distance tree of results</a>
+<a href="#" class="toolsCtr hidden " view="dflt" minslct="2" frm="sbmtMultiAln" seqlist="selSeqsMl" disabled="disabled" title="See multple alignment of query and target sequences for the selected sequences with expect value better than 0.001">Multiple alignment</a>
+
+<a aria-haspopup="true" aria-expanded="false" role="button" class="jig-ncbipopper button_config" title="Show/hide columns" id="button_config" href="#dsConfig"><span class="accsb">Show/hide columns of the table presenting sequences producing significant alignments </span></a>
+
+<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsConfig" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
+<div class="tl">Available columns</div>
+<input checked="checked" id="chkDs" value="2" type="checkbox"><label class="shownInl" for="chkDs">Description</label><br>
+<input checked="checked" id="chkMS" value="3" type="checkbox"><label class="shownInl" for="chkMs">Max Score</label><br>
+<input checked="checked" id="chkTS" value="4" type="checkbox"><label class="shownInl" for="chkTs">Total Score</label><br>
+<input checked="checked" id="chkCov" value="5" type="checkbox"><label class="shownInl" for="chkCov">Coverage</label><br>
+<input checked="checked" id="chkEval" value="6" type="checkbox"><label class="shownInl" for="chkEval">E-value</label><br>
+<input checked="checked" id="chkIdnt" value="7" type="checkbox"><label class="shownInl" for="chkIdnt"><span class="">Ident</span><span class="hidden">N</span></label><br>
+<input checked="checked" id="chkAcc" value="8" type="checkbox"><label class="shownInl" for="chkAcc">Accession</label><br>
+<button class="cfg rdf" id="dscRsDf">Restore Defaults</button>
+<button class="cfg" id="dscOk">Ok</button>
+<button class="cfg cnc" id="dscCnc">Cancel</button>
+</div> <!-- dsConfig -->
+
+<input id="cfcDsInf" defval="2,3,4,5,6,7,8" value="2,3,4,5,6,7,8" type="hidden">
+</div>
+<div class="ui-ncbigrid-outer-div caption-exists">
+<div class="ui-ncbigrid-inner-div">
+<table id="dscTable" class="jig-ncbigrid  ui-ncbigrid" data-jigconfig="" cellpadding="0" cellspacing="0">
+<caption class="hdnHeader">Sequences producing significant alignments:</caption>
+<thead>
+<tr class="first">
+  <th class="c0" id="c0"><span>Select for downloading or viewing reports</span></th>
+  <th class="dflnDth c2" id="c2">Description</th>
+  <th class=" c3" id="c3">
+
+  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=1&amp;HSP_SORT=1" class="dcs" title="Sort by max score">Max score</a>
+  </th>
+  <th class=" c4" id="c4">
+  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=2&amp;HSP_SORT=1" class="dcs" title="Sort by total score">Total score</a>
+  </th>
+  <th class=" c5" id="c5">
+  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=4&amp;HSP_SORT=0" class="dcs" title="Sort by query coverage">Query cover</a>
+  </th>
+  <th class="sel c6" id="c6">
+  <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=0&amp;HSP_SORT=0" class="dcs" title="Sort by E value">E value</a>
+  </th>
+  <th class="c7" id="c7">
+<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;DISPLAY_SORT=3&amp;HSP_SORT=3" class="dcs" title="Sort by ident">Ident</a>
+</th>
+
+  <th class="c1" id="c8">Accession</th>
+</tr>
+</thead>
+<tbody>
+<tr id="dtr_557804451" ind="1" class="odd dflLnk">
+<td class="l c0"><span class="ind">1</span><input id="chk_1" class="cb" name="getSeqGi" value="557804451" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_1" class="accsb">Select seq pdb|3J5A|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="1" accs="pdb|3J5A|A" seqfsta="gi|557804451" gi="557804451" seqid="557804451" id="deflnDesc_1" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804451">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nucltop&amp;blast_rank=1&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J5A_A">3J5A_A</a>
+</td>
+</tr><tr id="dtr_557804395" ind="2" class="even dflLnk">
+<td class="l c0"><span class="ind">2</span><input id="chk_2" class="cb" name="getSeqGi" value="557804395" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_2" class="accsb">Select seq pdb|3J58|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="2" accs="pdb|3J58|A" seqfsta="gi|557804395" gi="557804395" seqid="557804395" id="deflnDesc_2" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804395">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nucltop&amp;blast_rank=2&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J58_A">3J58_A</a>
+</td>
+</tr><tr id="dtr_557804339" ind="3" class="odd dflLnk">
+<td class="l c0"><span class="ind">3</span><input id="chk_3" class="cb" name="getSeqGi" value="557804339" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_3" class="accsb">Select seq pdb|3J56|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="3" accs="pdb|3J56|A" seqfsta="gi|557804339" gi="557804339" seqid="557804339" id="deflnDesc_3" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804339">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nucltop&amp;blast_rank=3&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J56_A">3J56_A</a>
+</td>
+</tr><tr id="dtr_557804283" ind="4" class="even dflLnk">
+<td class="l c0"><span class="ind">4</span><input id="chk_4" class="cb" name="getSeqGi" value="557804283" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_4" class="accsb">Select seq pdb|3J54|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="4" accs="pdb|3J54|A" seqfsta="gi|557804283" gi="557804283" seqid="557804283" id="deflnDesc_4" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804283">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nucltop&amp;blast_rank=4&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J54_A">3J54_A</a>
+</td>
+</tr><tr id="dtr_557804227" ind="5" class="odd dflLnk">
+<td class="l c0"><span class="ind">5</span><input id="chk_5" class="cb" name="getSeqGi" value="557804227" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_5" class="accsb">Select seq pdb|3J52|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="5" accs="pdb|3J52|A" seqfsta="gi|557804227" gi="557804227" seqid="557804227" id="deflnDesc_5" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804227">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nucltop&amp;blast_rank=5&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J52_A">3J52_A</a>
+</td>
+</tr><tr id="dtr_557804195" ind="6" class="even dflLnk">
+<td class="l c0"><span class="ind">6</span><input id="chk_6" class="cb" name="getSeqGi" value="557804195" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_6" class="accsb">Select seq pdb|3J51|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="6" accs="pdb|3J51|A" seqfsta="gi|557804195" gi="557804195" seqid="557804195" id="deflnDesc_6" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804195">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804195?report=genbank&amp;log$=nucltop&amp;blast_rank=6&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J51_A">3J51_A</a>
+</td>
+</tr><tr id="dtr_557804163" ind="7" class="odd dflLnk">
+<td class="l c0"><span class="ind">7</span><input id="chk_7" class="cb" name="getSeqGi" value="557804163" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_7" class="accsb">Select seq pdb|3J50|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="7" accs="pdb|3J50|A" seqfsta="gi|557804163" gi="557804163" seqid="557804163" id="deflnDesc_7" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804163">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804163?report=genbank&amp;log$=nucltop&amp;blast_rank=7&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J50_A">3J50_A</a>
+</td>
+</tr><tr id="dtr_557804083" ind="8" class="even dflLnk">
+<td class="l c0"><span class="ind">8</span><input id="chk_8" class="cb" name="getSeqGi" value="557804083" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_8" class="accsb">Select seq pdb|3J4X|A</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="8" accs="pdb|3J4X|A" seqfsta="gi|557804083" gi="557804083" seqid="557804083" id="deflnDesc_8" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804083">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)</a>
+</div>
+</td>
+<td class="c3">32.2</td>
+<td class="c4">77.3</td>
+<td class="c5">100%</td>
+<td class="c6">8e-04</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804083?report=genbank&amp;log$=nucltop&amp;blast_rank=8&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J4X_A">3J4X_A</a>
+</td>
+</tr><tr id="dtr_485601478" ind="9" class="odd dflLnk">
+<td class="l c0"><span class="ind">9</span><input id="chk_9" class="cb" name="getSeqGi" value="485601478" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_9" class="accsb">Select seq pdb|3J3F|5</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a title="Go to alignment for Chain 5, Structure Of The H. Sapiens 60s Rrna" class="deflnDesc" hsp="8" len="63" ind="9" accs="pdb|3J3F|5" seqfsta="gi|485601478" gi="485601478" seqid="485601478" id="deflnDesc_9" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601478">Chain 5, Structure Of The H. Sapiens 60s Rrna</a>
+</div>
+</td>
+<td class="c3">18.3</td>
+<td class="c4">  128</td>
+<td class="c5">100%</td>
+<td class="c6">   12</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601478?report=genbank&amp;log$=nucltop&amp;blast_rank=9&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3F_5">3J3F_5</a>
+</td>
+</tr><tr id="dtr_485601474" ind="10" class="even dflLnk">
+<td class="l c0"><span class="ind">10</span><input id="chk_10" class="cb" name="getSeqGi" value="485601474" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_10" class="accsb">Select seq pdb|3J3E|5</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a title="Go to alignment for Chain 5, Structure Of The D. Melanogaster 60s Rrna" class="deflnDesc" hsp="4" len="31" ind="10" accs="pdb|3J3E|5" seqfsta="gi|485601474" gi="485601474" seqid="485601474" id="deflnDesc_10" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601474">Chain 5, Structure Of The D. Melanogaster 60s Rrna</a>
+</div>
+</td>
+<td class="c3">18.3</td>
+<td class="c4">63.4</td>
+<td class="c5">100%</td>
+<td class="c6">   12</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601474?report=genbank&amp;log$=nucltop&amp;blast_rank=10&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3E_5">3J3E_5</a>
+</td>
+</tr><tr id="dtr_357380483" ind="11" class="odd dflLnk">
+<td class="l c0"><span class="ind">11</span><input id="chk_11" class="cb" name="getSeqGi" value="357380483" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_11" class="accsb">Select seq pdb|3J0O|8</label></td>
+<td class="lim l c2">
+<div class="lim n">
+<a title="Go to alignment for Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2" class="deflnDesc" hsp="1" len="9" ind="11" accs="pdb|3J0O|8" seqfsta="gi|357380483" gi="357380483" seqid="357380483" id="deflnDesc_11" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_357380483">Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2</a>
+</div>
+</td>
+<td class="c3">18.3</td>
+<td class="c4">18.3</td>
+<td class="c5">56%</td>
+<td class="c6">   12</td><td class="c7">100%</td>
+<td class="c1 l lim">
+<a href="http://www.ncbi.nlm.nih.gov/nucleotide/357380483?report=genbank&amp;log$=nucltop&amp;blast_rank=11&amp;RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J0O_8">3J0O_8</a>
+</td>
+</tr>
+</tbody>
+</table>
+</div></div>
+<!--</pre>  -->
+</div><!--/#descriptions-->
+</div><!-- descrInfo -->
+</div><!--ARIA-->
+</div>
+</form><!-- this is the end tag for the <form in blastcgi templates -->
+<form id="dwdlSubmit" action="" method="post" class="getseq">
+<input name="" value="" id="selDnSeqs" type="hidden">
+</form>
+<form class="getseq" method="post" seqsform="getSeqAlignment1" action="http://www.ncbi.nlm.nih.gov/sites/entrez" target="lnkPHWP1JNZ014" id="submitterTop">
+<input name="db" value="Nucleotide" type="hidden">
+<input id="selSeqs" name="term" value="" type="hidden">
+<input name="doptcmdl" value="docsum" type="hidden">
+<input name="cmd" value="search" type="hidden">
+</form>
+<form class="getseq" method="get" action="http://www.ncbi.nlm.nih.gov/projects/sviewer/" target="lnkPHWP1JNZ014" id="sbmtGraphics">
+<input id="ridParam" value="PHWP1JNZ014" type="hidden">
+<input id="seqViewParams" name="RID" value="" type="hidden">
+<input name="appname" value="ncbiblast" type="hidden">
+<input name="link_loc" value="fromDescr" type="hidden">
+<input name="tracks" value="[key:sequence_track,ShowLabel:true]" type="hidden">
+<input name="id" value="" type="hidden">
+</form>
+<form class="getseq" method="post" action="http://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl|59987&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;ns=100" id="sbmtTreeView" target="lnkPHWP1JNZ014">
+<input id="selSeqsTr" name="sequenceSet" value="" type="hidden">
+<input id="scrWidth" name="screenWidth" value="" type="hidden">
+<input id="scrHeight" name="screenHeight" value="" type="hidden">
+</form>
+<form class="getseq" method="post" action="?CMD=submit&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl|59987&amp;numSeqs=100" id="sbmtMultiAln" target="lnkPHWP1JNZ014">
+<input id="selSeqsMl" name="sequenceSet" value="" type="hidden">
+</form>
+<form class="getseq" enctype="text/plain" method="post" action="http://blast.ncbi.nlm.nih.gov/blast/SEQDUMP/seqdump.cgi" id="sbmtFASTA">
+<input name="RID" value="PHWP1JNZ014" type="hidden">
+<input name="DATABASE" value="" type="hidden">
+<input name="ALIGNDB_BATCH_ID" value="" type="hidden">
+<input name="ALIGNDB_MASTER_ALIAS" value="" type="hidden">
+<input name="ALIGNDB_CGI_HOST" value="" type="hidden">
+<input name="ALIGNDB_CGI_PATH" value="" type="hidden">
+<input name="SERVICE_TYPE" value="plain" type="hidden">
+<input name="DBTYPE" value="nucl" type="hidden">
+<input name="DOWNLOAD_TYPE" value="" type="hidden">
+<input name="ALIGN_SEQ_LIST" value="" type="hidden">
+</form><!-- used in redesign -->
+<iframe id="RSIFrameAln" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="NCBI%20Blast%20reference%20example_files/plinkcgi_002.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe>
+<div id="alignView" class=" ">
+<h2 class="resArr">
+<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showAlign" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="alignInfo" title="Show/hide Alignments">
+<span class="ui-ncbitoggler-master-text">Alignments</span>
+<span class="ui-icon ui-icon-plus-minus-big-open"></span>
+</a>
+</h2>
+
+<div class="ui-helper-reset" aria-live="assertive">
+<div aria-hidden="false" id="alignInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
+<div id="alignments" class="blRes">
+<span id="alnStart"></span><div seqlist="gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227" indexes="1-5" id="alnShow_1" class="alnMsg"><div class="alnMsgS hidden" id="alnMsg_1">Loading alignment...<span class="db"> for sequences gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227 Reading indexes 1-5</span></div><div id="alnShowReal_1" class="alnMsgR"><form name="getSeqAlignment1">
+<div class="alnHdr cnf" id="alnHdr_557804451" seqid="557804451" accs="pdb|3J5A|A">
+<a name="557804451"></a>
+<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804451" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804451" title="Download information for pdb|3J5A|A"><span>Download</span></a>
+<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804451" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
+<div><input seqfsta="gi|557804451" name="dwn_557804451" checked="checked" id="dwFST_557804451" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804451">FASTA (complete sequence)</label></div>
+<div><input seqfsta="gi|557804451" name="dwn_557804451" id="dwFSTAl_557804451" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804451">FASTA (aligned sequences)</label></div>
+<div class=""><input name="dwn_557804451" id="dwGenBank_557804451" getgi="557804451" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804451">GenBank (complete sequence)</label></div>
+<div>
+<button class="cfg" id="dw_cont_557804451">Continue</button>
+<button class="cfg cnc">Cancel</button>
+</div>
+</div> <!-- dsDownload -->
+<span class="csLinks" id="csLinks_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics">Graphics</a></span>
+
+<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
+<select id="sa_557804451" onchange="SortHSPAlnSel(event,this)">
+<option selected="selected" value="0">E value</option>
+<option value="1"> Score</option>
+<option value="3">Percent identity</option>
+<option value="2">Query start position</option>
+<option value="4">Subject start position</option>
+</select>
+</div>
+<span class="alnSeqLinks">
+<a title="Go to next alignment for pdb|3J58|A" class="gbd toolsCtr navNext" ref="ordinalpos=1&amp;currseq=557804451" id="alnNxt_557804451" onclick="goToNextAlign('dtr_557804451',true);"><span>Next</span></a>
+<a disabled="disabled" class="gbd toolsCtr navPrev" ref="ordinalpos=1&amp;currseq=557804451" id="alnPrv_557804451" onclick="goToNextAlign('dtr_557804451',false);"><span>Previous</span></a>
+<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J5A|A" id="alnDsc_557804451" onclick="goToDefLine('dtr_557804451');" href="#dtr_557804451"><span>Descriptions</span></a>
+</span>
+</div>
+<div class="oneSeqAln" id="aln_557804451">
+<div id="dln_557804451">
+<div class="dlfRow">
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)
+<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J5A|A">pdb|3J5A|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
+</div>
+</div>
+<div class="relInf" id="relInf_557804451"><label>Related Information</label></div>
+<!--
+<pre>
+<@aln_gene_info@>
+</pre>
+-->
+<div class="alnAll" id="alnAll_557804451"><div id="hd_557804451_1">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
+<span id="hsp557804451_1" class="alnParLinks">
+<a init="on" class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack hidden" href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #1</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>32.2 bits(16)</td>
+<td>8e-04<span class="sumN ">()</span></td>
+<td>16/16(100%)</td>
+<td>0/16(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804451_1">
+<pre>Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+</pre>
+</div>
+<div id="hd_557804451_2">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
+<span id="hsp557804451_2" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #2</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>16.4 bits(8)</td>
+<td>   47<span class="sumN ">()</span></td>
+<td>8/8(100%)</td>
+<td>0/8(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804451_2">
+<pre>Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+</pre>
+</div>
+<div id="hd_557804451_3">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
+<span id="hsp557804451_3" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #3</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804451_3">
+<pre>Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+</pre>
+</div>
+<div id="hd_557804451_4">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
+<span id="hsp557804451_4" class="alnParLinks">
+<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #4</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804451_4">
+<pre>Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+</pre>
+</div>
+</div> <!-- alnAll_557804451 -->
+</div> <!-- aln_557804451 -->
+<div class="alnHdr cnf" id="alnHdr_557804395" seqid="557804395" accs="pdb|3J58|A">
+<a name="557804395"></a>
+<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804395" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804395" title="Download information for pdb|3J58|A"><span>Download</span></a>
+<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804395" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
+<div><input seqfsta="gi|557804395" name="dwn_557804395" checked="checked" id="dwFST_557804395" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804395">FASTA (complete sequence)</label></div>
+<div><input seqfsta="gi|557804395" name="dwn_557804395" id="dwFSTAl_557804395" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804395">FASTA (aligned sequences)</label></div>
+<div class=""><input name="dwn_557804395" id="dwGenBank_557804395" getgi="557804395" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804395">GenBank (complete sequence)</label></div>
+<div>
+<button class="cfg" id="dw_cont_557804395">Continue</button>
+<button class="cfg cnc">Cancel</button>
+</div>
+</div> <!-- dsDownload -->
+<span class="csLinks" id="csLinks_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics">Graphics</a></span>
+
+<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
+<select id="sa_557804395" onchange="SortHSPAlnSel(event,this)">
+<option selected="selected" value="0">E value</option>
+<option value="1"> Score</option>
+<option value="3">Percent identity</option>
+<option value="2">Query start position</option>
+<option value="4">Subject start position</option>
+</select>
+</div>
+<span class="alnSeqLinks">
+<a title="Go to next alignment for pdb|3J56|A" class="gbd toolsCtr navNext" ref="ordinalpos=2&amp;currseq=557804395" id="alnNxt_557804395" onclick="goToNextAlign('dtr_557804395',true);"><span>Next</span></a>
+<a title="Go to previous alignment for pdb|3J5A|A" class="gbd toolsCtr navPrev" ref="ordinalpos=2&amp;currseq=557804395" id="alnPrv_557804395" onclick="goToNextAlign('dtr_557804395',false);"><span>Previous</span></a>
+<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J58|A" id="alnDsc_557804395" onclick="goToDefLine('dtr_557804395');" href="#dtr_557804395"><span>Descriptions</span></a>
+</span>
+</div>
+<div class="oneSeqAln" id="aln_557804395">
+<div id="dln_557804395">
+<div class="dlfRow">
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)
+<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J58|A">pdb|3J58|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
+</div>
+</div>
+<div class="relInf" id="relInf_557804395"><label>Related Information</label></div>
+<!--
+<pre>
+<@aln_gene_info@>
+</pre>
+-->
+<div class="alnAll" id="alnAll_557804395"><div id="hd_557804395_1">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
+<span id="hsp557804395_1" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack hidden" href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #1</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>32.2 bits(16)</td>
+<td>8e-04<span class="sumN ">()</span></td>
+<td>16/16(100%)</td>
+<td>0/16(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804395_1">
+<pre>Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+</pre>
+</div>
+<div id="hd_557804395_2">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
+<span id="hsp557804395_2" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #2</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>16.4 bits(8)</td>
+<td>   47<span class="sumN ">()</span></td>
+<td>8/8(100%)</td>
+<td>0/8(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804395_2">
+<pre>Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+</pre>
+</div>
+<div id="hd_557804395_3">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
+<span id="hsp557804395_3" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #3</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804395_3">
+<pre>Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+</pre>
+</div>
+<div id="hd_557804395_4">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
+<span id="hsp557804395_4" class="alnParLinks">
+<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #4</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804395_4">
+<pre>Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+</pre>
+</div>
+</div> <!-- alnAll_557804395 -->
+</div> <!-- aln_557804395 -->
+<div class="alnHdr cnf" id="alnHdr_557804339" seqid="557804339" accs="pdb|3J56|A">
+<a name="557804339"></a>
+<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804339" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804339" title="Download information for pdb|3J56|A"><span>Download</span></a>
+<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804339" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
+<div><input seqfsta="gi|557804339" name="dwn_557804339" checked="checked" id="dwFST_557804339" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804339">FASTA (complete sequence)</label></div>
+<div><input seqfsta="gi|557804339" name="dwn_557804339" id="dwFSTAl_557804339" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804339">FASTA (aligned sequences)</label></div>
+<div class=""><input name="dwn_557804339" id="dwGenBank_557804339" getgi="557804339" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804339">GenBank (complete sequence)</label></div>
+<div>
+<button class="cfg" id="dw_cont_557804339">Continue</button>
+<button class="cfg cnc">Cancel</button>
+</div>
+</div> <!-- dsDownload -->
+<span class="csLinks" id="csLinks_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics">Graphics</a></span>
+
+<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
+<select id="sa_557804339" onchange="SortHSPAlnSel(event,this)">
+<option selected="selected" value="0">E value</option>
+<option value="1"> Score</option>
+<option value="3">Percent identity</option>
+<option value="2">Query start position</option>
+<option value="4">Subject start position</option>
+</select>
+</div>
+<span class="alnSeqLinks">
+<a title="Go to next alignment for pdb|3J54|A" class="gbd toolsCtr navNext" ref="ordinalpos=3&amp;currseq=557804339" id="alnNxt_557804339" onclick="goToNextAlign('dtr_557804339',true);"><span>Next</span></a>
+<a title="Go to previous alignment for pdb|3J58|A" class="gbd toolsCtr navPrev" ref="ordinalpos=3&amp;currseq=557804339" id="alnPrv_557804339" onclick="goToNextAlign('dtr_557804339',false);"><span>Previous</span></a>
+<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J56|A" id="alnDsc_557804339" onclick="goToDefLine('dtr_557804339');" href="#dtr_557804339"><span>Descriptions</span></a>
+</span>
+</div>
+<div class="oneSeqAln" id="aln_557804339">
+<div id="dln_557804339">
+<div class="dlfRow">
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)
+<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J56|A">pdb|3J56|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
+</div>
+</div>
+<div class="relInf" id="relInf_557804339"><label>Related Information</label></div>
+<!--
+<pre>
+<@aln_gene_info@>
+</pre>
+-->
+<div class="alnAll" id="alnAll_557804339"><div id="hd_557804339_1">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
+<span id="hsp557804339_1" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack hidden" href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #1</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>32.2 bits(16)</td>
+<td>8e-04<span class="sumN ">()</span></td>
+<td>16/16(100%)</td>
+<td>0/16(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804339_1">
+<pre>Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+</pre>
+</div>
+<div id="hd_557804339_2">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
+<span id="hsp557804339_2" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #2</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>16.4 bits(8)</td>
+<td>   47<span class="sumN ">()</span></td>
+<td>8/8(100%)</td>
+<td>0/8(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804339_2">
+<pre>Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+</pre>
+</div>
+<div id="hd_557804339_3">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
+<span id="hsp557804339_3" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #3</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804339_3">
+<pre>Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+</pre>
+</div>
+<div id="hd_557804339_4">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
+<span id="hsp557804339_4" class="alnParLinks">
+<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #4</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804339_4">
+<pre>Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+</pre>
+</div>
+</div> <!-- alnAll_557804339 -->
+</div> <!-- aln_557804339 -->
+<div class="alnHdr cnf" id="alnHdr_557804283" seqid="557804283" accs="pdb|3J54|A">
+<a name="557804283"></a>
+<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804283" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804283" title="Download information for pdb|3J54|A"><span>Download</span></a>
+<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804283" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
+<div><input seqfsta="gi|557804283" name="dwn_557804283" checked="checked" id="dwFST_557804283" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804283">FASTA (complete sequence)</label></div>
+<div><input seqfsta="gi|557804283" name="dwn_557804283" id="dwFSTAl_557804283" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804283">FASTA (aligned sequences)</label></div>
+<div class=""><input name="dwn_557804283" id="dwGenBank_557804283" getgi="557804283" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804283">GenBank (complete sequence)</label></div>
+<div>
+<button class="cfg" id="dw_cont_557804283">Continue</button>
+<button class="cfg cnc">Cancel</button>
+</div>
+</div> <!-- dsDownload -->
+<span class="csLinks" id="csLinks_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics">Graphics</a></span>
+
+<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
+<select id="sa_557804283" onchange="SortHSPAlnSel(event,this)">
+<option selected="selected" value="0">E value</option>
+<option value="1"> Score</option>
+<option value="3">Percent identity</option>
+<option value="2">Query start position</option>
+<option value="4">Subject start position</option>
+</select>
+</div>
+<span class="alnSeqLinks">
+<a title="Go to next alignment for pdb|3J52|A" class="gbd toolsCtr navNext" ref="ordinalpos=4&amp;currseq=557804283" id="alnNxt_557804283" onclick="goToNextAlign('dtr_557804283',true);"><span>Next</span></a>
+<a title="Go to previous alignment for pdb|3J56|A" class="gbd toolsCtr navPrev" ref="ordinalpos=4&amp;currseq=557804283" id="alnPrv_557804283" onclick="goToNextAlign('dtr_557804283',false);"><span>Previous</span></a>
+<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J54|A" id="alnDsc_557804283" onclick="goToDefLine('dtr_557804283');" href="#dtr_557804283"><span>Descriptions</span></a>
+</span>
+</div>
+<div class="oneSeqAln" id="aln_557804283">
+<div id="dln_557804283">
+<div class="dlfRow">
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)
+<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J54|A">pdb|3J54|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
+</div>
+</div>
+<div class="relInf" id="relInf_557804283"><label>Related Information</label></div>
+<!--
+<pre>
+<@aln_gene_info@>
+</pre>
+-->
+<div class="alnAll" id="alnAll_557804283"><div id="hd_557804283_1">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
+<span id="hsp557804283_1" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack hidden" href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #1</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>32.2 bits(16)</td>
+<td>8e-04<span class="sumN ">()</span></td>
+<td>16/16(100%)</td>
+<td>0/16(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804283_1">
+<pre>Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+</pre>
+</div>
+<div id="hd_557804283_2">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
+<span id="hsp557804283_2" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #2</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>16.4 bits(8)</td>
+<td>   47<span class="sumN ">()</span></td>
+<td>8/8(100%)</td>
+<td>0/8(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804283_2">
+<pre>Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+</pre>
+</div>
+<div id="hd_557804283_3">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
+<span id="hsp557804283_3" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #3</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804283_3">
+<pre>Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+</pre>
+</div>
+<div id="hd_557804283_4">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
+<span id="hsp557804283_4" class="alnParLinks">
+<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #4</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804283_4">
+<pre>Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+</pre>
+</div>
+</div> <!-- alnAll_557804283 -->
+</div> <!-- aln_557804283 -->
+<div class="alnHdr cnf" id="alnHdr_557804227" seqid="557804227" accs="pdb|3J52|A">
+<a name="557804227"></a>
+<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804227" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804227" title="Download information for pdb|3J52|A"><span>Download</span></a>
+<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804227" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic">
+<div><input seqfsta="gi|557804227" name="dwn_557804227" checked="checked" id="dwFST_557804227" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804227">FASTA (complete sequence)</label></div>
+<div><input seqfsta="gi|557804227" name="dwn_557804227" id="dwFSTAl_557804227" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804227">FASTA (aligned sequences)</label></div>
+<div class=""><input name="dwn_557804227" id="dwGenBank_557804227" getgi="557804227" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;rettype=gb&amp;retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804227">GenBank (complete sequence)</label></div>
+<div>
+<button class="cfg" id="dw_cont_557804227">Continue</button>
+<button class="cfg cnc">Cancel</button>
+</div>
+</div> <!-- dsDownload -->
+<span class="csLinks" id="csLinks_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics">Graphics</a></span>
+
+<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
+<select id="sa_557804227" onchange="SortHSPAlnSel(event,this)">
+<option selected="selected" value="0">E value</option>
+<option value="1"> Score</option>
+<option value="3">Percent identity</option>
+<option value="2">Query start position</option>
+<option value="4">Subject start position</option>
+</select>
+</div>
+<span class="alnSeqLinks">
+<a title="Go to next alignment for pdb|3J51|A" class="gbd toolsCtr navNext" ref="ordinalpos=5&amp;currseq=557804227" id="alnNxt_557804227" onclick="goToNextAlign('dtr_557804227',true);"><span>Next</span></a>
+<a title="Go to previous alignment for pdb|3J54|A" class="gbd toolsCtr navPrev" ref="ordinalpos=5&amp;currseq=557804227" id="alnPrv_557804227" onclick="goToNextAlign('dtr_557804227',false);"><span>Previous</span></a>
+<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J52|A" id="alnDsc_557804227" onclick="goToDefLine('dtr_557804227');" href="#dtr_557804227"><span>Descriptions</span></a>
+</span>
+</div>
+<div class="oneSeqAln" id="aln_557804227">
+<div id="dln_557804227">
+<div class="dlfRow">
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)
+<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J52|A">pdb|3J52|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
+</div>
+</div>
+<div class="relInf" id="relInf_557804227"><label>Related Information</label></div>
+<!--
+<pre>
+<@aln_gene_info@>
+</pre>
+-->
+<div class="alnAll" id="alnAll_557804227"><div id="hd_557804227_1">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
+<span id="hsp557804227_1" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack hidden" href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #1</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>32.2 bits(16)</td>
+<td>8e-04<span class="sumN ">()</span></td>
+<td>16/16(100%)</td>
+<td>0/16(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804227_1">
+<pre>Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+</pre>
+</div>
+<div id="hd_557804227_2">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
+<span id="hsp557804227_2" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #2</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>16.4 bits(8)</td>
+<td>   47<span class="sumN ">()</span></td>
+<td>8/8(100%)</td>
+<td>0/8(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804227_2">
+<pre>Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+</pre>
+</div>
+<div id="hd_557804227_3">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
+<span id="hsp557804227_3" class="alnParLinks">
+<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #3</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804227_3">
+<pre>Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+</pre>
+</div>
+<div id="hd_557804227_4">
+<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
+<span id="hsp557804227_4" class="alnParLinks">
+<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a>
+<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&amp;currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a>
+<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a>
+</span>
+</div>
+<table class="alnParams">
+<caption class="hdnHeader">Alignment statistics for match #4</caption>
+<tbody><tr>
+<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
+</tr>
+<tr>
+<td>14.4 bits(7)</td>
+<td>  186<span class="sumN ">()</span></td>
+<td>7/7(100%)</td>
+<td>0/7(0%)</td>
+<td>Plus/Plus</td>
+<td class="aln_frame "></td>
+</tr></tbody></table>
+<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
+</div>
+<div id="ar_557804227_4">
+<pre>Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+</pre>
+</div>
+</div> <!-- alnAll_557804227 -->
+</div> <!-- aln_557804227 -->
+</form>
+
+</div></div>
+<pre>
+</pre>
+</div><!--/#alignments-->
+</div><!-- alignInfo -->
+</div><!--ARIA-->
+
+</div><!-- alignView -->
+<form><!-- this is the start tag for the </form in blastcgi templates - needs to be changed-->
+<!-- not used - verify -->
+<!-- not used - verify -->
+
+
+                </form>
+				</div><!-- /#content -->
+				<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="reformat" id="reformat">
+				   <input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden">
+				   <input name="ENTREZ_QUERY" value="" type="hidden">
+                   <input name="CDD_RID" value="" type="hidden">
+                   <input name="CDD_SEARCH_STATE" value="" type="hidden">
+                   <input name="RID" value="PHWP1JNZ014" type="hidden">
+				   <input name="STEP_NUMBER" value="" type="hidden">
+				   <input name="CMD" value="Web" type="hidden">
+				   <input name="PAGE_TYPE" value="BlastFormatting" type="hidden">
+
+				   <!-- TO DO: test all of those changes -->
+				   <!-- Psi blast params  PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> -->
+				   <!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> -->
+				   <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
+                 </form>
+
+                 <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="setSavedOptions" id="setSavedOptions">
+					<input name="PAGE_TYPE" value="BlastSearch" type="hidden">
+					<input name="VIEW_SEARCH" value="true" type="hidden">
+					<input name="CMD" value="Web" type="hidden">
+					<!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
+				</form>
+
+				<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="saveOptions" id="saveOptions">
+					<input name="SAVE" value="true" type="hidden">
+					<input name="CMD" value="GetSaved" type="hidden">
+					<!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from formatter> -->
+				</form>
+        </div><!-- /#content-wrap -->
+
+
+<div id="footer">
+   <div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
+   <p id="orgns">
+      <a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
+      <a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
+      <a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
+      <a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
+   </p>
+
+   <p>
+      <a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html" title="NCBI intellectual property statement">Copyright</a> |
+      <a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer" title="About liability, endorsements, external links, pop-up advertisements">Disclaimer</a> |
+      <a href="http://www.nlm.nih.gov/privacy.html" title="NLM privacy policy">Privacy</a> |
+      <a href="http://www.nlm.nih.gov/accessibility.html" title="About using NCBI resources with assistive technology">Accessibility</a> |
+      <a href="http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html" title="How to get help, submit data, or provide feedback">Contact</a> |
+      <a href="mailto:blast-help@ncbi.nlm.nih.gov" title="How to get help, submit data, or provide feedback">Send feedback</a>
+   </p>
+</div>
+   </div><!--/#wrap-->
+
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/utils.js"></script>
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/toggle.js"></script>
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/remote_data_provider.js"></script>
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/results.js"></script><link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/firefox-descriptions.css" media="screen">
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/blast.js"></script>
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/format.js"></script>
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/formatRes.js"></script>
+<script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/InstrumentPageStarterJS.js"></script>
+
+
+
+<div class="ui-ncbiautocomplete-holder shadow" aria-live="assertive"><ul class="ui-ncbiautocomplete-options" role="listbox" aria-activedescendant=""></ul><div class="ui-ncbiautocomplete-actions shadow"><a href="#" class="ui-ncbiautocomplete-link-pref">Preferences</a><a href="#" class="ui-ncbiautocomplete-link-off">Turn off</a></div></div><ul class="print-log"><li></li></ul></body></html>
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+function(c){c=c.originalEvent;var e=d(c);jQuery(c.target);(new Date).getTime();(new Date).getTime();var g=jQuery(c.target),k=g.id||"",j=g.name||"",t=g.sid||"",y=g.href||"",A=g.innerText||g.textContent||"";if(A.length>50)A=A.substr(0,50);var B=g.getAttribute?g.getAttribute("ref")||g.ref||"":"",w=g.className?g.className.replace(/^\s?/,"").replace(/\s?$/,"").split(/\s/g).join(",")||"":"";c=[];var v=[],u=g.parentNode;if(u)for(var s=0;s<6&&u!==null;s++){(parId=u.id)&&c.push(parId);if(parClassName=u.className)v=
+v.concat(parClassName.split(/\s/));u=u.parentNode}u=ncbi.sg.getInstance();var f=u.currentPageHitId||"";f=[];k.length>0&&f.push("link_id="+encodeURIComponent(k));j.length>0&&f.push("link_name="+encodeURIComponent(j));t.length>0&&f.push("link_sid="+encodeURIComponent(t));y.length>0&&f.push("link_href="+encodeURIComponent(y));A.length>0&&f.push("link_text="+encodeURIComponent(A));w.length>0&&f.push("link_class="+encodeURIComponent(w));s=u.getBrowserWidthHeight();s.width!==null&&f.push("browserwidth="+
+encodeURIComponent(s.width));s.height!==null&&f.push("browserheight="+encodeURIComponent(s.height));for(var i in e){s=e[i];s!==undefined&&f.push(i.toLowerCase()+"="+s.toString())}f.push("jsevent=hovernext");B.length>0&&f.push(B);if(typeof jQuery!=="undefined")if(e=jQuery(g).attr("sg")){e=e.split(/\}\s*,\s*\{/);for(s=0;s<e.length;s++){g=e[s].match(/name\s*:\s*'(.+)',\s*selector\s*:\s*'(.+)'/);if(g.length===3){i="cust_"+g[1];g=jQuery(g[2]).val();f.push(i+"="+encodeURIComponent(g))}}}c.length>0&&f.push("ancestorId="+
+c.join(","));v.length>0&&f.push("ancestorClassName="+v.join(",").replace(/\s+/g," ").replace(/(^\s|\s$)/g,""));u.addScrollDetailsAr(f,1800-f.join("&").length,true);c=f.join("&");f=ncbi.sg.getInstance().currentPageHitId||"";c+="&ncbi_phid="+f;ncbi.sg.getInstance()._storeNext("hovernext",c,null)});jQuery(document).on("mouseup mousedown",function(c){!jQuery(c.target).is("a[ref*='itool=Abstract-nondef']")&&jQuery(c.target).parents("a[ref*='itool=Abstract-nondef']").length==0&&!jQuery(c.target).is("#disc_col a")&&
+jQuery(c.target).parents("#disc_col a").length==0&&ncbi.sg.getInstance().setCookie("hovernext","")})}});
+
+;
+// This code creates window.console if it doesn't exist.
+// It also creates stub functions for those functions that are missing in window.console.
+// (Safari implements some but not all of the firebug window.console methods--this implements the rest.)
