blast2html: NCBI Blast reference example.html annotate

annotate NCBI Blast reference example.html @ 51:b15a20c2372a

fix python 2 compatibility

author	Jan Kanis <jan.code@jankanis.nl>
date	Wed, 21 May 2014 18:34:35 +0200
parents	344cd76f6fd2
children

rev	line source
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2 <html xmlns="http://www.w3.org/1999/xhtml"><head>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	3
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	5 <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	6 <meta name="jig" content="ncbitoggler ncbiautocomplete ncbilocalnav ncbigrid ncbipopper">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	7 <meta name="ncbitoggler" content="animation:'none'">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	8 <meta name="ncbipopper" content="animation:'none',closeEvent: 'click',openEvent: 'click',destPosition: 'top right',triggerPosition: 'bottom right'">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	9
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	10 <meta name="ncbi_app" content="blast">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	11 <meta name="ncbi_pdid" content="blastresults">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	12 <meta name="ncbi_stat" content="false">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	13 <meta name="ncbi_sessionid" content="8A8E11EE2CABF371_0000SID">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	14 <meta name="ncbi_phid" content="5AAB74D7368F2C81000000000000C9C8">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	15 <script type="text/javascript"> var ncbi_startTime = new Date(); </script>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	16 <title>NCBI Blast:Nucleotide Sequence (16 letters)</title>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	17 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jig.js"></script><link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/jig.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_002.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_005.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_004.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_004.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_007.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_003.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_007.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_003.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_008.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_008.js"></script><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_005.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_009.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_006.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_006.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_002.css">
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	18 <script type="text/javascript"> jQuery.getScript("/core/alerts/alerts.js", function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	19 galert(['div#header', 'body > *:nth-child(1)'])
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	20 });</script>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	21 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/main.css" media="screen">
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	22 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/blastRes.css" media="screen">
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	23 <!--[if IE]>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	24 <link rel="stylesheet" type="text/css" href="css/descriptionsIE.css" media="screen" />
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	25 <![endif]-->
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	26 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/print.css" media="print">
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	27 <!--[if lte IE 6]>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	28 <link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	29 <![endif]-->
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	30 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/blastReq.css" media="screen">
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	31 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/results.css" media="screen">
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	32 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/dynFormatRes.css" media="screen">
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	33
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	34 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	35
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	36 <body id="type-a" class="noToggleCheck ">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	37 <div id="wrap">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	38 <div id="header">
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	39 <div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov/" title="NCBI Home Page"><img src="NCBI%20Blast%20reference%20example_files/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page"></a>BLAST <span id="trdm"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	40 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	41 <div id="search">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	42
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	43 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	44 <script language="JavaScript" type="text/javascript"><!--
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	45 // --></script><table class="medium1" style="border:2px solid #336699;" id="myncbi_off" cellpadding="2" cellspacing="0"><tbody><tr><td align="left" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td align="right" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img src="NCBI%20Blast%20reference%20example_files/myncbihelpicon.gif" alt="My NCBI help" border="0"></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to sign in" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Sign In]</a> <a href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to register for an account" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Register]</a></td></tr></tbody></table></div>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	46 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	47 <a class="skp" href="#content-wrap">Jump to Page Content</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	48 <ul id="nav">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	49 <li class="first "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	50 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	51 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	52 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	53 </ul>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	54 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	55
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	56 <div id="content-wrap">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	57
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	58 <div id="breadcrumb" class="inlineDiv">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	59 <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	60 <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	61 <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=">blastn suite</a>/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	62 <strong>Formatting Results - PHWP1JNZ014</strong>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	63 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	64 <div class="inlineDiv resHeader resPage">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	65
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	66 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	67 <ul class="print-log-res"><li></li></ul>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	68
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	69 <!-- CDD info for old design -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	70
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	71
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	72
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	73
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	74
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	75
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	76
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	77
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	78 <div id="content">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	79
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	80 <!--<ul id="msg" class="msg"><li class="info"><p class=""></p><p class=""></p><p class=""></p></li></ul>-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	81 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	82 <a href="#" class="resLink resPage" id="searchOptions" submitform="setSavedOptions">Edit and Resubmit</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	83 <a href="#" class="resLink resPage hidden" id="saveSearchOptions" submitform="saveOptions">Save Search Strategies</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	84 <span class="reslink resPage">[Sign in above to save your search strategy]</span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	85 <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="#">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	86 <span class="ui-ncbitoggler-master-text">Formatting options </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	87 <span class="ui-icon ui-icon-triangle-1-e"></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	88 </a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	89 <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="#">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	90 <span class="ui-ncbitoggler-master-text">Download</span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	91 <span class="ui-icon ui-icon-triangle-1-e"></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	92 </a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	93 <span id="hnr">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	94 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	95 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	96 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	97 <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	98 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	99 <input name="QUERY_INDEX" value="0" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	100 <input name="_PGR" value="2" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	101 <input id="seqViewUrl" value="http://www.ncbi.nlm.nih.gov/projects/sviewer" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	102 <input name="CMD" value="Get" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	103 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	104 <!-- Reformat and downlaod for new design -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	105 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	106 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	107 <table class="options blastn ">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	108 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	109 <td class="frh" colspan="2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	110 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	111 <div class="tb">Formatting options</div>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	112 <input id="onPageReformat" src="NCBI%20Blast%20reference%20example_files/reformat.jpg" class="blastbutton" alt="Reformat" mouseovimg="css/images/reformatOver.jpg" mouseoutimg="css/images/reformat.jpg" mousedownimg="css/images/reformatDown.jpg" mouseupimg="css/images/reformatOver.jpg" border="0" type="image">
