Mercurial > repos > jankanis > blast2html
diff Blast output page example.html @ 0:bad241dc701f
add example input blast xml and output html page
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Tue, 06 May 2014 17:05:58 +0200 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example.html Tue May 06 17:05:58 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="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&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li> + <li class="recent "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&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&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&PAGE_TYPE=BlastHome">BLAST</a>/ + <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&PAGE_TYPE=BlastSearch&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="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&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&ALIGNMENTS=100&CMD=Get">Text</a> +<a class="xgl" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get">XML</a> +<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=Alignment&CMD=Get">ASN.1</a> +<a id="hitText" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get">Hit Table(text)</a> +<a id="hitCvs" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=CSV&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&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&RECENT_RESULTS=on&RID=PHWP1JNZ014&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&RID=PHWP1JNZ014&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=PSSM_Scoremat&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&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&db=nucleotide&term=59987&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&cmd=Retrieve&list_uids=9254694&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&RID=PHWP1JNZ014&FORMAT_OBJECT=TaxBlast&NCBI_GI=off&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_BLOCK_ON_RESPAGE=Top&MASK_COLOR=1&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&blastRID=PHWP1JNZ014&queryID=lcl%7C59987&entrezLim=&ex=&exl=&exh=&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> +<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> +<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> +<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> +<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> +</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/1.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="83"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/3.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="83"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/6.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/white.gif" height="4" width="83"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/9.gif" height="13" width="10"></td> +<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> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example_files/2.gif" height="13" width="10"></td> +<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> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%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="Blast%20output%20page%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="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="#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="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="#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="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="#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> +</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="#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@&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&rettype=gb&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&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&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&RID=PHWP1JNZ014&FORMAT_TYPE=CSV&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&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&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwText">Text</label></div> +<div><input name="dwn" id="dwXML" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwXML">XML</label></div> +<div><input name="dwn" id="dwASN" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=Alignment&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&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=1&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&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=2&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&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=4&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&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=0&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&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&DISPLAY_SORT=3&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&log$=nucltop&blast_rank=1&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J5A_A">3J5A_A</a> +</td> +</tr><tr id="dtr_557804395" ind="2" class="even dflLnk"> +<td class="l c0"><span class="ind">2</span><input id="chk_2" class="cb" name="getSeqGi" value="557804395" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_2" class="accsb">Select seq pdb|3J58|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="2" accs="pdb|3J58|A" seqfsta="gi|557804395" gi="557804395" seqid="557804395" id="deflnDesc_2" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804395">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nucltop&blast_rank=2&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&log$=nucltop&blast_rank=3&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J56_A">3J56_A</a> +</td> +</tr><tr id="dtr_557804283" ind="4" class="even dflLnk"> +<td class="l c0"><span class="ind">4</span><input id="chk_4" class="cb" name="getSeqGi" value="557804283" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_4" class="accsb">Select seq pdb|3J54|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="4" accs="pdb|3J54|A" seqfsta="gi|557804283" gi="557804283" seqid="557804283" id="deflnDesc_4" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804283">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nucltop&blast_rank=4&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&log$=nucltop&blast_rank=5&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J52_A">3J52_A</a> +</td> +</tr><tr id="dtr_557804195" ind="6" class="even dflLnk"> +<td class="l c0"><span class="ind">6</span><input id="chk_6" class="cb" name="getSeqGi" value="557804195" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_6" class="accsb">Select seq pdb|3J51|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="6" accs="pdb|3J51|A" seqfsta="gi|557804195" gi="557804195" seqid="557804195" id="deflnDesc_6" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804195">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804195?report=genbank&log$=nucltop&blast_rank=6&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&log$=nucltop&blast_rank=7&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J50_A">3J50_A</a> +</td> +</tr><tr id="dtr_557804083" ind="8" class="even dflLnk"> +<td class="l c0"><span class="ind">8</span><input id="chk_8" class="cb" name="getSeqGi" value="557804083" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_8" class="accsb">Select seq pdb|3J4X|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="8" accs="pdb|3J4X|A" seqfsta="gi|557804083" gi="557804083" seqid="557804083" id="deflnDesc_8" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804083">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804083?report=genbank&log$=nucltop&blast_rank=8&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&log$=nucltop&blast_rank=9&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3F_5">3J3F_5</a> +</td> +</tr><tr id="dtr_485601474" ind="10" class="even dflLnk"> +<td class="l c0"><span class="ind">10</span><input id="chk_10" class="cb" name="getSeqGi" value="485601474" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_10" class="accsb">Select seq pdb|3J3E|5</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain 5, Structure Of The D. Melanogaster 60s Rrna" class="deflnDesc" hsp="4" len="31" ind="10" accs="pdb|3J3E|5" seqfsta="gi|485601474" gi="485601474" seqid="485601474" id="deflnDesc_10" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601474">Chain 