+(function() {
+    var names = [ "log", "debug", "info", "warn", "error", "assert", "dir", "dirxml", "group",
+                  "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd" ];
+
+    if (typeof(console) === 'undefined' || typeof console === "function" ) {
+      //"typeof function" is needed see PP-769
+      console = {};
+    }
+
+    for (var i = 0; i < names.length; ++i) {
+       if (typeof(console[names[i]]) === 'undefined') {
+          console[names[i]] = function() { return false; };
+       }
+    }
+    ncbi.sg.getInstance().init();
+})();
Binary file NCBI Blast reference example_files/addOrg.jpg has changed
Binary file NCBI Blast reference example_files/black.gif has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/blast.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,308 @@
+
+function printfire()
+{
+    // Firefox
+    if (document.createEvent && window.dispatchEvent) {
+        printfire.args = arguments;
+        var ev = document.createEvent("Events");
+        ev.initEvent("printfire", false, true);
+        window.dispatchEvent(ev);
+    }
+}
+//This functions handle setting defaults for protein or nulcleotide suite  search page when
+//one of blast program radio buttons is clicked - not used now
+function AdjustMoreOptionsStyle()
+{
+	var optsEl = document.getElementById("moreopts");
+	if(optsEl && optsEl.style.height != "0px") {
+		optsEl.style.height = optsEl.scrollHeight + "px";
+	}
+}
+
+//Strip (taxid:XXX) from organism list selection
+//sgRunFunc="AdjustOrganism();"
+function AdjustOrganism()
+{
+	var words = $("qorganism").value.split(" (taxid");
+	$("qorganism").value = words[0];
+}
+
+
+/* JS Common to all BLAST pages */
+
+
+function setResultsTarget()
+{
+	//var newWin = $("newwin");
+	var newWin = this;
+	var searchFrm = $(newWin.getAttribute("form"));
+	if(newWin && newWin.checked == true) {
+		if(newWin.getAttribute("winType") == "random") {
+			searchFrm.target = "Blast_Results_for_" + Math.floor(Math.pow(10,10) *Math.random());
+		}
+		else {
+			searchFrm.target = $("resPageTarget").value;
+		}
+	}
+	else {
+		searchFrm.target = "";
+	}
+}
+
+function diffFromDefault(elem)
+{
+    var currentVal = "";
+    var ret = 0;
+
+    if (!(elem)) return;
+    var defVal = elem.getAttribute("defVal"); //Default value
+    var elShowDiff = utils.getParent(elem);
+    if(!elem.type) {//div element for example
+        //Check if parent elem has "hide" class
+        if(utils.hasClass(utils.getParent(elem), "hide")) {
+            currentVal = "hide";
+        }
+        else {
+            currentVal = "show";
+        }
+        elShowDiff = elem;
+    }
+    else if(elem.type == "select-one") {
+        if(elem[elem.selectedIndex].value) currentVal = elem[elem.selectedIndex].value;
+        //If Default value is not specified - the first one in the selection list is the default
+        if (!defVal && elem[0].value) defVal = elem[0].value;
+    }
+    else if(elem.type == "select-multiple") {
+	    currentVal = "";//for now
+    }
+    else if(elem.type == "checkbox") {
+        //alert("defVal1=" + elem.id + " " + defVal);
+        //var defVal = elem.defVal; //Default value
+        //alert("defVal2=" + defVal);
+        if(elem.checked == true) currentVal = "checked"
+        else  currentVal = "unchecked";
+    }
+    else {
+        currentVal = elem.value;
+    }
+
+
+    var numdiff = parseInt($("NUM_DIFFS").value,10);
+    var optsNumDiff = parseInt($("NUM_OPTS_DIFFS").value,10);
+    if(defVal != currentVal) {
+        if(!utils.hasClass(elShowDiff, "nondef")) {
+            utils.addClass(elShowDiff, "nondef");
+            numdiff++;
+            if(utils.hasClass(elem,"opts")) optsNumDiff++;
+        }
+        ret = 1;
+    }
+    else {
+        if(utils.hasClass(elShowDiff, "nondef")) {
+            utils.removeClass(elShowDiff, "nondef");
+            //alert("noDiff-" + elem.id);
+            if(numdiff != 0) numdiff--;
+            if(utils.hasClass(elem,"opts")) optsNumDiff--;
+        }
+        ret=0;
+    }
+    $("NUM_DIFFS").value = numdiff;
+    $("NUM_OPTS_DIFFS").value = optsNumDiff;
+    if(numdiff > 0) {
+        $("diffMes").style.display = "inline";
+    }
+    else {
+        $("diffMes").style.display = "none";
+    }
+    //alert(elem.id + " " + $("NUM_DIFFS").value);
+    return ret;
+}
+
+function setDefalValue(elem)
+{
+    var currentVal;
+    var defVal = elem.getAttribute("defVal"); //Default value
+    if(elem.type == "select-one") {
+        //If Default value is not specified - the first one in the selection list is the default
+        if(!defVal) defVal = elem[0].value;
+        for(j=0; j < elem.options.length; j++) {
+		    if(elem.options[j].value == defVal) {
+		        elem.options[j].selected = true;
+		        break;
+		    }
+        }
+    }
+    else if(elem.type == "checkbox" || elem.type == "radio") {
+        if(!defVal) defVal = "checked";
+        if(defVal == "checked") elem.checked = true
+        else elem.checked = false;
+    }
+    else {
+        if(!defVal) defVal = "";
+        elem.value = defVal;
+    }
+
+    var elShowDiff = utils.getParent(elem);
+    if(utils.hasClass(elShowDiff, "nondef")) {
+        utils.removeClass(elShowDiff, "nondef");
+    }
+    //alert(elem.id + " " + $("NUM_DIFFS").value);
+}
+
+function newResultsWinInit() {
+    jQuery("[class='newwin']").each(function(index) {
+        utils.addEvent(this, "click", setResultsTarget, false);
+    });
+}
+
+function resetOrganismSuggest(orgEntryElem)
+{
+    //suggestHint is in the hidden field used for SRA
+    var defaultMessage = ($("suggestHint")) ? $("suggestHint").value : "Enter organism name or id--completions will be suggested";
+    var suggestHint = $("qorganism").getAttribute("suggestHint");
+    if(suggestHint) defaultMessage = suggestHint;
+    if(orgEntryElem.value == "") {
+        orgEntryElem.value = defaultMessage;
+    }
+    if(orgEntryElem.value == defaultMessage) {
+        utils.addClass(orgEntryElem,"orgHint");
+    }
+}
+
+function setupOrganismSuggest(orgEntryElem)
+{
+    resetOrganismSuggest(orgEntryElem);
+    utils.addEvent(orgEntryElem, "focus", function() {
+        clearOrgSuggest(orgEntryElem);
+     }, false);
+}
+
+function clearOrgSuggest(orgEntryElem)
+{
+    if(utils.hasClass(orgEntryElem,"orgHint")) {
+        orgEntryElem.value="";
+        utils.removeClass(orgEntryElem,"orgHint");
+    }
+}
+
+function InitCustomButton(bn)
+{
+  utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
+  utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
+  utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
+  utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);
+}
+
+function showHideElem(id,hide)
+{
+  if($(id)) {
+    if(hide) {
+	    if(!utils.hasClass($(id),"hidden")) utils.addClass($(id), "hidden");
+	}
+	else {
+	    if(utils.hasClass($(id),"hidden")) utils.removeClass($(id), "hidden");
+	}
+  }
+}
+
+function resetOrganismControls(orgEntryElem) {
+    resetOrganismSuggest(orgEntryElem);
+    if ($("orgExcl")) $("orgExcl").checked = false;
+    utils.replaceInHtml("", $("orgs"));
+    if ($("frOrgs")) utils.replaceInHtml("", $("frOrgs"));
+    if ($("numOrg")) $("numOrg").value = 1;
+}
+
+function AddOrgRow(e,orgName,exclName) {
+    e = e || window.event;
+    utils.preventDefault(e);
+    var checkedExclude = new Array();
+    var orgDict = jQuery($($("qorganism"))).ncbiautocomplete("option","dictionary");
+    orgDict = (!orgDict || orgDict == "") ? "taxids_sg" : orgDict;
+    var len = $("qorganism").getAttribute("size");
+
+    var newOrgFieldID = "qorganism" + $("numOrg").value;
+    var newOrgField = " <div><input name=\"" + orgName + $("numOrg").value + "\" size=\"" + len + "\" id=\"" + newOrgFieldID +
+                       "\" type=\"text\" data-jigconfig=\"dictionary:'" + orgDict + "'\" autocomplete=\"off\" class=\"jig-ncbiautocomplete multiOrg\" />";
+    if (exclName != "") {
+        newOrgField += "<span class=\"orgExcl\">" +
+                       "<input type=\"checkbox\" name=\"" + exclName + $("numOrg").value + "\" class=\"oExcl cb\" id=\"orgExcl" + $("numOrg").value + "\" />" +
+                       "<label for=\"orgExcl" + $("numOrg").value + "\" class=\"right oExclRl\">Exclude</label></span>";
+    }
+    newOrgField += "</div>";
+    if (navigator.userAgent.match(/ie/i)) {
+        for (i = 1; i < $("numOrg").value; i++) {
+            if ($("orgExcl" + i)) checkedExclude[i] = $("orgExcl" + i).checked;
+        }
+    }
+    if (!navigator.userAgent.match(/firefox/i)) {
+        jQuery($($(orgs))).append(newOrgField,true);
+    }
+    else {
+        utils.insertInHtml(newOrgField, $("orgs"));
+    }
+
+    if (navigator.userAgent.match(/ie/i)) {
+        for (i = 1; i < $("numOrg").value; i++) {
+            if ($("orgExcl" + i)) $("orgExcl" + i).checked = checkedExclude[i];
+        }
+    }
+    setupOrganismSuggest($(newOrgFieldID));
+    jQuery($($(newOrgFieldID))).ncbiautocomplete();
+    $("numOrg").value++;
+}
+
+function adjustOrgVal(orgEntryElem)
+{
+    //if (utils.hasClass($("searchForm").EQ_MENU, "orgHint")) $("searchForm").EQ_MENU.value = "";
+    clearOrgSuggest(orgEntryElem);
+    if ($("numOrg")) {
+        for (i = 1; i < $("numOrg").value; i++) {
+            if ($("qorganism" + i)) {
+                clearOrgSuggest($("qorganism" + i));
+            }
+        }
+    }
+}
+
+function getUrlCompForEntryField(elem) {
+    var url = "";
+    if (elem && elem.value != "") {
+        url = "&" + elem.name + "=" + escape(elem.value);
+    }
+    return url;
+}
+
+
+function getUrlCompForCheckedField(elem) {
+    var url = "";
+    if (elem && elem.checked) {
+        url = "&" + elem.name + "=" + elem.value;
+    }
+    return url;
+
+}
+
+function getUrlCompForOptionsField(elem) {
+    var url = "";
+    if (elem) {
+        url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
+    }
+    return url;
+}
+
+function getUrlCompForMultiOptionsField(elem) {
+    var url = "";
+    if (elem) {
+        for (i = 0; i < elem.options.length; i++) {
+            if (elem.options[i].selected) {
+                url += "&" + elem.name + "=" + elem.options[i].value;
+            }
+        }
+    }
+    return url;
+}
+
+
+utils.addEvent(window, 'load', newResultsWinInit, false);
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/blastReq.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,332 @@
+#msgR .info {
+background-color: #dfd;
+padding: 4px;
+border: solid 1px green;
+color: green;
+}
+
+dl.summary dt {
+float: left;
+width: 8em;
+clear:left;
+margin: 0;
+text-align: right;
+padding-right: 1em;
+color: #666;
+}
+
+dl.summary dd {
+padding-left: 0.5em;
+display: block;
+margin-left: 7em !important;
+margin: 0;
+}
+dl.summary dt, dl.summary dd {
+margin-bottom: 0.5em;
+}
+a.help
+{
+float:right;
+font-size: 110%;
+}
+
+dl.summary label {
+display: inline;
+}
+
+dl.summary tr th label {
+padding: 0;
+margin-right:0;
+}
+table.options {
+border: solid 1px #ccc;
+border-right: solid 1px #ccc;
+}
+
+table.options td,
+table.options td.frh {
+font-size: 90%;
+_font-size: 85%;
+}
+
+table.options label.rb {
+border-right: solid 1px #ccc;
+margin-right: 0.5em;
+padding-right: 2.0em;
+}
+
+table.options tr td {
+_font-size: 90%;
+padding-left: 0.5em;
+}
+
+table.options {
+/*border-collapse: collapse;*/
+margin-left: 0;
+padding-left: 0;
+width: 62em;
+}
+
+table.options td label {
+font-size: 90%;
+}
+
+table.options th label,
+table.options td label {
+margin-right: 0;
+_position: relative;
+_top: -0.1em;
+}
+
+table.options tr.hdr td,
+table.options tr.hdr th {
+padding: 2px;
+border: solid 1px #ccc;
+background-color: #ddd;
+}
+
+table.options td, table.options td.frh {
+padding: 0.25em 0;
+vertical-align: center;
+}
+
+table.options th {
+padding-right: 1em;
+text-align: right;
+padding-left: 1em;
+}
+
+/*
+*:focus{
+background-color: white !important;
+}
+*/
+
+table.options select,table.options input, #graphic input{
+border: solid 1px #888;
+padding: 1px;
+}
+
+select {
+font-size: 90%;
+}
+
+select option {
+padding-right: 0.5em;
+}
+
+input.cb, table.options input.cb {
+border: none;
+}
+
+select {
+margin-right:1em;
+}
+
+table.options tr {
+background-color: #eee;
+}
+
+table.options tr.odd {
+background-color: #e0e0e0;
+}
+
+table.options th {
+
+background-color: white;
+}
+
+table.options tr.paramSet td
+{
+	border-top: solid 2px white;
+}
+
+
+
+
+.resetAll
+{
+font-weight: normal;
+padding: 0.5em;
+font-size: 90%;
+margin-left:5em;
+}
+
+.button {
+background-color: #ccc;
+padding: 0.25em 0.25em;
+color: black;
+border: outset 3px #eee;
+_border: outset 3px #eee;
+font-size: 90%;
+_padding:0;
+font-weight: bold;
+height:25px;
+_height:22px;
+}
+
+.fbtn {
+margin-bottom: 0.5em;
+}
+
+.note {
+font-size: 80%;
+color: green;
+background-color: #ffc;
+margin-left: 2em;
+padding: 3px;
+}
+.instr {
+   margin-left: 1em;
+   color: #666;
+font-size: 90%;
+}
+.smaller {
+font-size: 90%;
+font-weight: normal;
+}
+
+/* Results Page styles */
+
+#ridRes
+{
+	background-color: #FC9;
+	padding:5px 5px;
+}
+
+
+span dd.hidden,dt.hidden,dd.hidden span
+{
+	display:none;
+}
+
+dl.query .query,
+dl.title .title,
+dl.entrez .entrez,
+dl.db .db
+{
+	display:block;
+}
+
+
+dl.entrez span.entrez
+{
+	display:inline;
+}
+
+.hidden {
+display: none;
+}
+.hide {
+display: none;
+}
+.shown {
+display: block;
+}
+
+
+
+table.megaBlast tr.psiBlast,
+table.blastn tr.psiBlast,
+table.blastx tr.psiBlast,
+table.tblastn tr.psiBlast,
+table.tblastx tr.psiBlast,
+table.discoMegablast tr.psiBlast
+{
+display: none;
+}
+
+
+table.GlobalAln .xgl,
+body.GlobalAln div.xgl,
+body.GlobalAln dt.xgl,
+body.GlobalAln dd.xgl,
+body.GlobalAln span.xgl,
+body.GlobalAln table.xgl
+{
+display: none;
+}
+
+.dispType
+{
+	/*background-color:White;
+	border:solid 1px black;*/
+	border-top:solid 2px gray;
+	border-left:solid 2px gray;
+	font-size:90%;
+	padding-left:2px;
+
+}
+
+.newwin {
+border: none;
+}
+
+table.options .helplink
+{
+    font-weight:bold;
+    position:absolute;
+    right:0;
+}
+
+div#query label
+{
+    display: inline;
+    font-weight:bold;
+    padding-right:1em;
+}
+#NEW_VIEW
+{
+    _margin-left:-2px;
+}
+
+
+table.blastp *.blastn,
+table.psiBlast *.blastn,
+table.phiBlast *.blastn,
+table.blastx *.blastn,
+table.tblastn *.blastn,
+table.tblastx *.blastn
+{
+display: none;
+}
+
+#formatTable th.col1 {
+width: 8em;
+vertical-align: top;
+}
+/*
+#formatTable .helplink span {
+position: relative;
+}
+*/
+#org
+{
+    margin-top:2em;
+}
+#qorganism
+{
+    /*display:block;*/
+}
+.fi
+{
+    position:relative;
+}
+
+a#organismHelp
+{
+    margin-top:-1.5em;
+}
+
+table.options tr.paramSet td.hd {
+padding-right: 1em;
+text-align: right;
+padding-left: 1em;
+background-color:White;
+font-weight:bold;
+border-top:none;
+}
+.oExcl
+{
+    margin-left:2px;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/blastRes.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,262 @@
+a#refPage
+{
+	margin-left:3em;
+}
+
+a.resLink
+{
+	margin-left:1em;
+	display:none;
+}
+
+a.resLinkhidden
+{
+	display:none;
+}
+
+
+#cddResults
+{
+	float:right;
+	margin-top:-2em;
+	margin-right:1em;
+	color:#336699;
+    font-size:100%;
+}
+
+#cddResults.showing {
+   background-image: url(images/down.gif);
+}
+
+
+
+div.inlineDiv
+{
+	display:inline;
+}
+
+span.reslink
+{
+	display:none;
+}
+
+div.statPage *.statPage,
+div.resPage *.resPage
+{
+	display:inline;
+}
+
+div.resHeader *.hidden
+{
+	display:none;
+}
+
+#cddInfo
+{
+    text-align:center;
+}
+#cddDesc
+{
+    font-weight:bold;
+}
+div#desctbl
+{
+border: solid 1px #018aac;
+/*min-width: 1000px;*/
+margin: none;
+width: 100%;
+background-color:White;
+/*line-height:0;
+_line-height:0;*/
+}
+
+table#descs
+{
+font-family: Verdana, Sans-Serif;
+font-size: 90%;
+_font-size: 86%;
+border-collapse: collapse;
+/*min-width: 600px;*/
+width: 100%;
+}
+
+table#descs th a {
+text-decoration: none;
+color: #00c;
+}
+
+table#descs th a:visited {
+color: #00c;
+}
+
+table#descs th a:hover {position: relative;
+text-decoration: underline;
+}
+
+table#descs tr th.l,
+table#descs tr td.l {
+text-align: left;
+}
+
+table#descs tr th.sp {
+background-color: #def;
+}
+
+table#descs tr th,
+table#descs tr td {
+text-align: center;
+padding: 1px 4px;
+}
+
+table#descs tr.first th {
+padding-left:18px;
+border-left: solid 1px #A0ceff;
+border-top: solid 1px #A0ceff;
+border-bottom: solid 1px #018aac;
+border-right: solid 1px #018aac;
+padding-right: 8px;
+/*background-color: #01d5ff;*/
+background-color: #9cf;
+/*font-size: 92%;*/
+white-space:normal;
+line-height: 1.2em
+}
+
+
+table#descs td {
+border: solid 1px #ccc;
+border-width: 0px 1px;
+white-space:nowrap;
+overflow: hidden;
+}
+
+.slink {
+font-size: 90%;
+font-weight: normal;
+}
+
+table#descs tr.first th.sel {
+background: #9cf url(images/up.gif) no-repeat center left;
+padding-left: 18px;
+padding-right: 18px;
+}
+
+div.lim
+{
+/*overflow: hidden;-this used to work in Firefox 2- comment for now and set the width */
+width: 35em;
+display: inline-block;
+height: 1.3em;
+}
+
+table#descs tr:hover {
+background-color: #def;
+}
+
+pre
+{
+	font-size:110%;
+	_font-size:100%;
+	line-height:1;
+}
+
+#msg
+{
+    white-space:normal;
+    border-color:#cccccc;
+    padding:0;
+    margin: 0;
+    margin-top:2px;
+}
+#msg li
+{
+    display:none;
+    padding:0;
+    margin: 0;
+    text-indent: 0;
+}
+#msg li.warning, #msg li.error ,#msg li.info
+{
+    display:block;
+}
+
+#msg ul
+{
+    margin:0;
+    padding:0;
+}
+
+table#statInfo
+{
+    border: solid 1px #ccc;
+    background-color: #eee;
+    width: 100%;
+}
+
+table#statInfo tr.odd {
+background-color: #e0e0e0;
+}
+
+.READY, .UNKNOWN
+{
+    display:none;
+}
+
+p.WAITING
+{
+    margin-top:1em;
+}
+
+#frmPage
+{
+	margin-left:1em;
+}
+
+span.Gene_PubMedLinks
+{
+    color: Green; font-weight: bold;
+}
+
+ul.msg li p
+{
+    display:none;
+}
+
+.msg li p.warning, .msg li p.error, .msg li p.success,.msg li p.info
+{
+    display:block;
+}
+
+.mdlbox
+{
+    white-space:pre;
+    background-color:Transparent;
+    border:none;
+}
+
+#blastErr
+{
+    white-space:normal;
+}
+
+
+
+#RSIFrameNoRes,#RSIFrameDesc,#RSIFrameAln
+{
+    border:none;
+    width:519px;
+    height:35px;
+    margin:0px auto;
+}
+
+
+a.ui-ncbitoggler.hidden, a.ui-ncbitoggler-open.hidden
+{
+    display:none;
+}
+
+.smn {
+  display: inline-block;
+  height: 16px;
+  width: 16px;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/dynFormatRes.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,623 @@
+/* style changes for redesign begin*/
+a.gbd
+{
+    text-decoration:none;
+}
+
+tr.dflLnk td span
+{
+    font-size:78%;
+    display:none;
+    text-align:center;
+}
+a.dflSeq
+{
+    color:#369;
+    text-decoration:underline;
+    width:auto;
+}
+table.defln tr.dflLnk a
+{
+	margin-right:auto;
+	padding-left:0;
+}
+
+.alnParLinks
+{
+    float:right;
+}
+
+.alnSeqLinks
+{
+    float:right;
+    margin-right:1em;
+}
+
+
+.seqlinks select
+{
+    padding:0;
+}
+
+.dlfRow div
+{
+    font-size:90%;
+}
+
+.dlfRow
+{
+    display:inline;
+    font-size:110%;
+}
+
+.dlfRow.hidden
+{
+    display:none;
+}
+.dlfRow label
+{
+    font-size:87%;
+    display:inline;
+    color:#606060;
+    font-weight:bold;
+}
+
+.dlfRow span.r label
+{
+    padding-left:0.8em;
+}
+
+
+div.relInf
+{
+    font-family: Verdana, Sans-Serif;
+    font-size: 80%;
+    float:right;
+    width:21%;
+    border-top:solid 2px gray;
+    margin-top:-1em;
+    margin-right:3.5em;
+    left:3em;
+    max-width:25em;
+    padding-left:1em;
+    position:relative;
+    white-space:normal;
+}
+
+div.relInf a
+{
+    padding-right:0.2em;
+}
+
+.rlLink
+{
+    padding-left:0.2em;
+}
+.relInf label
+{
+    font-size:110%;
+    color:brown;
+    font-weight:bold;
+}
+div#content
+{
+    min-width:70em;
+}
+
+.dflLnk a
+{
+	font-size:90%;
+}
+a.dflSeq
+{
+    width:auto;
+    font-weight:normal;
+}
+
+
+#cntDesc,#cntDesc_psiw
+{
+    margin-bottom:0.2em;
+    display:inline-block;
+    width:20em;
+}
+#cntDesc span,#cntDesc_psiw span
+{
+    margin-right:0.5em;
+}
+
+#cntDesc a,#cntDesc input,#cntDesc_psiw a,#cntDesc_psiw input
+{
+    margin-left:0.5em;
+}
+
+#cntSelNone,#cntShAll
+{
+    margin-left:0.2em;
+}
+
+.toolsCtr
+{
+    color:Blue;
+}
+
+table.ui-ncbigrid th span.slink a
+{
+  display:inline;
+  padding-right: 0;
+}
+table.ui-ncbigrid th.sp
+{
+    font-weight:bold;
+}
+
+table.ui-ncbigrid th span.slink
+{
+    margin-left:0.2em;
+}
+
+table.ui-ncbigrid td {
+ white-space:nowrap;
+}
+table.ui-ncbigrid td.c3
+{
+    /*padding-left:0.8em;*/
+}
+table.ui-ncbigrid caption
+{
+    font-size:0;
+    line-height:0;
+}
+#content h3.cap,#content h3.cap a.ui-ncbitoggler.ui-widget, #content h3.cap a.ui-ncbitoggler-open
+{
+    color:#4d4d4d;
+    text-align:left;
+    margin:0 0 0.5em 0;
+}
+
+#content div.cap,#content div.cap a.ui-ncbitoggler.ui-widget, #content div.cap a.ui-ncbitoggler-open
+{
+    color:#4d4d4d;
+    text-align:left;
+    margin:0 0 0.5em 0;
+    letter-spacing:-1px;
+    font-size:110%;
+    font-weight:bold;
+}
+
+#descriptions div.caption-exists {
+  margin: 0;
+}
+
+/**********decrition toolbar styles *********/
+
+div.cnf {
+  -moz-border-bottom-colors: none;
+  -moz-border-image: none;
+  -moz-border-left-colors: none;
+  -moz-border-right-colors: none;
+  -moz-border-top-colors: none;
+  background: url("images/cnf.png") repeat scroll 0 0 transparent;
+  border-style: solid none none;
+  border-width: 1px medium medium;
+  /*clear: left;*/
+  height: 22px;
+  /*overflow: auto;*/
+  width: 100%;
+}
+
+ul.ui-ncbilocalnav li.has-child a.button_config {
+  background: url("/portal/portal3rc.fcgi/3493904/img/81796") no-repeat scroll right center transparent !important;
+  width: 22px;
+  height:22px;
+  margin-left:12em;
+}
+
+#li-config
+{
+    float:right;
+    width:17em;
+}
+div#descTblCtrl ul.ui-ncbilocalnav li
+{
+    border-right:none;
+}
+
+
+.cfg
+{
+    font-size:90%;
+}
+
+
+.oneSeqAln .hsp label
+{
+    color:#606060;
+    font-size:95%;
+    padding-right:0.5em;
+}
+
+.oneSeqAln pre
+{
+    margin-top:0.5em;
+}
+
+.aln_feat label
+{
+  color: #606060;
+  font-size: 95%;
+  padding-right: 0.5em;
+}
+.oneSeqAln .dflLnk.aln_feat
+{
+    padding-bottom:1em;
+}
+div.oneSeqAln h4
+{
+    border:none;
+    font-size:100%;
+    font-weight:normal;
+    letter-spacing:normal;
+    margin:0;
+}
+
+.oneSeqAln .dflLnk
+{
+    width:56em;
+}
+.aln_feat a
+{
+    margin-left:1em;
+    display:block;
+}
+.dflLnk.aln_feat div
+{
+  /*display:inline-block;  */
+  margin-left:5em;
+  margin-top:-1em;
+}
+.aln_frame.shown
+{
+    display:block;
+}
+/*align params styles change */
+
+table.alnParams
+{
+    border-left:none;
+    border-right:none;
+    margin-top:0.5em;
+    width:49em;
+}
+
+table.alnParams th
+{
+    background-color:Transparent;
+    border:none;
+    text-align:left;
+}
+
+table.alnParams td
+{
+   border:none;
+}
+
+
+.alnAll
+{
+    line-height:normal;
+    margin-top:1em;
+}
+
+.alnAll div
+{
+    width:70%;
+}
+
+/**new config staff begin**/
+.popDl
+{
+    display:none;
+}
+.popDl div
+{
+    margin-top:0.5em;
+}
+.popDl div.tl
+{
+    margin-top:0;
+    font-weight:bold;
+}
+a.button_config {
+  background: url("images/cnfButn.png") no-repeat scroll right center transparent !important;
+  width: 22px;
+  height:22px;
+  margin-left:12em;
+  float:right;
+}
+
+a.toolsCtr,span.csLinks a
+{
+    margin-left:8px;
+    float:left;
+    cursor:pointer;
+}
+
+a.toolsCtr[disabled] {
+  cursor: default;
+}
+
+
+a.toolsCtr SPAN
+{
+	color: #14376c;
+	/*line-height: 22px;*/
+	padding-left: 15px;
+	background-repeat: no-repeat;
+	background-position:left center;
+}
+
+a.toolsCtr[disabled] SPAN,a.toolsCtr[disabled]
+{
+    color:#C2C2C2;
+}
+
+a.dnld span
+{
+	background-image: url("images/dndl.png");
+}
+
+a.dnld[disabled] span
+{
+	background-image: url("images/dndl_dsb.png");
+}
+
+a.dialog
+{
+	padding-right: 18px;
+	background:transparent url(images/dialog.png) no-repeat scroll right center;
+	text-decoration:none;
+}
+
+a.dialog[disabled] {
+    background-image: url("images/dialog_dsb.png");
+}
+
+
+a.alnNav span
+{
+	background-image: url("images/align_Normal.png");
+}
+
+a.alnNav
+{
+    text-decoration:none;
+}
+
+
+a.navNext span
+{
+	background-image: url("images/next_Normal.png");
+}
+
+
+a.navNext[disabled] span
+{
+	background-image: url("images/next_Inactive.png");
+}
+
+
+a.navPrev span
+{
+	background-image: url("images/prev_Normal.png");
+}
+
+
+a.navPrev[disabled] span
+{
+	background-image: url("images/prev_Inactive.png");
+}
+
+
+a.navBack span
+{
+	background-image: url("images/table_Normal.png");
+}
+
+.alnRn
+{
+    float:left;
+}
+
+
+/* styles to change per discusssion with Mark begin*/
+.dflLnk a
+{
+	padding-left:0;
+}
+
+
+table.ui-ncbigrid th {
+  padding-left:0.3em;
+  padding-right:0;
+  text-align:center;
+}
+
+table.ui-ncbigrid td {
+  padding-left:0.4em;
+  padding-right:0.4em;
+  text-align:center;
+}
+
+table.ui-ncbigrid td.c2,table.ui-ncbigrid td.c1 {
+  text-align:left;
+}
+
+table.ui-ncbigrid td.c3{
+  padding:0.363em 0.25em;
+}
+
+
+table.ui-ncbigrid th a {
+  padding-right: 5px;
+}
+table.ui-ncbigrid th.c0
+{
+    width:25px;
+    padding:0;
+}
+
+.dflnDth
+{
+    width:100%;
+}
+div.lim {
+  width: 14em;
+}
+
+table.ui-ncbigrid th.c8,table.ui-ncbigrid th.c9 {
+  padding-right: 0.3em;
+}
+.c8,.c9
+{
+    font-size:80%;
+}
+
+
+td.lim.l.c2,td.lim.l.c1
+{
+    overflow:hidden;
+}
+a.spr
+{
+    border-right:none;
+}
+
+
+.psiInp
+{
+    margin-left:1em;
+    margin-top:0.5em;
+}
+
+
+.c8 input
+{
+    border:none;
+}
+table.ui-ncbigrid td.c8
+{
+    padding-left:1.5em;
+}
+
+tr.psi_new td
+{
+    background-color:#FFFF99;
+    border-top:solid 4px white;
+    border-spacing:3px;
+    border-collapse:collapse;
+    line-height:normal;
+}
+/* accessibility setting */
+tr.dflLnk td span.psiNw,tr.first th span,a.button_config span, a span.accsb,.dflLnk label.accsb
+{
+    display:inline;
+    position:absolute;
+    left:-9999px;
+}
+
+div.tgl
+{
+    margin-top:-1em;
+}
+.shcl
+{
+    float:right;
+}
+
+/* styles to change per discusssion with Mark end*/
+
+.alnRn a
+{
+    padding-right:1em;
+}
+.alnAll .moreHsps
+{
+    font-family: Verdana, Sans-Serif;
+    font-size: 75%;
+    margin-top:-2.5em;
+    width:58%;
+}
+.erm
+{
+    background-color:#FFFFCC;
+    padding:0.5em;
+}
+
+#debug,.ind,.alnMsgS .db,.erm .db
+{
+    display:none;
+}
+
+.tmsAln label
+{
+    font-size:93%;
+    display:inline;
+    color:#606060;
+    font-weight:bold;
+}
+.alnAll .tmsAln, .tmsAln div
+{
+    width:100%;
+    margin-bottom:-1em;
+}
+.tmsAlnPar
+{
+    margin-top:-1em;
+}
+/*debug info styles begin */
+
+
+/* use those styles only in debug version
+
+.alnMsg
+{
+    border:solid 1px black;
+}
+
+.alnMsgS.hidden,.alnMsgS .db
+{
+    display:block;
+}
+
+.oneSeqAln
+{
+    border:1px solid #C8C8C8;
+}
+
+#debug,tr.dflLnk td span.ind
+{
+    display:inline;
+}
+.c0
+{
+    width:30px;
+}
+/*debug info styles end */
+
+
+
+/**new config staff end**/
+/*
+ul.ui-ncbilocalnav li, ul.ui-ncbilocalnav {
+  background-color: #F4F4F4;
+  background-image: -moz-linear-gradient(center top , #FFFFFF, #F4F4F4);
+}
+ul.ui-ncbilocalnav li {
+  border-right: 1px solid #C4C4C4;
+}
+*/
+/**********decrition toolbar styles end*********/
+
+
+/* style chenges for redesign end*/
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/firefox-descriptions.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,3 @@
+table.dbInfo caption {
+
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/format.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,270 @@
+
+function UpdateDisplayTypes(displayTypes) {
+    dispMenu = displayTypes.options;
+    for(i=0; i < dispMenu.length; i++) {
+	    //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") ||
+	    if($("stepNumber").value == "" || $("stepNumber").value < 2) {
+			if(dispMenu[i].value.indexOf("PSSM") != -1) {
+				dispMenu[i--] = null;
+				//break;
+			}
+		}
+	}
+}
+
+function GetIndexByValue(selectElem,val) {
+    var idx = 0;
+    var opts = selectElem.options;
+    for(i=0; i < opts.length; i++) {
+        if(opts[i].value == val) {
+            idx = i;
+            break;
+        }
+    }
+    return idx;
+}
+
+function resetAdvView(show)
+{
+    var advView = $("advView");
+    if(show) {
+        if(utils.hasClass(advView, "hidden")) {
+            utils.removeClass(advView, "hidden");
+        }
+    }
+    else {
+        utils.addClass(advView, "hidden");
+    }
+}
+
+
+function ShowOrHide(hide,elem)
+{
+    if(hide) {
+        if(!utils.hasClass(elem, "hidden")) {
+            utils.addClass(elem, "hidden");
+        }
+    }
+    else {
+        if(utils.hasClass(elem, "hidden")) {
+            utils.removeClass(elem, "hidden");
+        }
+    }
+}
+
+function UpdateFormatTypes(form) {
+    var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value;
+    var hideAdvView = false;
+    bioseqFormatHide = true;
+    pssmFormatHide = true;
+    pssmScFormatHide = true;
+    formatTypeHide = true;
+	if (selectedObjType == "Alignment") {
+		formatObjectSelectedIndex = 0; //HTML
+		formatTypeHide = false;
+		hideAdvView = true;
+	}
+    if (selectedObjType == "PSSM") {
+		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text");
+		pssmFormatHide = false;
+    }
+    if (selectedObjType == "PSSM_Scoremat") {
+		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");
+		pssmScFormatHide = false;
+    }
+    else if (selectedObjType == "Bioseq") {
+		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");
+		bioseqFormatHide = false;
+    }
+    form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex;
+	ShowOrHide(formatTypeHide,form.FORMAT_TYPE);
+	if ($("bioseqFormat")) {
+	    ShowOrHide(bioseqFormatHide,$("bioseqFormat"));
+	    $("bioseqFormat").readOnly=true;
+	}
+	if ($("pssmFormat")) {
+	    ShowOrHide(pssmFormatHide,$("pssmFormat"));
+	    $("pssmFormat").readOnly=true;
+	}
+	if ($("pssmScFormat")) {
+	    ShowOrHide(pssmScFormatHide,$("pssmScFormat"));
+	    $("pssmScFormat").readOnly=true;
+	}
+	resetAdvView(hideAdvView);
+}
+
+function ResetForm()
+{
+    //var defValNodes = cssQuery(".reset");
+    defValNodes = $("FormatForm").elements;
+	for(i=0; i < defValNodes.length; i++) {
+	  if(utils.hasClass(defValNodes[i],"reset"))
+	                 setDefalValue(defValNodes[i]);
+	}
+	if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
+	    UpdateFormatTypes($("FormatForm"));
+	    UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
+	}
+	if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH)
+	else $("FormatForm").I_THRESH.value="";
+	//resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
+	resetOrganismControls($("FormatForm").FORMAT_ORGANISM);
+	//TO DO: add threshold
+}
+
+function LimitByHitlistSize(list)
+{
+    var listBreak = false;
+    var optSel = false;
+    for(i=0; i < list.options.length; i++) {
+        var optVal = parseInt(list.options[i].value ,10);
+        var hitListSize = parseInt($("maxNumSeq").value ,10);
+        if(list.options[i].selected) optSel = true;
+        if(optVal >= hitListSize)  {
+            if(!optSel) {list.options[i].selected = true;}
+            list.options.length = i + 1;
+            break;
+        }
+    }
+}
+
+function AddFormatOrgField(e) {
+    AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE");
+}
+
+function initSubmit() {
+
+
+}
+
+function adjustFormatOptions()
+{
+    var alignView = $("FormatForm").ALIGNMENT_VIEW;
+    var formatType = $("FormatForm").FORMAT_TYPE;
+    var queryAnch =  formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
+    var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch;
+    dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities");
+
+    UpdateDescriptions(dynFormatPW);
+    if (dynFormatPW) {
+        jQuery("#frmAln").addClass("hidden");
+        if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
+        jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE
+        jQuery("#scf").removeClass("hidden");//show CDS_FEAT
+        $("FormatForm").SHOW_LINKOUT.checked = true;
+    }
+    else {
+        if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex;
+
+        jQuery("#frmAln").removeClass("hidden");
+        if (dynFormatQA) {
+            if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
+        }
+        else {
+            jQuery("#shl").removeClass("hidden");
+        }
+        if (queryAnch) {
+            jQuery("#scf").addClass("hidden"); //hide CDS_FEAT
+        }
+        else {//pairwise old_view=false
+            jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT
+        }
+        jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE
+    }
+    if ($("blastSpec").value == "VecScreen") {
+        adjustVecscreen(dynFormatPW);
+    }
+}
+
+function adjustVecscreen(dynFormatPW)
+{
+    var dfltDescrInd = 0; //0
+    var dfltDynDescrInd = 5; //1000
+    var dfltAlnInd = 6; //1000
+    if (dynFormatPW) {
+        utils.addClass($("lr"), "hidden");
+        $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd;
+    }
+    else {
+        utils.removeClass($("lr"), "hidden");
+        $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd;
+    }
+    $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd;
+}
+
+
+function UpdateDescriptions(removeZero)
+{
+    if (removeZero) {
+        dispMenu = $("FormatForm").DESCRIPTIONS;
+        dispMenu.remove(0);
+    }
+    else {
+        dispMenu = $("FormatForm").DESCRIPTIONS;
+        if (dispMenu.options[0].value != "0") {
+            if (navigator.userAgent.match(/ie/i)) {
+                dispMenu.add(new Option("0", "0"), 0);
+            }
+            else {
+                dispMenu.add(new Option("0", "0"), dispMenu[0]);
+            }
+        }
+	}
+}
+
+function InitDynFormatOptions()
+{
+    if ($("OLD_VIEW")) {
+        utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false);
+        utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false);
+        utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false);
+        adjustFormatOptions();
+    }
+}
+
+function InitFormatPage()
+{
+    if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
+        UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
+        UpdateFormatTypes($("FormatForm"));
+        list = $("FormatForm").FORMAT_OBJECT;
+        utils.addEvent(list, "change", function() {
+            UpdateFormatTypes($("FormatForm"));
+                               },
+	                           false);
+    }
+    utils.addEvent($("resetAll"), "click",  ResetForm, false);
+    if($("maxNumSeq") != null) {
+    if($("maxNumSeq").value != "") {
+        LimitByHitlistSize($("FormatForm").DESCRIPTIONS);
+        LimitByHitlistSize($("FormatForm").ALIGNMENTS);
+        LimitByHitlistSize($("FormatForm").NUM_OVERVIEW);
+    }
+    }
+    setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
+    utils.addEvent($("FormatForm"), "submit", function() {
+                            adjustOrgVal($("FormatForm").FORMAT_ORGANISM);},
+                    false);
+
+    if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false);
+    InitDynFormatOptions();
+	/* add this code if decide image for View Report
+	var imgButtons = jQuery("[class='viewReport']");
+    for (var i = 0; i < imgButtons.length; i++) {
+      var l = imgButtons[i];
+      utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false);
+      utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false);
+      utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false);
+      utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false);
+      utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false);
+   }
+   */
+}
+
+utils.addEvent(window, 'load', InitFormatPage, false);
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/formatRes.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1542 @@
+// JScript source code
+/*************************new code begin *******************************************************/
+
+function getHiddenFieldVal(elemName) {
+    var val;
+    var elem = document.getElementsByName(elemName);
+    if (elem) {
+        val = (elem.length > 1) ? elem[0].value : elem.value;
+    }
+    return val;
+}
+
+function getHiddenFieldParamString(elemName) {
+    var ret = "";
+    var val = getHiddenFieldVal(elemName);
+    if (val) {
+        ret = "&" + elemName + "=" + val;
+    }
+    return ret;
+}
+
+function elementInViewport(el) {
+    if (!el) return;
+    var rect = el.getBoundingClientRect();
+
+    var myWidth = 0, myHeight = 0;
+    if (typeof (window.innerWidth) == 'number') {
+        //Non-IE
+        myWidth = window.innerWidth;
+        myHeight = window.innerHeight;
+    } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) {
+        //IE 6+ in 'standards compliant mode'
+        myWidth = document.documentElement.clientWidth;
+        myHeight = document.documentElement.clientHeight;
+    } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) {
+        //IE 4 compatible
+        myWidth = document.body.clientWidth;
+        myHeight = document.body.clientHeight;
+    }
+    //window.alert('Width = ' + myWidth);
+    //window.alert('Height = ' + myHeight);
+
+
+    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth)
+    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth)
+    return (rect.top >= 0 && rect.bottom <= myHeight);
+}
+
+function DisplayAlignFromDescription(elem) {
+    var alignView = $("FormatForm").ALIGNMENT_VIEW;
+    if (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities") {
+        DisplayDynamicAlign(elem);
+    }
+    else {
+        location.href = "#" + elem.getAttribute("seqID");
+    }
+}
+
+//<a class="deflnDesc" hsp=<hsp_num> ind="<index>" gi="<gi>" id="deflnDesc_gi" href="#AlnHdrgi">desc</a>
+//<div class="alnHdr" gi="<gi>" id="alnHdr_<index>">
+function DisplayDynamicAlign(elem) {
+    var currGi = elem.getAttribute("gi");
+    var currInd = elem.getAttribute("ind");
+    var stat = elem.getAttribute("stat");
+    if (!currInd || !currGi) return;
+
+    if (!stat || stat == "") {
+        //Get 4(5) aligns before currInd and 4(5) aligns after
+        ReadCurrentSeqAligns(currInd, 5);
+    }
+    else if (stat == "read") {
+        var indexes = getCurrIndexRange(currInd);
+        if (indexes) {
+            var msgID = "alnShow_" + indexes[0];
+            location.href = "#" + msgID;
+        }
+    }
+    else {
+        //error status handling
+    }
+}
+
+
+function goToNextAlign(dtrID, next) {
+    var currInd = parseInt($(dtrID).getAttribute("ind"));
+    var rid = $("Rid").value;
+    nextInd = (next) ? currInd + 1 : currInd - 1;
+
+    if ($("deflnDesc_" + nextInd)) {
+        currGi = $("deflnDesc_" + nextInd).getAttribute("seqID");
+        scrollToGI = currGi;
+        if (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "") {
+
+            if (!next) {
+                ReadPrevSeqAligns(currInd, 5, scrollToGI);
+            }
+            else {
+                //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!!
+                ReadNextSeqAligns(currInd, 5, scrollToGI);
+            }
+
+        }
+        else {
+            location.href = "#" + scrollToGI;
+        }
+    }
+}
+
+function goToDefLine(dtrID) {
+    if ($("psiInp")) {
+        var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table
+        togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1";
+        jQuery($(togglerID)).ncbitoggler("open");
+    }
+}
+
+/*
+readAln.rid = rid;
+readAln.startIndex = parseInt(currInd);
+readAln.numSeq = parseInt(maxNumAligns);
+
+readAln.insertAfterID = insertAfterID;
+readAln.seqList = giList;
+readAln.scrollToSeqID = scrollToGI;
+*/
+function ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) {
+    var lastDispIdx = 0;
+    var rid = $("Rid").value;
+
+    var readAln = new Object();
+    readAln.seqList = ""; //giList
+    readAln.rid = rid;
+
+    currInd = parseInt(currInd);
+
+    if (currInd != 0 && $("deflnDesc_" + currInd)) {
+        var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_<ind>
+        //alert(par.id);
+        if (par) par = utils.getParent(par); //"alnShow_<ind>
+        //alert(par.id);
+        if (par) readAln.insertAfterID = par.id;
+    }
+    else {
+        readAln.insertAfterID = "alnStart";
+    }
+
+
+
+    readAln.startIndex = currInd + 1;
+    readAln.numSeq = maxNumAligns;
+
+    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next");
+
+    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : "";
+    readAln.hspSort = 0;
+    ReadSeqAlignByIndex(readAln);
+}
+
+function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) {
+    var lastDispIdx = 0;
+    var rid = $("Rid").value;
+
+    var readAln = new Object();
+    readAln.seqList = ""; //giList
+    readAln.rid = rid;
+
+    currInd = parseInt(currInd);
+
+
+    //sets readAln.insertAfterID and returns lastDispIdx;
+    //Find the index of the previously displayed alignment
+    lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
+
+    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
+    readAln.numSeq = currInd - readAln.startIndex;    //stopIndex = currInd
+
+    checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev");
+
+    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID");
+    readAln.hspSort = 0;
+    ReadSeqAlignByIndex(readAln);
+}
+
+//When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd
+function ReadCurrentSeqAligns(currInd, maxNumAligns) {
+    var rid = $("Rid").value;
+    var readAln = new Object();
+    readAln.seqList = ""; //giList
+    readAln.rid = rid;
+
+    currInd = parseInt(currInd);
+
+
+    //sets readAln.insertAfterID and returns lastDispIdx;
+    //Find the index of the previously displayed alignment
+    var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
+
+    //lastDispIdx = parseInt(lastDispIdx);
+    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
+    readAln.numSeq = parseInt(maxNumAligns * 2);
+
+    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr");
+
+    readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID");
+    readAln.hspSort = 0;
+    ReadSeqAlignByIndex(readAln);
+    g_DisableAutoCheck = true;
+    location.href = "#alnShow_" + readAln.startIndex;
+}
+
+
+
+
+function setupDynHSPParams(readAln)
+{
+    var currSeqInd = readAln.startIndex;
+    hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp"));
+    alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len"));
+    var maxDispLen = parseInt($("maxDispAlnLen").value);//20000
+    var minDispLen = parseInt($("minDispAlnLen").value);//2000
+    if (alnLen > maxDispLen) {
+        var lenPerMatch = alnLen / hspNum;
+        readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch);
+        readAln.AlignDbPageNum = 0;
+        $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize);
+    }
+}
+
+
+
+function getCurrSeqsAlnLen(currSeqInd)
+{
+    var alnLen = 0;
+    if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") || $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) {
+        alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len");
+    }
+    alnLen = (alnLen) ? parseInt(alnLen) : 0;
+    return alnLen;
+}
+
+function checkTotalAlignLen(startIndex,stopIndex)
+{
+    var dispAlnLen = 0;
+    var maxDispLen = parseInt($("maxDispAlnLen").value);
+    for (var i = startIndex; i <= stopIndex; i++) {
+        alnLen = getCurrSeqsAlnLen(i);
+        if (alnLen == 0) break;
+        dispAlnLen += alnLen;
+    }
+    return dispAlnLen;
+}
+//Get total align length for seq currSeqInd and
+//"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs
+function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType)
+{
+    var startIndex = readAln.startIndex;
+    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
+    if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current
+        startIndex = Math.max(startIndex, currSeqInd - countSeqs);
+        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs);
+    }
+    else if(dispType == "prev") {
+        startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs);
+        stopIndex = currSeqInd - 1;
+    }
+    else {//next
+        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1);
+    }
+    var totAlnLen = checkTotalAlignLen(startIndex,stopIndex);
+    return totAlnLen;
+}
+
+function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType)
+{
+    var maxDispLen = parseInt($("maxDispAlnLen").value);
+    var totAlnLen = 0;
+    var exc = false;
+    for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) {
+        totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType);
+        if(totAlnLen > maxDispLen) {
+            break;
+        }
+    }
+    if (totAlnLen > maxDispLen) {
+        if (numSeq != 0) numSeq--;
+        if (dispType == "curr") {
+            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq);
+            //prev + 1(curr) + next
+            readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq;
+        }
+        else if (dispType == "prev") {
+            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq);
+            readAln.numSeq = numSeq + 1;
+        }
+        else { //"next" - readAln.startIndex stays
+            readAln.numSeq = numSeq + 1;
+        }
+
+        if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") {
+            setupDynHSPParams(readAln);
+        }
+
+        exc = true;
+    }
+    return exc;
+}
+
+
+//readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set
+function ReadSeqAlignByIndex(readAln) {
+    var numAligns = 0;
+    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
+
+        if (!$("deflnDesc_" + i)) {
+            break;
+        }
+        if (!$("deflnDesc_" + i).getAttribute("stat") || $("deflnDesc_" + i).getAttribute("stat") == "") {
+            currGi = $("deflnDesc_" + i).getAttribute("seqFSTA");
+            if (readAln.seqList != "") readAln.seqList += ",";
+            readAln.seqList += currGi;
+            numAligns++;
+        }
+        else {
+            break;
+        }
+    }
+    if (readAln.seqList != "") {
+        readAln.numSeq = parseInt(numAligns);
+        ReadSeqAlignForSeqList(readAln);
+    }
+}
+
+
+var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2...