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	113 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	114 </td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	115 <tr class="paramSet xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	116 <td class="hd"><label for="FORMAT_OBJECT">Show</label></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	117 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	118 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	119 <input id="FORMAT_OBJECT" value="Alignment" name="FORMAT_OBJECT" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	120 <label for="FORMAT_TYPE" id="nft">Alignment as</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	121 <select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defval="HTML">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	122 <option value="HTML" selected="selected">HTML</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	123 <option value="Text">Plain text</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	124
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	125 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	126
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	127 <span id="advView" class="">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	128 <span class=""><input name="OLD_VIEW" id="OLD_VIEW" class="cb reset" defval="unchecked" false="" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	129 <label for="OLD_VIEW">Old View</label></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	130 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	131 <a class="resetAll" id="resetAll">Reset form to defaults</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	132 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	133 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	134 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	135 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	136 These options control formatting of alignments in results pages. The
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	137 default is HTML, but other formats (including plain text) are available.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	138 PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	139 The Advanced view option allows the database descriptions to be sorted by various indices in a table.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	140 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	141 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	142 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	143 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	144 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	145 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	146
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	147 <tr class="odd paramSet">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	148 <td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	149 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	150 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	151 <select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defval="Pairwise" class="reset">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	152 <option value="Pairwise" selected="selected">Pairwise</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	153 <option value="PairwiseWithIdentities">Pairwise with dots for identities</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	154 <option value="QueryAnchored">Query-anchored with dots for identities</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	155 <option value="QueryAnchoredNoIdentities">Query-anchored with letters for identities</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	156 <option value="FlatQueryAnchored">Flat query-anchored with dots for identities</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	157 <option value="FlatQueryAnchoredNoIdentities">Flat query-anchored with letters for identities</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	158
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	159 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	160
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	161
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	162 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	163 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	164 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	165 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	166 Choose how to view alignments.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	167 The default "pairwise" view shows how each subject sequence aligns
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	168 individually to the query sequence. The "query-anchored" view shows how
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	169 all subject sequences align to the query sequence. For each view type,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	170 you can choose to show "identities" (matching residues) as letters or
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	171 dots.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	172 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	173 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	174 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	175 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	176 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	177 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	178
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	179 <tr class="paramSet">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	180 <td class="hd"><label>Display</label></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	181 <td class="cb">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	182 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	183 <input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" class="cb reset" defval="checked" checked="checked" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	184 <label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	185
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	186 <span class="hidden" id="shl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	187 <input name="SHOW_LINKOUT" id="SHOW_LINKOUT" class="cb reset" defval="checked" checked="checked" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	188 <label class="rb" for="SHOW_LINKOUT">Linkout</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	189 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	190 <span class="hidden" id="gts">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	191 <input name="GET_SEQUENCE" id="GET_SEQUENCE" class="cb reset" defval="checked" checked="checked" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	192 <label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	193 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	194
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	195 <input name="NCBI_GI" id="NCBI_GI" class="cb reset" defval="unchecked" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	196 <label class="rb" for="NCBI_GI">NCBI-gi</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	197 <span id="scf">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	198 <input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" class="cb reset blastn" defval="unchecked" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	199 <label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	200 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	201 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	202 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	203 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	204 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	205 <li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	206 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	207 </li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	208 <li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	209 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	210 </li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	211 <li>Sequence Retrieval: Show buttons to download matching sequences.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	212 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	213 </li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	214 <li>NCBI-gi: Show NCBI gi identifiers.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	215 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	216 </li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	217 <li>CDS feature: Show annotated coding region and translation.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	218 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	219 </li></ul>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	220 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	221 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	222 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	223 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	224
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	225
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	226 <tr class="paramSet odd xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	227 <td class="hd"><label>Masking</label></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	228 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	229 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	230 <label for="MASK_CHAR"> Character: </label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	231 <select name="MASK_CHAR" id="MASK_CHAR" class="reset" defval="2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	232 <option value="0">X for protein, n for nucleotide</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	233 <option value="2" selected="selected">Lower Case</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	234 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	235 <label for="MASK_COLOR"> Color:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	236 <select name="MASK_COLOR" id="MASK_COLOR" class="reset" defval="1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	237 <option value="0">Black
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	238 </option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	239
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	240 <option value="1" selected="selected">Grey
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	241 </option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	242
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	243 <option value="2">Red
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	244 </option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	245
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	246 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	247 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	248 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	249 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	250 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	251 <li>Masking Character: Display masked (filtered) sequence regions as
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	252 lower-case or as specific letters (N for nucleotide, P for protein).