5, Structure Of The D. Melanogaster 60s Rrna</a> +</div> +</td> +<td class="c3">18.3</td> +<td class="c4">63.4</td> +<td class="c5">100%</td> +<td class="c6"> 12</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601474?report=genbank&log$=nucltop&blast_rank=10&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&log$=nucltop&blast_rank=11&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&blastRID=PHWP1JNZ014&queryID=lcl|59987&entrezLim=&ex=&exl=&exh=&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&blastRID=PHWP1JNZ014&queryID=lcl|59987&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&rettype=gb&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&log$=nuclalign&blast_rank=1&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&rid=PHWP1JNZ014[557804451]&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]&v=752:2685&appname=ncbiblast&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&currseq=557804451" id="alnNxt_557804451" onclick="goToNextAlign('dtr_557804451',true);"><span>Next</span></a> +<a disabled="disabled" class="gbd toolsCtr navPrev" ref="ordinalpos=1&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&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J5A|A">pdb|3J5A|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804451"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804451"><div id="hd_557804451_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=961&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&rid=PHWP1JNZ014[557804451]&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]&v=961:976&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=2591&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&rid=PHWP1JNZ014[557804451]&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]&v=2591:2598&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=839&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&rid=PHWP1JNZ014[557804451]&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]&v=839:845&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=2027&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&rid=PHWP1JNZ014[557804451]&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]&v=2027:2033&appname=ncbiblast&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&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&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&rettype=gb&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&log$=nuclalign&blast_rank=2&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&rid=PHWP1JNZ014[557804395]&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]&v=752:2685&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J58|A">pdb|3J58|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804395"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804395"><div id="hd_557804395_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=961&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&rid=PHWP1JNZ014[557804395]&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]&v=961:976&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=2591&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&rid=PHWP1JNZ014[557804395]&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]&v=2591:2598&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=839&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&rid=PHWP1JNZ014[557804395]&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]&v=839:845&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=2027&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&rid=PHWP1JNZ014[557804395]&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]&v=2027:2033&appname=ncbiblast&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&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&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&rettype=gb&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&log$=nuclalign&blast_rank=3&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&rid=PHWP1JNZ014[557804339]&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]&v=752:2685&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J56|A">pdb|3J56|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804339"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804339"><div id="hd_557804339_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=961&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&rid=PHWP1JNZ014[557804339]&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]&v=961:976&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=2591&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&rid=PHWP1JNZ014[557804339]&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]&v=2591:2598&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=839&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&rid=PHWP1JNZ014[557804339]&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]&v=839:845&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=2027&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&rid=PHWP1JNZ014[557804339]&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]&v=2027:2033&appname=ncbiblast&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&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&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&rettype=gb&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&log$=nuclalign&blast_rank=4&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&rid=PHWP1JNZ014[557804283]&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]&v=752:2685&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J54|A">pdb|3J54|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804283"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804283"><div id="hd_557804283_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=961&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&rid=PHWP1JNZ014[557804283]&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]&v=961:976&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=2591&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&rid=PHWP1JNZ014[557804283]&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]&v=2591:2598&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=839&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&rid=PHWP1JNZ014[557804283]&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]&v=839:845&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=2027&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&rid=PHWP1JNZ014[557804283]&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]&v=2027:2033&appname=ncbiblast&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&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&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&rettype=gb&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&log$=nuclalign&blast_rank=5&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&rid=PHWP1JNZ014[557804227]&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]&v=752:2685&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J52|A">pdb|3J52|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804227"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804227"><div id="hd_557804227_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=961&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&rid=PHWP1JNZ014[557804227]&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]&v=961:976&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=2591&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&rid=PHWP1JNZ014[557804227]&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]&v=2591:2598&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=839&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&rid=PHWP1JNZ014[557804227]&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]&v=839:845&appname=ncbiblast&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&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&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&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=2027&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&rid=PHWP1JNZ014[557804227]&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]&v=2027:2033&appname=ncbiblast&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&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&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 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