+//Find the range of indexes of displayed alignments for currAlnInd
+//Returns array of 2 startIndex, stopIndex
+function getCurrIndexRange(currAlinInd) {
+    var currRange;
+    var ranges = g_DisplayeAlignsRanges.split(",");
+    for (var i = 0; i < ranges.length; i++) {
+        var indexes = ranges[i].split("-");
+        if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) {
+            currRange = indexes;
+            break;
+        }
+    }
+    return currRange;
+}
+
+
+//Find the index of the previous  displayed alignment
+function getPrevDisplyedAlignInfo(currInd, readAln) {
+    readAln.insertAfterID = "alnStart";
+    lastDispIdx = 0;
+    for (var i = currInd - 1; i >= 1; i--) {
+        indexes = getCurrIndexRange(i);
+        if (indexes) {
+            lastDispIdx = indexes[1];
+            readAln.insertAfterID = "alnShow_" + indexes[0];
+            break;
+        }
+    }
+    return parseInt(lastDispIdx);
+}
+
+
+//setReadStatus
+function setSeqAlnReadStatus(readAln, status) {
+    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
+        if ($("deflnDesc_" + i)) {
+            jQuery($($("deflnDesc_" + i))).attr("stat", status);
+            if (status == "disp") {
+                g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex;
+            }
+        }
+    }
+}
+
+/*
+readAln.rid = rid;
+readAln.seqList = giList;
+readAln.startIndex = parseInt(idx);
+readAln.insertAfterID = insertAfterID;
+readAln.numSeq = parseInt(numSeq);
+readAln.scrollToSeqID = scrollToGI;
+*/
+function SendReadSeqAlinRequest(readAln) {
+    blastUrl = "t2g.cgi";
+
+    var rp = new RemoteDataProvider(blastUrl);
+
+
+    rp.onSuccess = function(obj) {
+        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
+
+        if ($("alnShow_" + readAln.startIndex)) {
+            var moreHspsLink = getNextHspsLink(readAln);
+            jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, {
+                'widgets': ['ncbipopper', 'ncbitoggler'],
+                'configs': {
+                    'ncbipopper': { hasArrow: true, arrowDirection: 'top' }
+                }
+            });
+            setSeqAlnReadStatus(readAln, "disp");
+            jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
+            //Saves start and stop indexes of loaded alignments in global variables
+            saveIdxesForAutomaticLoad(readAln);
+            jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) {
+                var seqID = this.getAttribute("seqID");
+                if(seqID) initAlignBatch(seqID);
+            });
+
+        }
+
+        if (readAln.scrollToSeqID) {
+            location.href = "#" + readAln.scrollToSeqID;
+        }
+
+    };
+    rp.onError = function(obj) {
+        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
+        jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
+        $("alnShowReal_" + readAln.startIndex).innerHTML = "<div class=\"erm\" id=\"erm_" + readAln.startIndex + "\">Error loading alignment ...<span class=\"db\">requests:" + this.iActiveRequests + " status:" + obj.status +
+                          "</span><a class=\"gbd\" href=\"#\" onclick=\"ReSubmitReadSeqAligns(event," + readAln.startIndex + ")\">Try again<\a></div>";
+    }
+    var params = constructURLParams(readAln);
+    if (readAln.numSeq == 1) {
+        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
+    }
+    params += "&SEQ_LIST_START=" + readAln.startIndex;
+
+    var formatParams = constructFormatParams();
+    params += formatParams;
+
+    //alert(params);
+    rp.Request(params);
+}
+
+
+function constructURLParams(readAln) {
+    var params;
+
+    if ($("useAlignDB") && $("useAlignDB").value == "true") {
+
+        var alignDbParams = "&USE_ALIGNDB=true";
+        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
+        if (batchID) {
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID");
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS");
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST");
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH");
+        }
+        alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList;
+        alignDbParams += "&HSP_SORT=" + readAln.hspSort;
+
+        if (readAln.hasOwnProperty("AlignDbPageNum")) {
+            alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum;
+            alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize;
+            alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum;
+        }
+
+        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams;
+    }
+    else {
+        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort;
+    }
+    if ($("phiPtInd")) {
+        params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value;
+    }
+    return params;
+}
+
+/*
+readAln.rid = rid;
+readAln.seqList = giList;
+readAln.startIndex = parseInt(idx);
+readAln.insertAfterID = insertAfterID;
+readAln.numSeq = parseInt(numSeq);
+readAln.scrollToSeqID = scrollToGI;
+*/
+/*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes
+2. Insert another div with id="alnShowReal_index and class="alnMsgR"
+3. For "alnShow_index" set atrr indexes="startInd-stopInd"
+4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this
+5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes
+6. Send read request
+*/
+
+function ReadSeqAlignForSeqList(readAln) {
+    var text = "<div id=\"alnShow_" + readAln.startIndex + "\" class=\"alnMsg\"><div class=\"alnMsgS\" id=\"alnMsg_" + readAln.startIndex + "\">Loading alignment...<span class=\"db\"> for sequences " + readAln.seqList;
+    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
+    var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : "";
+    text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "</span></div>";
+    text += "<div id=\"alnShowReal_" + readAln.startIndex + "\" class=\"alnMsgR\"></div></div>";
+    var debugControl = "<div id=\"debug\"></div>";
+    if (!$("debug")) {
+        jQuery($($("descriptions"))).before(debugControl);
+    }
+    if (!$("alnShow_" + readAln.startIndex)) {
+        jQuery($($(readAln.insertAfterID))).after(text);
+        jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex);
+        jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList);
+        g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex;
+        setSeqAlnReadStatus(readAln, "read");
+        $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex;
+
+        if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ",";
+        g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex;
+
+        SendReadSeqAlinRequest(readAln);
+    }
+    else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) {
+        jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden");
+        jQuery($("erm_" + readAln.startIndex)).remove();
+        SendReadSeqAlinRequest(readAln);
+    }
+}
+
+
+function ReSubmitReadSeqAligns(e,currInd) {
+    var rid = $("Rid").value;
+    if ($("alnShow_" + currInd)) {
+        var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes");
+        var range = indexRange.split("-");
+
+
+        var readAln = new Object();
+        readAln.seqList = ""; //giList
+        readAln.rid = rid;
+        readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist");
+        readAln.startIndex = parseInt(range[0]);
+        readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1;
+        readAln.hspSort = 0;
+        ReadSeqAlignForSeqList(readAln);
+        utils.preventDefault(e);
+    }
+}
+
+
+var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read"
+var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N
+var g_DisableAutoCheck = false;
+
+var g_autoStartIdx = new Array();
+var g_autoStopIdx = new Array();
+
+function saveIdxesForAutomaticLoad(readAln) {
+    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
+    g_autoStartIdx.push(readAln.startIndex); //1,20,25
+    g_autoStopIdx.push(stopIndex);  //4,24,29
+    $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex;
+}
+
+function getNextHspsLink(readAln)
+{
+    var moreHspsLink = ""
+    if (readAln.hasOwnProperty("AlignDbPageNum")) {
+        var nextPageNum = readAln.AlignDbPageNum + 1;
+        var currHspInd = readAln.AlignDbPageSize * nextPageNum;
+        var argstring = readAln.startIndex + "," + currHspInd;
+        var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId");
+        var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs");
+        var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
+        var prevHspInd = readAln.AlignDbPageSize * nextPageNum;
+        var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize);
+        var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1);
+
+        moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID);
+        moreHspsLink = moreHspsLink.replace(/@accs@/g, accs);
+        moreHspsLink = moreHspsLink.replace("@argstring@", argstring);
+        moreHspsLink = moreHspsLink.replace(/@segs@/g, segs);
+        moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps);
+        moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize);
+        moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd);
+        moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi);
+    }
+    return moreHspsLink;
+}
+
+
+function ReadNextHSPSet(currSeqInd, currHSPNum) {
+    var readAln = new Object();
+
+    readAln.rid = $("Rid").value;
+    readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA");
+    readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId");
+    dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps");
+    readAln.startIndex = currSeqInd;
+    readAln.numSeq = 1;
+    if (dynHsps) {
+        readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps);
+        readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve
+    }
+    if (currHSPNum != 0) {
+        readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1);
+        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum;
+    }
+    var sortLink = $("sa_" + readAln.gi);
+    readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0;
+    SendReadSeqAlinSortHSPRequest(readAln);
+}
+
+function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) {
+    ReadNextHSPSet(currSeqInd, currHSPNum);
+    utils.preventDefault(e);
+}
+
+
+
+function checkAutoAlignArray() {
+    var stop = false;
+    var start = false;
+    var currAlignViewPos = $("alignView").getBoundingClientRect().top;
+    if (currAlignViewPos < g_alignViewPos) {//scrolling down
+        g_alignViewPos = currAlignViewPos;
+        if (g_DisableAutoCheck) {
+            g_DisableAutoCheck = false;
+            return;
+        }
+        for (i = 0; i < g_autoStopIdx.length; i++) {
+            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) {
+                //alert("Reading more aligns scrolling down!");
+                var nextInd = parseInt(g_autoStopIdx[i] + 1);
+                var currInd = g_autoStopIdx[i];
+                if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "")) {
+                    ReadNextSeqAligns(currInd, 5);
+                    stop = true;
+                    break;
+                }
+            }
+        }
+        if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array
+    }
+    else if (currAlignViewPos > g_alignViewPos) {//scrolling up
+        g_alignViewPos = currAlignViewPos;
+        //here maybe return if autoStop found!!!
+        /* commenting automic read when scroll up */
+        for (i = 0; i < g_autoStartIdx.length; i++) {
+            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) {
+                //alert("Reading more aligns scrolling up!");
+                var currInd = g_autoStartIdx[i];
+                //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!!
+                if (currInd > 1) {
+                    ReadPrevSeqAligns(currInd, 5);
+                    start = true;
+                    break;
+                }
+            }
+        }
+        if (start) g_autoStartIdx.splice(i, 1);
+    }
+    /*end of comment*/
+}
+
+var g_alignViewPos = 0;
+
+function checkAutoAlignLoad() {
+
+
+    checkAutoAlignArray();
+
+    if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) {
+        //alert("bottom!");
+
+        if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") {
+            //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex
+            ReadNextSeqAligns(g_MaxDisplayedIndex, 5);
+        }
+    }
+}
+
+
+function GetPatternLocResults()
+{
+    form = $("results");
+    if (!form.PHI_PTTRN_INDEX) {
+        var el = document.createElement("input");
+        el.name = "PHI_PTTRN_INDEX";
+        el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
+        form.appendChild(el);
+    }
+    else {
+        form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
+    }
+    form.submit();
+}
+
+function goToNextHSP(elem, next) {
+    var par = jQuery(elem).parent(); //parent span with class="alnParLinks"
+    var parts = par[0].id.split("_"); //"hsp<seqid>_hspnum "hsp207524544_2"
+    if (parts[0].indexOf("nxHsp") != -1) {
+        parts[0] = parts[0].replace("nxHsp", "hsp");
+    }
+    nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1)
+
+    gotoElem = jQuery($(nextID));
+    if (gotoElem[0]) {
+        a = jQuery(gotoElem).offset();
+        window.scroll(0, a.top);
+    }
+
+    else {
+        retrieveNextHSP(parts[0],parts[1]);
+    }
+
+}
+
+
+//parts[0]//hsp<seqid>,    parts[1] hspnum
+function retrieveNextHSP(currLinkID, currHSPNum)
+{
+    var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id
+    var currSeqInd, totalHsps;
+    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
+        currSeqInd = parseInt(this.getAttribute("ind"));
+        totalHsps = parseInt(this.getAttribute("hsp"));
+        dynHsps = this.getAttribute("dynHsps");
+    });
+    currHSPNum = parseInt(currHSPNum);
+    if (currHSPNum < totalHsps && dynHsps) {
+        ReadNextHSPSet(currSeqInd, currHSPNum);
+    }
+}
+/********Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error********************************/
+function getUrlCompForEntryField(elem) {
+    var url = "";
+    if (elem && elem.value != "") {
+        url = "&" + elem.name + "=" + escape(elem.value);
+    }
+    return url;
+}
+
+
+function getUrlCompForCheckedField(elem) {
+    var url = "";
+    if (elem && elem.checked) {
+        url = "&" + elem.name + "=" + elem.value;
+    }
+    return url;
+
+}
+
+function getUrlCompForOptionsField(elem) {
+    var url = "";
+    if (elem) {
+        url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
+    }
+    return url;
+}
+/****************************************/
+
+function constructFormatParams() {
+    var formatParams = "";
+
+    if ($("queryList")) {
+        formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value;
+    }
+
+
+    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT);
+    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE);
+    formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI);
+    formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW);
+    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR);
+    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR);
+    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW);
+    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH);
+    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW);
+    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH);
+    formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH);
+
+
+    formatParams += getHiddenFieldParamString("BUILD_NAME");
+
+    var serviceType = "";
+    if ($("serviceType").value == "sra") {
+        serviceType = "sra";
+    }
+    else if ($("clientType").value == "TMSmart_restricted") {
+        serviceType = "restricted";
+    }
+    if (serviceType != "") {
+        formatParams += "&BOBJSRVC=" + serviceType;
+    }
+    if ($("currQuery").value != "") {
+        formatParams += "&CURR_QUERY_ID=" + $("currQuery").value;
+    }
+
+    return formatParams;
+}
+
+//readAln.seqList contains one gi only for this
+function SendReadSeqAlinSortHSPRequest(readAln) {
+    blastUrl = "t2g.cgi";
+    var rp = new RemoteDataProvider(blastUrl);
+
+
+    rp.onSuccess = function(obj) {
+        var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : "";
+        var alnHtml = obj.responseText + moreHspsLink;
+        initHSPRequest(readAln, obj.responseText + moreHspsLink,false);
+        if (readAln.scrollToSeqID) {
+            location.href = "#" + readAln.scrollToSeqID;
+        }
+    };
+    rp.onError = function(obj) {
+        var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
+        var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
+        if (!$(msgID)) {
+            var msg = "<div class=\"erm\" att=\"1\" id=\"" + msgID + "\">Error loading alignment ...<span class=\"db\">status:" + obj.status +
+                          "</span><a class=\"gbd\" href=\"#\" onclick=\"ReadNextHSPSetEvt(event," + readAln.startIndex + "," + currHspInd +
+                          ")\">Try again <span class=\"attmt\"></span> <\a></div>";
+            initHSPRequest(readAln, msg, true);
+        }
+        else {
+            var attNum = parseInt($(msgID).getAttribute("att")) + 1;
+            $(msgID).setAttribute("att", attNum);
+            jQuery($(msgID)).find(".attmt").each(function(index) {
+                jQuery(this).html(", attempt " + attNum);
+            });
+        }
+    }
+
+    var params = constructURLParams(readAln);
+    if (readAln.AlignDbPageSize) {
+        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
+    }
+    params += "&SORT_ONE_ALN=on";
+    var formatParams = constructFormatParams();
+
+    params += formatParams;
+
+    //alert(params);
+    rp.Request(params);
+}
+function initHSPRequest(readAln, alnHtml, err) {
+    var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
+    if (currHspInd != 0) {
+        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd;
+        jQuery($(readAln.insertAfterID)).after(alnHtml);
+        moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1);
+        jQuery($(moreHspsID)).remove();
+        if (!err) {
+            errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
+            jQuery($(errMsgID)).remove();
+        }
+    }
+    else {
+        jQuery($("alnAll_" + readAln.gi)).html(alnHtml);
+    }
+}
+
+function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544"
+    var readAln = new Object();
+
+
+    var desLineID = sortLink.id.replace("sa", "dtr"); //tr id
+    var seqInd;
+
+    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
+        seqInd = this.getAttribute("ind");
+    });
+
+    ReadNextHSPSet(parseInt(seqInd), 0);
+}
+
+
+function configDescriptions(e,btn,dlgId)
+{
+    var suffix = PsiBelowThresh(dlgId);
+    var colmnsInfId = "cfcDsInf" + suffix;
+    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
+    var showAllColId = "shcl" + suffix;
+    var chkBoxes = $C("checkbox", "type", $(dlgId), "input");
+    if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = "";
+    for (i = 0; i < chkBoxes.length; i++) {
+        var check;
+        if (utils.hasClass(btn, "cnc")) {//cancel
+            if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) {
+                check = true;
+            }
+            else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) {
+                check = false;
+            }
+        }
+        else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) {
+            check = true;
+        }
+        if (typeof (check) != 'undefined') {
+            chkBoxes[i].checked = check;
+            showHideCol(tblID,parseInt(chkBoxes[i].value), !check);
+        }
+        if (!utils.hasClass(btn, "cnc")) {
+            if (chkBoxes[i].checked) { //OK
+                if ($(colmnsInfId).value != "") $(colmnsInfId).value += ",";
+                $(colmnsInfId).value += chkBoxes[i].value;
+            }
+        }
+    }
+    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
+        jQuery($(showAllColId)).removeClass("hidden");
+    }
+    else {
+        jQuery($(showAllColId)).addClass("hidden");
+    }
+
+    var chConfig = $("cfcDsSave").value != $(colmnsInfId).value;
+
+    var cfds = document.getElementsByName("CONFIG_DESCR");
+    if (cfds) {
+        for (i = 0; i < cfds.length; i++) {
+            cfds[i].value = $(colmnsInfId).value;
+        }
+    }
+    $("cfcDsSave").value = $(colmnsInfId).value;
+    if (chConfig) SaveConfigTable();
+    jQuery(document.body).click();
+    utils.preventDefault(e);
+}
+
+
+
+function initDescConfig()
+{
+    initConfigColumns("dsConfig");
+    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
+        initConfigColumns("dsConfig_psiw");
+    }
+}
+
+
+function initConfigColumns(cnfDlgID)
+{
+    var suffix = PsiBelowThresh(cnfDlgID);
+    //cnfDlgID is "dsConfig[_psiw]"
+    var colmnsInfId = "cfcDsInf" + suffix;
+    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
+    var showAllColId = "shcl" + suffix;
+
+    if (navigator.userAgent.match(/ie/i)) {
+        if ($("FormatForm").NCBI_GI.checked || $("serviceType").value == "sra") {
+            jQuery($(tblID)).find("th.c1").each(function(index) {
+                db = getHiddenFieldVal("DATABASE");
+                var width = (db.match(/WGS/i) || db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em";
+                jQuery(this).css("width", width);
+            });
+        }
+    }
+
+    jQuery($(tblID)).find("tr.first").each(function(index) {
+        jQuery(this).find("a.dcs").each(function(index) {
+           jQuery(this).bind("click", function(e) { checkConfig(this); });
+        });
+    });
+
+    jQuery($(cnfDlgID)).find("button").each(function(index) {
+        jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); });
+    });
+
+
+    jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); });
+
+    $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR");
+    if ($(colmnsInfId).value == "" || $(colmnsInfId).value == "undefined") {
+        $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval");
+    }
+    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
+        jQuery($(showAllColId)).removeClass("hidden");
+    }
+    else {
+        jQuery($(showAllColId)).addClass("hidden");
+    }
+    var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input")
+    for (i = 0; i < chkBoxes.length; i++) {
+        jQuery(chkBoxes[i]).bind("click", configColumn);
+        if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) {
+            chkBoxes[i].checked = true;
+        }
+        else {
+            //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value);
+            showHideCol($(tblID), chkBoxes[i].value, true);
+        }
+    }
+}
+function showAllCol(e,elem)
+{
+    var suffix = PsiBelowThresh(elem.id);
+    var rdf = "dscRsDf" + suffix;
+    jQuery($(rdf)).click();//click "restore defaults'
+    utils.preventDefault(e);
+}
+
+
+function configColumn() {
+    var suffix = PsiBelowThresh(this.id);
+    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
+
+    cCls = "c" + this.value;
+    if (this.checked) {//show
+        showHideCol(tblID,parseInt(this.value), false);
+    }
+    else {
+        showHideCol(tblID,parseInt(this.value), true);
+    }
+}
+
+function showHideCol(tblID, columnIndex, hide) {
+
+    if ($("Transcr")) {
+        colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden");
+        hide = hide && !colHidden;
+        show = !hide && colHidden;
+    }
+    else {
+        show = !hide;
+    }
+    if (hide) {
+        jQuery($(tblID)).ncbigrid("hideColumn", columnIndex);
+    }
+    else if (show) {
+        jQuery($(tblID)).ncbigrid("showColumn", columnIndex);
+    }
+    if ($("Transcr") && (hide || show) ) {
+        var colsp = parseInt($("Transcr").getAttribute("colspan"));
+        colsp = (hide) ? colsp - 1 : colsp + 1;
+        $("Transcr").setAttribute("colSpan", colsp);
+        if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp);
+    }
+}
+
+function checkConfig(lnk) {
+    var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value;
+    lnk.href = lnk.href + cnfCol + "#sort_mark";
+}
+
+function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists
+{
+    var dflLineLinks = $C(seqID, "gi", document, "a");
+    for (i = 0; i < dflLineLinks.length; i++) {
+        jQuery(dflLineLinks[i]).click();
+        break;
+    }
+    location.href = dflLineLinks[i].href;
+}
+
+
+
+function initDescSelect()
+{
+
+    jQuery("#cntDesc").find("a").each(function(index) {
+        jQuery(this).bind("click", configDescrSelect);
+    });
+    jQuery("#cntSelN").click();
+    jQuery("#descTblCtrl").find("a[view]").each(function(index) {
+        jQuery(this).bind("click", DisplaySelectedView);
+    });
+    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
+        jQuery("#cntDesc_psiw").find("a").each(function(index) {
+            jQuery(this).bind("click", configDescrSelect);
+        });
+        jQuery("#cntSelN_psiw").click();
+        jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) {
+            jQuery(this).bind("click", DisplaySelectedView);
+        });
+    }
+
+
+    //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });??
+
+}
+
+function DisplaySelectedView(e) {
+    if (this.getAttribute("view") == "graph") {    //seqviewer
+        ViewSelectedSeqViewer(e,this);
+    }
+    else {
+        if (this.getAttribute("view") == "tree") {    //seqviewer
+            $("scrWidth").value = screen.width;
+            $("scrHeight").value = screen.height;
+        }
+        ViewSelectedSeqsEx(e, this);
+    }
+}
+
+function PsiBelowThresh(elemID)
+{
+    var suffix = "";
+    if (elemID.indexOf("_psiw") != -1) {
+        suffix = "_psiw";
+    }
+    return suffix;
+}
+
+function ViewSelectedSeqsEx(e,elem) {
+    var sbmForm = elem.getAttribute("frm");
+    var seqList = elem.getAttribute("seqList");
+
+    var cnfElem = utils.getParent(elem); //.cnf div
+    var suffix = PsiBelowThresh(cnfElem.id);
+    var tblID = "dscTable" + suffix;
+
+    $(seqList).value = createSelseqString(tblID,true);
+    $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces
+    if ($(seqList).value.indexOf("dbSNP") != -1) {
+        $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp
+        elem.href = $(sbmForm).action + $(seqList).value;
+        elem.target = "new";
+    }
+    else {
+        $(sbmForm).submit();
+        utils.preventDefault(e);
+    }
+}
+
+function ViewSelectedSeqsTree(e) {
+    $("scrWidth").value = screen.width;
+    $("scrHeight").value = screen.height;
+}
+
+function initSeqViewerGet(seqList) {
+    if (seqList.length >= 2000) {
+        seqList = seqList.substr(0,2000);
+        lastComma = seqList.lastIndexOf(",");
+        seqList = seqList.substr(0,lastComma);
+    }
+    $("seqViewParams").name = "RID";
+    $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]";
+}
+
+function ViewSelectedSeqViewer(e, elem)
+{
+    var cnfElem = utils.getParent(elem); //.cnf div
+    var suffix = PsiBelowThresh(cnfElem.id);
+    var tblID = "dscTable" + suffix;
+
+    //change to false when new verison of seqVier is installed in production
+    var seqList = createSelseqString(tblID, false);
+    $("sbmtGraphics").action = $("seqViewUrl").value;
+
+    var rp = new RemoteDataProvider("url2nc.cgi");
+    rp.onSuccess = function(obj) {
+        var jsnResp = JSON.parse(obj.responseText);
+        ncid = jsnResp.ncid;
+
+        if (ncid != "") {
+            $("seqViewParams").name = "rkey";
+            $("seqViewParams").value = ncid;
+        }
+        else {
+            initSeqViewerGet(seqList);
+        }
+        $("sbmtGraphics").submit();
+    };
+    rp.onError = function(obj) {
+        initSeqViewerGet(seqList);
+        $("sbmtGraphics").submit();
+        utils.preventDefault(e);
+    }
+    var params = $("ridParam").value + "[" + seqList + "]";
+    rp.Request(params, "POST");
+    utils.preventDefault(e);
+}
+
+function configDescrSelect(e) {
+    var sel = this.getAttribute("sel");
+    if (sel) {
+        var selNum = 0;
+        var check = (sel == "all") ? true : false;
+
+        var suffix = PsiBelowThresh(this.id);
+        var tblID = "dscTable" + suffix;
+        var toolbarID = "descTblCtrl" + suffix;
+        var selElID = "slcNum" + suffix;
+
+        jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
+            jQuery(this)[0].checked = check;
+            if (check) selNum++;
+        });
+        enableDescrLinks(selNum, toolbarID, selElID);
+    }
+    utils.preventDefault(e);
+}
+
+
+
+function enableDescrLinks(selNum, toolbarID, selElID) {
+    jQuery($(toolbarID)).find("a[minSlct]").each(function(index) {
+        var minSelected = this.getAttribute("minSlct");
+        minSelected = parseInt(minSelected);
+        if (selNum >= minSelected) {
+            this.removeAttribute("disabled");
+        }
+        else {
+            this.setAttribute("disabled", "disabled");
+        }
+    });
+    $(selElID).innerHTML = selNum;
+}
+
+
+
+function configDescrLinks(e, elem)
+{
+
+    ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false");
+    var par = jQuery(elem).parents(".jig-ncbigrid");//parent table
+    if (par) {
+        var suffix = PsiBelowThresh(par[0].id);
+        var tblID = "dscTable" + suffix;
+        var toolbarID = "descTblCtrl" + suffix;
+        var selElID = "slcNum" + suffix;
+
+        var currSelNum = parseInt($(selElID).innerHTML);
+        var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1;
+        enableDescrLinks(selNum, toolbarID, selElID);
+    }
+}
+/***Download code begin****/
+
+function initDownLoadPopup(dwnDialog) {
+
+    jQuery(dwnDialog).find("button").each(function(index) {
+        jQuery(this).bind("click", execDownLoad);
+    });
+
+    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
+}
+
+function initDescDownLoad() {
+    initDownLoadPopup($("dsDownload"));
+
+    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
+        initDownLoadPopup($("dsDownload_psiw"));
+    }
+}
+
+function initAlignDownLoad(navObj)
+{
+    var seqID = navObj.seqID;
+    var dwnDialog = $("dlgDwnl_" + seqID);
+    jQuery(dwnDialog).find("button").each(function(index) {
+        jQuery(this).bind("click", execDownLoad);
+    });
+
+    var dwnFSTW = $("dwFST_" + seqID);//whole seq
+    var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions
+
+    if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID);
+    if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID);
+
+    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
+}
+
+
+function execDownLoad(e) {
+    if (!utils.hasClass(this, "cnc")) {
+        par = utils.getParent(this);
+        dwnDialog = utils.getParent(par); //parent dialog with popDl class
+        var descr = (this.id == "dw_cont" || this.id == "dw_cont_psiw") ? true : false;
+        jQuery(dwnDialog).find("input").each(function(index) {
+            if (this.checked) {
+                submitDownLoad(this, descr);
+            }
+        });
+    }
+    jQuery(document.body).click();
+    utils.preventDefault(e);
+}
+
+function submitDownLoad(radioElem, descr) {
+    var toolURL = radioElem.getAttribute("url");
+    if (toolURL) {
+        if (descr) {
+            var getGi = radioElem.getAttribute("getGi");
+            getGi = (getGi) ? true : false;
+
+            var tblID = "dscTable";
+            var suffix = PsiBelowThresh(radioElem.id);
+            tblID += suffix;
+
+            $("selDnSeqs").value = createSelseqString(tblID,getGi);
+        }
+        else {
+            var seqfsta = radioElem.getAttribute("seqfsta");
+            $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi");
+        }
+        var addParams = "";
+        if (radioElem.getAttribute("addParam")) {
+            addParams = addDwnlParams();
+        }
+        var submitName = radioElem.getAttribute("sbName")
+        $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST";
+        $("dwdlSubmit").action = toolURL + addParams;
+        $("dwdlSubmit").submit();
+    }
+    else {
+        var sbFunction = radioElem.getAttribute("sbFunc");
+        if (sbFunction) {
+            eval(sbFunction + "(radioElem, descr)");
+        }
+    }
+}
+
+
+function initDownLoadFSTA(radioElem, descr)
+{
+    if (descr) {
+
+        var tblID = "dscTable";
+        var suffix = PsiBelowThresh(radioElem.id);
+        tblID += suffix;
+
+        $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false);
+    }
+    else {
+        $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta");
+    }
+    $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType");
+
+    $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE");
+    if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox
+        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
+        if (batchID) {
+            $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID");
+            $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS");
+            $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST");
+            $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH");
+        }
+    }
+    $("sbmtFASTA").submit();
+}
+
+function createSelseqString(tblID,getGi) {
+    var selSeqs = "";
+    jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
+        if (jQuery(this)[0].checked) {
+            if (selSeqs != "") selSeqs += ",";
+            if (getGi) {
+                selSeqs += jQuery(this)[0].value;
+            }
+            else {
+                var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc");
+                selSeqs += $(linkID).getAttribute("seqFSTA");
+            }
+        }
+    });
+    return selSeqs;
+}
+
+/***Download code end****/
+
+/***Init navigation code begin **/
+
+function initNavigation(navObj) {
+    initNextAlnLink(navObj, true);
+    initNextAlnLink(navObj, false);
+}
+
+
+function initNavInfo(navObj) {
+    var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind"));
+    nextInd = currInd + 1;
+    prevInd = currInd - 1;
+
+    navObj.currSeqID = "";
+    navObj.nextSeqID = "";
+    navObj.prevSeqID = "";
+
+    if ($("deflnDesc_" + nextInd)) {
+        navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs");
+        if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA");
+    }
+    if ($("deflnDesc_" + prevInd)) {
+        navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs");
+        if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA");
+    }
+    if ($("deflnDesc_" + currInd)) {
+        navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA");
+    }
+}
+
+
+function initNextAlnLink(navObj, next) {
+
+    var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID);
+    var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID;
+
+    if (nextLinkEl) {
+        if (nextSeqid != "") {
+            var text = (next) ? "next" : "previous";
+            nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid);
+        }
+        else {
+            nextLinkEl.setAttribute("disabled", "disabled");
+        }
+    }
+}
+function scan(link) {
+    var init = link.getAttribute("init");
+    if (!init) {
+        ncbi.sg.scanLinks(link);
+        link.setAttribute("init","on");
+    }
+}
+
+function initWidth(seqID) {
+    var lineLengthElem = $("FormatForm").LINE_LENGTH;
+    var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
+    if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
+
+    var relWidth = (lineLength > 90) ? "12%" : "15%";
+    var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
+    lineLength = (lineLength + parseInt(17)) * charWidth;
+    var width = lineLength + "px";
+    jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) {
+        jQuery(this).css("width", width);
+    });
+    jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) {
+        jQuery(this).css("width", width);
+    });
+    jQuery($("relInf_" + seqID)).css("width", relWidth);
+}
+
+
+/***Init navigation code end **/
+function initAlignBatch(seqID)
+{
+    var navObj = new Object();
+    navObj.seqID = seqID;
+    initNavInfo(navObj);
+
+    initAlignDownLoad(navObj);
+    initNavigation(navObj);
+    ncbi.sg.scanLinks($("alnNxt_" + seqID));
+    ncbi.sg.scanLinks($("alnPrv_" + seqID));
+    if ($("serviceType").value == "vecscreen") {
+        utils.addClass($("alnDsc_" + seqID), "hidden");
+    }
+    ncbi.sg.scanLinks($("alnDwnld_" + seqID));
+    jQuery($("csLinks_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("relInf_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("rng_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("dln_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    initWidth(seqID);
+/*
+    jQuery($("alnHdr_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("aln_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+*/
+}
+
+function SaveConfigTable() {
+    blastUrl = "fmtsave.cgi";
+
+
+    var rp = new RemoteDataProvider(blastUrl);
+
+
+    rp.onSuccess = function(obj) {
+        //alert("success");
+    };
+    rp.onError = function(obj) {
+        //alert("error");
+    }
+
+    var program = getHiddenFieldVal("PROGRAM");
+    var rid = getHiddenFieldVal("RID");
+    var blastSpec = getHiddenFieldVal("BLAST_SPEC");
+    var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value;
+    if(blastSpec) {
+        params += "&BLAST_SPEC=" + blastSpec;
+    }
+    rp.Request(params,"POST");
+}
+
+function removeRID() {
+    var rid = document.getElementsByName("RID");
+    for (var i = 0; i <= rid.length; i++) {
+        jQuery(rid[i]).remove();
+    }
+}
+
+function initAdvancedView()
+{
+    if ($("dsConfig")) {
+
+        var alnView = getHiddenFieldVal("ALIGNMENT_VIEW");
+        if (alnView == "Pairwise" || alnView == "PairwiseWithIdentities") {
+            var rid = getHiddenFieldVal("RID");
+            ReadNextSeqAligns(0, 5);
+            g_alignViewPos = $("alignView").getBoundingClientRect().top;
+            utils.addEvent(window, "scroll", checkAutoAlignLoad, false);
+        }
+        list = $("phiPtInd");
+        if (list) {
+            utils.addEvent(list, "change", GetPatternLocResults, false);
+        }
+        initDescConfig();
+        initDescSelect();
+        initDescDownLoad();
+        if ($("psiInp")) {
+            var nextIter = document.getElementsByName("NEXT_I");
+            for (var i = 0; i < nextIter.length; i++) {
+                utils.addEvent(nextIter[i], "click", removeRID, false);
+            }
+        }
+    }
+}
+
+//takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4"
+function initjQry()
+{
+    var oldCreate = jQuery.ui.ncbipopper.prototype._create;
+    jQuery.ui.ncbipopper.prototype._create = function() {
+        var destSelector = this.options.destSelector || this.options.sourceSelector || this.element.prop("hash");
+        this.options.destSelector = destSelector.replace(/\./g, "\\.");
+        oldCreate.apply(this, arguments);
+    }
+}
+utils.addEvent(window,
+				"load", initAdvancedView,
+				false);
+
+initjQry()
+
+/* If user agent has "safari" in it, include safari-specific stylesheet. */
+if (navigator.userAgent.match(/ie/i)) {
+    document.write("<link rel='stylesheet' type='text/css' href='css/ie-descriptions.css'  media='screen'/>");
+}
+/*****************************new code end*********************************************************************/
Binary file NCBI Blast reference example_files/helix.gif has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jig.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+.ui-helper-hidden{display:none;}.ui-helper-hidden-accessible{position:absolute;left:-99999999px;}.ui-helper-reset{margin:0;padding:0;border:0;outline:0;line-height:1.3;text-decoration:none;font-size:100%;list-style:none;}.ui-helper-clearfix:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-helper-clearfix{display:inline-block;}/* required comment for clearfix to work in Opera \*/ * html .ui-helper-clearfix{height:1%;}.ui-helper-clearfix{display:block;}/* end clearfix */ .ui-helper-zfix{width:100%;height:100%;top:0;left:0;position:absolute;opacity:0;filter:Alpha(Opacity=0);}.ui-state-disabled{cursor:default!important;}.ui-icon{display:block;text-indent:-99999px;overflow:hidden;background-repeat:no-repeat;}.ui-widget-overlay{position:absolute;top:0;left:0;width:100%;height:100%;}.ui-widget{font-size:1.1em;}.ui-widget-content{border:1px solid #aaa;background:#fff url(images/ui-bg_flat_75_ffffff_40x100.png) 50% 50% repeat-x;color:#222;}.ui-widget-content a{color:#222;}.ui-widget-header{border:1px solid #aaa;background:#ccc url(images/ui-bg_highlight-soft_75_cccccc_1x100.png) 50% 50% repeat-x;color:#222;font-weight:bold;}.ui-widget-header a{color:#222;}.ui-state-default,.ui-widget-content .ui-state-default{border:1px solid #d3d3d3;background:#e6e6e6 url(images/ui-bg_glass_75_e6e6e6_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#555;}.ui-state-default a,.ui-state-default a:link,.ui-state-default a:visited{color:#555;text-decoration:none;}.ui-state-hover,.ui-widget-content .ui-state-hover,.ui-state-focus,.ui-widget-content .ui-state-focus{border:1px solid #999;background:#dadada url(images/ui-bg_glass_75_dadada_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#212121;}.ui-state-hover a,.ui-state-hover a:hover{color:#212121;text-decoration:none;}.ui-state-active,.ui-widget-content .ui-state-active{border:1px solid #aaa;background:#fff url(images/ui-bg_glass_65_ffffff_1x400.png) 50% 50% 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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery.js	Thu May 15 16:59:18 2014 +0200
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+this.element.find("li").not(":has(ul)").find("a").off("click",this._unselectEverythingFnc)},_addAjaxEvents:function(){if(this.element.find(">li:has(a.expandDown)").not(":has(ul)").length>0){var a=this;this._ajaxEnterFnc=function(){a._loadAjaxContent()};this.element.on("mouseenter",this._ajaxEnterFnc)}},_loadAjaxContent:function(){var a=this;this.element.off("mouseenter",this._ajaxEnterFnc);this._ajaxEnterFnc=null;var d=this.element.find("a.expandDown"),b=d.eq(0).prop("href").split("#");jQuery("<div/>").load(b[0],
+function(){a._handleAjaxLoadCallback(this,d)})},_handleAjaxLoadCallback:function(a,d){var b=jQuery(a);d.each(function(){var c=jQuery(this),e=c.prop("href").split("#")[1];e=b.find("#"+e);if(e[0].tagName.toLowerCase()==="li")e=e.find(">ul");c.parent().append(e)});this._createMenus();this._addEvents()},_checkFocus:function(){function a(){d.element.find("a:focus").length===0&&d._unselectEverything()}var d=this;window.setTimeout(a,10)},_addListeners:function(){var a=this;this.element.find(">ul").andSelf().on("ncbibasicmenuunselected",
+function(d,b,c,e){e==="click"&&a.closeSub(c)}).on("ncbibasicmenuselected",function(d,b,c,e){if(e==="click")a.openSub(c);else{d=c.siblings().find("ul:visible");if(d.length>0){d.each(function(){a.closeSub(jQuery(this))});c.parent("ul").hasClass("ui-ncbimenu")&&a.openSub(c)}}}).on("ncbibasicmenuactiondown ncbibasicmenuactionright",function(d,b){b=jQuery(b);var c=b.find(">ul");if(b.hasClass("selected"))c.length===1&&c.not(":visible")&&a.openSub(b);else b.find(">a").click();c.length===1&&window.setTimeout(function(){c.ncbibasicmenu("selectFirstItem")},
+10)}).on("ncbibasicmenuactionup ncbibasicmenuactionleft ncbibasicmenuescape",function(d,b){b=jQuery(b);d=b.find(">ul");if(d.length>0&&d.is(":visible"))a.closeSub(jQuery(b));else{b=b.parent("ul").parent("li");b.find(">a").focus();a.closeSub(b)}})},_destroyListeners:function(){this.element.find("ul").andSelf().off("ncbibasicmenuunselected").off("ncbibasicmenuselected")},openSub:function(a){var d=a.find(">ul");if(d.length===1){this._isActive=true;var b=a.parent().find("li:has(ul:visible)");b.length>
+0&&this.closeSub(b);if(a.parent().hasClass("orientation_hort")){b="left bottom";var c="fit flip"}else{b="right center";c="flip fit"}d.show().position({of:a,my:"left top",at:b,collision:c}).attr("aria-hidden","false")}},closeSub:function(a){(a.is("li")?a.find("ul"):a).find("ul").andSelf().not(".ui-ncbimenu").hide().attr("aria-hidden","true").end().ncbibasicmenu("removeAllSelections").find("li.selected").removeClass("selected")},_unselectEverything:function(){this.closeSub(this.element.find("ul:visible").andSelf());
+this._isActive=false}});
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_002.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+.ui-ncbigrid-outer-div{min-width:300px;}table.ui-ncbigrid td{padding:.363em .637em;}table.ui-ncbigrid th{padding:.308em .539em;text-align:left;border-left:0;border-top:0;font-weight:normal;}table.ui-ncbigrid thead th{border-bottom:1px solid #d4dfe9;border-right:1px solid #cfcfcf;background:#F0F0F0;background:-moz-linear-gradient(top,#FFF 0,#F0F0F0 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#F0F0F0));}table.ui-ncbigrid tbody th{line-height:1.333em;color:#333;font-size:.923em;border-bottom:1px solid #d4dfe9;border-right:1px solid #cfcfcf;background:#FAFAFA;background:-moz-linear-gradient(top,#FFF 0,#FAFAFA 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#FAFAFA));}table.ui-ncbigrid th:last-child{border-right:0;*margin-right:-1px;}table.ui-ncbigrid td{border:0;}table.ui-ncbigrid td input[type="checkbox"]{margin:0;}table.ui-ncbigrid thead,table.ui-ncbigrid tbody,table.ui-ncbigrid colgroup,table.ui-ncbigrid col,table.ui-ncbigrid tr{border:0!important;}table.ui-ncbigrid,table.ui-ncbigrid thead,table.ui-ncbigrid caption{margin:0;}.ui-ncbigrid-outer-div{position:relative;zoom:1;margin:1em 0 2.8em 0;}div.caption-exists,div.filterToolbar-exists{margin:3em 0;}table.ui-ncbigrid{border-width:0;}.ui-ncbigrid-inner-div{border-color:#97b0c8;border-style:solid;}.ui-ncbigrid-inner-div{border-width:0 0 1px 0;clear:both;}.ui-ncbigrid-outer-div{border:1px solid #97b0c8;}.ui-ncbigrid-outer-div:after{clear:both;content:'.';display:block;height:0;visibility:hidden;font-size:0;}.ui-ncbigrid-header-wrapper{height:auto;max-width:100%;}.ui-ncbigrid-header-wrapper table.ui-ncbigrid{border:0;height:auto;}.ui-ncbigrid-header-wrapper thead{border-width:1px 0 0 0;}table.ui-ncbigrid caption{color:#4D4D4D;font-size:.923em;font-weight:bold;padding:0;position:absolute;text-align:left;top:-2.077em;zoom:1;}.ui-ncbigrid-filter-toolbar{clear:both;display:block;font-size:.923em;line-height:27px;position:absolute;right:0;text-align:right;top:-2.417em;width:auto;}.ui-ncbigrid-filter-toolbar input[type="text"]{font-size:inherit!important;height:1.091em;padding:0;margin-right:-1px;}.ui-ncbigrid-paged-toolbar{display:block;clear:both;width:100%;}.ui-ncbigrid-paged-countItems,.ui-ncbigrid-checkbox-toolbar{font-size:.923em;}.ui-ncbigrid-paged-toolbar div{float:left;display:inline-block;width:auto;margin-right:1em;}.ui-ncbigrid-paged-toolbar .ui-ncbigrid-paged-pageControl{margin-right:0;}.ui-ncbigrid-paged-countItems{text-align:center;}.ui-ncbigrid-paged-pageControl{text-align:right;font-size:.923em;}.ui-ncbigrid-paged-pageControl .prev{margin-left:.2em;margin-right:.6em;}.ui-ncbigrid-paged-pageControl .next{margin-left:.6em;margin-right:.2em;}.ui-ncbigrid-paged-toolbar-bottom{border-top:0;}.ui-ncbigrid-select-question{clear:both;text-align:center;display:none;padding:.385em 0 .308em;border-style:solid;border-color:#d4dfe9;border-width:1px 0;background:-moz-linear-gradient(top,#FFF 0,#F5F5F5 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#F5F5F5));font-size:.923em;}.ui-ncbigrid-select-question-footer{background:#fff;border-bottom:0;}.ui-ncbigrid-select-question .ui-ncbigrid-select-row-count{font-weight:bold;}.ui-ncbigrid-select-question a{margin-left:.583em;}.ui-ncbigrid-checkbox-toolbar label{margin-left:1em;}.ui-ncbigrid-checkbox-toolbar label:first-child{margin-left:0;}.ui-ncbigrid-checkbox-toolbar a,.ui-ncbigrid-checkbox-toolbar a:visited{color:#369;}.ui-ncbigrid-checkbox-toolbar,.ui-ncbigrid-paged-toolbar{width:auto;}.ui-ncbigrid-checkbox-toolbar{float:left;clear:left;padding:.416em .416em .416em .583em;line-height:1.75em;}.ui-ncbigrid-paged-toolbar{float:right;clear:right;padding:.385em .385em .385em .539em;line-height:1.615em;}table.ui-ncbigrid{border-collapse:separate;width:100%;}div.ui-ncbigrid-scroll{height:20em;overflow-y:auto;overflow-x:hidden;}div.ui-ncbigrid-scroll table.ui-ncbigrid{border-top:0;border-bottom:0;width:100%;}div.ui-ncbigrid-scroll table.ui-ncbigrid caption,div.ui-ncbigrid-scroll>table.ui-ncbigrid>thead>tr>th{visibility:hidden;line-height:0;border-bottom:0;border-top:0;padding-top:0;padding-bottom:0;}div.ui-ncbigrid-scroll table.ui-ncbigrid tbody tr:first-child td{border-top:0;}div.ui-ncbigrid-header-wrapper{width:100%;overflow:hidden;}div.ui-ncbigrid-hort-scroll{overflow-x:auto;}tr.ui-ncbigrid-rowHidden{display:none;}table.ui-ncbigrid th.sortAsc a,table.ui-ncbigrid th.sortDsc a,table.ui-ncbigrid th.sortNone a{padding-right:21px;background-repeat:no-repeat;background-position:right center;color:#333;}table.ui-ncbigrid th.sortAsc,table.ui-ncbigrid th.sortDsc{background:#fff;}table.ui-ncbigrid th.sortAsc a{background-image:url('../img/sorted_asc.gif');}table.ui-ncbigrid th.sortDsc a{background-image:url('../img/sorted_dsc.gif');}table.ui-ncbigrid th.sortNone a{background-image:none;color:#14376c;}table.ui-ncbigrid th.sortNone a:hover{background-image:url('../img/sorted_non.gif');color:#985735;}table.ui-ncbigrid th a{display:block;text-decoration:none;_width:100%;padding-right:21px;border:0;}table.ui-ncbigrid th a:hover,table.ui-ncbigrid th a,table.ui-ncbigrid th a:active{border:0!important;}table.ui-ncbigrid th,table.ui-ncbigrid th a{color:#14376c;}table.ui-ncbigrid tbody tr.ui-ncbigrid-checkbox-selected td,table.ui-ncbigrid tr.ui-ncbigrid-row-selected td{background-color:#eaf0f4;}table.ui-ncbigrid tbody tr.ui-ncbigrid-checkbox-hover td,table.ui-ncbigrid tr.ui-ncbigrid-row-hover>td{background-color:#D5DEE3;}table.ui-ncbigrid tr.ncbigrid-row-filtered{display:none;}td.ui-ncbigrid-column-hidden,th.ui-ncbigrid-column-hidden{display:none;}table.ui-ncbigrid tbody tr.ui-ncbigrid-high>td{background-color:#eaf0f4;}.ui-ncbigrid-paged-pageControl{margin-top:0;}.ui-ncbigrid-paged-pageControl input[type="text"]{height:1.091em;font-size:inherit!important;padding:0;}.ui-ncbigrid-paged-pageControl span.page_link{color:#ccc;padding:1px 7px;}.ui-ncbigrid-paged-pageControl a.page_link{border:1px solid #ddd;padding:2px 6px;*padding:0 4px;white-space:nowrap;text-decoration:none;}.ui-ncbigrid-paged-pageControl a.page_link:hover{color:#985735;}.ui-ncbigrid tbody tr.collapsed{display:none;}.ui-ncbigrid tbody tr th span.collapsableTbodyIcon{float:left;margin-right:.833em;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big{background-position:left -30px;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big-open{background-position:left 0;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big,.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big-open{background-color:transparent;background-image:url("../img/ncbitoggler-plus-minus-big.gif");background-repeat:no-repeat;margin-left:-0.1em;top:.2em;}.ui-ncbigrid-collapsable,.ui-ncbigrid-collapsable span{cursor:pointer;}table.ui-ncbigrid .ignoreCollapse{cursor:default;}.ui-ncbigrid-outer-div .ui-ncbigrid-outer-div{margin:0;*position:static;}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_002.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,22 @@
+(function(e){e.widget("ui.ncbitoggler",{styles:{ariaWrapper:"ui-ncbitoggler-live",groupMasterReplaceNode:"span.ui-ncbitoggler-group-replace-txt",groupMasterStateClose:"ui-ncbitoggler-group-master-to-close",groupMasterStateOpen:"ui-ncbitoggler-group-master-to-open",master:"ui-ncbitoggler",masterOpen:"ui-ncbitoggler-open",target:"ui-ncbitoggler-slave",targetOpen:"ui-ncbitoggler-slave-open",icon:"ui-icon-triangle-1-e",iconOpen:"ui-icon-triangle-1-s",iconPlusMinusBig:"ui-icon-plus-minus-big",iconPlusMinusBigOpen:"ui-icon-plus-minus-big-open",
+iconArrowStop:"ui-icon-arrowthickstop-1-s",iconArrowStopOpen:"ui-icon-arrowthickstop-1-n"},options:{animation:"slide",closedAppendText:"",cookieNamePrefix:"jig-tog-rem-",indicator:"small-arrow",initOpen:false,isIcon:true,liveRegions:true,openedAppendText:"",remember:false,speed:50,targets:""},_cachedTargetData:{},_create:function(){this._setOption("disabled",false);this.appendTextNode=this.initTargetsClass=this.iconSpan=this.startOpen=this.rememberCookie=this.remember=this.cookieName=this.addedHref=
+null;var a=this.element,b=a[0],c=this.styles,d=this,f=this.options.isIcon;a.data("isOpen",false);a.addClass("ui-widget ui-ncbitoggler");f||a.addClass("ui-ncbitoggler-no-icon");var g=a.attr("href");!g?(this.addedHref=true):(this.addedHref=false);this._validate(g);a.children("span.ui-ncbitoggler-master-text").length===0&&a.contents().filter(function(){return this.nodeType===3}).each(function(){var h=e(this);jQuery.trim(this.nodeValue).length>0&&h.wrap('<span class="ui-ncbitoggler-master-text"></span>')});
+if(this.options.openedAppendText!==""||this.options.closedAppendText!==""){this.appendTextNode=a.children("span.ui-ncbitoggler-appended-text");if(this.appendTextNode.length===0)if(!this.initOpen){this.appendTextNode=e('<span class="ui-ncbitoggler-appended-text">'+this.options.closedAppendText+"</span>");a.find(".ui-ncbitoggler-master-text").after(this.appendTextNode)}}if(this.remember=this.options.remember||false){g=this.element.attr("id");if(!g){window.console&&console.error&&console.error("ncbitoggler: master node "+
+b+" must have a unique id attribute when remembering state");return}this.cookieName=this.options.cookieNamePrefix+g;this.rememberCookie=e.cookie(this.cookieName)}if(this.startOpen=this.rememberCookie?this.rememberCookie==="open"?true:false:a.hasClass("jig-ncbitoggler-open")||a.hasClass(c.masterOpen)||this.options.initOpen?true:false){this.element.data("isOpen",true);a.removeClass(this.styles.master);a.addClass(c.masterOpen);this._targetsOpen=true}else{this.element.data("isOpen",false);a.removeClass(this.styles.masterOpen);
+a.addClass(c.master)}f&&this._initMasterIcon();this.targets=this._getTargets();this.targets.addClass("ui-ncbitoggler").removeClass("ui-ncbitoggler-disabled ui-state-disabled");if(this.startOpen){this.targets.removeClass(c.target);this.targets.addClass(c.targetOpen);this.initTargetsClass=c.targetOpen}else{this.targets.removeClass(c.targetOpen);this.targets.addClass(c.target);this.initTargetsClass=c.target}this._initAria();this._doGrouping();a.click(function(h){d.toggle(h,d)});this._saveReferences()},
+_getGroupMaster:function(){for(var a=this.styles,b=this.element[0].className.split(/\s+/),c=0;c<b.length;c++){var d=b[c].match(/ui-ncbitoggler-group-(.+)$/);if(d){d=d[1];var f=e("a.ui-ncbitoggler-group-open-"+d+", a.ui-ncbitoggler-group-close-"+d,this.options.contextNode);if(f.length===1){f.hasClass("ui-ncbitoggler-group-open-"+d)&&f.addClass(a.groupMasterStateOpen);f.hasClass("ui-ncbitoggler-group-close-"+d)&&f.addClass(a.groupMasterStateClose);return f}}}},_doGrouping:function(){var a=this._getGroupMaster();
+if(a){var b=this,c=this.styles,d=a.data("togglers");this.element.id||e.ui.jig._generateId(this.widgetName);if(!this.element[0].id)this.element[0].id=e.ui.jig._generateId(this.widgetName);if(typeof d==="undefined"){a.data("togglers",[]);a.data("togglers").push(this.element)}else d.push(this.element);var f=a.find(c.groupMasterReplaceNode);a.click(function(g){g.preventDefault();g=a.data("togglers");g=g[g.length-1][0];if(a.hasClass(c.groupMasterStateOpen)){b.open();f.length>0&&f.text(b.options.groupMasterCloseReplaceText);
+b.element[0]===g&&a.removeClass(c.groupMasterStateOpen).addClass(c.groupMasterStateClose)}else{b.close();f.length>0&&f.text(b.options.groupMasterOpenReplaceText);b.element[0]===g&&a.removeClass(c.groupMasterStateClose).addClass(c.groupMasterStateOpen)}})}},_initAria:function(){var a=this.startOpen;this.element.attr({role:"button","aria-expanded":a});this.options.liveRegions&&this.targets.each(function(){var b=e(this);b.find("table").length===0&&!b.parent("div").hasClass("ui-helper-reset")&&b.wrap('<div class="ui-helper-reset" aria-live="assertive">');
+b.attr("aria-hidden",a?"false":"true")})},_validate:function(a){var b=this.element,c=["a"],d=b[0].tagName.toLowerCase();if(e.inArray(d,c)===-1)throw new Error("ncbitoggler: master node must be one of the following elements: "+c.toString());a||b.attr("href","#")},_initMasterIcon:function(){var a=this.element,b=this.styles;if(this.options.indicator=="plus-minus-big"){this.iconOpenClass=b.iconPlusMinusBigOpen;this.iconCloseClass=b.iconPlusMinusBig}else if(this.options.indicator=="arrow-stop"){this.iconOpenClass=
+b.iconArrowStopOpen;this.iconCloseClass=b.iconArrowStop}else{this.iconOpenClass=b.iconOpen;this.iconCloseClass=b.icon}this.iconSpan=a.find("span.ui-icon");if(this.iconSpan.length===0){this.iconSpan=e('<span class="ui-icon"></span>');this.startOpen?this.iconSpan.addClass(this.iconOpenClass):this.iconSpan.addClass(this.iconCloseClass);a.append(this.iconSpan)}else if(this.startOpen){this.iconSpan.removeClass(this.iconCloseClass);this.iconSpan.addClass(this.iconOpenClass)}},getSlaves:function(){return this._targets},
+getTargets:function(){return this.getSlaves()},_getTargets:function(){var a=this.element,b=a.attr("toggles")||a.attr("data-ncbitoggler-toggles");if(b)jQuery.ui.jig._isConsole("warn")&&console.warn('The attributes "toggles" and "data-ncbitoggler-toggles" are deprecated. Please use the "targets" attribute instead (see documentation).');else b=this.options.targets;if(b&&typeof b=="object"){b=b;a="";for(var c in b)a+=c+", ";a=a.replace(/,\s$/,"");c=e(a)}else if(b){c=e(b);if(c.length===0){this.isSibling=
+false;c=b.split(/ +/);b="";for(a=0;a<c.length;a++)b+=a!==c.length-1?"#"+c[a]+",":"#"+c[a];c=e(b)}}else if(a.parent(":header").length>0){a.parent(":header").parent().css("zoom","1");this.isSibling=true;c=a.parent(":header").css("zoom","1").next()}else{this.isSibling=true;c=a.next()}return this._targets=this._normalizeTargets(c)},_normalizeTargets:function(a){var b=[];a.each(function(){var c=this,d=e(this);if(d.hasClass("ui-helper-reset"))c=d.children().get(0);b.push(c)});return ret=e(b)},_getCachedTargetData:function(a){return this._cachedTargetData[a]},
+_cacheTargetData:function(a,b){this._cachedTargetData[a]=b},_openAjaxTarget:function(a,b){var c=this,d=this._getCachedTargetData(a);d?e(a).html(d):e.get(b,function(f){c._cacheTargetData(a,f);e(a).html(f)})},_openTargets:function(){if(!(this._targetsOpening||this._targetsClosing||this._targetOpen)){this._targetsOpening=true;var a=this.targets,b=this.styles;a.removeClass(b.target).addClass(b.targetOpen).attr("aria-hidden","false");var c=this.options.targets;if(typeof c=="object"){var d=this;for(targetSel in c)(function(f){d._openAjaxTarget(f,
+c[f])})(targetSel)}b=this.options.openedAppendText;b!==""&&this.appendTextNode.html(b);a.css("display","");this._targetsOpening=false;this._targetsOpen=true}},_closeTargets:function(){if(!(this._targetsOpening||this._targetsClosing||!this._targetsOpen)){this._targetsClosing=true;var a=this.targets,b=this.styles;a.removeClass(b.targetOpen).addClass(b.target).attr("aria-hidden","true");b=this.options.closedAppendText;b!==""&&this.appendTextNode.html(b);a.css("display","");this._targetsOpen=this._targetsClosing=
+false}},_fixHasLayout:function(a){window.setTimeout(function(){a.targets.addClass("foo").removeClass("foo")},1)},open:function(a){var b=this.element,c=this;if(!b.hasClass(this.styles.master))return b;this.updateState("open");if(this.options.animation==="slide")this.targets.slideToggle(this.options.speed,function(){c._openTargets();e.browser.msie&&c._fixHasLayout(c);b.data("isOpen",true);b.trigger("ncbitoggleropen");a&&a()});else{this._openTargets();e.browser.msie&&c._fixHasLayout(c);b.data("isOpen",
+true);b.trigger("ncbitoggleropen");a&&a()}this._updateReferences("open");return b},close:function(a){var b=this.element,c=this;if(!b.hasClass(this.styles.masterOpen))return b;this.updateState("closed");if(this.options.animation==="slide")this.targets.slideToggle(this.options.speed,function(){c._closeTargets();b.trigger("ncbitogglerclosed").trigger("ncbitogglerclose");b.data("isOpen",false);a&&a()});else{this._closeTargets();b.data("isOpen",false);b.trigger("ncbitogglerclosed");a&&a()}this._updateReferences("closed");
+return b},toggle:function(a,b,c){var d=arguments.length;if(d===0||d===1){b=this;if(d===1)c=arguments[0]}else a.preventDefault();this.element.hasClass(this.styles.master)?b.open(c):b.close(c)},updateState:function(a){var b=this.element;a||(a=b.hasClass(styles.master)?"open":"closed");var c=this.styles.master,d=this.styles.masterOpen,f=this.iconCloseClass,g=this.iconOpenClass;if(a=="closed"){c=this.styles.masterOpen;d=this.styles.master;f=this.iconOpenClass;g=this.iconCloseClass}b.removeClass(c).addClass(d).attr("aria-expanded",
+a=="closed"?"false":"true");this.options.isIcon&&this.iconSpan.removeClass(f).addClass(g);this.remember&&e.cookie(this.cookieName,a)},_removeHandlers:function(){this.element.unbind("click")},destroy:function(){e.Widget.prototype.destroy.apply(this,arguments);var a=this.element,b=this.styles;a.removeClass(b.master+" "+b.masterOpen+" ui-state-disabled ui-widget ui-ncbitoggler-disabled").removeAttr("role").removeAttr("aria-expanded");this.targets.removeClass("ui-ncbitoggler ui-ncbitoggler-slave ui-ncbitoggler-slave-open ui-state-disabled ui-ncbitoggler-disabled");
+this.targets.removeAttr("aria-hidden");if(this.options.isIcon){b=a.find("span.ui-icon")[0];a[0].removeChild(b)}this.targets.each(function(){var d=jQuery(this),f=d.parent("div.ui-helper-reset");if(f.length>0){d.insertBefore(f);f.remove()}});b=a.find("span.ui-ncbitoggler-master-text");var c=b.html();b.remove();a.html(c);this._removeHandlers();return this},disable:function(){e.Widget.prototype.disable.apply(this,arguments);this._removeHandlers();this.targets.addClass("ui-ncbitoggler-disabled ui-state-disabled");
+return this},enable:function(){e.Widget.prototype.enable.apply(this,arguments);this.targets.removeClass("ui-ncbitoggler-disabled ui-state-disabled");var a=this;this.element.click(function(b){a.toggle(b,a)});return this},_saveReferences:function(){var a=this;this._targets.each(function(){typeof e(this).data("ncbitoggler-masters")==="undefined"&&e(this).data("ncbitoggler-masters",[]);e(this).data("ncbitoggler-masters").push(a.element)})},_updateReferences:function(a){var b=this;e.each(this._targets.data("ncbitoggler-masters"),
+function(){b.element!=this&&e(this).ncbitoggler("updateState",a)})}})})(jQuery);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_003.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+.ui-ncbibasicmenu{list-style-type:none;min-width:200px;}.ui-ncbibasicmenu,.ui-ncbibasicmenu>li{padding:0;margin:0;}.ui-ncbibasicmenu li ul li{background-color:#FFF;}.ui-ncbibasicmenu li ul li a:hover,.ui-ncbibasicmenu li ul li.selected a:hover{background-color:#4C96DF;color:#FFF;}.oneLevel li a,.ui-ncbibasicmenu li a{display:block;text-decoration:none;background-color:#FCFCFC;border:1px solid #FCFCFC;border-width:1px 0;color:#14376C;font-size:13px;font-weight:normal;margin:0;padding:.2em .9em;text-decoration:none;}.oneLevel li a:hover,.ui-ncbibasicmenu>li>a:hover{background-color:#E3F8FF;}.oneLevel li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbibasicmenu>li.ui-ncbimenu-item-no-hlt>a:hover,.oneLevel li.ui-ncbimenu-item-skip a:hover,.ui-ncbibasicmenu>li.ui-ncbimenu-item-skip>a:hover{background-color:#FCFCFC;}.oneLevel li a:focus,.ui-ncbibasicmenu>li>a:focus{outline:1px dashed #000;}.oneLevel li.selected a,.ui-ncbibasicmenu>li.selected>a{color:#FFF;background-color:#4C96DF;}.oneLevel li.selected a:hover,.ui-ncbibasicmenu>li.selected>a:hover{color:#FFF;}.oneLevel li.selected.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbibasicmenu>li.selected.ui-ncbimenu-item-no-hlt>a:hover,.oneLevel li.selected.ui-ncbimenu-item-skip a:hover,.ui-ncbibasicmenu>li.selected.ui-ncbimenu-item-skip>a:hover{color:inherit;background-color:#FCFCFC;}.orientation_hort>li{display:inline;float:left;}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_003.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+(function(){jQuery.widget("ui.ncbilocalnav",jQuery.ui.ncbimenu,{_create:function(){this.options.isSubMenuLimited=true;jQuery.ui.ncbimenu.prototype._create.apply(this,arguments)},_addClasses:function(){this.element.addClass("ui-ncbilocalnav");jQuery.ui.ncbimenu.prototype._addClasses.apply(this,arguments)},_destroyClasses:function(){this.element.removeClass("ui-ncbilocalnav");jQuery.ui.ncbimenu.prototype._destroyClasses.apply(this,arguments)}})})();
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_004.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+div.ui-ncbiautocomplete-holder{position:absolute;top:0;left:0;border:1px solid #5a5a5a;display:none;font-family:Arial,helvetica,sans-serif;font-size:inherit;border-style:solid;border-color:#777;border-width:1px;}ul.ui-ncbiautocomplete-options{height:218px;overflow:auto;overflow-x:hidden;overflow-y:auto;width:100%;margin:0;padding:0;list-style-type:none;font-weight:normal;cursor:pointer;background-color:#FFF;}ul.ui-ncbiautocomplete-options li span{font-weight:normal;}ul.ui-ncbiautocomplete-options li{padding:.2em;padding-left:.8em;padding:.231em .461em;white-space:nowrap;overflow:hidden;width:100%;color:#14376c;text-overflow:ellipsis;}ul.ui-ncbiautocomplete-options li:last-child{padding-bottom:.6em;}ul.ui-ncbiautocomplete-options li.ui-ncbiautocomplete-options-high{background-color:#DAEEF4;text-decoration:none;color:#015;}.ui-ncbiautocomplete-actions{background-color:#CECECE;line-height:inherit;padding:5px;border:1px solid #777;*zoom:1;*display:block;margin:1px -1px 0 -1px;min-height:15px;}.ui-ncbiautocomplete-actions:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-ncbiautocomplete-actions{display:inline-block;}.ui-ncbiautocomplete-actions a{display:inline;float:left;color:#015;text-decoration:none;}.ui-ncbiautocomplete-actions .ui-ncbiautocomplete-link-pref-right{text-align:right;float:right;}.ui-ncbiautocomplete-link-pref{text-indent:-9999px;background:url("../img/gear.png") no-repeat;width:15px;height:16px;}a.ui-ncbiautocomplete-link-off:hover,a.ui-ncbiautocomplete-link-pref:hover{text-decoration:underline;color:#015;}li.ui-ncbiautocomplete-show-more{width:100%!important;background:#C3D2DB!important;border-top:1px solid #5A5A5A;}li.ui-ncbiautocomplete-show-more.ui-ncbiautocomplete-options-high{text-decoration:underline!important;}iframe.ui-ncbiautocomplete-iframe{position:absolute;top:0;left:0;height:200px;z-index:1000;display:none;filter:alpha(opacity=1);}.shadow{-webkit-box-shadow:.4em .4em .5em rgba(153,153,153,.9);-moz-box-shadow:.4em .4em .5em rgba(153,153,153,.9);box-shadow:.4em .4em .5em rgba(153,153,153,.9);}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_004.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,53 @@
+jQuery.widget("ui.ncbiautocomplete",{options:{webserviceUrl:"/portal/utils/autocomp.fcgi",isUrlRelative:false,dictionary:"",responseFormat:"old",disableUrl:null,prefUrl:null,zIndex:1001,isEnabled:true,hasRelatedMatches:false,minLength:2,expandPauseTime:400,maxListLimit:null,isCrossDomain:false,disableCache:false,requireValidation:false,queryParameter:"q"},_create:function(){if(this.options.localData&&!this.options.dictionary)this.options.dictionary="local";this._storeTitleAttribute();this._createOptionsBox();
+this._addAttributes();this._setHandlers();this._setWebServicePath();this._lastEnteredTerm="";this._setSGData()},_storeTitleAttribute:function(){this.element.data("ncbiautocompleteOriginalTitle",this.element.attr("title"))},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);this.element.removeAttr("title");this._destroyAria();this._destroyHandlers();var a=this.element.data("ncbiautocompleteOriginalTitle");a&&this.element.attr("title",a)},_destroyOptionsBox:function(){jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox!=
+null&&jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox.remove()},_destroyHandlers:function(){this.element.off("keypress keydown keyup cut paste")},_destroyAria:function(){this.element.removeAttr("aria-haspopup").removeAttr("aria-autocomplete").removeAttr("role").removeAttr("autocomplete")},_activeRequest:null,_keys:{up:38,down:40,enter:13,escape:27,tab:9,shift:16},_setSGData:function(){this.sgData={jsevent:"autocomplete",userTyped:"",hasScrolled:false,usedArrows:false,selectionAction:"",optionSelected:"",
+optionIndex:-1,optionsCount:-1}},_addAttributes:function(){this.element.attr({title:"Use up and down arrows to choose an item from the autocomplete.","aria-haspopup":true,"aria-autocomplete":"list",role:"textbox"})},_setHandlers:function(){var a=this;jQuery(this.element).focus(function(){a._focused()}).keypress(function(c){a._keyPress(c,"press")}).keydown(function(c){a._keyPress(c,"down")}).keyup(function(c){a._keyUp(c)}).bind("cut paste",function(){a._changeFired()}).attr("AUTOCOMPLETE","OFF");var b=
+jQuery(this.element)[0];b.autocomplete="off";b.AUTOCOMPLETE="OFF";jQuery(window).resize(function(){a._isActive&&a._positionOptionsBox()});jQuery(document).click(function(c){a._checkClickEvent(c)});jQuery(this._gol.optionsBox).hover(function(){if(a._isActive)a._isOptionsBoxFocused=true},function(){if(a._isActive)a._isOptionsBoxFocused=false})},_isOptionsBoxFocused:false,_createOptionsBox:function(){if(jQuery.ui.ncbiautocomplete._globalOptionsList===null){jQuery.ui.ncbiautocomplete._globalOptionsList=
+{};var a=jQuery("div.grid");a=a.length===1?a:jQuery(document.body);jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox=jQuery("<div class='ui-ncbiautocomplete-holder shadow' aria-live='assertive'></div>").appendTo(a);jQuery.ui.ncbiautocomplete._globalOptionsList.optionsList=jQuery("<ul class='ui-ncbiautocomplete-options' role='listbox' aria-activedescendant=''></ul>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox));jQuery.ui.ncbiautocomplete._globalOptionsList.optionsActions=
+jQuery("<div class='ui-ncbiautocomplete-actions shadow'></div>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox));jQuery.ui.ncbiautocomplete._globalOptionsList.prefLink=jQuery("<a href='#' class='ui-ncbiautocomplete-link-pref'>Preferences</a>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsActions));jQuery.ui.ncbiautocomplete._globalOptionsList.turnOffLink=jQuery("<a href='#' class='ui-ncbiautocomplete-link-off'>Turn off</a>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsActions));
+jQuery.ui.ncbiautocomplete._globalOptionsList.isIE6=jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<7;if(jQuery.ui.ncbiautocomplete._globalOptionsList.isIE6)jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox.iframe=jQuery("<iframe src='javascript:\"\";' class='ui-ncbiautocomplete-iframe' marginwidth='0' marginheight='0' align='bottom' scrolling='no' frameborder='0'></iframe>").appendTo(document.body)}this._gol=jQuery.ui.ncbiautocomplete._globalOptionsList},_positionOptionsBox:function(){if(this._gol.activeElement){var a=
+jQuery(this.element),b=jQuery(this._gol.activeElement);a=a.attr("id")||a[0];b=b.attr("id")||b[0];a!==b&&this._hideOptions()}var c=this;if(this._gol.activeElement!==this.element){b=this.options.prefUrl!==null?"block":"none";a=this.options.disableUrl!==null?"block":"none";var e=b==="block"||a==="block"?"block":"none";jQuery(this._gol.prefLink).css("display",b).attr("href",this.options.prefUrl).unbind("click").click(function(){c._prefLinkClick()});jQuery(this._gol.turnOffLink).css("display",a).unbind("click").click(function(m){c.turnOff();
+m.preventDefault()});jQuery(this._gol.optionsActions).css("display",e);jQuery(this._gol.optionsActions).children(":nth-child(2)").addClass("ui-ncbiautocomplete-link-pref-right")}else this._gol.activeElement=this.element;e=this.element;var d=jQuery(this._gol.optionsBox),f=false;if(e.parent().hasClass("jig-ncbiclearbutton-wrap")){e=e.parent();f=true;d.addClass("ui-ncbiautocomplete-holder-clearfix")}else d.removeClass("ui-ncbiautocomplete-holder-clearfix");b=e.outerWidth();a=e.outerHeight();e=e.offset();
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+i-k+h+"px");d.css("zIndex",f-1)}},_isActive:false,_focused:function(){this._gol.activeElement!==this.element&&this._hideOptions();this._setActivedescendant();this._positionOptionsBox();if(this.options.isEnabled){this._isActive=true;this._hasBeenEscaped=false}this.options.minLength===0&&this.options.localData&&this._keyUp({})},_lastEnteredTerm:null,_isCached:false,_hasBeenEscaped:false,_lastKeyPressDwnUpScroll:new Date,_lastFoundMatch:null,_findMatchInCache:function(a){this._lastFoundMatch=null;if(typeof this._localCache[this.options.dictionary]===
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+true;return b},_timerTriggerEnterEvent:null,_clearTriggerEnterEvent:function(){this._timerTriggerEnterEvent=null},_triggerEnterEvent:function(){var a=this;if(!this._timerTriggerEnterEvent){this._timerTriggerEnterEvent=window.setTimeout(function(){a._clearTriggerEnterEvent()},50);this.element.trigger("ncbiautocompleteenter",this.sgData);this.element.trigger("ncbiautocompletechange",this.sgData);this._sgSend()}},_triggerTabEvent:function(){this.element.trigger("ncbiautocompletetab",this.sgData);this.element.trigger("ncbiautocompletechange",
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+d?"enter":"tab";this.element.attr("valueId",this.element.attr("_optValue")||null);if(d)this._triggerEnterEvent();else{this._sentTab||this._triggerTabEvent();this._sentTab=true;window.setTimeout(function(){e._sentTab=false},10)}}this._hideOptions(true);if(d){a.stopPropagation();a.preventDefault();return false}}else a.keyCode===this._keys.tab&&this._hideOptions(true);else if(a.keyCode===this._keys.tab)if(!this._tabCalled){this._hideOptions(true);this._tabCalled=true;window.setTimeout(function(){e._tabCalled=
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+9)if(l)j.attr("partialText",j.html()).attr("isIEExpand",true).css("width",r-28+"px");else{var t=n.toLowerCase().indexOf("<span>"),u=n.toLowerCase().indexOf("</span>"),z=function(g){var o=false;if(g>=t&&g<t+6){g=g-t;g=t+g;o=true}if(g>=u&&g<u+7){g=g-u;g=u+g}return{cutLoc:g,addSpan:o}},x=function(g,o,v,A,s){n.indexOf("Journal of magnetic");g=z(g);var p=n.substr(0,g.cutLoc)+(g.addCloseSpan?"</span>":"")+"&hellip;";j.html(p);if(p===A){if(j.height()!==w&&typeof s!=="undefined")p=s;j.attr("partialText",
+p).css("white-space","nowrap")}else if(j.height()===w){o=p.toString()+"";s=Math.floor((g.cutLoc+v)/2);x(s,g.cutLoc,v,p,o)}else{v=Math.floor((parseInt(g.cutLoc,10)+parseInt(o,10))/2);x(v,o,g.cutLoc,p,s)}};j.css("white-space","normal").css("width",r-22+"px");var B=j.height();j.html(".");var w=j.height();j.html(n);B>w&&x(y,0,n.length)}});a.scrollTop(0);this._removeHighlight("mouse");this._hideOptionsIfOffPage()}}},_filteredCache:function(a,b){var c=true,e="l"+(this.options.maxListLimit||"n");if(a===
+null)c=false;else{if(b){b=b;if(typeof this._localCache[this.options.dictionary]==="undefined")this._localCache[this.options.dictionary]={};else if(typeof this._localCache[this.options.dictionary][e]==="undefined")this._localCache[this.options.dictionary][e]={}}else b=this._localCache[this.options.dictionary][e][a];b.matchedText=a;var d=this.options.minLength===0&&a.length===0;if(!this.options.hasRelatedMatches){c=a.replace(/([\^\$\\\?\(\)\[\]\*\+\{\}\|\/\.\,])/g,"\\$1");c=new RegExp(c,"ig");for(var f=
+b.matches.join("!!!~~~!!!").split("!!!~~~!!!"),i=f.length-1;i>=0;i--)!d&&f[i].match(c)===null&&f.splice(i,1);b.matches=f;this._localCache[this.options.dictionary][e][a]=b;c=f.length>0}}c?this._displayOptions(this._localCache[this.options.dictionary][e][a]):this._hideOptions()},_removeHighlight:function(a){if(!(a==="mouse"&&new Date-this._lastKeyPressDwnUpScroll<100)){var b=this;jQuery("li",this._gol.optionsList).removeClass("ui-ncbiautocomplete-options-high").each(function(){b._collapseOption(this)})}},
+_addHightlightMouse:function(a){if(new Date-this._lastKeyPressDwnUpScroll>100){this._resetCurrentIndex();this._currIndex=jQuery(a).prevAll("li").length;this._addHightlight(a)}},_addHightlight:function(a){this._removeHighlight();jQuery(a).addClass("ui-ncbiautocomplete-options-high");var b=this;this._expandTimer&&window.clearTimeout(this._expandTimer);this._expandTimer=window.setTimeout(function(){b._expandOption(a)},this.options.expandPauseTime)},_expandOption:function(a){if(jQuery(a).hasClass("ui-ncbiautocomplete-options-high")){a=
+jQuery(a).attr("isExpanded",true);var b=a.attr("fullText");if(a.html()!==b||a.attr("isIEExpand")){a.html(b).css("text-overflow","").css("white-space","normal").css("-o-text-overflow","");this._scrollIntoView()}}},_collapseOption:function(a){a=jQuery(a);a.attr("isIEExpand")?a.css("text-overflow","ellipsis").css("white-space","nowrap").css("-o-text-overflow","ellipsis"):a.css("white-space","nowrap").html(a.attr("partialText"))},_optionClicked:function(a){a=jQuery(a);if(a.hasClass("ui-ncbiautocomplete-show-more"))this._gotoShowAll();
+else{var b=this._cleanUpSelectionText(a);a=a.attr("valueId")||null;this.sgData.optionSelected=b;this.sgData.optionIndex=this._currIndex;this.sgData.valueId=a;this.sgData.selectionAction="click";this._sgSend();b=jQuery(this.element).val(b);b.attr("valueid",a);b.trigger("ncbiautocompleteoptionclick",this.sgData);b.trigger("ncbiautocompletechange",this.sgData)}this._isOptionsBoxFocused=false;this._hideOptions()},isOptionsBoxOpen:function(){return jQuery(this._gol.optionsBox).css("display")==="block"},
+_hideOptions:function(a){this._gol.activeElement=null;if(!(this._isOptionsBoxFocused&&!a)){var b=jQuery(this._gol.optionsBox);a&&jQuery(this._gol.optionsBox).css("display","none");b.attr("aria-activedescendant")===this.element.attr("id")&&b.attr("aria-activedescendant","");this._gol.isIE6&&jQuery(this._gol.optionsBox.iframe).css("display","none");this._resetCurrentIndex();this._isActive=false;this._lastEnteredTerm=null;b=jQuery(this._gol.optionsBox);var c=jQuery(this._gol.optionsList);b.css("display",
+"none");c.html("");this._lastTextInTextbox=b=this.element.val();if(this.options.requireValidation&&b.length>0&&this.options.isEnabled&&(!this.element.is(":focus")||a))this._trigger((b.length<this.options.minLength?false:this.isInDictionary(b))?"validselection":"invalidselection")}},_setTextCursorToEnd:function(a){var b=this.element;jQuery(b).val(a);if(b.createTextRange){a=b.createTextRange();a.moveStart("character",b.value.length);a.collapse();a.select()}},_resetCurrentIndex:function(){this._currIndex=
+-1},_cleanUpSelectionText:function(a){return jQuery.trim(a.attr("acValue")).replace(/&amp;/gi,"&").replace(/\\"/g,'"')},_currIndex:-1,_moveSelection:function(a){if(this._isActive){this.sgData.usedArrows=true;var b=jQuery("li",this._gol.optionsList).length;this._currIndex+=a;this._removeHighlight();a=this._lastEnteredTerm;var c="";if(!(a===null||a.length<this.options.minLength)){if(this._currIndex<0||this._currIndex>=b)this._currIndex=this._currIndex===-2?b-1:-1;if(this._currIndex!==-1){b=jQuery("li:eq("+
+this._currIndex+")",this._gol.optionsList);this._addHightlight(b);if(this._currIndex===this.options.maxListLimit){this.sgData.optionSelected="";this.sgData.valueId=""}else{a=this._cleanUpSelectionText(b);c=b.attr("valueId")||null;this.sgData.optionSelected=a;this.sgData.valueId=c}}else{this.sgData.optionSelected="";this.sgData.valueId=""}this.element.attr("_optValue",c);this.element.attr("valueId",c);this._setTextCursorToEnd(a);this._scrollIntoView();this.sgData.optionIndex=this._currIndex}}},_scrollIntoView:function(){var a=
+jQuery("li:eq("+this._currIndex+")",this._gol.optionsList);if(a.length!==0){var b=jQuery(this._gol.optionsList),c=b.height(),e=b.scrollTop(),d=a[0].offsetTop;a=a.height();if(d-c+a>e){e=jQuery("li:eq("+(this._currIndex+1)+")",this._gol.optionsList);b.scrollTop((e.length===1?e[0].offsetTop:d+a+10)-c)}else d<e&&b.scrollTop(d)}},enableAutocomnplete:function(){this.options.isEnabled=true},disableAutocomnplete:function(){this.disableAutocomplete()},disableAutocomplete:function(){this._isOptionsBoxFocused=
+this.options.isEnabled=false;this._hideOptions()},turnOff:function(a){this.disableAutocomplete();var b=this.element.data("ncbiautocompleteOriginalTitle");b&&this.element.attr("title",b);if(!a){typeof ncbi!=="undefined"&&ncbi.sg&&ncbi.sg.ping&&ncbi.sg.ping(this.element[0],"autocompleteoffclick","dictionary="+this.options.dictionary);this.element.trigger("ncbiautocompletedisableclicked");a=this.options.disableUrl;if(a!==null&&a.length>0){b=jQuery.ui.jig._getFncFromStr(a);typeof b==="function"?b():jQuery.get(a)}}},
+_prefLinkClick:function(){typeof ncbi!=="undefined"&&ncbi.sg&&ncbi.sg.ping&&ncbi.sg.ping(this.element[0],"autocompleteprefclick","dictionary="+this.options.dictionary)},_checkClickEvent:function(a){if(this._isActive)if(jQuery(this.element)[0]!=a.target){this._isActive=this._isOptionsBoxFocused=false;this._hideOptions()}},_sgSend:function(){typeof ncbi!=="undefined"&&typeof ncbi.sg!=="undefined"&&typeof ncbi.sg.ping!=="undefined"&&ncbi.sg.ping(this.sgData,false)},getSgData:function(){return this.sgData},
+_gotoShowAll:function(){var a=jQuery(this.element),b=a.val();a.trigger("ncbiautocompleteshowall",{value:b,dictionary:this.options.dictionary})},_hideOptionsIfOffPage:function(){if(this.options.maxListLimit){var a=this,b=jQuery(".ui-ncbiautocomplete-options li"),c=b.eq(0).outerHeight()||20,e=jQuery(this._gol.optionsBox),d=jQuery(window).height(),f=e.position().top,i=f+e.outerHeight()-(document.body.scrollTop||document.documentElement.scrollTop||window.pageYOffset||0);if(b.last().hasClass("ui-ncbiautocomplete-show-more")){var k=
+f+"-"+d+"-"+i;if(!this.choppedDetails)this.choppedDetails={};var h=this.choppedDetails[k],m=0,q=function(){i=f+e.outerHeight()-(document.body.scrollTop||document.documentElement.scrollTop||window.pageYOffset||0);if(i>d){b=jQuery(".ui-ncbiautocomplete-options li");var r=b.length-2;if(r>=0){b.eq(r).remove();sz=c*(b.length-1);b.closest(".ui-ncbiautocomplete-holder").height(sz).css("min-height",sz+"px");b.closest(".ui-ncbiautocomplete-options").height(sz).css("overflow-y","hidden");m++;q()}}else a.choppedDetails[k].count=
+m};if(h){var l=h.count;if(l>0){h=2*h.length-l-b.length-2;b.filter(":lt("+(b.length-1)+")").filter(":gt("+h+")").remove();b=jQuery(".ui-ncbiautocomplete-options li");sz=c*b.length;b.closest(".ui-ncbiautocomplete-holder").height(sz).css("min-height",sz+"px");b.closest(".ui-ncbiautocomplete-options").height(sz).css("overflow-y","hidden")}m=l}else this.choppedDetails[k]={count:0,length:b.length};q()}else{l=Math.floor((d-f)/c)*c;h=b.length*c;if(l>h)l=h;b.closest(".ui-ncbiautocomplete-holder").height(l).css("min-height",
+l+"px");b.closest(".ui-ncbiautocomplete-options").height(l).css("overflow-y","auto")}}},isValid:function(){return this.isInDictionary(this.element.val())},isInDictionary:function(a){var b=false;if(a&&a.length>=this.options.minLength&&this.options.dictionary&&this.options.dictionary.length>0&&this.options.isEnabled){var c=false,e="l"+(this.options.maxListLimit||"n"),d=a.toLowerCase();if(this._localCache[this.options.dictionary]&&this._localCache[this.options.dictionary][e]){e=this._localCache[this.options.dictionary][e];
+c=true;if(e[d])b=this._isValidCheck(d,e[d].matches);else for(var f in e)if(b=this._isValidCheck(d,e[f].matches))break}if(!b&&!c)b=this._validSeverCall(a)}return b},_isValidCheck:function(a,b){var c=false;if(b){c=jQuery.inArray(a.toLowerCase(),b)>-1;if(!c){var e=new RegExp("(^|@)("+a.toLowerCase()+")(@|$)","i");jQuery.each(b,function(d,f){if(f.match(e)){c=true;return false}})}}return c},_customFormat:function(a){if(typeof this.options.responseProcessor==="string")this.options.responseProcessor=jQuery.ui.jig._getFncFromStr(this.options.responseProcessor);
+this._displayOptions({matchedText:this._lastEnteredTerm,matches:this.options.responseProcessor.call(this,a),isCompleteList:0})}});jQuery.ui.ncbiautocomplete._globalOptionsList=null;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_005.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+a.ui-ncbitoggler{color:#22c;}a.ui-ncbitoggler,a.ui-ncbitoggler-open{padding-left:16px;position:relative;display:block;}a.ui-ncbitoggler-no-icon{padding-left:0;}a.ui-ncbitoggler span.ui-icon-plus-minus-big,a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open{background-color:transparent;background-image:url(../img/ncbitoggler-plus-minus-big.gif);background-repeat:no-repeat;top:.2em;margin-left:-0.1em;}a.ui-ncbitoggler span.ui-icon-plus-minus-big{background-position:left -30px;}a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open{background-position:left 0;}.ui-ncbitoggler-slave,.ui-ncbitoggler-slave-open{margin:.2em 0 0 16px;}.ui-ncbitoggler-slave{display:none;}.ui-ncbitoggler-slave-open{display:block;}a.ui-ncbitoggler span.ui-icon,a.ui-ncbitoggler-open span.ui-icon{display:inline;position:absolute;left:0;_left:-1em;}a.ui-ncbitoggler-disabled{outline:none;}a.ui-ncbitoggler-disabled:active{outline:none;color:#551A8B;}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_005.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,2 @@
+(function(){var d=jQuery.ui.button.prototype._create;jQuery.ui.button.prototype.options.color="ui-ncbibutton-gray";jQuery.ui.button.validColors=["ui-ncbibutton-gray","ui-ncbibutton-copper","ui-ncbibutton-blue"];jQuery.ui.button.classColors=["jig-ncbibutton-gray","jig-ncbibutton-copper","jig-ncbibutton-blue"];var e=function(){d.apply(this,arguments);this._addClasses()};jQuery.widget("ui.ncbibutton",jQuery.ui.button,{_create:function(){e.apply(this,arguments)},_getColor:function(){for(var a=this.options.color,
+f=this.element[0].className,c=jQuery.ui.button.classColors,b=0;b<c.length;b++)if(f.indexOf(c[b])!==-1){a=jQuery.ui.button.validColors[b];break}if(a.indexOf("ui-ncbibutton-")!==0)a="ui-ncbibutton-"+a;if(jQuery.inArray(a,jQuery.ui.button.validColors)===-1){typeof console!=="undefined"&&console.warn&&console.warn("The color you picked: "+this.options.color+" is not a valid color choice.\n Valid colors: "+jQuery.ui.button.validColors.join(", "));a=jQuery.ui.button.validColors[0]}return a},_addClasses:function(){this.buttonElement.addClass("ui-ncbibutton").addClass(this._getColor()).removeClass("ui-button ui-widget")}})})();
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_006.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+.ui-ncbipopper-wrapper{position:fixed;top:0;left:0;z-index:11;display:none;}.ui-ncbipopper-wrapper-relative-parent{position:fixed!important;}.ui-ncbipopper-basic{border:3px solid #3e72a6;background-color:#fff;color:#303030;padding:1em;text-align:left;-moz-border-radius:6px;-webkit-border-radius:6px;border-radius:6px;}button.ui-ncbipopper-close-button-generated{display:block;float:right;margin:-1.25em -1.3em 0 0;font-size:small;width:1.7em;text-align:center;padding:0;border:0;}button.ui-ncbipopper-close-button-generated,button.ui-ncbipopper-close-button-generated:active{margin:-0.615em;height:14px;width:13px;background-image:url(../img/ui-popper-closebutton.png);background-color:transparent;background-repeat:no-repeat;}button.ui-ncbipopper-close-button-generated .ui-button-text{color:transparent;text-shadow:none;}div.ui-ncbipopper-arrow-image{position:absolute;top:100px;left:100px;width:7px;height:7px;z-index:11;display:none;background-image:url(../img/ncbipopper-arrow.png);background-repeat:no-repeat;}div.ui-ncbipopper-arrow-left{background-position:center left;height:28px;}div.ui-ncbipopper-arrow-right{background-position:center right;height:28px;}div.ui-ncbipopper-arrow-top{background-position:top center;width:28px;}div.ui-ncbipopper-arrow-bottom{background-position:bottom center;width:28px;}.brieflinkpopdesc{font-size:.846em;margin-top:.4em;}.portlet .brieflinkpop{width:350px;}.portlet .brieflinkpop a{font-size:1em;}.portlet .brieflinkpopperctrl{display:inline-block;}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_006.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,75 @@
+jQuery.widget("ui.ncbigrid",{options:{isScrollable:false,height:"10em",hortScrollbarEnabled:false,width:null,isPageable:false,currentPage:1,isPageToolbarHideable:true,pageSize:10,isSortable:false,columnTypes:[],sortFunctions:[],isPresorted:false,sortColumn:-1,sortColumnDir:1,sortRowIndex:0,titleAscending:"sort ascending",titleDescending:"sort descending",ariaLabelAscending:"activate to sort column ascending",ariaLabelDescending:"activate to sort column descending",regExp:false,checkboxToolbarEnabled:false,
+filterToolbarEnabled:false,filterToolbarIsCaseInsensitive:null,filterToolbarColumnIndex:null,filterToolbarIsInverse:null,isLoadingMessageShown:true,loadingText:"Loading",collapseRowsEnabled:false,addCommas:false},_init:function(){},_create:function(){this._isStartPageOne=this.options.currentPage===1;this._wrapTable();this._addBasicStyles();this._checkIfCSSIsScrollable();this._attachLoadingMessageListener();if(this.options.isScrollable||this.options.isSortable||this.options.isPageable||this.options.checkboxToolbarEnabled||
+this.options.filterToolbarEnabled)this._addAriaRolesAndStates();this._addRowClickWatcher();this.options.isScrollable&&this._createScrollable();if(this.options.isPageable||this.options.isPagable){this.options.isPageable=true;this._createPageGrid()}if(this.options.isSortable){this._createSortGrid();this.updateAriaTH()}else this._enableCollapseTbodyRows();this.options.checkboxToolbarEnabled&&this._createCheckboxSelectors();this.options.filterToolbarEnabled&&this._createFilterBarControl();this._addRowHoverEvent();
+this._addContentsAdjustmentEvent();this._adjustContents()},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);this.options.isScrollable&&this._destroyScrollable();if(this.options.isPageable||this.options.isPagable)this._destroyPageGrid();this._destroyRowHoverEvent()},_addBasicStyles:function(){this.element.addClass("ui-ncbigrid").attr("cellpadding","0").attr("cellspacing","0")},_checkIfCSSIsScrollable:function(){if(this.element.hasClass("jig-ncbigrid-scroll"))this.options.isScrollable=
+true},_wrapTable:function(){var a=this.element.parent().parent();if(!a.hasClass("ui-ncbigrid-outer-div")){this.element.wrap('<div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"></div></div>');a=this.element.parent().parent()}this.element.find("caption").length>0&&a.addClass("caption-exists");var b=this.options.width;b&&a.css("width",b)},_addRowHoverEvent:function(){jQuery(this.element).on("mouseenter","tbody > tr",function(){var a=jQuery(this);a.hasClass("ignoreHoverHighlight")||
+a.addClass("ui-ncbigrid-row-hover")}).on("mouseleave","tbody > tr",function(){jQuery(this).removeClass("ui-ncbigrid-row-hover")})},_destroyRowHoverEvent:function(){jQuery(this.element).off("mouseenter mouseleave","tr")},_addContentsAdjustmentEvent:function(){var a=this;this.element.on("ncbigridupdated",function(){a._adjustContents()})},_getNumCommaIndices:function(){var a=this.options.columnTypes;if(!a)return[];for(var b=[],c=0;c<a.length;c++)if(a[c]=="numComma"||a[c]=="numberComma")b.push(c);return b},
+_getCommaSeparatedValue:function(a){var b=parseInt(a);if(isNaN(b))return a;else{a=a.split(".");b=a[0].replace(/(\d)(?=(\d\d\d)+(?!\d))/g,"$1,");return a[1]?b+"."+a[1]:b}},_adjustContentsForCommas:function(){var a=this._getNumCommaIndices();if(a.length){var b=this;jQuery(this.element).find("tbody td").each(function(){var c=jQuery(this),d=c.parent().find("td").index(c);jQuery.inArray(d,a)!=-1&&c.html(b._getCommaSeparatedValue(c.html()))})}},_adjustContents:function(){this.options.addCommas&&this._adjustContentsForCommas()},
+_addAriaRolesAndStates:function(){var a=this.element;a.attr("id")||a.attr("id",jQuery.ui.jig._generateId(this.widgetName));a.parent().parent().attr("role","grid").attr("tabindex","0");a.children("thead").children("tr").attr("role","row").children("th").attr({"aria-controls":a.attr("id"),role:"columnheader",tabindex:"0"});a.children("tbody").attr({role:"alert","aria-live":"polite","aria-relevant":"text"})},updateAriaTH:function(){if(this.options.isSortable){var a=this;this.element.parent().parent().find("div, table").attr("tabindex",
+"0").end().find("thead").find("th").each(function(b,c){b="";var d=a.options.ariaLabelAscending;if(jQuery(c).is(".sortDsc")){b="descending";d=a.options.ariaLabelAscending}else if(jQuery(c).is(".sortAsc")){b="ascending";d=a.options.ariaLabelDescending}c=jQuery(c).children("a");jQuery(c).attr("aria-label",jQuery(c).text()+": "+d);b==""?jQuery(c).removeAttr("aria-sort"):jQuery(c).attr("aria-sort",b)})}},_createScrollable:function(){this._storeRefs();this._addScrollClasses();this._copyCaptionHeader();
+this._setWidthHeight();this._setWidths();this._registerScrollableListeners()},_destroyScrollable:function(){this._removeScrollClasses();if(this.parts){this.parts.scrollWrapper.removeClass("ui-ncbigrid-scroll");this.parts.headerWrapper.remove();for(var a in this.parts)this.parts[a]=null;this.parts=null}this._windowResize&&jQuery(window).unbind("resize",this._windowResize)},_storeRefs:function(){var a=this.element;this.parts={table:a,ths:a.find("> thead th")}},_addScrollClasses:function(){var a=this.element,
+b=a.parent().addClass("ui-ncbigrid-scroll");this.parts.scrollWrapper=b;if(jQuery.browser.webkit){var c=navigator.userAgent;c.indexOf("AppleWebKit")>0&&c.indexOf("Chrome")==-1&&a.addClass("safari")}this.options.hortScrollbarEnabled&&b.addClass("ui-ncbigrid-hort-scroll")},_removeScrollClasses:function(){this.element.removeClass("ui-ncbigrid").removeClass("safari").parent().removeClass("ui-ncbigrid-scroll")},_copyCaptionHeader:function(){var a=this.element,b=a.parent();b.parent();var c=a.find("caption").clone();
+a=a.find("> thead").clone();c=jQuery("<div class='ui-ncbigrid-header-wrapper'></div>").append("<table cellpadding='0' cellspacing='0' class='ui-ncbigrid ui-ncbigrid-header'></table>").find("table").append(c).append(a).end();c.insertBefore(b);b=c.find("caption");b.wrapInner("<div></div>");this.parts.captionDiv=b.find("div");this.parts.headerWrapper=c;this.parts.headerThs=c.find("thead th")},_setWidthHeight:function(){this.options.height!==null&&this.parts.scrollWrapper.height(this.options.height)},
+_setWidths:function(){function a(j){jQuery(this).width(h[j])}var b=this.parts,c=b.table,d=b.ths,e=b.scrollWrapper,g=b.headerWrapper;b=b.headerThs;var f=jQuery.browser.msie;if(!this.options.hortScrollbarEnabled&&c.data("isMinSet")!==true&&this.element.is(":visible")){var i=c.outerWidth();if(c.width()>e.width()){e.css("min-width",i+16);c.data("isMinSet",true)}}var h=[];d.each(function(){var j=0;if(jQuery(this).is(":visible"))j=jQuery(this).width()+0;h.push(j)});d=c.height()>e.height()?16:0;f=this.options.isSortable&&
+f&&parseInt(jQuery.browser.version,10)<8?d:0;c.parent().parent().find("table.ui-ncbigrid-header").width(c.width()+2-f);c=e.width()-d;g.width(c);this.parts.captionDiv&&this.parts.captionDiv.width(c);b.each(a)},_handleScroll:function(a,b,c){function d(){g._handleScroll(a,b,true)}var e=a.scrollLeft;b.scrollLeft=e;this.parts.captionDiv&&this.parts.captionDiv.css("margin-left",e+"px");var g=this;if(!c){window.setTimeout(d,1);window.setTimeout(d,5)}},_registerScrollableListeners:function(){var a=this;this._windowResize=
+function(){a._setWidths()};jQuery(window).resize(this._windowResize);var b=this.element.parent().parent().find(".ui-ncbigrid-header-wrapper")[0];this.element.parent().scroll(function(){a._handleScroll(this,b)});this.element.bind("ncbigridupdated",function(){a._setWidths()});this.element.bind("resetScroll",function(){a._resetScrollToTop()})},_resetScrollToTop:function(){this.parts.scrollWrapper.scrollTop(0)},_createPageGrid:function(){this._createPageBars();this._addPagingEvents();this._gotoPage(this.options.currentPage)},
+_destroyPageGrid:function(){if(this._pageBars){this._removePagingEvents();this._removePageBars()}},_pagingControlsHTML:'                                         <div class="ui-ncbigrid-paged-toolbar">                                                <div class="ui-ncbigrid-paged-countItems">Items <span class="ui-ncbigrid-paged-startRow">1</span> - <span class="ui-ncbigrid-paged-endRow">10</span> of <span class="ui-ncbigrid-paged-totalRows">10</span></div>                                                <div class="ui-ncbigrid-paged-pageControl pagination">                        <a href="#" class="ui-ncbigrid-paged-pageControl-first page_link" title="Goto First Page">&lt;&lt; First</a>                        <span class="ui-ncbigrid-paged-pageControl-first page_link" title="Inactive Goto First Page">&lt;&lt; First</span>                        <a href="#" class="ui-ncbigrid-paged-pageControl-previous page_link prev" title="Goto Previous Page">&lt; Prev</a>                        <span class="ui-ncbigrid-paged-pageControl-previous page_link prev" title="Inactive Goto Previous Page">&lt; Prev</span>                        <label>Page</label> <input type="text" value="1" size="2" title="current page number"/> of <span class="ui-ncbigrid-paged-endPage">2</span>                        <a href="#" class="ui-ncbigrid-paged-pageControl-next next page_link" title="Goto Next Page">Next &gt;</a>                        <span class="ui-ncbigrid-paged-pageControl-next next page_link" title="Inactive Goto Next Page">Next &gt;</span>                        <a href="#" class="ui-ncbigrid-paged-pageControl-last page_link" title="Goto Last Page">Last &gt;&gt;</a>                        <span class="ui-ncbigrid-paged-pageControl-last page_link" title="Inactive Goto Last Page">Last &gt;&gt;</span>                        </div>                                            </div>',
+_createPageBars:function(){this._pageToolBar_top=jQuery(this._pagingControlsHTML).addClass("ui-ncbigrid-paged-toolbar-top");this._pageToolBar_bottom=jQuery(this._pagingControlsHTML).addClass("ui-ncbigrid-paged-toolbar-bottom");var a=this.element,b=a.parent().parent();b.prepend(this._pageToolBar_top);b.append(this._pageToolBar_bottom);b.children(".ui-ncbigrid-paged-toolbar-top").children(".ui-ncbigrid-paged-countItems").attr("id",jQuery.ui.jig._generateId("ui-ncbigrid-paged-countItems"));a.attr("aria-describedby",
+this._pageToolBar_top.children(".ui-ncbigrid-paged-countItems").attr("id"));this._pageBars=this._pageToolBar_top.add(this._pageToolBar_bottom);this._pageBars.find(":input").each(function(c,d){jQuery(d).attr("id",jQuery.ui.jig._generateId("ui-ncbigrid-paged-current-page")).prev().attr("for",jQuery(d).attr("id"))})},_removePageBars:function(){this._pageToolBar_top.remove();this._pageToolBar_top=null;this._pageToolBar_bottom.remove();this._pageBars=this._pageToolBar_bottom=null;this.element.removeAttr("aria-describedby")},
+_addPagingEvents:function(){var a=this,b=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-first"),c=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-previous"),d=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-next"),e=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-last"),g=this._pageBars.find("input");b.click(function(f){a.gotoFirstPage();f.preventDefault()});c.click(function(f){a.gotoPrevPage();f.preventDefault()});d.click(function(f){a.gotoNextPage();f.preventDefault()});e.click(function(f){a.gotoLastPage();
+f.preventDefault()});g.keypress(function(f){if(f.keyCode===13){a.gotoPage(this.value.replace(/,/g,""));f.preventDefault()}})},_removePagingEvents:function(){this._pageBars.find("a").unbind("click").end().find("input").unbind("keypress")},_showHidePageToolbar:function(){if(this._pageBars)if(this.options.isPageToolbarHideable)parseInt(this.getRowCount())<=parseInt(this.options.pageSize)?this._pageBars.hide():this._pageBars.show()},_setPage:function(){this.element.trigger("resetScroll");this.element.trigger("pagechanged");
+var a=this._getCurrentPage(),b=this.getMaxPage();this._showHidePageToolbar();this._updateRows(a,b);this._updateButtons(a,b);this._updatePagingText(a,b);this._updateGoto(a,b);this._updateItemRange(a,b);this._pageBars.find(".ui-ncbigrid-paged-pageControl").attr({"aria-valuemin":"1","aria-controls":this.element.attr("id"),"aria-valuemax":b,"aria-valuenow":a});this._notifyGridUpdated()},_updateRows:function(a){var b=this.options.pageSize,c=this.getRowCount();a=(a-1)*b;var d=a+b;b=this.element.find("> tbody > tr:not(.ncbigrid-row-filtered)");
+var e=this.element.find("> tbody").length>1,g=0;if(e&&a>0)g=b.filter(":lt("+a+")").filter(":has(th)").length;var f="";if(d<c)f+=":lt("+(d+g)+")";if(a>0)f+=":gt("+(a-1+g)+")";c=b;if(f.length>0){b.not(".ui-ncbigrid-rowHidden").addClass("ui-ncbigrid-rowHidden");c=b.filter(f)}c.removeClass("ui-ncbigrid-rowHidden");if(e){a=c.filter(":has(th)").length;if(a>0){b=0;for(c=c.last().next();b<a&&c.length===1;){if(!c.hasClass("ncbigrid-row-filtered")){c.has("th")||b++;c.removeClass("ui-ncbigrid-rowHidden")}c=
+c.next()}}}this._notifyGridUpdated()},_updateButtons:function(a,b){var c=b===2,d=a===1,e=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-previous,a.ui-ncbigrid-paged-pageControl-first").css("display",d?"none":"inline").filter("a.ui-ncbigrid-paged-pageControl-first");d=this._pageBars.find("span.ui-ncbigrid-paged-pageControl-previous,span.ui-ncbigrid-paged-pageControl-first").css("display",d?"inline":"none").filter("span.ui-ncbigrid-paged-pageControl-first");b=a===b||b==0;a=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-next,a.ui-ncbigrid-paged-pageControl-last").css("display",
+b?"none":"inline").filter("a.ui-ncbigrid-paged-pageControl-last");b=this._pageBars.find("span.ui-ncbigrid-paged-pageControl-next,span.ui-ncbigrid-paged-pageControl-last").css("display",b?"inline":"none").filter("span.ui-ncbigrid-paged-pageControl-last");c&&e.add(d).add(a).add(b).css("display","none")},_updatePagingText:function(a,b){if(b<1)b=1;if(this.options.addCommas)b=this._getCommaSeparatedValue(""+b);this._pageBars.find("div.ui-ncbigrid-paged-pageControl").find("span.ui-ncbigrid-paged-endPage").html(b)},
+_updateGoto:function(a){if(this.options.addCommas)a=this._getCommaSeparatedValue(""+a);this._pageBars.find("input").val(a)},_updateItemRange:function(a){var b=parseInt(this.options.pageSize,10),c=this.getRowCount();a=(a-1)*b+1;b=a+b-1;if(b>c)b=c;if(c==0)a=0;if(this.options.addCommas){c=this._getCommaSeparatedValue(""+c);a=this._getCommaSeparatedValue(""+a);b=this._getCommaSeparatedValue(""+b)}var d=this._pageBars.find("div.ui-ncbigrid-paged-countItems");d.find("span.ui-ncbigrid-paged-startRow").html(a);
+d.find("span.ui-ncbigrid-paged-endRow").html(b);d.find("span.ui-ncbigrid-paged-totalRows").html(c)},_getCurrentPage:function(){return this.options.currentPage},getCurrentPage:function(){return this._getCurrentPage()},getMaxPage:function(){return Math.ceil(this.getRowCount()/this.options.pageSize)},getRowCount:function(){return jQuery(this.element).find("> tbody > tr:not(.ncbigrid-row-filtered):not(:has(> th))").length},getHeaderRowCount:function(){return jQuery(this.element).find("tbody > tr:has(th)").length},
+gotoFirstPage:function(){this._gotoPage(1)},gotoLastPage:function(){this._gotoPage(this.getMaxPage())},gotoNextPage:function(){this._gotoPage(this._getCurrentPage()+1)},gotoPrevPage:function(){this._gotoPage(this._getCurrentPage()-1)},gotoPage:function(a){this._gotoPage(parseInt(a,10))},_gotoPage:function(a){if(isNaN(a)||a<1)a=1;else if(a>this.getMaxPage()){a=this.getMaxPage();if(a<1)a=1}this.options.currentPage=a;this._pagingSelectAllQuestions&&this._pagingSelectAllQuestions.hide();this._setPage()},
+_createSortGrid:function(){var a=this.options.sortColumn;if(this.options.sortColumn!==-1){a=a-1;this.options.sortColumn=a!==-1?a:0}this._indexGrid();this._addSortEvents();this._setSortHeaders();this._checkInitialState();this._notifyGridUpdated()},_destroySortGrid:function(){},reindex:function(){for(var a=0;a<this.element.find("tbody tr:eq(0) td").length;a++)this.element.data("sort_order_col_"+a,null);this.element.data("rows",null);this._indexGrid()},_indexGrid:function(){var a=this,b=this.element.find("> tbody");
+if(b.length===0)this._isIndexed=false;else for(var c=0;c<b.length;c++)(function(d,e){function g(){for(var o=0;o<50&&k<m;o++){var p=l[k],q=a.getRowValues_DOM(p);if(q.length==0){a._enableCollapseTbodyRows(p);i.push(p);j++}else{q.unshift(k-j,p);f.push(q);h.push(q)}k++}if(k<m)window.setTimeout(g,0);else{a.element.data("tbody"+e+"-rows",h);a.element.data("tbody"+e+"-header",i);a._presort(f,e)}}var f=[],i=[],h=[],j=0,l=jQuery(d).find("> tr"),k=0,m=l.length;if(m===0)a._isIndexed=false;else{a._isIndexed=
+true;g()}})(b[c],c)},_presort:function(a,b){function c(h){var j=g.options.sortFunctions[h-2];j||(j=g.element.find("> thead th:eq("+(h-2)+")").data("sortfunc"));if(j)if(typeof j==="function")return j;else if(j.indexOf("fnc:")===0){j=j.substr(4,j.length).split(".");for(var l=window[j[0]],k=1;k<j.length;k++)l=l[j[k]];return g.options.sortFunctions[h]=l}return null}function d(h,j,l){function k(n){if(n.length<2)return n;var r=parseInt(n.length/2),s=n.slice(0,r);n=n.slice(r,n.length);return m(k(s),k(n))}
+function m(n,r){for(var s=[];n.length&&r.length;){var u=false;(u=o?-g.options.sortColumnDir==o.call(g,{data:n[0][j],row:jQuery(n[0][1])},{data:r[0][j],row:jQuery(r[0][1])}):n[0][j]<=r[0][j])?s.push(n.shift()):s.push(r.shift())}for(;n.length;)s.push(n.shift());for(;r.length;)s.push(r.shift());return s}var o=c(j),p=jQuery.browser.msie?100:1E3,q=0,t=[];(function(){for(var n=0;n<p&&q<h.length;n++){t.push(h[q]);q++}q<h.length?setTimeout(arguments.callee,0):l(k(t),j)})()}function e(h,j){var l=0,k=[];(function(){for(var m=
+0;m<50&&l<h.length;m++){k.push(h[l][0]);l++}l<h.length?setTimeout(arguments.callee,0):g.element.data("tbody"+b+"-sort_order_col_"+(j-2),k)})()}for(var g=this,f=a[0].length,i=2;i<f;i++)this._getColumnType(i-2)!=="none"&&d(a,i,e)},_getColumnType:function(a){var b=this.options.columnTypes[a];b||(b=this.element.find("> thead th:eq("+a+")").data("columntype"));return b||"str"},getColumnType:function(a){return this._getColumnType(a-1)},getRowValues:function(a){if(typeof a==="number")a=this.element.find("tbody tr:eq("+
+a+")");var b=[];a=a[0].getElementsByTagName("td");for(var c=a.length,d=0;d<c;d++)b.push(this._getCellValueHelper(a[d].innerHTML,d));return b},getRowValues_DOM:function(a){var b=[];a=jQuery(a).children("td");for(var c=a.length,d=0;d<c;d++)b.push(this._getCellValueHelper(a[d].textContent||a[d].innerText||"",d));return b},_getCellValue:function(a,b){return this._getCellValueHelper(a.html(),b)},_getCellValueHelper:function(a,b){var c=this._getColumnType(b);switch(c){case "num":case "number":case "float":return a!==
+undefined&&a.length>0?parseFloat(a):Number.POSITIVE_INFINITY;case "int":return a!==undefined&&a.length>0?parseInt(a,10):Number.POSITIVE_INFINITY;case "numberComma":case "numComma":a=(a||"").replace(/[, ]/g,"");return a.length>0?parseFloat(a):Number.POSITIVE_INFINITY;case "date":return new Date(a);case "str-insensitive":return a.toLowerCase();case "str":default:if(typeof c==="function")return c(a);else if(c.indexOf("fnc:")===0){c=c.substr(4,c.length).split(".");for(var d=window[c[0]],e=1;e<c.length;e++)d=
+d[c[e]];this.options.columnTypes[b]=d;return d(a)}else return a||""}},getCellValue:function(a,b){if(typeof a==="number")a=this.element.find("tbody tr:eq("+a+")");return this._getCellValue(a.find("td:eq("+b+")"),b)},_addSortEvents:function(){function a(e){b._getColumnType(e)!=="none"&&jQuery(this).wrapInner(d).find("a").data("index",e)}var b=this,c=this.element.find("> thead tr:eq("+this.options.sortRowIndex+") th");this.element.bind("ncbigridcontentchanged",function(){b.reindex()});var d="<a href='#' title='"+
+this.options.titleAscending+"'></a>";c.each(a);c=c;if(this.parts&&this.parts.headerThs){this.parts.headerThs.each(a);c=c.add(this.parts.headerThs)}c.find("a").click(function(e){b._sort(jQuery(this).data("index"));e.preventDefault()})},sort:function(a,b){this._sort(a-1,b)},_sort:function(a,b){if(this._isIndexed){this.options.isPageable&&this.element.trigger("resetCheckboxes");var c=b;if(b===undefined)c=this.options.sortColumn!==a?1:-1*this.options.sortColumnDir;this.options.sortColumn=a;this.options.sortColumnDir=
+c;this.element.trigger("ncbigridshowloadingbar");this._setSortHeaders();this._waitForCache()}},_setSortHeaders:function(){var a=this.element.find("> thead tr:eq("+this.options.sortRowIndex+") th"),b=null;if(this.parts&&this.parts.headerThs)b=this.parts.headerThs;a.add(b).removeClass("sortAsc sortDsc").addClass("sortNone").find("a").attr("title",this.options.titleAscending);var c=this.options.sortColumn;if(this.options.sortColumn!==-1){var d=this.options.sortColumnDir===1?"sortAsc":"sortDsc",e=this.options.sortColumnDir===
+1?this.options.titleDescending:this.options.titleAscending;a.eq(c).addClass(d).removeClass("sortNone").find("a").attr("title",e);b&&b.eq(c).addClass(d).removeClass("sortNone").find("a").attr("title",e)}this.options.isSortable&&this.updateAriaTH()},_waitForCache:function(){for(var a=this,b=this.options.sortColumn,c=this.element.find("tbody"),d=0;d<c.length;d++)(function(e){var g=a.element.data("tbody"+e+"-sort_order_col_"+b);if(g)a._setTheRows(g,e);else{var f=arguments.callee;setTimeout(function(){f(e)},
+10)}})(d)},_setTheRows:function(a,b){var c=this.element.data("tbody"+b+"-header"),d=this.element.data("tbody"+b+"-rows");b=this.element.find("tbody:eq("+b+")");var e=jQuery("<tbody>"),g=c.length;if(g>0)for(var f=0;f<g;f++)e.append(c[f]);if(this.options.sortColumnDir==1)for(f=0;f<a.length;f++){c=d[a[f]][1];e.append(c)}else for(f=a.length-1;f>=0;f--){c=d[a[f]][1];e.append(c)}b.replaceWith(e);this.element.trigger("ncbigridhideloadingbar");if(this.options.isPageable)if(this._isStartPageOne)this.gotoFirstPage();
+else{this._gotoPage(this.options.currentPage);this._isStartPageOne=true}this.element.trigger("ncbigridcolumnsorted",[this.options.sortColumn+1,this.options.sortColumnDir])},_checkInitialState:function(){!this.options.isPresorted&&this.options.sortColumn!==-1&&this._sort(this.options.sortColumn,this.options.sortColumnDir)},_checkboxControlsHTML:'                                         <div class="ui-ncbigrid-checkbox-toolbar">                        \t\t\t\t\t\t<label>Select:</label>\t\t\t\t\t\t<a href="#" class="ui-ncbigrid-select-all">All</a>\t\t\t\t\t\t<a href="#" class="ui-ncbigrid-select-none">None</a>\t\t\t\t\t\t<label>Selected:</label>\t\t\t\t\t\t<span class="ui-ncbigrid-selected-text">0</span>                                            </div>',
+_pagingSelectAllQuestionHTML:'<div class="ui-ncbigrid-select-question">All <span class="ui-ncbigrid-select-row-count">10</span> items on this page are <span class="selectText1">selected</span>. <a href="#" class="ui-ncbigrid-select-question-all"><span class="selectText2">Select</span> all rows in table</a> <a href="#" class="ui-ncbigrid-select-question-cancel">Cancel</a></div>',_createCheckboxSelectors:function(){this._createCheckboxBar();this._addCheckboxEvents();this._updateCount()},_createCheckboxBar:function(){this._checkboxToolBar_top=
+jQuery(this._checkboxControlsHTML).addClass("ui-ncbigrid-checkbox-toolbar-top");this._checkboxToolBar_bottom=jQuery(this._checkboxControlsHTML).addClass("ui-ncbigrid-checkbox-toolbar-bottom");var a=this.element.parent().parent();a.prepend(this._checkboxToolBar_top);if(this.options.isPageable){this._checkboxToolBar_bottom.insertBefore(this._pageToolBar_bottom);this._addSelectAllQuestionToolbar()}else a.append(this._checkboxToolBar_bottom);a.find(".ui-ncbigrid-checkbox-toolbar").attr("aria-controls",
+this.element.attr("id"));this._chekboxBars=this._checkboxToolBar_top.add(this._checkboxToolBar_bottom)},_addCheckboxEvents:function(){var a=this;this._chekboxBars.find("a.ui-ncbigrid-select-all").click(function(b){a.checkAll();a._askSelectAllQuestion();b.preventDefault()});this._chekboxBars.find("a.ui-ncbigrid-select-none").click(function(b){a.uncheckAll();a._askSelectAllQuestion(true);b.preventDefault()});jQuery(this.element).on("click","tbody",function(b){a._rowClicked(b)});this.element.bind("resetCheckboxes",
+function(){a.uncheckAll()});this._addSelectAllQuestionToolbarEvents()},_addSelectAllQuestionToolbar:function(){if(this.options.checkboxToolbarEnabled){this._pagingSelectAllQuestion_top=jQuery(this._pagingSelectAllQuestionHTML).addClass("ui-ncbigrid-select-question-header");this._pagingSelectAllQuestion_bottom=jQuery(this._pagingSelectAllQuestionHTML).addClass("ui-ncbigrid-select-question-footer");this._pagingSelectAllQuestion_top.insertAfter(this._pageToolBar_top);this._pagingSelectAllQuestion_bottom.insertAfter(this._pageToolBar_bottom);
+this._pagingSelectAllQuestions=this._pagingSelectAllQuestion_top.add(this._pagingSelectAllQuestion_bottom);this._pagingSelectAllQuestions.find(".ui-ncbigrid-select-question-all").attr("aria-controls",this.element.attr("id"))}},_addSelectAllQuestionToolbarEvents:function(){if(this.options.checkboxToolbarEnabled){var a=this;this._pagingSelectAllQuestions.find("a.ui-ncbigrid-select-question-all").click(function(b){a[a._askAllSelectionMode](true);a._pagingSelectAllQuestions.hide();b.preventDefault()});
+this._pagingSelectAllQuestions.find("a.ui-ncbigrid-select-question-cancel").click(function(b){a._pagingSelectAllQuestions.hide();b.preventDefault()});this.element.bind("ncbigridpagechanged checkboxrowclicked",function(){a._pagingSelectAllQuestions&&a._pagingSelectAllQuestions.hide()})}},_askSelectAllQuestion:function(a){this._askAllSelectionMode=a?"uncheckAll":"checkAll";if(this.options.isPageable)if(parseInt(this.getRowCount())>=parseInt(this.options.pageSize)){this._pagingSelectAllQuestions.show();
+this._updateSelectPageCount(a)}else this._pagingSelectAllQuestions.hide()},_updateSelectPageCount:function(a){var b=this.element.find("> tbody > tr > td > input[type=checkbox]:visible").length;this._pagingSelectAllQuestions.find(".ui-ncbigrid-select-row-count").html(b);this._pagingSelectAllQuestions.find(".selectText1").html(a?"deselected":"selected");this._pagingSelectAllQuestions.find(".selectText2").html(a?"Deselect":"Select")},_updateCount:function(){var a=this.element.find("tbody input[type=checkbox]");
+a=a.length>0?a.filter(":checked").length:this.element.find("tbody tr.ui-ncbigrid-row-selected").length;this._chekboxBars.find("span.ui-ncbigrid-selected-text").html(a)},_checkHelper:function(a,b){if(b){b=jQuery(this.element).find("> tbody > tr:not(.ncbigrid-row-filtered) > td > input[type=checkbox]");this._trigger(a?"checkall":"uncheckall",null,[a]);this._checkAllState=a}else b=a&&this.options.isPageable?this.element.find("> tbody > tr > td > input[type=checkbox]:visible"):this.element.find("> tbody > tr > td >  input[type=checkbox]");
+b.attr("checked",a);b=b.length===0?this.element.find("tbody tr").data("row-selected",a):b.closest("tr");a?b.addClass("ui-ncbigrid-row-selected"):b.removeClass("ui-ncbigrid-row-selected");this._updateCount()},checkAll:function(a){this._checkHelper(true,a);this._trigger("selectallclicked",null,[{acrossAllPages:a}])},uncheckAll:function(a){this._checkHelper(false,a);this._trigger("selectnoneclicked",null,[{acrossAllPages:a}])},_rowClicked:function(a){var b=jQuery(a.target||a.srcElement);a=null;if(b.is("input[type=checkbox]")){a=
+b;var c=a.is(":checked")}else if(!b.is("a")){a=b.closest("tr").find("input[type=checkbox]");c=!a.is(":checked");a.attr("checked",c)}b=b.closest("tr");if(a&&a.length===0){c=!b.data("row-selected");b.data("row-selected",c)}c?b.addClass("ui-ncbigrid-row-selected"):b.removeClass("ui-ncbigrid-row-selected");this.element.trigger("checkboxrowclicked");this._updateCount()},_filterBarControlsHTML:'                                         <div class="ui-ncbigrid-filter-toolbar">                        \t\t\t\t\t\t\t<label>Filter:</label>\t\t\t\t\t\t\t<input type="text" name="gridFilter" />                                            </div>',
+_createFilterBarControl:function(){this._createFilterBar();this._addFilterEvents()},_createFilterBar:function(){this._filterToolBar=jQuery(this._filterBarControlsHTML);var a=this.element.parent().parent();a.prepend(this._filterToolBar).children(".ui-ncbigrid-filter-toolbar").attr("aria-controls",this.element.attr("id"));a.addClass("filterToolbar-exists");var b=jQuery.ui.jig._generateId("gridFilter");a.children(".ui-ncbigrid-filter-toolbar").children(":input").attr("id",b).prev().attr("for",b)},_addFilterEvents:function(){var a=
+this;this._filterToolBar.find("input[type=text]").keyup(function(b){a._filterGrid(b,this)})},_filterGrid:function(a,b){if(!this._lastRunFilter)this._lastRunFilter="";a=b.value;b=this.options.filterToolbarIsCaseInsensitive||null;var c=this.options.filterToolbarColumnIndex||null,d=this.options.filterToolbarIsInverse||null;this._lastRunFilter.length>0&&a.indexOf(this._lastRunFilter)!==0&&this.removeFilterRows();this._lastRunFilter=a;if(this._lastRunFilter.length>0){var e=false;if(this.options.regExp)try{a=
+RegExp(a.replace(/(^\/)|(\/$)/g,""))}catch(g){e=true}e||this.filterRows(a,b,c,d)}},_custFilterCnt:0,filterRows:function(a,b,c,d){function e(){p.options.isPageable&&p._gotoPage(0);p.element.trigger("ncbigridfilterapplied",[a,b,c,g,f]).trigger("ncbigridhideloadingbar");p._notifyGridUpdated()}if(!(typeof a=="undefined"||a.length===0)){this.element.trigger("ncbigridshowloadingbar");if(!jQuery.isArray(a)){orgTxt=a;a=[[a,b,c,d]]}d=f=jQuery("tbody tr:not(.ncbigrid-row-filtered)",this.element);for(var g,
+f,i=0;i<a.length;i++){var h=a[i],j=h[0],l=h[2],k=h[3];h="";if(typeof l!="undefined"&&l!==null)h=":nth-child("+l+")";k=k?"not-":"";var m="",o=null;if(typeof j==="function"){m="-functionTest";o=this._custFilterCnt;this._custFilterCnt=o+1;o="filter_temp_"+o;jQuery.ui.jig[o]=j;j="jQuery.ui.jig."+o}else if(j.constructor&&j.constructor.toString().indexOf("RegExp")>0)m="-regexp";else if(b)m="-insensitive";f=l!==null?f.find("td"+h+":"+k+"contains"+m+"("+j+")").parent():f.filter(":"+k+"contains"+m+"("+j+")");
+if(o)jQuery.ui.jig[o]=null}var p=this;if(d){g=d.not(f);var q=g.length,t=0;(function(){for(;t<q;){g.eq(t).addClass("ncbigrid-row-filtered").attr("isfiltered","true");t++}e()})()}else e()}},removeFilterRows:function(a,b,c,d,e){function g(){if(l){jQuery.ui.jig[l]=null;a=j}m.options.isPageable&&m._gotoPage(0);m.element.trigger("ncbigridfilterremoved",[a,b,c]);m.options.isPageable?m._gotoPage(m.options.currentPage):m._notifyGridUpdated()}var f=null;if(typeof a!="undefined"&&a.length>0){if(typeof d==="undefined")d=
+true;var i="",h="";if(d||e){i=":not(";h=")"}var j=d="",l=null;if(typeof a==="function"){d="-functionTest";var k=this._custFilterCnt;this._custFilterCnt=k+1;l="filter_temp_"+k;j=jQuery.ui.jig[l]=a;a="jQuery.ui.jig."+l}else if(a.constructor&&a.constructor.toString().indexOf("RegExp")>0)d="-regexp";else if(b)d="-insensitive";e=e?"not-":"";if(typeof c!="undefined"&&c!==null){i="tbody tr[isfiltered='true'] td:nth-child("+c+")"+i+":"+e+"contains"+d+"("+a+")"+h;f=this.element.find(i).parent()}else{i="tbody tr[isfiltered='true']"+
+i+":contains"+d+"("+a+")"+h;f=this.element.find(i)}}else f=this.element.find("tr.ncbigrid-row-filtered");var m=this;if(f!==null){var o=f.length,p=0;(function(){for(;p<o;){f.eq(p).removeClass("ncbigrid-row-filtered").attr("isfiltered","false");p++}g()})()}else g()},showColumn:function(a){var b=this.element;if(this.options.isScrollable)b=b.add(this.parts.headerWrapper.find("table"));b.children().find(">tr>*:nth-child("+a+")").removeClass("ui-ncbigrid-column-hidden");this._setColumnHiddenData(a,false);
+this.element.trigger("showColumn",[a]);this._notifyGridUpdated()},hideColumn:function(a){var b=this.element;if(this.options.isScrollable)b=b.add(this.parts.headerWrapper.find(">table"));b.children().find(">tr>*:nth-child("+a+")").addClass("ui-ncbigrid-column-hidden");this._setColumnHiddenData(a,true);this.element.trigger("hideColumn",[a]);this._notifyGridUpdated()},_setColumnHiddenData:function(a,b){var c=this.element.data("dataHiddenCols");c||(c=[]);c[a]=b;this.element.data("dataHiddenCols",c)},
+getHiddenShownColumns:function(){var a=[],b=[],c=this.element.data("dataHiddenCols");if(c)for(var d in c)c[d]?a.push(d):b.push(d);return{hidden:a,shown:b}},_attachLoadingMessageListener:function(){var a=this;this.element.bind("ncbigridshowloadingbar",function(){a._showLoadingMessage()}).bind("ncbigridhideloadingbar",function(){a._hideLoadingMessage()})},_showLoadingMessage:function(){if(this.options.isLoadingMessageShown){if(!this.isPopperAttached){this.element.parent().parent().ncbipopper({triggerPosition:"top center",
+destPosition:"top center",hasArrow:false,closeEvent:"custom",openEvent:"custom",openAnimation:"none",closeAnimation:"none",destText:this.options.loadingText,isDestElementCloseClick:false,isDocumentElementCloseClick:false,isEscapeKeyClose:false,isTriggerElementCloseClick:false});this.isPopperAttached=true}this.element.parent().parent().ncbipopper("open")}},_hideLoadingMessage:function(){this.options.isLoadingMessageShown&&this.element.parent().parent().ncbipopper("close")},_addRowClickWatcher:function(){var a=
+this;jQuery(this.element).on("click","tbody",function(b){b=jQuery(b.srcElement||b.target).closest("td");if(b.length===1){var c=b.closest("tr");a.element.trigger("ncbigridrowclick",[{row:c,cell:b,rowIndex:c[0].rowIndex,cellIndex:b[0].cellIndex}])}})},_notifyGridUpdated:function(){this.element.trigger("ncbigridupdated")},_notifyGridContentChanged:function(){this.element.trigger("ncbigridcontentchanged")},addHTMLRowData:function(a,b,c,d){var e=this.getRowCount(),g="";if(typeof b=="undefined")g=":last-child";
+else{if(b>e)b=e;else if(b<0){b=1;c="before"}g=":nth-child("+b+")"}b=d!==undefined?":eq("+d+")":"";if(e===0)jQuery("tbody"+b+g,this.element).append(a);else c&&c.toLowerCase()==="before"?jQuery("tbody"+b+" tr"+g,this.element).before(a):jQuery("tbody"+b+" tr"+g,this.element).after(a);this.options.isPageable?this._gotoPage(this.options.currentPage):this._notifyGridUpdated();this._notifyGridContentChanged()},_deleteRowHelper:function(a,b){b=b!==undefined?":eq("+b+")":"";a?this.element.find("tbody"+b+" tr"+
+a).remove():this.element.find("tbody"+b).empty()},deleteAllRows:function(){this._deleteRowHelper();this.options.isPageable&&this._gotoPage(0);this._notifyGridUpdated();this._notifyGridContentChanged()},deleteRow:function(a,b){if(typeof a!="undefined"){a=jQuery.isArray(a)?a.sort():[a];for(var c=a.length-1;c>=0;c--)this._deleteRowHelper(":nth-child("+a[c]+")",b);this.options.isPageable&&this._gotoPage(this.options.currentPage);this._notifyGridUpdated();this._notifyGridContentChanged()}},getCellData:function(a,
+b,c){if(!(typeof a=="undefined"||typeof b=="undefined")){a=jQuery("tbody"+(c!==undefined?":eq("+c+")":"")+" tr:nth-child("+a+") td:nth-child("+b+")",this.element);if(a.length==0)return null;return this._getCellValue(a,b)}},getColumnCount:function(a){a=a===false?":visible":"";a=jQuery(this.element).find("tbody tr:not(.ui-ncbigrid-rowHidden):eq(0) td"+a).length;if(a===0)a=jQuery(this.element).find("> thead tr:last th").length;return a},getColumnData:function(a,b){if(typeof a==="undefined")return null;
+else if(jQuery.isArray(a)){for(var c=[],d=0;d<a.length;d++){if(a[d]<=0||a[d]>this.getColumnCount())c.push(null);c.push(this._getColumnDataHelper(a[d]),b)}return c}else{if(a<=0||a>this.getColumnCount())return null;return this._getColumnDataHelper(a,b)}},_getColumnDataHelper:function(a,b){var c=[],d=this,e=this._getColumnType(a-1);if(e==="str"||!e)e="str-sensitive";jQuery("tbody"+(b!==undefined?":eq("+b+")":"")+" tr td:nth-child("+a+")",this.element).each(function(g,f){c.push(d._csColumnTypeConversion(f,
+e,true))});if(c.length!==0)return c},getRowData:function(a,b){if(typeof a!=="undefined")if(jQuery.isArray(a)){for(var c=[],d=0;d<a.length;d++)c.push(this._getRowDataHelper(a[d]),b);return c}else return this._getRowDataHelper(a,b)},_getRowDataHelper:function(a,b){var c=[],d=this;jQuery("tbody"+(b!==undefined?":eq("+b+")":"")+" tr:nth-child("+a+") td",this.element).each(function(e){c.push(d._getCellValue(jQuery(this),e))});if(c.length!==0)return c},highlightRows:function(a,b,c,d){var e=jQuery.browser.msie&&
+parseFloat(jQuery.browser.version)<7;if(!(typeof a=="undefined"||a.length===0)){this.element.trigger("ncbigridshowloadingbar");var g=[],f=b?"-insensitive":"";d=d?"not-":"";if(a.constructor&&a.constructor.toString().indexOf("RegExp")>0){f="-regexp";d=""}typeof c!="undefined"?jQuery("tbody tr td"+(":nth-child("+c+")")+":"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).parent();h="ui-ncbigrid-high";if(e)h=i.hasClass("ui-ncbigrid-row-even")?"ui-ncbigrid-row-even-high-IE6":"ui-ncbigrid-row-odd-high-IE6";
+i.addClass(h);jQuery.inArray(i,g)===-1&&g.push(i)}):jQuery("tbody tr:"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h);h="ui-ncbigrid-high";if(e)h=i.hasClass("ui-ncbigrid-row-even")?"ui-ncbigrid-row-even-high-IE6":"ui-ncbigrid-row-odd-high-IE6";i.addClass(h);g.push(i)});this.element.trigger("ncbigridhighlightapplied",[a,b,c,g]).trigger("ncbigridhideloadingbar");return{highlightedRows:g}}},removeHighlightRows:function(a,b,c,d){var e=jQuery.browser.msie&&parseFloat(jQuery.browser.version)<
+7;if(typeof a!="undefined"&&a.length>0){var g=[],f=b?"-insensitive":"";d=d?"not-":"";if(a.constructor&&a.constructor.toString().indexOf("RegExp")>0){f="-regexp";d=""}typeof c!="undefined"?jQuery("tbody tr td"+(":nth-child("+c+")")+":"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).parent().removeClass("ui-ncbigrid-high");e&&i.removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6");jQuery.inArray(i,g)===-1&&g.push(i)}):jQuery("tbody tr:"+d+"contains"+
+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).removeClass("ui-ncbigrid-high");e&&i.removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6");g.push(i)})}else{jQuery(".ui-ncbigrid-high",this.element).removeClass("ui-ncbigrid-high");e&&jQuery(".ui-ncbigrid-row-odd-high-IE6, .ui-ncbigrid-row-even-high-IE6",this.element).removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6")}this.element.trigger("ncbigridhighlightremoved",[a,
+b,c])},setCellData:function(a,b,c,d){jQuery("tbody"+(d!==undefined?":eq("+d+")":"")+" tr:nth-child("+a+") td:nth-child("+b+")",this.element).text(c);this.element.trigger("ncbigridcellchange",[a,b,this.getCellData(a,b)]);this._notifyGridUpdated();this._notifyGridContentChanged()},setRowData:function(a,b,c){jQuery("tbody"+(c!==undefined?":eq("+c+")":"")+" tr:nth-child("+a+") td",this.element).each(function(d,e){jQuery(e).text(b[d])});this.element.trigger("ncbigridrowchange",[a,this.getRowData(a,c)]);
+this._notifyGridUpdated();this._notifyGridContentChanged()},_enableCollapseTbodyRows:function(a){if(this.options.collapseRowsEnabled){a||(a=jQuery(this.element).find("tbody tr:has(th)"));var b=this;jQuery(a).each(function(){jQuery(this).addClass("ui-ncbigrid-collapsable").find("th").eq(0).prepend('<span class="collapsableTbodyIcon ui-icon ui-icon-plus-minus-big-open"></span>').find("span").click(function(c){c.stopPropagation();b._collapseTbodyRows(this.parentNode.parentNode)}).end().end().not(".ignoreCollapse").click(function(){b._collapseTbodyRows(this.parentNode)})})}},
+_collapseTbodyRows:function(a){jQuery(a).find("th span.collapsableTbodyIcon").toggleClass("ui-icon-plus-minus-big").toggleClass("ui-icon-plus-minus-big-open").end().siblings().toggleClass("collapsed")}});jQuery.extend(jQuery.expr[":"],{"contains-insensitive":function(a,b,c){return(a.textContent||a.innerText||"").toLowerCase().indexOf((c[3]||"").toLowerCase())>=0}});
+jQuery.extend(jQuery.expr[":"],{"contains-regexp":function(a,b,c){a=jQuery.trim(a.textContent||a.innerText||"");c=c[3];b=c.match(/\/([gi]+)$/);b=b!==null?b[1]:"";c=c.replace(/\/[gi]?$/,"").replace(/^\//,"");return a.match(new RegExp(c,b))!==null}});jQuery.extend(jQuery.expr[":"],{"contains-functionTest":function(a,b,c){a=a.textContent||a.innerText||"";return jQuery.ui.jig._getFncFromStr(c[3])(a)}});
+jQuery.extend(jQuery.expr[":"],{"not-contains":function(a,b,c){return(a.textContent||a.innerText||"").indexOf(c[3]||"")===-1}});jQuery.extend(jQuery.expr[":"],{"not-contains-insensitive":function(a,b,c){return(a.textContent||a.innerText||"").toLowerCase().indexOf((c[3]||"").toLowerCase())===-1}});
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_007.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+html .ui-ncbimenu>li>a{color:#fff;}.jig-ncbimenu li.offscreen_noflow{position:absolute;left:-1000px;}.jig-ncbimenu{clear:both;}.jig-ncbimenu ul{display:none;}.jig-ncbimenu>li{display:inline;float:left;}ul.ui-ncbibasicmenu li{display:block;margin:0;}.ui-ncbimenu li>a{background-color:transparent;border:0;}.ui-ncbimenu ul{-moz-border-radius:6px;-webkit-border-radius:6px;border-radius:6px;border:1px solid #CCC;-webkit-box-shadow:.4em .4em .5em rgba(0,0,0,.3);-moz-box-shadow:.4em .4em .5em rgba(0,0,0,.3);box-shadow:.4em .4em .5em rgba(0,0,0,.3);}.ui-ncbimenu li.active a{background-color:#4c96df;}.ui-ncbimenu>li a:focus{outline:0;}.ui-ncbimenu li a.expandDown{padding-right:20px;background:url("../img/arrow-sprite.png") no-repeat scroll 96% -6% #FFF;}.ui-ncbimenu li a.expandRight{background:url("../img/arrow-sprite.png") no-repeat scroll 96% 106% #FFF;}.ui-ncbimenu>li>a.expandDown,.ui-ncbimenu>li>a.expandRight{background-color:transparent;}.ui-ncbimenu li>a:hover.expandRight{background:url("../img/arrow-sprite.png") no-repeat scroll 96% 106% #4C96DF;}.ui-ncbimenu li.ui-ncbimenu-item-no-hlt>a:hover.expandRight,.ui-ncbimenu li.ui-ncbimenu-item-skip>a:hover.expandRight{background-color:transparent;}.ui-ncbimenu li ul{display:none;z-index:200;}ul.ui-ncbimenu li ul li a{background-color:#fff;}.ui-ncbimenu ul{position:absolute;display:none;}.ui-ncbimenu>li a:hover,.ui-ncbimenu li.selected>a{background-color:#4C96DF;color:#fff;}.ui-ncbimenu li ul.ncbibasicmenu li.ui-ncbimenu-item-no-hlt,.ui-ncbimenu li ul.ncbibasicmenu li.ui-ncbimenu-item-skip{background-color:#FFF;}.ui-ncbimenu li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu li.selected.ui-ncbimenu-item-no-hlt>a,.ui-ncbimenu li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu li.selected.ui-ncbimenu-item-skip>a{color:#fff;}.ui-ncbimenu li ul li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu li ul li.selected.ui-ncbimenu-item-no-hlt>a,.ui-ncbimenu li ul li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu li ul li.selected.ui-ncbimenu-item-skip>a{color:#14376C;background-color:transparent;}.ui-ncbimenu .oneLevel li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu.ui-ncbibasicmenu>li.ui-ncbimenu-item-no-hlt>a:hover,.ui-ncbimenu .oneLevel li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu.ui-ncbibasicmenu>li.ui-ncbimenu-item-skip>a:hover{background-color:transparent;}.ui-ncbimenu .ui-ncbimenu-item-leaf{margin:0 .75em 0 0;}.ui-ncbimenu .ui-ncbimenu-item-leaf>a:hover{background-color:transparent;}.ui-ncbimenu:before,.ui-ncbimenu:after{content:"";display:table;}.ui-ncbimenu{*zoom:1;}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_007.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,14 @@
+jQuery.widget("ui.ncbibasicmenu",{options:{defaultSelection:-1,allowMultipleSelections:false,orientation:"vertical",preventDefaultCheck:true,stopPropagationCheck:true,normalizeSubsToOneLevel:false,disableSelect:false},styles:{itemNoHilite:"ui-ncbimenu-item-no-hlt",itemSkip:"ui-ncbimenu-item-skip"},_init:function(){this._loadedOnce&&this.rescan();this._loadedOnce=true},_create:function(){this._setSelectorString();this._addClasses();this._formatList();this._addEvents();this._setUpDefaults();this._setTabIndex();
+this._addAria()},rescan:function(){this._addClasses();this._setTabIndex();this._addAria();this._destroyFocusEvents();this._setUpFocusEvents()},destroy:function(){this._destroyTabIndex();this._destroyClasses();this._destroyEvents();this._destroyAria();this._destroyFormatList()},_setSelectorString:function(){var a=">";if(this.options.normalizeSubsToOneLevel){a="";this.element.addClass("oneLevel")}this._liSelector=a+"li:not(.ui-ncbimenu-item-skip)"},_addClasses:function(){this.isVert=this.options.orientation===
+"vertical";var a="ui-ncbibasicmenu";this.isVert||(a+=" orientation_hort");this.element.addClass(a)},_destroyClasses:function(){this.element.removeClass("ui-ncbibasicmenu")},_setUpDefaults:function(){this.selectedOption=this.options.defaultSelection;if(this.selectedOption!==-1){var a=this.element.find(this._liSelector+">a");if(this.options.allowMultipleSelections)for(var b=0;b<this.selectedOption.length;b++)this._makeSelection(a.eq(this.selectedOption[b]),"load");else this._makeSelection(a.eq(this.selectedOption),
+"load")}},_formatList:function(){},_destroyFormatList:function(){},_setTabIndex:function(){var a=this.element.find(this._liSelector+">a").attr("tabindex","-1"),b=this.element.find(this._liSelector+".selected>a");if(b.length>0)b=b.eq(0);else{var c=0;for(b=a.eq(0);b.is("."+this.styles.itemSkip+" a")&&c<a.length-1;){c+=1;b=a.eq(c)}}this.options.nested||b.removeAttr("tabindex")},_destroyTabIndex:function(){this.element.find(this._liSelector+">a").removeAttr("tabindex")},_addEvents:function(){this._setUpKeyListener();
+this._setUpClickEvents();this._setUpFocusEvents();this._setUpHoverEvents()},_destroyEvents:function(){this._destroyKeyListener();this._destroyClickEvents();this._destroyFocusEvents();this._destroyHoverEvents()},_setUpKeyListener:function(){if(!this._menuKeyListener){var a=this;this._menuKeyListener=function(b){if(a.element.is(":visible"))if(a._keyPressDetected(b.keyCode)){b.preventDefault();a.options.stopPropagationCheck&&b.stopPropagation()}};jQuery(document).keydown(this._menuKeyListener)}},_destroyKeyListener:function(){if(this._menuKeyListener){jQuery(window).unbind("keydown",
+this._menuKeyListener);this._menuKeyListener=null}},_setUpClickEvents:function(){var a=this;this._ulClickEvent=function(b){var c=b.srcElement||b.target;if(c){a.options.disableSelect||a._makeSelection(jQuery(c),"click");a.options.stopPropagationCheck&&b.stopPropagation();a.options.preventDefaultCheck&&jQuery(c).siblings("ul").length===1&&b.preventDefault()}};this.element.on("click.ncbibasicmenu",this._ulClickEvent)},_destroyClickEvents:function(){this.element.off("click",this._ulClickEvent)},_setUpFocusEvents:function(){var a=
+this;this._focusFnc=function(){a._menuFocused(this)};this._blurFnc=function(){a._menuBlured(this)};this.element.find(this._liSelector+">a").on("blur",this._blurFnc).on("focus",this._focusFnc)},_destroyFocusEvents:function(){this.element.find(this._liSelector+">a").off("blur",this._blurFnc).off("focus",this._focusFnc)},focus:function(){this._menuFocused(null)},_menuFocused:function(a){this._lastAnchor=a;this._isFocused=true},_menuBlured:function(a){if(this._lastAnchor==a)this._isFocused=false},removeFocus:function(){this._menuBlured()},
+_setUpHoverEvents:function(){var a=this;this._mouseEnterFnc=function(b){b=jQuery(b.target).closest("li");!b.hasClass(a.styles.itemNoHilite)&&!b.hasClass(a.styles.itemSkip)&&b.addClass("hover")};this.mouseLeaveFnc=function(){jQuery(this).removeClass("hover")};this.element.on("mouseenter","li",this._mouseEnterFnc).on("mouseleave","li",this.mouseLeaveFnc)},_destroyHoverEvents:function(){this.element.off("mouseenter",this._mouseEnterFnc).off("mouseleave",this.mouseLeaveFnc);this.mouseLeaveFnc=this._mouseEnterFnc=
+null},_makeSelection:function(a,b){var c=a.parent("li");if(c.length===1){var d=c.hasClass("selected");this.options.allowMultipleSelections||this._removeAllSelections();if(!c.hasClass(this.styles.itemSkip)){c.hasClass(this.styles.itemNoHilite)||c[d?"removeClass":"addClass"]("selected");var e=d?"unselected":"selected";b!=="menunav"&&this._trigger(e,"x",[a,c,b]);if(b==="click"||b==="load")this.selectedOption=this.element.find(this._liSelector+".selected").index();else d||c.find(">a").focus()}}this._setTabIndex()},
+_keys:{up:38,down:40,left:37,right:39,enter:13,escape:27,tab:9},_keyPressDetected:function(a){var b=this._keys,c=false;if(this._isFocused&&this.element.has(this._liSelector+">a:focus"))switch(a){case b.up:this._upDownPressed(-1);c=true;break;case b.down:this._upDownPressed(1);c=true;break;case b.left:this._leftRightPressed(-1);c=true;break;case b.right:this._leftRightPressed(1);c=true;break;case b.enter:this._enterSelected();c=false;break;case b.escape:this._escapeTyped();c=false;break;case b.tab:this._trigger("tab");
+default:c=false}return c},_upDownPressed:function(a){this.isVert?this._moveSelection(a):this._trigger(a===1?"actiondown":"actionup","x",this.focusedElement())},_leftRightPressed:function(a){this.isVert?this._trigger(a===1?"actionright":"actionleft","x",this.focusedElement()):this._moveSelection(a)},focusedElement:function(){return this.selectedOption!==-1?this.element.find(this._liSelector).eq(this.selectedOption):this.element.find(this._liSelector+":has(>a:focus)")},moveSelection:function(a){this._moveSelection(a)},
+_getNextIndex:function(a,b,c){a=a+b;if(a<0)a=c-1;else if(a>c-1)a=0;return a},_moveSelection:function(a){for(var b=this.element.find(this._liSelector+">a"),c=this._getNextIndex(this.selectedOption,a,b.length);b.eq(c).closest("li").hasClass(this.styles.itemSkip);)c=this._getNextIndex(c,a,b.length);this.selectedOption=c;this._makeSelection(b.eq(c),"keyboard")},removeAllSelections:function(){this.selectedOption=-1;this._removeAllSelections();this._setTabIndex()},_removeAllSelections:function(){this.element.find(this._liSelector).removeClass("selected")},
+_enterSelected:function(){this._trigger("enter")},_escapeTyped:function(){this._trigger("escape","x",this.focusedElement())},_addAria:function(){var a=this.element.parents('[role="menubar"]'),b=this.element.find(this._liSelector),c=b.find(">a");this.element.attr("role",a.length===0?"menubar":"menu");b.attr("role","presentation");c.attr("role","menuitem")},_destroyAria:function(){var a=this.element.find(this._liSelector),b=a.find(">a");this.element.removeAttr("role");a.removeAttr("role");b.removeAttr("role")},
+selectFirstItem:function(){this.selectedOption=0;this._moveSelection(0)}});
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_008.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1 @@
+ul.jig-ncbilocalnav,ul.ui-ncbilocalnav{list-style:none;margin:0;padding:0;width:100%;}ul.jig-ncbilocalnav:after,ul.ui-ncbilocalnav:after{content:".";display:block;height:0;clear:both;visibility:hidden;*zoom:1;*display:block;}ul.jig-ncbilocalnav li,ul.ui-ncbilocalnav li{float:left;position:relative;list-style:none;display:block;}ul.jig-ncbilocalnav li a,ul.ui-ncbilocalnav li a{color:#444;text-decoration:none;display:block;padding:.15em 1em .15em 1em;zoom:1;}ul.jig-ncbilocalnav ul{display:none;}ul.ui-ncbilocalnav ul{margin:0;margin-left:0!important;display:none;border-width:1px 0 0 1px;width:200px;padding-left:0;-moz-box-shadow:.4em .4em .5em #999;-webkit-box-shadow:.4em .4em .5em #999;box-shadow:.4em .4em .5em #999;_margin-top:1px;}ul.ui-ncbilocalnav li.open ul{display:block;position:absolute;left:-1px;}ul.ui-ncbilocalnav li:first-child{margin-left:1.333em;}ul.ui-ncbilocalnav ul li:first-child{margin-left:0;}ul.ui-ncbilocalnav ul li{float:none;display:block;position:relative;*line-height:125%;zoom:1;}ul.ui-ncbilocalnav li.has-child ul{z-index:1003;}ul.ui-ncbilocalnav li:first-child{border-left:1px solid #b0b0b0;}ul.ui-ncbilocalnav ul li:first-child{border-left:0;}ul.ui-ncbilocalnav{border-top:1px solid #c4c4c4;border-bottom:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul{border-left:1px solid #b0b0b0;}ul.ui-ncbilocalnav li{border-right:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul li{border-bottom:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul li:first-child{border-top:1px solid #b0b0b0;}ul.ui-ncbilocalnav li.active{border-right:1px solid #c4c4c4;*z-index:1005;}ul.ui-ncbilocalnav li.active ul li{*z-index:1006;}ul.ui-ncbilocalnav li.active,ul.ui-ncbilocalnav li.active ul li,ul.ui-ncbilocalnav li.hover,ul.ui-ncbilocalnav li.hover ul li{*z-index:1006;}ul.ui-ncbilocalnav li.selected>ul>li a{margin:0 .75em;padding:.15em 1.5em .15em .25em;}ul.ui-ncbilocalnav li.selected a{color:#444!important;background-color:transparent!important;}ul.ui-ncbilocalnav li.hover>a,ul.ui-ncbilocalnav li.hover.selected>a,ul.ui-ncbilocalnav li.selected>a{background-color:transparent!important;color:#444!important;}ul.ui-ncbilocalnav,ul.ui-ncbilocalnav li{background-color:#F4F4F4;background-image:-webkit-gradient(linear,left top,left bottom,from(#fff),to(#F4F4F4));background-image:-webkit-linear-gradient(top,#fff,#F4F4F4);background-image:-moz-linear-gradient(top,#fff,#F4F4F4);background-image:-ms-linear-gradient(top,#fff,#F4F4F4);background-image:-o-linear-gradient(top,#fff,#F4F4F4);background-image:linear-gradient(top,#fff,#F4F4F4);}ul.ui-ncbilocalnav li.hover,ul.ui-ncbilocalnav li.selected{background-color:#E0E0E0;background-image:-webkit-gradient(linear,left top,left bottom,from(#F2F2F2),to(#E0E0E0));background-image:-webkit-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-moz-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-ms-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-o-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:linear-gradient(top,#F2F2F2,#E0E0E0);}ul.ui-ncbilocalnav li li.hover{background-color:#EDEDED;background-image:-webkit-gradient(linear,left top,left bottom,from(#DEDEDE),to(#EDEDED));background-image:-webkit-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-moz-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-ms-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-o-linear-gradient(top,#DEDEDE,#EDEDED);background-image:linear-gradient(top,#DEDEDE,#EDEDED);}.ui-ncbilocalnav>li>a.expandDown{background:url(../img/ncbilocalnav-arrow.png) no-repeat right 8px!important;_background-position:right 11px!important;padding:.15em 1.5em .15em .25em;margin:0 .75em;color:#444;}ul.ui-ncbilocalnav li.selected ul li a{background-image:none!important;zoom:1;}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_008.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,14 @@
+(function(b){var h,i,j,g,l=function(){var a=b(this).find(":ui-button");setTimeout(function(){a.button("refresh")},1)},k=function(a){var c=a.name,e=a.form,f=b([]);if(c)f=e?b(e).find("[name='"+c+"']"):b("[name='"+c+"']",a.ownerDocument).filter(function(){return!this.form});return f};b.widget("ui.button",{options:{disabled:null,text:true,label:null,icons:{primary:null,secondary:null}},_create:function(){this.element.closest("form").unbind("reset.button").bind("reset.button",l);if(typeof this.options.disabled!==
+"boolean")this.options.disabled=this.element.propAttr("disabled");this._determineButtonType();this.hasTitle=!!this.buttonElement.attr("title");var a=this,c=this.options,e=this.type==="checkbox"||this.type==="radio",f="ui-state-hover"+(!e?" ui-state-active":"");if(c.label===null)c.label=this.buttonElement.html();if(this.element.is(":disabled"))c.disabled=true;this.buttonElement.addClass("ui-button ui-widget ui-state-default ui-corner-all").attr("role","button").bind("mouseenter.button",function(){if(!c.disabled){b(this).addClass("ui-state-hover");
+this===h&&b(this).addClass("ui-state-active")}}).bind("mouseleave.button",function(){c.disabled||b(this).removeClass(f)}).bind("click.button",function(d){if(c.disabled){d.preventDefault();d.stopImmediatePropagation()}});this.element.bind("focus.button",function(){a.buttonElement.addClass("ui-state-focus")}).bind("blur.button",function(){a.buttonElement.removeClass("ui-state-focus")});if(e){this.element.bind("change.button",function(){g||a.refresh()});this.buttonElement.bind("mousedown.button",function(d){if(!c.disabled){g=
+false;i=d.pageX;j=d.pageY}}).bind("mouseup.button",function(d){if(!c.disabled)if(i!==d.pageX||j!==d.pageY)g=true})}if(this.type==="checkbox")this.buttonElement.bind("click.button",function(){if(c.disabled||g)return false;b(this).toggleClass("ui-state-active");a.buttonElement.attr("aria-pressed",a.element[0].checked)});else if(this.type==="radio")this.buttonElement.bind("click.button",function(){if(c.disabled||g)return false;b(this).addClass("ui-state-active");a.buttonElement.attr("aria-pressed","true");
+var d=a.element[0];k(d).not(d).map(function(){return b(this).button("widget")[0]}).removeClass("ui-state-active").attr("aria-pressed","false")});else{this.buttonElement.bind("mousedown.button",function(){if(c.disabled)return false;b(this).addClass("ui-state-active");h=this;b(document).one("mouseup",function(){h=null})}).bind("mouseup.button",function(){if(c.disabled)return false;b(this).removeClass("ui-state-active")}).bind("keydown.button",function(d){if(c.disabled)return false;if(d.keyCode==b.ui.keyCode.SPACE||
+d.keyCode==b.ui.keyCode.ENTER)b(this).addClass("ui-state-active")}).bind("keyup.button",function(){b(this).removeClass("ui-state-active")});this.buttonElement.is("a")&&this.buttonElement.keyup(function(d){d.keyCode===b.ui.keyCode.SPACE&&b(this).click()})}this._setOption("disabled",c.disabled);this._resetButton()},_determineButtonType:function(){this.type=this.element.is(":checkbox")?"checkbox":this.element.is(":radio")?"radio":this.element.is("input")?"input":"button";if(this.type==="checkbox"||this.type===
+"radio"){var a=this.element.parents().filter(":last"),c="label[for='"+this.element.attr("id")+"']";this.buttonElement=a.find(c);if(!this.buttonElement.length){a=a.length?a.siblings():this.element.siblings();this.buttonElement=a.filter(c);if(!this.buttonElement.length)this.buttonElement=a.find(c)}this.element.addClass("ui-helper-hidden-accessible");(a=this.element.is(":checked"))&&this.buttonElement.addClass("ui-state-active");this.buttonElement.attr("aria-pressed",a)}else this.buttonElement=this.element},
+widget:function(){return this.buttonElement},destroy:function(){this.element.removeClass("ui-helper-hidden-accessible");this.buttonElement.removeClass("ui-button ui-widget ui-state-default ui-corner-all ui-state-hover ui-state-active  ui-button-icons-only ui-button-icon-only ui-button-text-icons ui-button-text-icon-primary ui-button-text-icon-secondary ui-button-text-only").removeAttr("role").removeAttr("aria-pressed").html(this.buttonElement.find(".ui-button-text").html());this.hasTitle||this.buttonElement.removeAttr("title");
+b.Widget.prototype.destroy.call(this)},_setOption:function(a,c){b.Widget.prototype._setOption.apply(this,arguments);if(a==="disabled")c?this.element.propAttr("disabled",true):this.element.propAttr("disabled",false);else this._resetButton()},refresh:function(){var a=this.element.is(":disabled");a!==this.options.disabled&&this._setOption("disabled",a);if(this.type==="radio")k(this.element[0]).each(function(){b(this).is(":checked")?b(this).button("widget").addClass("ui-state-active").attr("aria-pressed",
+"true"):b(this).button("widget").removeClass("ui-state-active").attr("aria-pressed","false")});else if(this.type==="checkbox")this.element.is(":checked")?this.buttonElement.addClass("ui-state-active").attr("aria-pressed","true"):this.buttonElement.removeClass("ui-state-active").attr("aria-pressed","false")},_resetButton:function(){if(this.type==="input")this.options.label&&this.element.val(this.options.label);else{var a=this.buttonElement.removeClass("ui-button-icons-only ui-button-icon-only ui-button-text-icons ui-button-text-icon-primary ui-button-text-icon-secondary ui-button-text-only"),
+c=b("<span></span>",this.element[0].ownerDocument).addClass("ui-button-text").html(this.options.label).appendTo(a.empty()).text(),e=this.options.icons,f=e.primary&&e.secondary,d=[];if(e.primary||e.secondary){if(this.options.text)d.push("ui-button-text-icon"+(f?"s":e.primary?"-primary":"-secondary"));e.primary&&a.prepend("<span class='ui-button-icon-primary ui-icon "+e.primary+"'></span>");e.secondary&&a.append("<span class='ui-button-icon-secondary ui-icon "+e.secondary+"'></span>");if(!this.options.text){d.push(f?
+"ui-button-icons-only":"ui-button-icon-only");this.hasTitle||a.attr("title",c)}}else d.push("ui-button-text-only");a.addClass(d.join(" "))}}});b.widget("ui.buttonset",{options:{items:":button, :submit, :reset, :checkbox, :radio, a, :data(button)"},_create:function(){this.element.addClass("ui-buttonset")},_init:function(){this.refresh()},_setOption:function(a,c){a==="disabled"&&this.buttons.button("option",a,c);b.Widget.prototype._setOption.apply(this,arguments)},refresh:function(){var a=this.element.css("direction")===
+"rtl";this.buttons=this.element.find(this.options.items).filter(":ui-button").button("refresh").end().not(":ui-button").button().end().map(function(){return b(this).button("widget")[0]}).removeClass("ui-corner-all ui-corner-left ui-corner-right").filter(":first").addClass(a?"ui-corner-right":"ui-corner-left").end().filter(":last").addClass(a?"ui-corner-left":"ui-corner-right").end().end()},destroy:function(){this.element.removeClass("ui-buttonset");this.buttons.map(function(){return b(this).button("widget")[0]}).removeClass("ui-corner-left ui-corner-right").end().button("destroy");
+b.Widget.prototype.destroy.call(this)}})})(jQuery);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/jquery_009.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,46 @@
+document.times=0;
+jQuery.widget("ui.ncbipopper",{destTextCallbackCalledCount:0,options:{openMethod:"",openEvent:"mouseover",openAnimation:"slideDown",openAnimationTime:290,closeMethod:"",closeEvent:"mouseout",closeAnimation:"slideUp",closeAnimationTime:150,isEscapeKeyClose:true,isSourceElementCloseClick:false,isTriggerElementCloseClick:true,isTargetElementCloseClick:false,isDestElementCloseClick:false,isDocumentCloseClick:true,addCloseButton:false,adjustFit:"autoAdjust",delayTimeout:300,sourcePosition:"",destPosition:"top left",
+sourceSelector:"",destSelector:"",targetPosition:"",triggerPosition:"bottom right",sourceText:null,destText:null,multipleHandlesSelector:"",openAtTarget:false,hasArrow:false,arrowDirection:"left",groupName:null,width:null,height:null,cssClass:null,excludeBasicCssStyles:false,wrapElement:false,loadingText:"loading...",showLoadingMessage:true,isDestTextCacheable:true,resizable:false,openAtMousePosition:false},_create:function(){this._setUpDestElem();this._addEventHandlers();this._addEscapeListener();
+this._addDocumentClickListener();this._addResizeListener();this._addCloseButton();this._addSharingDetails();this._addPopperHover();this.addTriggerAria()},updateTriggers:function(){this._addEventHandlers();this._addDocumentClickListener();this.addTriggerAria()},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);var a=this.isPopperShared();this._destroyDestAria();this._destroyTriggerAria();this._removeSharingDetails();this._destroyCloseButton(a);this._destroyResizeListener();this._destroyDocumentClickListener();
+this._destroyEscapeListener();this._removeEventHandlers();this._destroyDestElem(a)},getDestElement:function(a){var b=this.destElem;if(!this.origDestElem)this.origDestElem=b;if(b){if(a&&this._isWaitingToBeAddedToDom){a=jQuery("div.grid");a=a.length===1?a:jQuery(document.body);b.appendTo(a);this._isWaitingToBeAddedToDom=true;this._getActualText(b)}}else{b=this.options.destSelector||this.options.sourceSelector||this.element.prop("hash");a=this.options.destText||this.options.sourceText;if(b){b=jQuery(b);
+if(b.length===0)b=this._createTextHolder()}else if(a)b=this._createTextHolder();else throw"The popper can not find the popper element or text to display";if(this.options.wrapElement){if(!b.parent().hasClass("ui-ncbipopper-wrapper")){b.wrap('<div style="display:none"></div>');b.show()}if(!this.origDestElem)this.origDestElem=b;b=b.parent()}this.destElem=b;this._addDestAria()}if(!this.origDestElem)this.origDestElem=this.destElem;return b},_createTextHolder:function(){var a=jQuery('<div><div class="ui-ncbipopper-content"></div></div>');
+this._isWaitingToBeAddedToDom=true;return a},_getActualText:function(a){if(!this.isFunctionResultCached){var b=this.options.destText||this.options.sourceText,c=this._getFunction(b);if(typeof c==="function")b=this._getText(c);a.css("display","none").attr("generated","true").find(".ui-ncbipopper-content").html(b)}},_getFunction:function(a){var b=null;if(jQuery.ui.jig&&jQuery.ui.jig._getFncFromStr)b=jQuery.ui.jig._getFncFromStr(a);else if(typeof a==="function")b=a;return b},getDestTextCallbackCalledCount:function(){return this.destTextCallbackCalledCount},
+_getText:function(a){if(!(this.options.isDestTextCacheable&&this.getTextCalled||this.callbackInProgress)){this.getTextCalled=true;a||(a=this._getFunction(this.options.destText||this.options.sourceText));var b=this;this.callbackInProgress=true;a=a.call(this.element[0],function(c){b._setHTML(c);b.destTextCallbackCalledCount++;b.callbackInProgress=false})||this.options.loadingText;if(a!==this.options.loadingText)this.isFunctionResultCached=this.options.isDestTextCacheable;return a}},reloadContent:function(){var a=
+this._getText(),b=this.getDestElement().find(".ui-ncbipopper-content");b&&b.html(a);return this.element},_setHTML:function(a){var b=this.getDestElement().find(".ui-ncbipopper-content");if(b){b.html(a);this.isFunctionResultCached=this.options.isDestTextCacheable;!this.options.showLoadingMessage&&!this.isPopperDisplayed&&this._openAnimation()}},_setUpDestElem:function(){var a=this.getDestElement().addClass("ui-ncbipopper-wrapper");this.options.excludeBasicCssStyles||a.addClass("ui-ncbipopper-basic");
+this.options.resizable&&a.resizable();var b=this.options.cssClass;b&&a.addClass(b);this.options.width!==null&&a.width(this.options.width);this.options.height!==null&&a.height(this.options.height);this._resetElementPosition(a);a.removeClass("offscreen_noflow").hide();a.data("isOpen",false)},_setArrowDirection:function(){if(this.options.hasArrow){var a=this.options.arrowDirection;this._arrow&&this._arrow.removeClass("ui-ncbipopper-arrow-top ui-ncbipopper-arrow-bottom  ui-ncbipopper-arrow-left  ui-ncbipopper-arrow-right").addClass("ui-ncbipopper-arrow-"+
+a)}},_setUpArrow:function(a,b,c){if(this.options.hasArrow){var d=this.options.arrowDirection;if(this._arrow)this._arrow.removeClass("ui-ncbipopper-arrow-top ui-ncbipopper-arrow-bottom  ui-ncbipopper-arrow-left  ui-ncbipopper-arrow-right").addClass("ui-ncbipopper-arrow-"+d);else this._arrow=jQuery('<div class="ui-ncbipopper-arrow-image ui-ncbipopper-arrow-'+d+'">&nbsp;</div>').appendTo(document.body);a=this._getPositionSettings(a,"arrow",c);this._arrow.show().position({my:a.dest,of:this._activeTrigger||
+a.triggerElement||this.element,at:a.trigger,offset:a.offset,collision:"none"});if(b||this._arrowOverlapsPopper())this._arrow.hide()}},_destroyDestElem:function(a){a||this.getDestElement().removeClass("ui-ncbipopper-wrapper ui-ncbipopper-basic ui-ncbipopper-wrapper-relative-parent").attr("style","").show();this.options.wrapElement&&this.origDestElem.unwrap();this.destElem=null},_addEventHandlers:function(){var a=this,b=this.element,c=this.options.multipleHandlesSelector;if(c&&c.length>0)b=b.add(c);
+var d=this.options.openMethod||this.options.openEvent,e=this.options.closeMethod||this.options.closeEvent;if(d===e&&e==="click"){this._openFunction=function(f){a._toggle(f,f.currentTarget);f.preventDefault()};b.on("click",this._openFunction)}else{c={timeout:this.options.delayTimeout};if(d==="mouseover")c.over=function(f){a._isOverTrigger=true;a.open(f,this)};else{c.over=function(){a._isOverTrigger=true};this._openFunction=function(f){if(d==="click")if(a.option.isTriggerElementCloseClick){a._toggle(f,
+this);f.preventDefault()}else{a.isOpen(this)||f.preventDefault();a.open(f,this)}else a.open(f,this)};b.on(d,this._openFunction)}if(e==="mouseout")c.out=function(){a._isOverTrigger=false;a.isOpen(this)&&!a._isOverPopper&&a.close()};else{c.out=function(){};this._closeFunction=function(f){a.close();e==="click"&&f.preventDefault()};b.on(e,this._closeFunction)}if(d==="mouseover"||e==="mouseout")b.hoverIntent(c);if(this.options.isTriggerElementCloseClick&&e!=="click"&&d!=="click"){this._closeFunction2=
+function(f){a.isOpen(b)&&a.close();f.preventDefault()};b.on("click",this._closeFunction2)}}if(this.options.isDestElementCloseClick){this._closeFunctionPopper=function(f){a.isOpen(b)&&a.close();f.preventDefault()};this.getDestElement().on("click",this._closeFunctionPopper)}},_removeEventHandlers:function(){var a=this.element,b=this.getDestElement(),c=this.options.multipleHandlesSelector;if(c&&c.length>0)a=a.add(c);a.off("mouseover mouseout");if(this._openFunction){a.off(this.options.openMethod||this.options.openEvent,
+this._openFunction);this._openFunction=null}if(this._closeFunction){a.off(this.options.closeMethod||this.options.closeEvent,this._closeFunction);this._closeFunction=null}if(this._closeFunction2){a.off("click",this._closeFunction2);this._closeFunction2=null}if(this._closeFunctionPopper){b.off("click",this._closeFunctionPopper);this._closeFunctionPopper=null}},_toggle:function(a,b){this.isOpen(b)?this.close():this.open(a,b);a&&a.preventDefault&&a.preventDefault();return this.element},_arrowOverlapsPopper:function(){var a=
+this.getDestElement(),b=Math.floor(a.position().top),c=Math.floor(a.position().left),d=Math.floor(c+a.outerWidth());a=Math.floor(b+a.height());var e=this._arrow,f=Math.floor(e.position().top),g=Math.floor(e.position().left);Math.floor(g+e.width());var h=Math.floor(f+e.height());c=g>c&&g<d||g+e.css("width")>c&&g+e.css("width")<d;b=f>b&&f<a||f+e.css("height")>b&&h+e.css("height")<a;return c&&b?true:false},_openAnimation:function(a){function b(){var k=d.outerHeight(),l=jQuery(window).height();k>l&&d.css({"max-height":l-
+45+"px",overflow:"auto"});jQuery(window).trigger("resize")}var c=this,d=this.getDestElement().data("isOpening",this.element).stop(true,true),e=this._arrow,f=this.options.openAnimation,g=function(){c._trigger("opencomplete");c.getDestElement().data("isOpening",null);jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<=7&&c._positionPopper(a,false,true);b()},h=function(k){e.fadeTo(0,0);window.setTimeout(function(){e.stop(true,true).show();c._arrowOverlapsPopper()||e.css("opacity",1)},k)};if(f===
+"none"||this.isOpen()){d.show();e&&h(0);g()}else{var j=this.options.openAnimationTime;if(e){var i=0;if(e==="top")i=0;else if(e==="bottom")i=j;else{i=parseInt(e.css("top"),10)-parseInt(d.css("top"),10);var m=d.height()||i;i=i/m*j;if(i>j)i=j}h(i)}d[f](j,g)}},open:function(a,b){if(!b)b=this.element;if(this.options.openAtTarget){if(this._activeTrigger!==b){this.getDestElement().hide();this.getDestElement().data("isOpen",false)}this._activeTrigger=b}else this._activeTrigger=this.element;b=this.getDestElement();
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+this._ncbipopperescapepressedFunction);this._ncbipopperescapepressedFunction=null}},_registerGlobalEscapeListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalEscapeRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalEscapeRegistered=true;var a=document,b="keypress";if(!jQuery.browser.msie&&!jQuery.browser.mozilla){a=window;b="keydown"}jQuery(a)[b](function(c){c.keyCode===27&&jQuery(document).trigger("ncbipopperescapepressed")})}},_addDocumentClickListener:function(){if(this.options.isDocumentCloseClick){this._registerGlobalClickListener();
+var a=this;this._ncbipopperdocumentclickFunction=function(b,c){a._checkDocumentClick(b,c)};jQuery(document).bind("ncbipopperdocumentclick",this._ncbipopperdocumentclickFunction)}},_destroyDocumentClickListener:function(){this._ncbipopperdocumentclickFunction&&jQuery(document).unbind("ncbipopperdocumentclick",this._ncbipopperdocumentclickFunction)},_registerGlobalClickListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalClickRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalClickRegistered=
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+false,d=this;jQuery(a).each(function(){if(d._isSameElementOrChild(jQuery(this),b))c=true});if(c)return}this.close()}}},_isSameElementOrChild:function(a,b){return a[0]==b[0]||jQuery(a).has(b).length===1},_addResizeListener:function(){this._registerGlobalResizeListener();var a=this;this.ncbipopperdocumentresizeFunction=function(b){a._pageResized(b)};jQuery(window).bind("ncbipopperdocumentresize",this.ncbipopperdocumentresizeFunction)},_destroyResizeListener:function(){if(this.ncbipopperdocumentresizeFunction){jQuery(window).unbind("ncbipopperdocumentresize",
+this.ncbipopperdocumentresizeFunction);this.ncbipopperdocumentresizeFunction=null}},_registerGlobalResizeListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalResizeRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalResizeRegistered=true;jQuery(window).on("resize scroll",function(){jQuery(window).trigger("ncbipopperdocumentresize")})}},_pageResized:function(a){if(this.isOpen()){this._positionPopper(a);this._setUpArrow(a)}},_addCloseButton:function(){if(this.options.addCloseButton){var a=
+this.getDestElement(),b=a.find(".ui-ncbipopper-close-button, .ncbipopper-close-button");if(b.length===0){b=jQuery("<button class='ui-ncbipopper-close-button ui-ncbipopper-close-button-generated'>x</button>").attr("generated","true").prependTo(a);b.ncbibutton({color:"blue"})}if(b){var c=this;this._closeButtonFunction=function(d){c.close();d.preventDefault()};b.on("click",this._closeButtonFunction)}}},_destroyCloseButton:function(a){this._closeButtonFunction&&this.getDestElement().find(".ui-ncbipopper-close-button, .ncbipopper-close-button").off("click",
+this._closeButtonFunction).filter(function(){return!a}).filter(".ui-ncbipopper-close-button-generated").ncbibutton("destroy").remove()},isPopperShared:function(){return(this.getDestElement().data("popperTriggers")||[]).length>1},_addSharingDetails:function(){var a=this.getDestElement(),b=a.data("popperTriggers")||[];b.push(this.element);a.data("popperTriggers",b)},_removeSharingDetails:function(){for(var a=this.getDestElement(),b=a.data("popperTriggers"),c=this.element[0],d=0;d<b.length;d++)if(b[d][0]==
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+this.getDestElement();if(this._arrow)a=a.add(this._arrow);var b=this,c={timeout:this.options.delayTimeout,over:function(){},out:function(){b._overPopper(false)}};jQuery(a).hoverIntent(c);jQuery(a).mouseenter(function(){b._overPopper(true);b._lastOver=new Date});jQuery(a).mouseleave(function(){new Date-b._lastOver<b.options.delayTimeout&&b._overPopper(false)}).mouseout(function(d){var e=jQuery(d.target||d.srcElement);if(e.hasClass("ui-ncbipopper-wrapper")||e.hasClass("ui-ncbipopper-arrow-image"))if(e.find(d.relatedTarget).length===
+0){b._isOverPopper=false;b._outTimer=window.setTimeout(function(){b._overPopper(false)},200)}})}},_destroyPopperHover:function(){var a=jQuery(this.getDestElement());a.unbind("mouseenter").unbind("mouseleave");a.removeProp("hoverIntent_t");a.removeProp("hoverIntent_s")},_overPopper:function(a){this._outTimer&&window.clearInterval(this._outTimer);if(a)this._pTimer=new Date;this._isOverPopper=a;if(!a)if(this._isOverTrigger){var b=this;window.setTimeout(function(){!b._isOverPopper&&!b._isOverTrigger&&
+b._overPopper(false)},300)}else this.close()},isOpen:function(a){if(!a)a=this._activeTrigger;a=jQuery(a);var b=jQuery(this._activeTrigger),c=this.getDestElement().data("popperTriggers");a=this.options.openAtTarget||c.length>1?a&&a.length&&b&&b.length&&b[0]===a[0]:true;return this.getDestElement().data("isOpen")&&a?true:false},_setParentsZIndex:function(a){if(jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<=7){var b=this.getDestElement().parents(),c=0;if(b.length>1){b.each(function(e){if(jQuery(this).css("position")===
+"relative"){c=e===0?0:e+1;return false}});b=b.eq(c);var d=b.css("position");b.data("orgPosition")||b.data("orgPosition",d);if(d==="static"||d==="relative"){d=a===1?b.data("orgPosition"):"relative";b.css({position:d,"z-index":a})}}}},addTriggerAria:function(a){var b=a;if(!a){b=this.element;if((a=this.options.multipleHandlesSelector)&&a.length>0)b=b.add(a)}b.attr("role","button").attr("aria-expanded",false).attr("aria-haspopup",true)},_destroyTriggerAria:function(){var a=this.element,b=this.options.multipleHandlesSelector;
+if(b&&b.length>0)a=a.add(b);a.removeAttr("role aria-expanded aria-haspopup")},_addDestAria:function(){this.getDestElement().attr("aria-live","assertive").attr("aria-hidden",true).addClass("ui-helper-reset")},_destroyDestAria:function(){this.getDestElement().removeAttr("aria-live aria-hidden").removeClass("ui-helper-reset")},_setAriaState:function(a,b,c){b=b?b:this.element;c=c?c:this.getDestElement();b.attr("aria-expanded",a);c.attr("aria-hidden",!a)}});jQuery.ui.ncbipopper.openGroups={};
+jQuery.ui.ncbipopper.globalEvents={isGlobalEscapeRegistered:false,isGlobalClickRegistered:false,isGlobalResizeRegistered:false};
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/main.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,337 @@
+/*
+LEGAL
+=====
+Copyright: Daemon Pty Limited 1995-2006, http://www.daemon.com.au & http://www.mollio.org/
+License: Released Under the "Common Public License 1.0", http://www.opensource.org/licenses/cpl.php
+Version: 010306
+*/
+body {padding: 0 0 10px;background: #fff url("images/body_bg-ncbi.gif") repeat-x 0 100%;color:#333;font:83%/1.5 arial,tahoma,verdana,sans-serif;}
+body { margin: 0; padding: 0; }
+/* LINKS */
+a,a:link,a:link,a:link,a:hover {text-decoration:underline;cursor:pointer}
+a:link {color:#369}
+/* Original: a:visited {color:#999} */
+a:visited {color:#664E99;}
+a:hover,a:active {color:#069}
+/* FORMS */
+form {margin: 0 0 1.5em}
+input {font-family: arial,tahoma,verdana,sans-serif;margin: 2px 0 0}
+label {display:block;padding: 5px 0}
+label br {clear:left}
+#desc {font-weight: bold;margin-bottom: 5px;}
+#desc a {font-weight: normal;}
+#logolink, #logolink img {float: left;border: 0;margin: 0;}
+
+/* TYPOGRAPHY */
+p, ul, ol {margin: 0 0 1.5em}
+/* Original: h1, h2, h3, h4, h5, h6 {letter-spacing: -1px;font-family: arial,verdana,sans-serif;margin: 1.2em 0 .3em;color:#000;border-bottom: 1px solid #eee;padding-bottom: .1em}*/
+h1, h2, h3, h4, h5, h6 { letter-spacing: -1px;font-family: arial,verdana,sans-serif;margin: 1.2em 0 .3em;color:#2A6979;border-bottom: 1px solid #ccc;padding-bottom: .1em}
+h1 {font-size: 196%;margin-top:.6em}
+h2 {font-size: 136%}
+h3 {font-size: 126%}
+h4 {font-size: 116%}
+h5 {font-size: 106%}
+h6 {font-size: 96%}
+.highlight {color:#4E8999; padding: 3px; border: solid 1px #ccc;}
+.featured { background-color: #ffc; padding: 0.25em 0.5em;margin:0; }
+.subdued {color:#999}
+
+small {font-size:11px}
+
+/* LISTS */
+ul {margin: .3em 0 1.5em 0;list-style-type:none}
+ul.related {margin-top: -1em}
+ol {margin: .5em .5em 1.5em}
+ol li {margin-left: 1.4em;padding-left: 0;background: none; list-style-type: decimal}
+.section li {line-height: 1.4em;padding-left: 25px;background: transparent url("images/sprites-ncbi.gif") no-repeat 0 0}*/
+li.doc {background-position: 3px -500px}
+ul.nomarker li {background:none;padding-left:0}
+dl {margin: 0 0 1em 0}
+dt {font-weight:bold;margin-top: 1.3em}
+dl dl {margin: 0 0 1.5em 30px}
+
+/* GENERAL */
+/*img {border:none} */
+hr {margin: 1em 0;background:#f2f2f2;height:1px;color:#f2f2f2;border:none;clear:both}
+.clear {clear:both;position:relative;font-size:0px;height:0px;line-height:0px}
+/* LAYOUT - HEADER */
+#header {background: #204174  url("images/sprites-ncbi.gif") repeat-x 0 100%;margin: 0 0 3px;padding: 0 0 8px;white-space:nowrap;}
+#header #site-name {font: 120% arial;letter-spacing: -.05em;margin: 0 ;padding:3px 0; color:#ffffff;font-weight: bold;}
+#header #site-name h1 {font-style: italic; letter-spacing: 0; color: #68a; margin:0 0 0 5em; position: relative; left: 200px;font-size:85%;border:none;padding-bottom:0;display:inline;}
+#header {min-width:770px;position:relative;}
+/* NAV - top horizontal nav */
+#nav, #nav ul {padding: 0;margin: 0;list-style: none}
+#nav {font-weight:bold;height:2.09em;font: bold 95% arial;margin: 0 105px 0 40px; width: 430px;}
+#nav li {background: #999;float: left;width: auto;display:block;margin: 0;border-bottom: 3px solid #666;border-right: 3px solid #252525;padding:0}
+#nav a, #nav a:link, #nav a:visited, #nav a:hover, #nav a:active {text-decoration:none;cursor:pointer;color:#fff;display: block;padding: 4px 10px 2px}
+#nav a:hover {color:#000}
+#nav li ul {border-left: 1px solid #ccc;background: #eee;width:22.8em;font-size:90%;margin-top:3px;position: absolute;font-weight:normal;left: -999em}
+#nav li:hover ul, #nav li.sfhover ul {left: 0;z-index:99999;}
+#nav li li {background:none;float:none;border:none;border: 1px solid #999;border-top:1px solid #fff;border-right:solid 1px #ccc;border-left:none;padding-left:0}
+#nav li li.last {border-bottom:solid 1px #ccc;}
+#nav li li a, #nav li li a:link, #nav li li a:visited, #nav li li a:hover {color:#000;padding: 3px 10px 2px;width:21em}
+#nav li li a:hover {color:#fff;background:#4E8999}
+#nav li.active {background: #4E8999;border-bottom: 3px solid #4E8999}
+#nav li.active a:link, #nav li.active a:visited, #nav li.active a:hover, #nav li.active a:active {}
+#nav li.active a:hover {color:#000}
+#nav li.active li {border:none;border-top: 1px solid #ccc;border-bottom: 1px solid #ccc;}
+#nav li.active li {border: solid 1px #ccc;border-right: solid 1px #4E8999;border-left: solid 1px #4E8999;}
+#nav li.active li.last {border-bottom: solid 1px #4E8999;}
+#nav li.active li a:link, #nav li.active li a:visited, #nav li.active li a:hover, #nav li.active li a:active {color:#000}
+#nav li.active li a:hover {background: #666 url("images/sprites-ncbi.gif") repeat-x 0 99%;color:#fff; filter:progid:DXImageTransform.Microsoft.AlphaImageLoader (src='images/sprites-ncbi.gif', sizingMethod='crop');}
+#nav li.active li.active a:link, #nav li.active li.active a:visited, #nav li.active li.active a:hover, #nav li.active li.active a:active {color:#fff;font-weight:bold;background: #666 url("images/sprites-ncbi.gif") repeat-x 0 99%; filter:progid:DXImageTransform.Microsoft.AlphaImageLoader (src='images/sprites-ncbi.gif', sizingMethod='crop');}
+
+/* hide from IE mac \*/
+#nav li {width:auto}
+/* end hiding from IE5 mac */
+
+/* SEARCH */
+#search {color:#fff;font-weight:bold;position:absolute;top:10px;right:4em}
+#search form {margin:0}
+#search input {width:8em;margin: 0 0 -1px;height:1.2em}
+#search label {padding:5px 0 0;display:inline}
+#search input.f-submit {width:auto;font-size:81%;margin:0 0 -.15em;height:1.95em}
+#content {margin: 0;}
+#type-d #content {margin: 0 0 0 40px;}
+#breadcrumb {margin-top:-5px;font-size:93%;font-weight:bold; margin-left: 1em; margin-bottom: 0; padding: 0 6px 0 12px;; background: url("images/right-arrow.gif") no-repeat center left;display:inline;}
+#breadcrumb strong{font-weight:bold;}
+#breadcrumb a:link, #breadcrumb a:visited {text-decoration:none}
+#breadcrumb a:hover, #breadcrumb a:active {text-decoration:underline}
+/* CODE - formatting for code inserted into body - more here: http://dizque.lacalabaza.net/temp/lipt/ */
+ol.code {font-family: monospace;position:relative}
+ol.code li {color: #666;margin-bottom: 1px}
+ol.code code {color: #000;display: block}
+ol.code .cmt {color: #4077d2}
+li.tab0 code {padding-left: 4em}
+li.tab1 code {padding-left: 8em}
+li.tab2 code {padding-left: 12em}
+li.tab3 code {padding-left: 16em}
+li.tab4 code {padding-left: 20em}
+li.tab5 code {padding-left: 24em}
+ol.code li  {background: #f3f3f3}
+p.note {margin: 1em;border: 1px solid #ddd;background: #f0f0f0;padding: 1em}
+
+/* LAYOUT TYPE A */
+#type-a #content-wrap { width: 100%; margin: 0; padding: 0; white-space:nowrap;margin-top:-0.3em;}
+#type-a #content { margin: 0 40px; }
+/* LAYOUT - FOOTER */
+#footer p {margin:0; padding: 0;padding-bottom:1.5em;}
+
+#footer a:link {color:#999}
+#footer {clear:both;border-top: 1px solid #E3E8EE;padding: 4px 10px 0 10px;font-size:86%;color:#999; margin: 0;}
+#breadcrumb a.help {margin-left: 1em;font-weight:normal;text-decoration: underline;}
+div#search {border: solid 1px #aaa;}
+div#search td{padding: 1px;}
+/* Mozilla-only rule */
+html > body div#search td{padding: 2px;font-weight: bold;font-size: 80%;}
+div#search {background-color: white;position: absolute;right: 4px;top: 4px;color: #369; /* new rule: text by default is white */}
+#jtitle{margin-left:1em;}
+.hidden {display: none;}
+.shown {display: block;}
+a#moreHelp {font-weight:bold;text-decoration:underline;font-size:80%;padding-left:5px;background:none;}
+/* These next two rules replace the text of <a class="helplink"><span>[?]</span></a>
+ * with a 16x16 help link image with transparent background
+ */
+.helpbox, .resBox {font-size: 95%;color: #666;border: solid 1px #ccc;background-color: #def;margin-left: 1em;padding: 0.5em;margin-bottom: 0.5em;zoom:1;}
+.help, .helpbox, .resBox {font-size: 95%;color: #666;white-space:normal;}
+.helplink {padding-left: 16px;background:transparent url(images/help.gif) center left no-repeat;list-style: none;}
+.helplink span {visibility: hidden;}
+a.helplink {text-decoration: none;}
+.helpbox a {background:none;text-decoration:underline;font-size:90%;}
+a.arrowlink:hover {text-decoration: underline;}
+a.arrowlink{
+   padding-left: 16px;
+   background-image: url(images/right.gif);
+   background-repeat: no-repeat;
+   background-position: center left;
+   -moz-outline-style: none;
+   text-decoration: none;
+   text-decoration: underline;
+}
+
+#orgns {float: right;}
+
+ul.msg, ul.msg li {
+padding:0;
+text-indent:0;
+margin: 0;
+}
+
+ul.msg {
+margin-top: 1em;
+}
+
+ul.msg li {
+margin-bottom: 3px;
+display: none;
+font-weight: bold;
+background: transparent url(images/gradient30down.png) repeat-x top left;
+}
+/* IE6 doesn't have alpha transparency, so hack it out */
+* html ul.msg li {
+background-image: none;
+}
+
+ul.msg li p, ul.msg li div.msInf  {
+padding: 3px;
+padding-left: 28px;
+margin:0;
+white-space:normal;
+}
+
+ul.msg li a.small {
+font-weight: normal;
+font-size: 90%;
+}
+
+ul.msg li.error {
+background-color: #fbb;
+border: solid 1px #c00;
+color: #c00;
+}
+
+ul.msg li.error p, ul.msg li.error div.msInf{
+background: transparent url(images/error.png) no-repeat 6px center;
+}
+
+ul.msg li.warning {
+background-color: #ffc;
+border: solid 1px #cc0;
+color: #444;
+}
+
+ul.msg li.warning p, ul.msg li.warning div.msInf {
+background: transparent url(images/warn.png) no-repeat 6px center;
+}
+
+ul.msg li.success {
+background-color: #dfd;
+border: solid 1px #0d0;
+color: #060;
+}
+
+ul.msg li.success p,ul.msg li.success div.msInf {
+background: transparent url(images/ok.png) no-repeat 6px center;
+}
+
+ul.msg li.info {
+background-color: #ace;
+color: #444;
+border: solid 1px #369;
+padding: 1px;
+}
+
+ul.msg li.info p,ul.msg li.info div.msInf {
+background: transparent url(images/info.png) no-repeat 6px center;
+}
+
+ul.msg li.warning,ul.msg li.error,ul.msg li.success,ul.msg li.info
+{
+    display:block;
+}
+ul.msg li p
+{
+    display:block;
+}
+
+ul.msg li.error p.warning {
+background: transparent url(images/warn.png) no-repeat 6px center;
+}
+
+ul.msg li .helpbox
+{
+    font-weight:normal;
+    margin-left:0;
+}
+
+a.errorHelp
+{
+/*float:right;
+margin-right:2em;
+margin-top:-2em;*/
+margin-left:0.5em;
+}
+
+.msInf a.shown
+{
+    display:inline;
+}
+
+#tryNew
+{
+    color:Red;
+}
+.orgHint
+{
+    color:#AAAAAA;
+}
+
+
+span.acPromt,.skp
+{
+    position:absolute;
+    left:-9999px;
+}
+
+
+
+#rgs
+{
+    margin-left:35em;
+    white-space:nowrap;
+}
+
+#trdm
+{
+    vertical-align:super;
+    font-size:small;
+}
+
+.print-log-res { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }
+.print-log-res li { list-style-image: none; }
+
+/* jig toggler adjustments */
+#content .ui-ncbitoggler.ui-widget, #content a.ui-ncbitoggler-open, #content  a.ui-ncbitoggler-slave-open
+{
+    font-size:100%;
+}
+
+.helplink.ui-widget
+{
+  display:inline;
+}
+
+
+#content a.ui-ncbitoggler.ui-widget, #content a.ui-ncbitoggler-open
+{
+color:#336699;
+}
+
+#moreHelp span
+{
+    visibility:visible;
+}
+
+
+#content #moreHelp.ui-ncbitoggler, #content #moreHelp.ui-ncbitoggler-open
+{
+    font-size:80%;
+}
+
+#content  .ui-ncbitoggler-slave-open
+{
+    line-height:1.4em;
+}
+
+div.ui-ncbiautocomplete-holder {
+  font-size: 80%;
+}
+ul.ui-ncbiautocomplete-options li span{ color: red;}
+.ytb,.section a.ytb
+{
+    margin-bottom:-5px;
+    background: url("/core/assets/guide/images/YouTube.png") no-repeat scroll left center transparent !important;
+    height:22px;
+    padding-left:55px;
+    font-weight:normal;
+}
\ No newline at end of file
Binary file NCBI Blast reference example_files/myncbihelpicon.gif has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/plinkcgi.html	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,11 @@
+<html xmlns:xs="http://www.w3.org/2001/XMLSchema"><head>
+<meta http-equiv="content-type" content="text/html; charset=UTF-8">
+  </head><body>
+    <p class="featured" id="prlink">
+      <a href="http://www.ncbi.nlm.nih.gov/projects/primer-blast/index.cgi?LINK_LOC=BlastDescAd" target="pr_win">
+        <img src="plinkcgi_data/primerAd.png" alt="New" border="0">
+      </a>
+    </p>
+
+
+</body></html>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/plinkcgi_002.html	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,11 @@
+<html xmlns:xs="http://www.w3.org/2001/XMLSchema"><head>
+<meta http-equiv="content-type" content="text/html; charset=UTF-8">
+  </head><body>
+    <p class="featured" id="prlink">
+      <a href="http://www.ncbi.nlm.nih.gov/projects/primer-blast/index.cgi?LINK_LOC=BlastAlnAd" target="pr_win">
+        <img src="plinkcgi_data/primerAd.png" alt="New" border="0">
+      </a>
+    </p>
+
+
+</body></html>
\ No newline at end of file
Binary file NCBI Blast reference example_files/plinkcgi_data/primerAd.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/print.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,305 @@
+/*
+LEGAL
+=====
+Copyright: Daemon Pty Limited 1995-2006, http://www.daemon.com.au & http://www.mollio.org/
+License: Released Under the "Common Public License 1.0", http://www.opensource.org/licenses/cpl.php
+Version: 010306
+*/
+
+
+body {font: 10pt arial,tahoma,verdana,sans-serif}
+h1, h2, h3, h4, h5, h6 {margin: 1em 0 .2em;font-family: arial,tahoma,verdana,sans-serif}
+
+* {float:none;position:static;background:#fff}
+p {margin: 0 0 1em}
+dt {font-weight:bold}
+
+#nav, #search, #nav-secondary,  #poweredby {display:none}
+
+/* =LINKS */
+a {border:none}
+a,a:link,a:link,a:link,a:hover {background:transparent;text-decoration:underline;cursor:pointer}
+a:link {color:#5291c4}
+a:visited {color:#666}
+a:hover {color:#ff9900;border:none}
+a:active {color:#0066cc}
+
+.teaserBox {clear:both;margin: 0 0 1em}
+
+.sponsors img {margin: .5em 0}
+
+#footer {margin: 1em 0}
+
+#jtitle {
+border-bottom:2px solid black;
+margin-top:0.25em;;
+margin-left:-1.5em;;
+margin-bottom: 2em;;
+font-size: 110%;;
+padding-bottoM:0.5em;;
+}
+
+/* TABLES */
+table {font-size: 9pt;margin: 0 0 1em;border-collapse:collapse;}
+
+	table th {border-bottom: 3px solid #000;vertical-align:top;padding: 1.5em 3px 3px;line-height:1.1;font: bold 145% arial;letter-spacing:0;text-align:left}
+	.table1 th.time {border-bottom: none;font: bold 89% verdana;color:#ff9c00;vertical-align:top;padding: 3px}
+	.table1 td {border: 1px solid #ddd;font-size: 9pt;padding: 3px;vertical-align:top}
+	.table1 td a {display:block;width:auto;font-weight:bold}
+	.table1 td a:link, .table1 td a:visited, .table1 td a:hover, .table1 td a:active {border:none;text-decoration:none}
+	.table1 th.sub {background: #aaa}
+	.table1 th.sub2 {background: #bbb;color:#000}
+	.table1 td ul li {background: #fff}
+
+
+#logolink img {
+display: none;
+}
+
+#site-name {
+font-size: 140%;
+font-weight: bold;
+padding: 3px;
+text-align:center;
+}
+
+div.resHeader {
+display:  none;
+}
+
+#content-wrap {
+margin : 0 0.25in;
+}
+
+#blHeader pre, #query pre {
+white-space: normal;
+}
+
+#blHeader pre p {
+display: none; /* Get rid of pointer to BLAST FAQs */
+}
+
+#graphic input {
+display: none;
+}
+
+#descs td { vertical-align: top; }
+td.lim { white-space: normal; padding-bottom: 0.5em;}
+#descs td { vertical-align: top; border-bottom: solid 1px #888; border-collapse: collapse; padding-top: 0;}
+
+#descs a {
+text-decoration: none;
+color: black;
+padding: 0;
+margin: 0;
+}
+
+#descs th {
+font-size: 110%;
+}
+
+#graphic table {
+margin: 0;
+}
+
+input {
+display: none;
+}
+
+#graphic h3 a {
+border-bottom:2px solid black;
+color:black;
+display:block;
+margin-bottom:2em;
+margin-top:3em;
+text-align:left;
+text-decoration:none;
+margin-left: -1.5em;
+}
+
+
+#graphic {page-break-after: always; }
+
+td.l a { padding: 0; margin-right: 1em !important; font-weight:bold;}
+#descs td {color: black;}
+
+/* Get rid of stupid long headers */
+#desctbl { margin-top: 1em; border-top: solid 1px #ccc; page-break-after: always;}
+#desctbl table thead { display: none; margin-top: 1em;}
+#desctbl table tr td { width: 4em; }
+#desctbl table td.lim { width: 40em; }
+
+#alignments { line-height: 0.9em; }
+#alignments center b {
+ display: block; z-index: 100; position: relative;
+}
+#alignments center b font { color: black; display: block; text-align: left; font-size: 120%; padding: 0 0 3px; border-bottom: solid 2px #444; margin-left: -1.5em; }
+
+div#alignments.blRes a { text-decoration: none; color: black; font-weight: bold; }
+
+#footer {
+display: none;
+}
+
+h1
+{
+font-size:120%;
+font-weight:bold;
+}
+#FormatForm,#FormatDownload,#showDetails,#queryHelp,#dbDetails,.reslink
+{
+    display:none;
+}
+#multipleSeqs,#queryInfo,.skp,.resLink,.seqlinks,.msg
+{
+   display:none;
+}
+
+#dbDetails,#refInfo,#seealso,#resStat,#showRefs,dd.hidden
+{
+    display:none;
+}
+/*
+#querysummary dl
+{
+ line-height:1.4em;
+}
+
+#querysummary dd
+{
+    margin-left:20%;
+    margin-top:-1.2em;
+}
+
+#querysummary dd a
+{
+    display:none;
+}
+*/
+
+#summary {
+font-size:1.2em;
+}
+#summary {
+margin-top:0pt;
+padding-bottom:1em;
+padding-top:0.5em;
+font-family:Verdana,Arial,Sans-Serif;
+font-size:90%;
+
+}
+#summarylists {
+margin:1em 0pt 0pt;
+overflow:hidden;
+}
+#querysummary {
+float:left;
+padding:0pt;
+width:49%;
+}
+
+#dbsummary {
+margin-left:51%;
+padding:0pt;
+}
+#summary dl {
+margin:0pt 0pt 0.5em;
+padding:0pt;
+}
+#summary dt, #summary dd {
+line-height:1.4em;
+}
+#summary dt {
+float:left;
+font-weight:bold;
+text-align:right;
+width:10em;
+margin-top:0;
+}
+#summary dd {
+margin-left:11em;
+white-space:normal !important;
+}
+#summary h3 {
+color:#444444;
+font-style:italic;
+margin-bottom:-0.5em;
+margin-top:0pt;
+text-align:center;
+}
+#ht,#graphic,#cddDesc
+{
+    text-align:center;
+}
+
+#ht
+{
+    font-weight:bold;
+}
+
+#graphic h3 a,#ovrInfo,#showCDD,.psiInp,.defln caption,#grView.hidden,#RSIFrameDesc
+{
+    display:none;
+}
+
+
+#grView.hidden.shown
+{
+    display:block;
+}
+
+.print-log-res { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }
+.print-log-res li { list-style-image: url("images/img_blast_results_gif"); }
+
+#SwitchDesign,#ytb,.fdb,#debug,.moreHsps,.shcl,#cntDesc,#descTblCtrl,.hdnHeader,td.c0,th.c0,.alnMsgS,.alnHdr,.relInf
+{
+    display:none;
+}
+
+h3.cap,#RSIFrameAln,.alnRn span, div.hsp .alnParLinks,.ui-ncbiautocomplete-link-pref,.ui-ncbiautocomplete-link-off
+{
+    display:none;
+}
+
+.alnAll
+{
+    margin-top:0.5emem;
+}
+.dlfRow
+{
+    line-height:1.5em;
+}
+
+span.r label
+{
+    margin-left:0.5em;
+}
+td.l a.deflnDesc
+{
+    font-weight:normal;
+    text-decoration:none;
+    color:inherit;
+}
+
+table.alnParams
+{
+    width:50em;
+}
+table.alnParams th
+{
+    font-size:100%;
+}
+
+table.alnParams td
+{
+    font-size:110%;
+    padding-top:0.5em;
+}
+
+.oneSeqAln
+{
+    border-top:1px solid gery;
+    margin-top:1em;
+    padding-top:1em;
+    width:60em;
+}
Binary file NCBI Blast reference example_files/query_no_scale.gif has changed
Binary file NCBI Blast reference example_files/reformat.jpg has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/remote_data_provider.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,79 @@
+//=========================================================================================================
+function RemoteDataProvider(sUrl) {
+    this.iActiveRequests = 0;
+    this.sUrl = sUrl;
+}
+
+//-------------------------------------------------------------------------------------------------------------
+RemoteDataProvider.prototype.GetHttpObj = function() {
+    var oHttpObj = null;
+    try {
+        oHttpObj = new ActiveXObject("Msxml2.XMLHTTP");
+    } catch(e) {
+        try {
+            oHttpObj = new ActiveXObject("Microsoft.XMLHTTP")
+        } catch(oc) {
+            oHttpObj = null;
+        }
+    }
+    if (!oHttpObj && typeof XMLHttpRequest != "undefined") {
+        oHttpObj = new XMLHttpRequest();
+    }
+    return oHttpObj;
+}
+
+//-------------------------------------------------------------------------------------------------------------
+RemoteDataProvider.prototype.Request = function(sRequest, method) {
+    var oHttpObj = this.GetHttpObj();
+    if (null == oHttpObj) return;
+
+    method = (!method) ? "GET" : "POST";
+    var sURL = (method == "GET") ? this.sUrl + "?" + sRequest : this.sUrl;        //alert(sURL);
+    this.iActiveRequests++;
+    var oThis = this;
+    oHttpObj.onreadystatechange = function () {
+        if (oHttpObj.readyState == 4 && oHttpObj.status == 200) {
+            oThis.onSuccess(oHttpObj);
+            oThis.iActiveRequests--;
+            oThis.onStop();
+        } else if(oHttpObj.readyState == 4 && oHttpObj.status != 200) {
+            oThis.onError(oHttpObj);
+            oThis.iActiveRequests--;
+            oThis.onStop();
+        }
+    };
+
+    if (oHttpObj.readyState != 0) oHttpObj.abort();
+    this.onStart();
+    oHttpObj.open(method, sURL, true);
+//    oHttpObj.setRequestHeader('Cache-Control', 'no-cache');
+    var params = (method == "GET") ? null : sRequest;
+    if (params) {
+        oHttpObj.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
+        oHttpObj.setRequestHeader("Content-length", params.length);
+        oHttpObj.setRequestHeader("Connection", "close");
+    }
+    oHttpObj.send(params);
+}
+
+//-------------------------------------------------------------------------------------------------------------
+RemoteDataProvider.prototype.onSuccess = function(obj) {
+    alert(["success:", this.iActiveRequests, obj.responseText]);
+}
+
+//-------------------------------------------------------------------------------------------------------------
+RemoteDataProvider.prototype.onStart = function() {
+//    alert(["start:", this.iActiveRequests]);
+}
+
+//-------------------------------------------------------------------------------------------------------------
+RemoteDataProvider.prototype.onStop = function() {
+//    alert(["start:", this.iActiveRequests]);
+}
+
+//-------------------------------------------------------------------------------------------------------------
+RemoteDataProvider.prototype.onError = function(obj) {
+    //alert(["error:", this.iActiveRequests, obj.status]);
+}
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/results.css	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1224 @@
+#summary {
+font-size:1.2em;
+}
+#summary {
+margin-top:0pt;
+padding-bottom:1em;
+padding-top:0.5em;
+font-family:Verdana,Arial,Sans-Serif;
+font-size:90%;
+
+}
+#summarylists {
+margin:1em 0pt 0pt;
+overflow:hidden;
+}
+#seealso {
+margin-left:2em;
+}
+#querysummary {
+float:left;
+padding:0pt;
+width:49%;
+}
+#dbsummary {
+margin-left:51%;
+padding:0pt;
+}
+#summary dl {
+margin:0pt 0pt 0.5em;
+padding:0pt;
+}
+#summary dt, #summary dd {
+line-height:1.4em;
+}
+#summary dt {
+float:left;
+font-weight:bold;
+text-align:right;
+width:10em;
+margin-top:0;
+}
+#summary dd {
+margin-left:11em;
+white-space:normal !important;
+overflow:hidden;
+}
+#summary h3 {
+color:#444444;
+font-style:italic;
+margin-bottom:-0.5em;
+margin-top:0pt;
+text-align:center;
+}
+
+#multipleSeqs {
+font-weight: bold;
+}
+#multipleSeqs a {
+font-size:80%;
+font-weight:normal;
+}
+#breadcrumb {
+background:transparent url(images/right-arrow.gif) no-repeat scroll left center;
+font-size:93%;
+font-weight:bold;
+margin-top:-5px;
+padding:0pt 6px 0pt 12px;
+}
+#breadcrumb a {
+color:#336699;
+}
+
+#jobTitle
+{
+color:#669;
+/*color:#2A6980;*/
+font-weight:bold;
+margin-bottom:-0.5em;
+}
+
+#type-a #content-wrap {white-space:normal; padding-bottom:2em;}
+
+#statInfo
+{
+    font-size:100%;
+}
+
+
+#resMsg
+{
+background-color:#FFFFCC;
+font-size:110%;
+/*margin-top:4em;
+padding-left:0.5em;*/
+text-align:center;
+}
+
+#seealso label
+{
+    display:inline;
+}
+
+#seealso a
+{
+    padding: 0,4px;
+}
+
+a.shown
+{
+    display:inline;
+}
+
+
+table.dbInfo
+{
+    width:50%;
+    border:solid 1px gray;
+    font-size:100%;
+    border-collapse:collapse;
+    margin-top:1em;
+}
+table.dbInfo td,
+table.dbInfo caption
+{
+   border:solid 1px gray;
+   padding: 1px 4px;
+}
+table.dbInfo caption {
+    background-color:#acf;
+    text-align:center;
+    border-bottom:none;
+    margin-bottom:-0.2em;
+    font-weight:bold;
+    margin-top:1em;
+}
+#resStat, #dbDetails
+{
+    padding-left:25%;
+}
+
+table.dbInfo td
+{
+    text-align:left;
+}
+
+table.dbInfo th {
+visibility:hidden;
+/*padding:0;*/
+}
+
+
+table.dbInfo th div {
+height:0;
+}
+
+table#Kappa pre
+{
+    font-size:120%;
+}
+
+
+/****** Mark new rules ************/
+/* override main.css rules */
+#type-a #content {
+margin: 0 2em;
+}
+
+#type-a h1 {
+font-size: 150%;
+margin-bottom: 1em;
+border-top: solid 1px #ccc;
+}
+
+#type-a h2 {
+font-size: 125%;
+color: #666;
+}
+
+#type-a h3 {
+border: none;
+font-size: 110%;
+}
+#graphic {
+text-align: center;
+margin: auto;
+}
+
+#multipleSeqs label {
+width: 9em;
+height: 1em;
+text-align: right;
+margin-right: 0;
+padding: 0 1em;
+float: left;
+}
+#multipleSeqs select {
+margin-right: 1em;
+font-size: 95%;
+}
+#multipleSeqs input {
+font-size: 95%;
+margin-top: -0.25em;
+margin-right: 1em;
+}
+label.other {
+font-size: 110%;
+font-weight: bold;
+}
+form#results
+{
+    display:none;
+}
+
+#hdLink
+{
+    margin-top:-1.2em;
+    float:right;
+}
+
+#hdTitle
+{
+    margin-left:5em;
+}
+.shownInl
+{
+    display:inline;
+}
+
+#psiHd
+{
+    margin-top:1em;
+}
+
+#phiInfo
+{
+    text-align:center;
+    color:Green;
+    font-size:110%;
+    margin-top:1em;
+}
+#ht
+{
+font-weight:bold;
+margin-bottom:-0.9em;
+margin-top:0.2em;
+text-align:center;
+}
+
+.psiThresh
+{
+    text-align:center;
+    color:Green;
+    font-weight:bold;
+}
+
+#psiThreshA span.shown,#psiThreshB span.shown
+{
+    display:inline;
+}
+
+a.resArr
+{
+    color:#666;
+    font-size:120%;
+    font-weight:bold;
+}
+
+a.arrowlink.showing
+{
+    background-image: url(images/down.gif);
+}
+
+#graphic table
+{
+    background-color:White;
+}
+
+#type-a #content
+{
+    background-color:#D3DFF5;
+    border:1px solid #888888;
+    padding:0 0.5em;
+    zoom:1;
+}
+
+.resBox
+{
+    background-color:#eee;
+    margin-right:1em;
+    color:#222;
+    zoom:1;
+}
+
+.resBox1
+{
+    background-color:white;
+}
+
+#tryNew,.hl
+{
+    color:Red;
+}
+
+/*#tryNew
+{
+    margin-right:20em;
+}*/
+
+
+div#vecSrceen {
+margin-bottom:0pt;
+margin-left:17%;
+margin-top:0pt;
+padding-left:2em;
+white-space:pre;
+width:64%;
+zoom:1;
+}
+
+.psiInp
+{
+    white-space:normal;
+    margin-bottom:1.5em;
+}
+
+.seqlinks label
+{
+    display:inline;
+}
+
+.seqlinks input
+{
+   margin-left:1em;
+}
+.seqlinks a.ln
+{
+   margin-left:2em;
+}
+
+.seqlinks a.lnt
+{
+   margin-left:0.5em;
+}
+
+form.getseq
+{
+    margin:0;
+}
+
+#queryList option.nohits
+{
+    color:Gray;
+}
+
+#queryList
+{
+    float:left;
+}
+
+p#qb
+{
+    margin-top:0;
+    margin-bottom:0;
+}
+
+#dn
+{
+    margin-left:5em;
+}
+
+#dnf
+{
+    font-size:80%;
+}
+
+/*#FormatForm
+{
+    margin-left:2em;
+}*/
+table.options
+{
+    width:80%;
+    margin-top:0.5em;
+    margin-left:10%;
+    border-collapse:collapse;
+    max-width:70em;
+}
+
+form.resbox label
+{
+    display:inline;
+}
+
+#onPageReformat
+{
+    position:absolute;
+    right:0.5em;
+    border:none;
+    padding-bottom:1px;
+    bottom:0.1em;
+}
+
+table.dwnl
+{
+    width:60%;
+    margin-left:20%;
+    height:3em;
+}
+table.dwnl td
+{
+    padding-right:0.5em;
+}
+/*
+a#showStat
+{
+    margin-left:-0.4em;
+}
+*/
+a.resArrowLinkB:hover,a.resArrowLinkW:hover {text-decoration: underline;}
+a.resArrowLinkB,a.resArrowLinkW{
+   padding-left: 12px;
+   background-image: url(images/rightSmallArrow.gif);
+   background-repeat: no-repeat;
+   background-position: center left;
+   -moz-outline-style: none;
+   text-decoration: none;
+   text-decoration: underline;
+}
+a.resArrowLinkB.showing
+{
+   background-image: url(images/downSmallArrow.gif);
+}
+
+a.resArrowLinkW{
+   background-image: url(images/rightSmallWArrow.gif);
+}
+
+a.resArrowLinkW.showing
+{
+    background-image: url(images/downSmallWArrow.gif);
+}
+td.dnl
+{
+    border-left:solid 1px gray;
+}
+.dnLinks a
+{
+    margin-left:1em;
+}
+
+.dnLinks
+{
+    text-align:center;
+}
+#tdal
+{
+    width:30em;
+}
+
+.dnHeader
+{
+    font-size:100%;
+    font-weight:bold;
+    text-align:center;
+}
+#dnHelp
+{
+    display:inline;
+    position:relative;
+    padding-left:0;
+}
+
+table td.frh
+{
+    background-color:#E0E0E0;
+    color:Gray;
+    text-align:center;
+}
+
+#type-a h3.tb,#type-a div.tb
+{
+    display:inline;
+    color:Gray;
+    letter-spacing:normal;
+    font-size:120%;
+    font-weight:bold;
+}
+
+#content a.resLink
+{
+	display:inline;
+}
+
+#content a.resLink.hide
+{
+	display:none;
+}
+
+ul.msg li p.info {
+background: transparent url(images/info.png) no-repeat 6px center;
+}
+
+.blRes
+{
+    background-color:White;
+    border:solid 1px #CCCCCC;
+    padding: 1em;
+    margin:1em;
+    /*font-size:110%;*/
+    zoom:1;
+}
+/* Check this for many results */
+div#content
+{
+    min-width:80em;
+}
+#hitmtImg
+{
+
+    padding:1em;
+    border:solid 2px gray;
+    padding-bottom:2em;
+}
+#qgr
+{
+    margin-top:-1.8em;
+    /*writing-mode:tb-rl;*/
+}
+#htmb
+{
+    margin-top:-2em;
+    margin-left:11em;
+    border:solid 1px gray;
+}
+
+#hitMatrixView
+{
+    margin-top:1em;
+}
+
+#hitMatrixInfo
+{
+    text-align:center;
+}
+
+#bl2ovrInfo
+{
+    text-align:left;
+}
+
+.newMln
+{
+    height:12px;
+    margin-left:-0.5em;
+}
+
+/***** New staff neew to remove all table#descs from blastRes.css, a.resArr, .psiThresh after formatter upadte *******/
+
+h2.resArr a
+{
+    color:#666;
+    font-size:105%;
+    font-weight:bold;
+    font-family:arial,tahoma,verdana,sans-serif;
+    white-space:nowrap;
+}
+
+h2.resArr
+{
+    border-bottom:none;
+    letter-spacing:normal;
+    margin:0;
+    padding:0;
+    width:15%;
+}
+
+.psiThresh h3
+{
+    text-align:center;
+    color:Green;
+    font-weight:bold;
+}
+
+/*#alignments
+{
+    font-size:115%;
+    font-family:Monospace;
+    white-space:pre;
+    line-height:1;
+}
+*/
+table.defln
+{
+font-family: Verdana, Sans-Serif;
+font-size: 80%;
+_font-size: 86%;
+border-collapse: collapse;
+width: 100%;
+border-bottom:1px solid #018AAC;
+}
+
+table.defln caption
+{
+font-weight:bold;
+text-align:left;
+}
+
+table.hideCap caption
+{
+visibility:hidden;
+height:0;
+font-size:1%;
+}
+
+table.defln th a {
+/*text-decoration: none;*/
+color: #00c;
+}
+
+table.defln th a:visited {
+color: #00c;
+}
+
+table.defln th a:hover {position: relative;
+text-decoration: underline;
+}
+
+table.defln tr th.l,
+table.defln tr td.l {
+text-align: left;
+}
+
+table.defln tr th.sp {
+background-color: #def;
+}
+
+table.defln tr th,
+table.defln tr td {
+text-align: center;
+padding: 1px 4px;
+}
+
+table.defln tr.first th {
+padding-left:18px;
+border-left: solid 1px #A0ceff;
+border-top: solid 1px #A0ceff;
+border-bottom: solid 1px #018aac;
+border-right: solid 1px #018aac;
+border-top: 1px solid #018AAC;
+padding-right: 8px;
+padding-bottom: 3px;
+background-color: #9cf;
+white-space:normal;
+line-height: 1.2em
+}
+
+
+table.defln td {
+border: solid 1px #ccc;
+border-width: 0px 1px;
+white-space:nowrap;
+overflow: hidden;
+}
+
+table.defln tr.first th.sel {
+background: #9cf url(images/up.gif) no-repeat center left;
+padding-left: 18px;
+padding-right: 18px;
+}
+
+table.defln tr:hover {
+/*background-color: #def;*/
+}
+
+/* accessebility styles */
+table.defln.noCaption caption
+{
+    display:none;
+}
+
+
+/* accessebility styles */
+.hdnHeader {
+/*visibility:hidden;*/
+font-size:0;
+height:0;
+}
+
+div.chs
+{
+    margin-bottom: -1em;
+}
+
+.psiInp label
+{
+    display:inline;
+}
+
+h3.tgl
+{
+    letter-spacing:normal;
+    margin:0;
+}
+h3.tgl a
+{
+    font-size:80%;
+    color:#222222;
+    font-family:Verdana,Sans-Serif;
+}
+div.tgl
+{
+    margin-top:0;
+    background-color:White;
+    border:none;
+}
+div.tgl table.defln a
+{
+    font-size:100%;
+}
+
+/************ new alignment styles ************/
+
+.sumN, .aln_frame
+{
+    display: none;
+}
+
+table.alnParams
+{
+    border:solid 1px #a0a0a0;
+    border-collapse:collapse;
+    font-family:Verdana,Arial,Sans-Serif;
+    font-size:87%;
+    width:60%;
+    margin-bottom:1em;
+}
+
+table.alnParams th
+{
+    background-color:#e8e8e8;
+    color:#606060;
+    border:solid 1px #a0a0a0;
+    padding: 1px 4px;
+    font-size:86%;
+}
+
+table.alnParams td
+{
+   border:solid 1px #a0a0a0;
+   padding: 1px 4px;
+   white-space:nowrap;
+}
+
+
+.aln_feat.hidden
+{
+width:0;
+padding:0;
+}
+
+a.sortAlnArrowLinkB
+{
+   padding-left: 12px;
+   background-image: url(images/downSmallArrow.gif);
+   background-repeat: no-repeat;
+   background-position: center left;
+}
+
+a.sortAlnArrowLinkW
+{
+   padding-left: 12px;
+   background-image: url(images/downSmallWArrow.gif);
+   background-repeat: no-repeat;
+   background-position: center left;
+}
+
+.seqlinks span
+{
+    margin-left:1em;
+}
+
+.alnSortSeq
+{
+	margin-bottom:2em;
+	display:inline;
+}
+
+.alnSortSeq a
+{
+    font-size:90%;
+}
+table.alnParams a
+{
+    display:block;
+    padding:3px 3px;
+    font-size:90%;
+}
+
+table.alSeqInf td
+{
+vertical-align:top;
+}
+td.alSeq
+{
+padding-left:1em;
+}
+
+td.alSeq.alFirst
+{
+white-space:nowrap;
+padding-left:0;
+}
+
+td.alTitle
+{
+font-size:90%;
+}
+
+img.imn
+{
+/*    width:30px;
+    height:15px;
+*/
+}
+
+img.imc
+{
+    width:15px;
+    height:15px;
+}
+td.l img.hidden
+{
+    display:inline;
+    visibility:hidden;
+}
+
+
+.dflLnk a
+{
+	padding-left:1em;
+	font-size:110%;
+}
+
+table.defln td.dflLnk
+{
+	text-align:left;
+	padding-bottom:0.5em;
+	font-size:11px;
+}
+
+.dflLnk label
+{
+	font-weight:bold;
+	display:inline;
+}
+.oneSeqAln .dflLnk
+{
+font-family: Verdana, Sans-Serif;
+font-size: 80%;
+padding-bottom:1em;
+width:60%;
+}
+
+table.alnDefln tr td.l
+{
+    text-align:left;
+}
+
+table.alnDefln td
+{
+    /*overflow:hidden;*/
+    white-space:nowrap;
+    vertical-align:top;
+}
+
+table.alnDefln td.lim
+{
+    white-space:normal;
+    font-size:98%;
+}
+
+/* check specific browser file */
+table.alnDefln div.lim
+{
+    width:35em;
+}
+
+table.defln tr.dflnAln.shown
+{
+    display:table-row;
+}
+
+table.alnDefln tr.shown
+{
+    display:table-row;
+}
+
+.alnDflLn label
+{
+    font-weight:bold;
+    display:inline;
+    font-size:80%;
+    color:#444444;
+    padding-right:3px;
+    padding-left:3px;
+}
+
+.alnDflLn
+{
+    margin-left:2em;
+}
+
+.alnSortSeq.alnDflLn
+{
+    margin-left:0.5em;
+    float:left;
+    position:absolute;
+}
+
+.alnDflLn input
+{
+   margin-left:1em;
+   border:none;
+}
+.alnDflLn label.hidden
+{
+    display:none;
+}
+
+h3.sAlnHdr
+{
+    color:#444444;
+    display:inline;
+    letter-spacing:normal;
+}
+
+h3.sAlnHdr a
+{
+    color:#444444;
+    text-decoration:none;
+    margin-left:2em;
+    font-size:85%;
+}
+
+.alnHdr
+{
+    padding-top:0.1em;
+    padding-bottom:0.1em;
+}
+
+.oneSeqAln
+{
+    padding-left:1em;
+    padding-top:0.2em;
+}
+
+table.defln tr.dflnAln td
+{
+    text-align:left;
+    border:none;
+    background-color:White;
+}
+
+table.defln tr.dflnAln td input.ch,table.defln tr.dflnAln td h3
+{
+    display:none;
+}
+
+
+tr.dflnAln .oneSeqAln
+{
+    font-size:120%;
+}
+
+tr.dflnAln .alnDflLn{
+
+    margin-left:0;
+}
+
+tr.dflnAln .alnHdr
+{
+   padding:0;
+}
+
+tr.dflnAln .alnHdr label
+{
+   font-size:90%;
+}
+.hil
+{
+background-color: #def;
+}
+
+
+table.defln tr.odd
+{
+    background-color:#f8f8f8;
+}
+
+table.defln tr.even
+{
+    background-color:#e8e8e8;
+}
+a.dflSeq
+{
+    color:Gray;
+    font-weight:bold;
+    text-decoration:none;
+    padding-left:0;
+    display:inline-block;
+    width:13em;
+}
+a.dflSeq.nogi
+{
+    color:#336699;
+    text-decoration:underline;
+}
+td.lim
+{
+    font-size:13px;
+}
+
+.ldsb
+{
+    padding-left:1em;
+    color:Gray;
+    font-size:110%;
+}
+
+a.spr
+{
+    padding-right:3px;
+    border-right:solid 1px;
+}
+
+
+
+#hlp11
+{
+    width:60%;
+    margin-left:22%;
+    margin-top:0.5em;
+}
+
+/* jig toggler styles */
+a.resLink.ui-ncbitoggler, a.jtg.ui-ncbitoggler,a.resLink.ui-ncbitoggler-open, a.jtg.ui-ncbitoggler-open
+{
+padding-left:13px;
+color:#336699;
+}
+
+a.resLink.ui-ncbitoggler,a.resLink.ui-ncbitoggler-open
+{
+    font-size:100%;
+}
+
+
+table.options .helplink
+{
+    font-size:100%;
+    display:inline;
+}
+
+
+span.ui-icon.ui-icon-triangle-1-e,span.ui-icon.ui-icon-triangle-1-s
+{
+   padding-left: 12px;
+   background-repeat: no-repeat;
+   -moz-outline-style: none;
+   text-decoration: underline;
+   /*height:18px;
+   width:20px;   */
+}
+
+
+
+span.ui-icon.ui-icon-triangle-1-e
+{
+   background-image: url(images/rightSmallArrow.gif);
+}
+
+span.ui-icon.ui-icon-triangle-1-s
+{
+    background-position: center left;
+    background-image: url(images/downSmallArrow.gif);
+}
+
+table.dbInfo.shown
+{
+    display:table;
+}
+
+#seealso a.hidden
+{
+    display:none;
+}
+
+#seealso a, #seealso a.hidden.shown
+{
+    display:inline-block;
+}
+
+
+a.ui-ncbitoggler.hidden.shown.jtg, a.ui-ncbitoggler-open.hidden.shown.jtg
+{
+    display:inline;
+}
+/**Comment those line to display ncbi-toggler native icon - begin *
+a.ui-ncbitoggler span.ui-icon-plus-minus-big, a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open
+{
+   padding-left: 16px;
+   background-image: url(images/down.gif);
+   background-repeat: no-repeat;
+   background-position: center left;
+   -moz-outline-style: none;
+   text-decoration: none;
+   text-decoration: underline;
+}
+
+a.ui-ncbitoggler span.ui-icon-plus-minus-big
+{
+   background-image: url(images/right.gif);
+}
+
+a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open
+{
+     background-image: url(images/down.gif);
+}
+*Comment those line to diplay ncbi-toggler native icon - end **/
+
+a.ui-ncbitoggler span.ui-icon-plus-minus-big, a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open {
+  background-image: url("images/ncbitoggler-plus-minus-big.gif");
+}
+a.helplink{display:inline}
+#summary .ui-widget
+{
+font-family:Verdana,Arial,Sans-Serif  !important;
+font-size:100%;
+}
+.resBox.ui-widget,.resbox.ui-widget
+{
+    font-size:100%;
+}
+
+.resetAll
+{
+    position:absolute;
+    padding:0;
+    right:0;
+    margin-right:5em;
+}
+
+#nft
+{
+    padding-right:1em;
+    vertical-align:baseline;
+}
+#advView
+{
+    margin-left:3em;
+}
+#SwitchDesign, a.fdb
+{
+    color:Red;
+}
+a.fdb
+{
+    margin-top: -1.5em;
+    float:right;
+    margin-right:5%;
+}
+#SwitchDesign
+{
+    left:50em;
+    right:10em;
+    position:absolute;
+    white-space:nowrap;
+}
+
+
+#brFtp
+{
+    margin-left:1em;
+}
+
+#hnr
+{
+    float:right;
+}
+
+#topLinks
+{
+    float:left;
+}
+#topLinksLeft
+{
+    float:right;
+}
+
+#summary h1
+{
+    border-top:none;
+}
+
+#dbPlusSpecies > div {
+  width: 50%;
+  margin-top:0.5em;
+  padding-bottom:0.1em;
+}
+
+#nextDbSet,#lastDbSet {
+  float: right;
+}
+#prevDbSet,#lastDbSet {
+  padding-left:0.5em;
+}
+#dbSpecies,#dbSpecies caption
+{
+    margin-top:auto;
+}
+.cpAdd
+{
+    font-size:80%;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/results.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,649 @@
+// JScript source code
+
+//Display Reformat page button only after the whole page is loaded
+
+function ReformatPageEvent()
+{
+	var refPageLink = document.getElementById("refPage");
+
+	//alert(refPageLink);
+	//alert(refPageLink.getAttribute("submitForm"));
+	var submitForm = refPageLink.getAttribute("submitForm");
+	alert(submitForm);
+	if(refPageLink && submitForm) {
+		utils.addEvent(refPageLink,
+					   "click",
+					   function() {
+							document.getElementById(submitForm).submit();
+						},
+						false);
+	}
+}
+
+
+function SubmitEvent(linkID)
+{
+
+	var link = document.getElementById(linkID);
+	//alert(link.getAttribute("submitForm"));
+	var submitForm = link.getAttribute("submitForm");
+	if(link && submitForm) {
+		utils.addEvent(link,
+					   "click",
+					   function() {
+							document.getElementById(submitForm).submit();
+						},
+						false);
+	}
+}
+
+
+function SubmitEventSave(linkID)
+{
+
+	var link = document.getElementById(linkID);
+	//alert(link.getAttribute("submitForm"));
+	var submitForm = link.getAttribute("submitForm");
+	if(link && submitForm) {
+		utils.addEvent(link,
+					   "click",
+					   function() {
+							//$(submitForm).CMD.value = "GetSaved";
+							document.getElementById(submitForm).submit();
+						},
+						false);
+	}
+}
+
+
+
+
+//This function creates submit form event on click
+//form submitted is defined in submitForm attribute
+//It also copies params from forms[0] (search paramateres) created by formatter
+function SubmitEventNew(linkID)
+{
+
+	var link = document.getElementById(linkID);
+	//alert(link.getAttribute("submitForm"));
+	if(!link) return;
+	var submitForm = link.getAttribute("submitForm");
+	if(link && submitForm) {
+		utils.addEvent(link,
+					   "click",
+					   function() {
+							document.forms[0].CMD.value = "";
+							if(document.forms[0].PAGE_TYPE) {
+								document.forms[0].PAGE_TYPE.value = "";
+							}
+							var s = document.forms[0].innerHTML;
+							var form = $(submitForm);
+							form.innerHTML = s + form.innerHTML;
+							form.submit();
+						},
+						false);
+	}
+}
+
+function GetResults()
+{
+    form = $("results");
+    form.QUERY_INDEX.value = $("queryList")[$("queryList").selectedIndex].value;
+    form.submit();
+}
+
+function isIdIn(id, idArray){
+  var idSeen=false;
+
+  for(i=0; i<idArray.length; i++){
+    if(id==idArray[i]){
+      idSeen=true;
+      break;
+    }
+  }
+  return idSeen;
+}
+
+function GetSelectedSeqString(formName)
+{
+    var selSeqs = "";
+    var idArray=new Array();
+    forms = document.getElementsByName(formName);
+    for(var j=0; j < forms.length; j++){
+      for(var i=0; i < forms[j].elements.length; i++){
+        var theElem=forms[j].elements[i];
+        if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"&&theElem.checked){
+          if(!isIdIn(theElem.value, idArray)){
+            idArray[idArray.length]=theElem.value;
+          }
+        }
+      }
+    }
+    selSeqs = idArray.join();
+    return selSeqs;
+}
+
+function ViewSelectedSeqs(e)
+{
+    var submitForm = $("submitterTop");
+    var targetForm = submitForm.getAttribute("seqsForm");
+    $("selSeqs").value = GetSelectedSeqString(targetForm);
+    submitForm.submit();
+    utils.preventDefault(e);
+}
+
+
+function ViewSelectedSeqTree()
+{
+    var submitForm = $("treesubmitterTop");
+    var targetForm = submitForm.getAttribute("seqsForm");
+    $("seqSet").value = GetSelectedSeqString(targetForm);
+    $("scrWidth").value = screen.width;
+    $("scrHeight").value = screen.height;
+    submitForm.submit();
+}
+
+function ViewTree(linkID) {
+    link = document.getElementById(linkID);
+    var target = link.target;
+    winRef = window.open(link.href + "&screenWidth=" + screen.width + "&screenHeight=" + screen.height, target);
+}
+
+function ViewSelectedSeqMultiAlign()
+{
+    var submitForm = $("multisubmitterTop");
+    var targetForm = submitForm.getAttribute("seqsForm");
+    $("seqSetM").value = GetSelectedSeqString(targetForm);
+    submitForm.submit();
+}
+
+
+
+function selectAllSeqs()
+{
+    var formName = this.getAttribute("seqsForm");
+    forms = document.getElementsByName(formName);
+    for(var j=0; j < forms.length; j++){
+        for(var i=0; i < forms[j].elements.length; i++){
+    //for(var i=0; i < document.forms[formName].elements.length; i++){
+            var theElem=forms[j].elements[i];
+            if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"){
+                theElem.checked=this.checked;
+            }
+        }
+    }
+    links = document.getElementsByName("selectAll");
+    for(var i=0; i < links.length;i++) {
+        if(links[i] != this)  links[i].checked = this.checked;
+    }
+}
+
+
+function InitSeqAlignLinks()
+{
+    var links = document.getElementsByName("getSeqs");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",ViewSelectedSeqs,false);
+    }
+    links = document.getElementsByName("treeView");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",ViewSelectedSeqTree,false);
+    }
+    links = document.getElementsByName("mltiAln");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",ViewSelectedSeqMultiAlign,false);
+    }
+    links = document.getElementsByName("selectAll");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",selectAllSeqs,false);
+    }
+
+    if($("showAlign"))
+        utils.addEvent($("showAlign"),"click",showHideLinks,false);
+}
+
+function InitDownLoad()
+{
+    var deltaBlast = ($("diThresh") && $("diThresh").value != "") ? true : false;
+    if (!deltaBlast && ($("stepNumber").value == "" || $("stepNumber").value < 2)) {
+        utils.addClass($("dnPSSMPar"),"hidden");
+    }
+}
+function Reformat()
+{
+    if(utils.hasClass($("FormatForm").FORMAT_ORGANISM,"orgHint"))  $("FormatForm").FORMAT_ORGANISM.value = "";
+
+    $("FormatForm").submit();
+}
+function InitCustomButton(bn)
+{
+  utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
+  utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
+  utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
+  utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);
+}
+
+function InitAllCustomButtons()
+{
+    if($("go")) InitCustomButton($("go"));
+    if($("dn")) InitCustomButton($("dn"));
+    if($("onPageReformat")) InitCustomButton($("onPageReformat"));
+}
+function showHideLinks()
+{
+    var links = document.getElementsByName("selectAll");
+    for(var i=0; i < links.length;i++) {
+        //This is done since IE does not recognize getElementsByName for span elem
+        var allLinks = utils.getParent(links[i]);
+        var removeClass,addClass;
+        if(utils.hasClass(allLinks,"shownInl")) {
+            removeClass="shownInl";
+            addClass="hidden";
+        }
+        else {
+            removeClass="hidden";
+            addClass="shownInl";
+        }
+        utils.removeClass(allLinks,removeClass);
+        utils.addClass(allLinks,addClass);
+    }
+}
+/*remove this function */
+function InitHelpLinks()
+{
+    for(var i=1; i <= 11;i++) {
+        InitToggleEvent($("hlp" + i));
+    }
+}
+//This function is used for collapsible deflines onmouseover="showInfo(this)"
+//Initialized in showdefline.cpp
+function showInfo(elem)
+{
+    var targetElem = $("info_" + elem.id);
+    if(!targetElem) return;
+    if(elem.getAttribute("init") == "on") return;
+
+    Toggle.addTarget(elem, targetElem);
+    elem.setAttribute("init","on");
+}
+
+function InitPsiBlast()
+{
+    //utils.addEvent($("ttt"),"keyup",SetHitlistSize,false);
+    var hts = document.getElementsByName("HITLIST_SIZE");
+    for(var i=0; i < hts.length;i++) {
+        utils.addEvent(hts[i],"keyup",SetHitlistSize,false);
+    }
+    if($("psiInp")) {
+        var numSubsets = $("psiInp").getAttribute("numSubsets");
+        for(var i=1; i <= numSubsets;i++) {
+            if ($("alnPos" + i)) InitToggleEvent($("alnPos" + i));
+            if ($("deflnG" + i)) InitToggleEvent($("deflnG" + i));
+            if ($("deflnB" + i)) InitToggleEvent($("deflnB" + i));
+        }
+    }
+}
+
+function SetHitlistSize()
+{
+    var hts = document.getElementsByName("HITLIST_SIZE");
+    for(var i=0; i < hts.length;i++) {
+        if(this != hts[i]) {
+            hts[i].value = this.value;
+        }
+    }
+}
+function InitToggleEvent(toggleNode)
+{
+    if(toggleNode) {
+        var srcid = toggleNode.getAttribute("toggle");
+        if(srcid) Toggle.addTarget(srcid, toggleNode);
+    }
+}
+
+function InitIFrameLinks()
+{
+    CheckIframe($("RSIFrameNoRes"),"prlink");
+    CheckIframe($("RSIFrameDesc"),"prlink");
+    CheckIframe($("RSIFrameAln"),"prlink");
+}
+
+function CheckIframe(iframe,contentElemID)
+{
+    if(!iframe) return;
+
+    var iframeDoc;
+
+    if(iframe.contentDocument) {//Firefox
+        iframeDoc = iframe.contentDocument;
+    }
+    else if (iframe.contentWindow) {//IE
+        iframeDoc = iframe.contentWindow.document;
+    }
+    else if(iframe.document) {
+        iframeDoc = iframe.document;
+    }
+    if(iframeDoc){
+        if(iframeDoc.getElementById(contentElemID)) {
+            utils.addClass(iframe,"shown");
+            utils.removeClass(iframe,"hidden");
+        }
+     }
+}
+
+
+function InitHitMatrix()
+{
+    if($("bl2seImg")) {
+
+        utils.addEvent($("hitmtImg"),"load",
+                        function() {
+						    utils.addClass($("bl2seImg"),"shown");
+                            utils.removeClass($("bl2seImg"),"hidden");
+
+						},
+						false);
+        utils.addEvent($("showHitMatrix"),"click",
+                        function() {
+                            $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
+                            if(utils.hasClass($("htmb"),"shown")) {
+							    utils.addClass($("htmb"),"hidden");
+                                utils.removeClass($("htmb"),"shown");
+                            }
+                            else {
+                                utils.addClass($("htmb"),"shown");
+                                utils.removeClass($("htmb"),"hidden");
+                            }
+						},
+						false);
+
+        if($("blastSpec") && $("blastSpec").value=="GlobalAln") {
+            $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
+        }
+    }
+}
+
+
+
+
+
+function SetFormSubmitEvent()
+{
+    var el = $("refPage");
+    if(el) {
+	    SubmitEventNew("refPage");
+	}
+	SubmitEventNew("frmPage");
+	el = $("searchOptions");
+	if(el) {
+	    SubmitEventNew("searchOptions");
+	}
+	el = $("saveSearchOptions");
+	if(el) {
+	    SubmitEventNew("saveSearchOptions");
+	}
+	//SubmitEventNew("breadCrSearchOptions");
+	list = $("queryList");
+	if(list) {
+        utils.addEvent(list,"change",GetResults,false);
+    }
+
+    list = $("go");
+	if(list) {
+        utils.addEvent(list,"click",GetResults,false);
+    }
+
+
+    list= $("onPageReformat");
+    if(list) {
+        utils.addEvent(list,"click",Reformat,false);
+    }
+
+    if ($("cddResults") && $("statInfo")) {
+        jQuery($("cddResults")).ncbitoggler('toggle');
+    }
+    //New design still uses toggle
+    if ($("showCDD")) {
+        InitToggleEvent($("cddInfo"));
+    }
+    InitToggleEvent($("refInfo"));
+    InitToggleEvent($("resStat"));
+    InitToggleEvent($("dbDetails"));
+    InitToggleEvent($("graphicInfo"));
+    InitToggleEvent($("descrInfo"));
+    InitToggleEvent($("alignInfo"));
+    InitToggleEvent($("ovrInfo"));
+    InitToggleEvent($("queryInfo"));
+    InitToggleEvent($("hitMatrixInfo"));
+    InitToggleEvent($("bl2ovrInfo"));
+    //Init only for PSI blastfse
+    if($("prevRID")) InitPsiBlast();
+    InitSeqAlignLinks();
+    InitAllCustomButtons();
+    if($("dnPSSMPar")) InitDownLoad();
+    InitHitMatrix();
+    if($("noRes")) {
+        if($("hitCvs")) utils.addClass($("hitCvs"),"hidden");
+        if($("hitText")) utils.addClass($("hitText"),"hidden");
+    }
+    InitIFrameLinks();
+    showDbDetails(); //fill behind the scene
+    if ($("showDetails") && utils.hasClass($("showDetails"), "shown")) {
+        utils.addEvent($("showDetails"), "click", showDbDetails, false);
+    }
+    initContentWidth();
+}
+
+function initContentWidth() {
+    var lineLengthElem = $("FormatForm").LINE_LENGTH;
+    if (lineLengthElem) {
+        var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
+        if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
+
+        var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
+        var minWidth = (lineLength + parseInt(17)) * charWidth;
+
+
+        var alignView = $("FormatForm").ALIGNMENT_VIEW;
+        var formatType = $("FormatForm").FORMAT_TYPE;
+        var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
+
+        var addWidth = ($("FormatForm").OLD_VIEW.checked || queryAnch) ? 250 : 350;
+
+        minWidth = minWidth + parseInt(addWidth) + "px";
+        jQuery($("content")).css("min-width", minWidth);
+    }
+
+}
+
+
+
+
+
+function ShowHideAlnDeflines(alnID, checkbx) {
+    var dflTableID = "dln_" + alnID;
+    if ($(dflTableID)) {
+        var rmClass, addClass;
+        if (checkbx.checked) {
+            rmClass = "hidden";
+            addClass = "shown";
+        }
+        else {
+            rmClass = "shown";
+            addClass = "hidden";
+        }
+        var elems = $C(rmClass, "class", $(dflTableID), "tr");
+        if (elems) {
+            //alert(elems.length);
+            for (var i = 0; i < elems.length; i++) {
+                utils.removeClass(elems[i], rmClass);
+                utils.addClass(elems[i], addClass);
+            }
+        }
+    }
+}
+
+function SortAln(e, sortLink, sortItem) {
+    var p = utils.getParent(sortLink);
+    var p = utils.getParent(p);
+    p_TD = utils.getParent(p);
+    p_TR = utils.getParent(p_TD);
+    if (utils.hasClass(p_TR, "dflnAln")) {
+        p_TD.innerHTML = "Reading seqaligns...";
+        var gi = p_TD.id.substr(2);
+        var rid = p_TD.getAttribute("rid");
+        getAlignSort(rid, gi, p_TD, sortItem);
+        e = e || window.event;
+        utils.preventDefault(e);
+        return;
+    }
+    var links = document.getElementsByName("alnSort");
+    if (links.length >= sortItem) {
+        var href = links[sortItem].href.replace(new RegExp("selectAllTop.*(&|$)"), "");
+        var hrefLn = sortLink.href.replace(new RegExp(".*#"), "");
+        sortLink.href = href + hrefLn;
+    }
+}
+
+
+
+var fullArr;
+var numDbs;
+function showDbDetails(e,dbSetIndex)
+{
+    if (!($("dbPlusSpecies"))) return; //No org display
+    if ($("dbPlusSpecies").getAttribute("init") == "on" && dbSetIndex == null) return;
+    $("dbPlusSpecies").setAttribute("init", "on");
+
+    dbInfoUrl = "getDBInfo.cgi";
+    var rp = new RemoteDataProvider(dbInfoUrl);
+    rp.minArr = 10;
+
+    if (!fullArr) {
+        var arr = $("results").DATABASE.value.split(" ");
+        numDbs = arr.length;
+        if (arr.length > rp.minArr) {
+            fullArr = new Array();
+            while (arr.length > 1) {
+                var arrNew = arr.splice(0, rp.minArr); //does not include stopindex
+                fullArr.push(arrNew);
+            }
+            if (!dbSetIndex) dbSetIndex = 0;
+        }
+    }
+
+    rp.onSuccess = function(obj) {
+        var navDB = document.createElement("div");
+        if (fullArr) {
+            var prevLink, nextLink, firstLink, lastLink;
+            if (this.currDbSetIndex >= 1) {
+                var firstStart = 1;
+                var firstEnd = firstStart + fullArr[0].length - 1;
+                firstLink = document.createElement("a");
+                jQuery(firstLink).attr("href", "#");
+                jQuery(firstLink).attr("id", "firstDbSet");
+                jQuery(firstLink).attr("onclick", "showDbDetails(event,0);");
+                jQuery(firstLink).attr("title", "Databases " + firstStart + "-" + firstEnd);
+                jQuery(firstLink).html("First " + this.minArr + " dbs");
+
+            }
+            if (this.currDbSetIndex >= 1) {
+                var prevStart = (this.currDbSetIndex - 1) * this.minArr + 1;
+                var prevEnd = prevStart + fullArr[this.currDbSetIndex - 1].length - 1;
+                prevLink = document.createElement("a");
+                jQuery(prevLink).attr("href", "#");
+                jQuery(prevLink).attr("id", "prevDbSet");
+                jQuery(prevLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex - 1) + ");");
+                jQuery(prevLink).attr("title", "Databases " + prevStart + "-" + prevEnd);
+                jQuery(prevLink).html("Prev " + this.minArr + " dbs");
+            }
+
+            if (this.currDbSetIndex < fullArr.length - 1) {
+                var nextStart = (this.currDbSetIndex + 1) * this.minArr + 1;
+                var nextEnd = nextStart + fullArr[this.currDbSetIndex + 1].length - 1;
+                nextLink = document.createElement("a");
+                jQuery(nextLink).attr("href", "#");
+                jQuery(nextLink).attr("id", "nextDbSet");
+                jQuery(nextLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex + 1) + ");");
+                jQuery(nextLink).attr("title", "Databases " + nextStart + "-" + nextEnd);
+                jQuery(nextLink).html("Next " + this.minArr + " dbs");
+            }
+            if (this.currDbSetIndex < fullArr.length - 1) {
+                var lastInd = fullArr.length - 1;
+                var lastStart = numDbs - fullArr[lastInd].length;
+                var lastEnd = numDbs;
+                lastLink = document.createElement("a");
+                jQuery(lastLink).attr("href", "#");
+                jQuery(lastLink).attr("id", "lastDbSet");
+                jQuery(lastLink).attr("onclick", "showDbDetails(event," + lastInd + ");");
+                jQuery(lastLink).attr("title", "Databases " + lastStart + "-" + lastEnd);
+                jQuery(lastLink).html("Last " + this.minArr + " dbs");
+            }
+
+
+            jQuery(navDB).attr("id", "addDbSet");
+            if (firstLink) jQuery(navDB).append(firstLink);
+            if (prevLink) jQuery(navDB).append(prevLink);
+            if (lastLink) jQuery(navDB).append(lastLink);
+            if (nextLink) jQuery(navDB).append(nextLink);
+        }
+
+        jQuery($("dbPlusSpecies")).html(navDB);
+        jQuery(navDB).after(obj.responseText);
+        if (fullArr) {
+            var cap = jQuery($("dbSpecies")).find("caption");
+            if (cap) {
+                var currStart = (this.currDbSetIndex) * this.minArr + 1;
+                var currEnd = currStart + fullArr[this.currDbSetIndex].length - 1;
+                var capText = cap.html() + "<div class=\"cpAdd\"> Databases " + currStart + "-" + currEnd;
+                cap.html(capText);
+            }
+        }
+    };
+    rp.onError = function(obj) {
+        $("dbPlusSpecies").innerHTML += "error, requests:" + this.iActiveRequests + " status:" + obj.status;
+    }
+    var dbs;
+    if (fullArr) {
+        rp.currDbSetIndex = dbSetIndex;
+        var currArr = fullArr[dbSetIndex];
+        dbs = currArr.join(",");
+    }
+    else {
+        dbs = $("results").DATABASE.value.replace(/ /g, ",");
+    }
+
+    rp.Request("CMD=getDBOrg&DATABASE=" + dbs, "POST");
+    if(e) utils.preventDefault(e);
+}
+
+function synchronizeCheck(id, formName, inputName, isChecked) {
+
+    for (var i = 0; i < document.forms[formName].elements.length; i++) {
+        var theElem = document.forms[formName].elements[i];
+        if (theElem.type == "checkbox" && theElem.name == inputName && id == theElem.value) {
+            theElem.checked = isChecked;
+
+        }
+    }
+
+}
+
+utils.addEvent(window,
+				"load", SetFormSubmitEvent,
+				false);
+
+
+/* If user agent has "safari" in it, include safari-specific stylesheet. */
+if (navigator.userAgent.match(/safari/i) || navigator.userAgent.match(/opera/i)) {
+document.write("<link rel='stylesheet' type='text/css' href='css/safari-descriptions.css'  media='screen'/>");
+}
+if (navigator.userAgent.match(/opera/i)) {
+document.write("<link rel='stylesheet' type='text/css' href='css/opera-descriptions.css'  media='screen'/>");
+}
+if (navigator.userAgent.match(/firefox/i) || navigator.userAgent.match(/safari/i)) {
+document.write("<link rel='stylesheet' type='text/css' href='css/firefox-descriptions.css'  media='screen'/>");
+}
+
+
+
Binary file NCBI Blast reference example_files/scale.gif has changed
Binary file NCBI Blast reference example_files/score.gif has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/toggle.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,174 @@
+
+Toggle = function(node) {
+   this.init(node);
+}
+
+/**
+* @class Creates a  new Toggle class with "node" as src
+* @return Reutrns a new toggle instance
+*/
+Toggle.prototype = {
+
+   init: function(node) {
+
+      // Subclass instance?
+      if (typeof(arguments[0]) == 'undefined') return;
+
+      var oThis = this;
+      this.node = node;
+
+      // Initialize "showing" variable based on presence of "showing" or
+      // "hiding" class. If neither, then showing. Be sure class is
+      // set to reflect variable value
+      node.showing =
+         utils.hasClass(node, "showing") || !utils.hasClass(node, "hiding");
+      utils.addClass(node, node.showing ? "showing" : "hiding");
+
+      // Set notifier for node
+      utils.addEvent(node, "click", function(e) {
+         e = e || window.event;
+         utils.preventDefault(e);
+
+         var theNode = utils.getTargetObj(e);
+
+         // Send message to global notifier, if one exists
+         if (typeof(Notifier) != 'undefined') {
+            var notifier = Notifier.getInstance();
+            // Notify before change
+            notifier.Notify(oThis, "change:" + theNode.id, !this.showing);
+         }
+
+         // Hide or show based on current state
+         if (this.showing) {
+             oThis.hide();
+         } else {
+             oThis.show();
+         }
+
+      }, false);
+
+      utils.addEvent(node, "selectstart", function(e) { utils.preventDefault(e); }, true);
+      utils.addEvent(node, "drag", function(e) { utils.preventDefault(e); }, true);
+
+      // Cache "this" for ID lookup
+      if (!node.id) {
+          node.id = utils.createNewId();
+      }
+      var m = Toggle.getSrcs();
+      m[node.id] = this;
+   },
+
+   // Hide targets, and set self to hiding.
+   hide: function() {
+       var oThis = this;
+
+       oThis.setHiding();
+       if (oThis.listeners) {
+           forEach(oThis.listeners, function(l) {
+               oThis.hideTarget(l);
+           });
+       }
+   },
+
+   // Show targets, and set self to showing.
+   show: function() {
+       var oThis = this;
+
+       oThis.setShowing();
+       if (oThis.listeners) {
+           forEach(oThis.listeners, function(l) {
+               oThis.showTarget(l);
+           });
+       }
+   },
+
+   // Set own presentation to "showing"
+   setShowing: function() {
+       utils.addClass(this.node, "showing");
+       utils.removeClass(this.node, "hiding");
+       this.node.showing = true;
+   },
+
+   // Set own presentation to "hiding"
+   setHiding: function() {
+       utils.addClass(this.node, "hiding");
+       utils.removeClass(this.node, "showing");
+       this.node.showing = false;
+   },
+
+   // Show a target
+   showTarget: function(l) {
+       utils.addClass(l, "shown");
+       utils.removeClass(l, "hidden");
+   },
+
+   // Hide a target
+   hideTarget: function(l) {
+      utils.addClass(l, "hidden");
+      utils.removeClass(l, "shown");
+   },
+
+   // Add a target to this toggle.
+   add: function(target) {
+      if (!this.listeners) {
+          this.listeners = new Array();
+      }
+      this.listeners[this.listeners.length] = target;
+
+      if (utils.hasClass(target, "hidden")) {
+        this.setHiding();
+        this.node.showing = false;
+      } else {
+        this.setShowing();
+        this.node.showing = true;
+      }
+   }
+}
+
+// Show/hide a "target" (a node controlled by the node with the given ID)
+Toggle.addTarget = function(srcid, target) {
+   var tn = Toggle.findOrMake(srcid);
+   tn.add(target);
+}
+
+// Assoc array of srcs indexed by their ids
+Toggle.getSrcs = function() {
+   if (!Toggle.srcs) {
+      Toggle.srcs = new Object();
+   }
+   return Toggle.srcs;
+}
+
+// Find or make toggle for given id
+Toggle.findOrMake = function(srcid) {
+   var ts = Toggle.getSrcs();
+   var tn = ts[srcid];
+   if (!tn) {
+      tn = new Toggle($(srcid));
+   }
+   return tn;
+}
+
+// This dispatches the call to Toggle.onload, which may be
+// overridden by instances (subclasses)
+Toggle._onload = function() {
+   Toggle.onload();
+}
+
+// A toggle source node controls other nodes that reference it by id using
+// their toggle= attribute. A node may be both a toggle source and destination.
+Toggle.onload = function() {
+//alert("toggle start");
+   if(utils.hasClass(document.body,"noToggleCheck")) return;
+
+   shnodes = jQuery("[toggle]");
+   // Now hook up dst nodes
+   forEach(shnodes, function(node) {
+      // Link toggle node to its source
+      var srcid = node.getAttribute("toggle");
+      Toggle.addTarget(srcid, node);
+   });
+    //alert("toggle 2 end");
+}
+
+utils.addEvent(window, 'load', Toggle._onload, false);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/utils.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,633 @@
+// $Id: utils.js,v 1.4 2014/02/26 14:47:32 zaretska Exp $
+
+utils = {
+
+KeyCode_TAB: 9,
+KeyCode_DELETE: 46,
+KeyCode_BACKSPACE: 8,
+KeyCode_LEFT_ARROW: 37,
+KeyCode_RIGHT_ARROW: 39,
+KeyCode_HOME: 36,
+KeyCode_END: 35,
+KeyCode_PAGE_UP: 33,
+KeyCode_PAGE_DOWN: 34,
+KeyCode_UP_ARROW: 38,
+KeyCode_DOWN_ARROW: 40,
+KeyCode_ESC: 27,
+KeyCode_ENTER: 13,
+KeyCode_SPACE: 32,
+KeyCode_SHIFT_KEY: 16,
+KeyCode_CTRL_KEY: 17,
+KeyCode_ALT_KEY: 18,
+KeyCode_LEFT_MS_WINDOWS_KEY: 91,
+KeyCode_RIGHT_MS_WINDOWS_KEY: 92,
+KeyCode_MS_MENU_KEY: 93,
+
+isObject: function(a) { return (a && typeof a == 'object'); },
+
+isArray: function(a) { return this.isObject(a) && a.constructor == Array; },
+
+insertInHtml: function(text, obj) {
+	if (document.all) {
+		obj.innerHTML += text;
+	} else {
+		var range = document.createRange();
+		range.setStartAfter(obj);
+		var docFrag = range.createContextualFragment(text);
+		obj.appendChild(docFrag);
+	}
+
+},
+
+replaceInHtml: function(text, obj) {
+	if (document.all) {
+		obj.innerHTML = text;
+	} else {
+		while (obj.hasChildNodes()) obj.removeChild(obj.firstChild);
+		var range = document.createRange();
+		range.setStartAfter(obj);
+		var docFrag = range.createContextualFragment(text);
+		obj.appendChild(docFrag);
+	}
+},
+
+
+getTargetObj: function(eEvent) {
+    var oTarget;
+    var e = eEvent || window.event;
+    if (e == null) return null;
+    if (e.srcElement == null)  {
+        oTarget = e.target;
+    } else {
+        oTarget = e.srcElement;
+    }
+    while ( oTarget && oTarget.nodeType != 1 ) oTarget = oTarget.parentNode;
+    return oTarget;
+},
+
+
+
+
+getParent: function(obj) {
+     if (obj) {
+         var result = obj.parentNode;
+         while (result && result.nodeType != 1) result = result.nextSibling;
+         if (result) return result;
+     }
+     return null;
+},
+
+getFirstChild: function(obj) {
+     if (obj) {
+         var result = obj.firstChild;
+         while (result && result.nodeType != 1) result = result.nextSibling;
+         if (result) return result;
+     }
+     return null;
+},
+
+getNextSibling: function(obj, tagName) {
+    if (obj) {
+        var result = obj.nextSibling;
+        if (tagName) {
+            var tn = tagName.toUpperCase();
+            while (result && result.tagName != tn) result = result.nextSibling;
+        } else {
+            while (result && result.nodeType != 1) result = result.nextSibling;
+        }
+        return result;
+    }
+    return null;
+},
+
+getPreviousSibling: function(obj, tagName) {
+     if (obj) {
+         var result = obj.previousSibling;
+         if (tagName) {
+             var tn = tagName.toUpperCase();
+             while (result && result.tagName != tn) result = result.previousSibling;
+         } else {
+             while (result && result.nodeType != 1) result = result.previousSibling;
+         }
+         return result;
+     }
+     return null;
+},
+
+removeChildren: function(oObj) {
+     if (!oObj || typeof oObj != "object") return;
+     while(oObj.hasChildNodes()) oObj.removeChild(oObj.firstChild)
+},
+
+insertAfter: function(parent, node, referenceNode) {
+	parent.insertBefore(node, referenceNode.nextSibling);
+},
+
+nextItem: function(item, nodeName) {
+    if (item == null) return;
+    var next = item.nextSibling;
+    while (next != null) {
+        if (next.nodeName == nodeName) return next;
+        next = next.nextSibling;
+    }
+    return null;
+},
+
+previousItem: function(item, nodeName) {
+    var previous = item.previousSibling;
+    while (previous != null) {
+        if (previous.nodeName == nodeName) return previous;
+        previous = previous.previousSibling;
+    }
+    return null
+},
+
+moveBefore: function(item1, item2) {
+    var parent = item1.parentNode;
+    parent.removeChild(item1);
+    parent.insertBefore(item1, item2);
+},
+
+moveAfter: function(item1, item2) {
+    var parent = item1.parentNode;
+    parent.removeChild(item1);
+    parent.insertBefore(item1, item2 ? item2.nextSibling : null);
+},
+
+
+
+
+createCookie: function(name, value, days) {
+    if (days) {
+        var date = new Date();
+        date.setTime(date.getTime() + (days * 24 * 60 * 60 * 1000));
+        var expires = '; expires=' + date.toGMTString();
+    } else expires = '';
+    document.cookie = name + '=' + value + expires + '; path=/';
+},
+
+readCookie: function(name) {
+    var nameEQ = name + '=';
+    var ca = document.cookie.split(';');
+    for (var i = 0; i < ca.length; i++) {
+        var c = ca[i];
+        while (c.charAt(0)==' ') c = c.substring(1, c.length);
+        if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length, c.length);
+    }
+    return "";
+},
+
+eraseCookie: function(name) {
+	document.cookie = name + "=null; expires=Thu, 01-Jan-1970 00:00:01 GMT; domain=nih.gov; path=/";
+	document.cookie = name + "; expires=Thu, 01-Jan-1970 00:00:01 GMT; domain=nih.gov; path=/";
+},
+
+addClass: function(element, className) {
+    if (!this.hasClass(element, className)) {
+        if (element.className) element.className += " " + className;
+        else element.className = className;
+    }
+},
+
+removeClass: function(element, className) {
+    var regexp = new RegExp("(^|\\s)" + className + "(\\s|$)");
+    element.className = element.className.replace(regexp, "$2");
+},
+
+hasClass: function(element, className) {
+    var regexp = new RegExp("(^|\\s)" + className + "(\\s|$)");
+    return regexp.test(element.className);
+},
+
+
+getXY: function (obj){
+     /*
+     +------------- w ----
+     | (x,y)
+     |
+     h
+     |
+     */
+     var b={x:0, y:0, w:obj.offsetWidth, h:obj.offsetHeight};
+
+     if (obj.offsetParent) {
+         while(obj) {
+             b.x += obj.offsetLeft;
+             b.y += obj.offsetTop;
+             obj = obj.offsetParent;
+         }
+     } else if (obj.x) {
+         b.x = obj.x;
+         b.y = obj.y;
+     }
+     return b;
+},
+
+/* Based on ppk (untested) */
+getEventXY: function(e) {
+    var xpos = 0;
+    var ypos = 0;
+    e = e || window.event;
+    xpos = e.pageX || (e.clientX + document.body.scrollLeft +
+                    document.documentElement.scrollLeft);
+    ypos = e.pageY || (e.clientY + document.body.scrollTop +
+                    document.documentElement.scrollTop);
+    return {x: xpos, y: ypos};
+},
+
+drawText: function (sText, sId, add) {
+    if (!sId) sId = "debug";
+    var obj = document.getElementById(sId);
+    if (obj) {
+        if (add)
+            this.insertInHtml("<br/>" + sText, obj);
+        else
+            this.replaceInHtml(sText, obj);
+    }
+},
+
+
+selectRange: function (oObj /*:object*/, iStart /*:int*/, iLength /*:int*/) {
+    if (!(oObj && oObj.value)) return;
+
+    if (oObj.createTextRange) {
+        //use text ranges for Internet Explorer
+        var oRange = oObj.createTextRange();
+        oRange.moveStart("character", iStart);
+        oRange.moveEnd("character", iLength - oObj.value.length);
+        oRange.select();
+    } else if (oObj.setSelectionRange) {
+        //use setSelectionRange() for Mozilla
+        oObj.setSelectionRange(iStart, iLength);
+    }
+    //set focus back to the textbox
+    oObj.focus();
+},
+
+getSelection: function() {
+     var text = "";
+     if (window.getSelection) {
+         text += window.getSelection();
+     } else if (document.getSelection) {
+         text += document.getSelection();
+     } else if (document.selection){        //IE
+         text += document.selection.createRange().text;
+     }
+     return text;
+},
+
+
+
+
+// http://ejohn.org/apps/jselect/event.html
+addEvent: function(obj, type, fn, b) {
+    if (obj.attachEvent) {
+        var name = "" + type + fn;
+//        name = name.substring(0, name.indexOf("\n"));   // IE  This doesn't work
+        obj["e" + name] = fn;
+        obj[name] = function(){ obj["e" + name](window.event);}
+        obj.attachEvent("on" + type, obj[name]);
+    } else {
+        obj.addEventListener(type, fn, b);
+        return true;
+    }
+},
+
+
+removeEvent: function(obj, type, fn, b) {
+    if (obj.detachEvent) {
+        var name = "" + type + fn;
+//        name = name.substring(0, name.indexOf("\n"));   //IE This doesn't work
+        if ("function" == typeof obj[name]) {
+            obj.detachEvent("on" + type, obj[name]);
+            obj[name] = null;
+            obj["e" + name] = null;
+        }
+    } else {
+      obj.removeEventListener(type, fn, b);
+      return true;
+    }
+},
+
+noBubbleEvent: function(e) {
+	if (e && e.stopPropagation) e.stopPropagation();
+	else window.event.cancelBubble = true;
+},
+
+targetEvent: function(e) {
+     if (e.srcElement == null) {
+         return e.target;
+     } else {
+         return window.event.srcElement;
+     }
+},
+
+preventDefault: function(e) {
+     if (e.preventDefault) e.preventDefault();
+     else window.event.returnValue = false;
+},
+
+relatedTarget: function(e) {
+    if (!e) var e = window.event;
+	if (e.relatedTarget)    return e.relatedTarget;
+	else if (e.toElement)   return e.toElement;
+    else if (e.fromElement) return e.fromElement;
+},
+
+readStyle: function(element, property) {
+    if (element.style[property]) {
+        return element.style[property];
+    } else if (element.currentStyle) {
+        return element.currentStyle[property];
+    } else if (document.defaultView && document.defaultView.getComputedStyle) {
+        var style = document.defaultView.getComputedStyle(element, null);
+        if (style) return style.getPropertyValue(property);
+    }
+    return "";
+},
+
+
+printObj: function (oObj, iLevel) {
+     var s = "";
+     var sIdent = "";
+     if (!iLevel) iLevel = 0;
+     for (var i = 0; i < iLevel; i++) {
+         sIdent += "__";
+     }
+     for (var i in oObj) {
+         var ss = [];
+         if ("string" == typeof oObj[i]) {
+             ss = oObj[i].split("<");
+         }
+         s += sIdent + " " + i + " : [" + (typeof oObj[i]) + "] : " + ss.join("&lt;") + "<br/>";
+ //        if (oObj[i] && "object" == typeof oObj[i] && iLevel < 2) {
+ //            s+= "<br/>-----" + typeof oObj[i] + " --- " + iLevel + "</br>";
+ //            s += this.printObj(oObj[i], iLevel + 1);
+ //        }
+     }
+     return s;
+},
+
+jsLoader:  {
+    sBase: "", /* Base is this directory */
+    oLoaded: [],
+    load: function (aScripts) {
+
+       var oS = document.getElementsByTagName("script");
+       var k = 0;
+       for (var j = 0; j < oS.length; j++) {
+           if (oS[j].src == "") continue;
+           this.oLoaded[k++] = oS[j].src;
+       }
+
+        var oHead = document.getElementsByTagName("head")[0];
+
+        for (var i = 0; i < aScripts.length; i++) {
+            var sNewSrc = this.sBase + aScripts[i];
+            var oS = document.getElementsByTagName("script");
+            var b = true;
+            for (var j = 0; j < this.oLoaded.length; j++) {
+                if (sNewSrc == this.oLoaded[j]) {
+//                    alert(sNewSrc + " : already loaded");
+                    b = false;
+                }
+            }
+
+            if (b) {
+                var oScript = document.createElement("script");
+                oScript.src = sNewSrc;
+                oScript.setAttribute("type", "text/javascript");
+                oHead.appendChild(oScript);
+                this.oLoaded[this.oLoaded.length] = sNewSrc;
+            }
+        }
+    }
+},
+
+// Create an id that doesn't exist in this document
+createNewId: function()
+{
+   var newid = null
+
+   while (!newid || document.getElementById(newid)) {
+       newid = "XID" + Math.round(Math.random() * 65536).toString(16)
+   }
+   return newid
+}
+
+};
+
+
+String.prototype.trimSpaces = function(trimMode) {
+    // 0 = trim begin and end
+    // 1 = trim begin only
+    // 2 = trim after only
+
+    var targetString = this;
+    var iPos = 0;
+    if (!trimMode) trimMode = 0;
+
+    if (trimMode==0 || trimMode==1) {
+        if (targetString.charAt(iPos)==" ") {
+            while(targetString.charAt(iPos)==" ") iPos++;
+            targetString = targetString.substr(iPos);
+        }
+    }
+
+    iPos = targetString.length-1;
+    if (trimMode==0 || trimMode==2) {
+        if (targetString.charAt(iPos) == " ") {
+            while(targetString.charAt(iPos) == " ") iPos--;
+            targetString = targetString.substr(0, iPos + 1);
+        }
+    }
+    return targetString;
+}
+
+
+
+
+/* Shortcuts */
+
+// Get elements by Id's
+function $() {
+  var elements = new Array();
+
+  for (var i = 0; i < arguments.length; i++) {
+    var element = arguments[i];
+    if (typeof element == 'string')
+      element = document.getElementById(element);
+
+    if (arguments.length == 1)
+      return element;
+
+    elements.push(element);
+  }
+
+  return elements;
+}
+
+// Get elements by AttributeValue for Attributename
+// http://www.dustindiaz.com/top-ten-javascript/ (but has some errors)
+function $C(attrValue, attrName, node, tag) {
+    //alert([attrValue, attrName, node, tag])
+    if ("*" == attrValue) {
+        return $AN(attrName, node, tag);
+    }
+	var oElements = new Array();
+	if (!node) node = document;
+	if (!tag) tag = '*';
+	if (!attrName) attrName = 'class';
+
+	var els = node.getElementsByTagName(tag);
+	var elsLen = els.length;
+	var pattern = new RegExp("(^|\\s)" + attrValue + "(\\s|$)");
+    var j = 0;
+	for (i = 0; i < elsLen; i++) {
+		if (attrName == "class" && pattern.test(els[i].className)) {
+            // IE behavior
+//            oElements.push(els[i]);
+            oElements[j++] = els[i];
+		} else if (pattern.test(els[i].getAttribute(attrName))) {
+			oElements[j++] = els[i];
+//			oElements.push(els[i]);
+		}
+	}
+    return oElements;
+}
+
+
+function $AN(attrName, node, tag) {
+	var oElements = new Array();
+	if (node == null) node = document;
+	if (tag == null)tag = '*';
+	var els = node.getElementsByTagName(tag);
+	for (i = 0; i < els.length; i++) {
+		if (els[i].getAttribute(attrName) != null) {
+			oElements.push(els[i]);
+		}
+	}
+	return oElements;
+}
+
+function dump(aMessage) {
+  var consoleService = Components.classes["@mozilla.org/consoleservice;1"]
+                                 .getService(Components.interfaces.nsIConsoleService);
+  consoleService.logStringMessage(aMessage);
+}
+
+
+// forEach iterators from Dean Edwards: http://dean.edwards.name/weblog/2006/07/enum/
+// generic enumeration
+Function.prototype.forEach = function(object, block, context) {
+    for (var key in object) {
+        if (typeof this.prototype[key] == "undefined") {
+            block.call(context, object[key], key, object);
+        }
+    }
+};
+
+// globally resolve forEach enumeration
+var forEach = function(object, block, context) {
+    if (object) {
+        var resolve = Object; // default
+        if (object instanceof Function) {
+            // functions have a "length" property
+            resolve = Function;
+        } else if (object.forEach instanceof Function) {
+            // the object implements a custom forEach method so use that
+            object.forEach(block, context);
+            return;
+        } else if (typeof object.length == "number") {
+            // the object is array-like
+            resolve = Array;
+        }
+        resolve.forEach(object, block, context);
+    }
+};
+
+//
+// Update Array class to JS 1.5 if not yet there.
+//
+
+// array-like enumeration
+if (!Array.forEach) { // mozilla already supports this
+    Array.forEach = function(object, block, context) {
+        for (var i = 0; i < object.length; i++) {
+            block.call(context, object[i], i, object);
+        }
+    };
+}
+
+if (!Array.prototype.indexOf)
+	Array.prototype.indexOf = function(item, startIndex) {
+		var len = this.length;
+		if (startIndex == null)
+			startIndex = 0;
+		else if (startIndex < 0) {
+			startIndex += len;
+			if (startIndex < 0)
+				startIndex = 0;
+		}
+		for (var i = startIndex; i < len; i++) {
+			var val = this[i] || this.charAt && this.charAt(i);
+			if (val == item)
+				return i;
+		}
+		return -1;
+	};
+
+if (!Array.prototype.lastIndexOf)
+	Array.prototype.lastIndexOf = function(item, startIndex) {
+		var len = this.length;
+		if (startIndex == null || startIndex >= len)
+			startIndex = len - 1;
+		else if (startIndex < 0)
+			startIndex += len;
+		for (var i = startIndex; i >= 0; i--) {
+			var val = this[i] || this.charAt && this.charAt(i);
+			if (val == item)
+				return i;
+		}
+		return -1;
+	};
+
+if (!Array.prototype.map)
+	Array.prototype.map = function(func, thisVal) {
+		var len = this.length;
+		var ret = new Array(len);
+		for (var i = 0; i < len; i++)
+			ret[i] = func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this);
+		return ret;
+	};
+
+if (!Array.prototype.filter)
+	Array.prototype.filter = function(func, thisVal) {
+		var len = this.length;
+		var ret = new Array();
+		for (var i = 0; i < len; i++) {
+			var val = this[i] || this.charAt && this.charAt(i);
+			if(func.call(thisVal, val, i, this))
+				ret[ret.length] = val;
+		}
+		return ret;
+	};
+
+if (!Array.prototype.every)
+	Array.prototype.every = function(func, thisVal) {
+		var len = this.length;
+		for (var i = 0; i < len; i++)
+			if (!func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this))
+				return false;
+		return true;
+	};
+
+if (!Array.prototype.some)
+	Array.prototype.some = function(func, thisVal) {
+		var len = this.length;
+		for (var i = 0; i < len; i++)
+			if (func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this))
+				return true;
+		return false;
+	};
+
Binary file NCBI Blast reference example_files/white.gif has changed