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	253 </li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	254 <li>Masking Color: Display masked sequence regions in the given color.</li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	255 </ul>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	256 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	257 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	258 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	259 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	260
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	261
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	262 <tr id="lr" class="paramSet xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	263 <td class="hd"><label>Limit results</label></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	264 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	265 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	266 <label for="FRM_DESCRIPTIONS">Descriptions:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	267 <select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defval="100">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	268
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	269 <option value="10">10</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	270 <option value="50">50</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	271 <option value="100" selected="selected">100</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	272
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	273
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	274
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	275
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	276
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	277
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	278 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	279
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	280 <label for="FRM_NUM_OVERVIEW">Graphical overview:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	281 <select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defval="100">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	282 <option value="0">0</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	283 <option value="10">10</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	284 <option value="50">50</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	285 <option value="100" selected="selected">100</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	286
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	287
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	288
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	289 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	290 <span class="hidden" id="frmAln">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	291 <label for="FRM_ALIGNMENTS">Alignments:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	292 <select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defval="100">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	293 <option value="0">0</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	294 <option value="10">10</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	295 <option value="50">50</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	296 <option value="100" selected="selected">100</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	297
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	298
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	299
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	300
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	301
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	302
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	303 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	304 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	305 <label for="FRM_LINE_LENGTH">Line length:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	306 <select name="LINE_LENGTH" id="FRM_LINE_LENGTH" class="reset" defval="60">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	307 <option value="60" selected="selected">60</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	308 <option value="90">90</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	309 <option value="120">120</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	310 <option value="150">150</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	311 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	312 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	313 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	314 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	315 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp5">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	316 <li>Descriptions: Show short descriptions for up to the given number of sequences.</li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	317 <li>Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.</li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	318 <li>Line lenghth: ....</li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	319 </ul>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	320 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	321 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	322 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	323 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	324
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	325 <tr class="paramSet odd xgl ">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	326 <td class="hd"></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	327 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	328 <div class="">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	329 <label for="qorganism">Organism</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	330 <span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	331 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	332 <input name="FORMAT_ORG_EXCLUDE" class="oExclR cb" id="orgExcl" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	333 <input value="1" name="FORMAT_NUM_ORG" id="numOrg" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	334 <label for="orgExcl" class="right">Exclude</label>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	335 <a href="#" title="Add organism" id="addOrg"><img src="NCBI%20Blast%20reference%20example_files/addOrg.jpg" id="addOrgIm" alt="Add organism" mouseovimg="css/images/addOrgOver.jpg" mouseoutimg="css/images/addOrg.jpg" mousedownimg="css/images/addOrgDown.jpg" mouseupimg="css/images/addOrgOver.jpg" border="0"></a>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	336 <div id="orgs">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	337
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	338 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	339 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	340 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	341 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	342 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	343 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp6">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	344 Show only sequences from the given organism.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	345 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	346 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	347 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	348 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	349 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	350 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	351
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	352 <tr class="paramSet xgl ">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	353 <td class="hd"></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	354 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	355 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	356 <label for="FORMAT_EQ_TEXT">Entrez query:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	357 <input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" class="reset" type="text">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	358 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	359 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	360 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	361 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp7">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	362 Show only those sequences that match the given Entrez query.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	363 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	364 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	365 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	366 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	367 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	368 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	369
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	370
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	371 <tr class="paramSet odd xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	372 <td class="hd"></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	373 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	374 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	375 <label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" class="reset" type="text">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	376 <label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" class="reset" type="text">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	377 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	378 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	379 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	380 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp8">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	381 Show only sequences with expect values in the given range.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	382 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	383 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	384 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	385 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	386 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	387 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	388 <tr class="paramSet xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	389 <td class="hd"></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	390 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	391 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	392 <label for="PERC_IDENT_LOW">Percent Identity Min:</label> <input name="PERC_IDENT_LOW" id="PERC_IDENT_LOW" size="10" class="reset" type="text">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	393 <label for="PERC_IDENT_HIGH">Percent Identity Max:</label> <input name="PERC_IDENT_HIGH" id="PERC_IDENT_HIGH" size="10" class="reset" type="text">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	394 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	395 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	396 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	397 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp10">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	398 Show only sequences with percent identity values in the given range.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	399 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	400 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	401 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	402 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	403 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	404 <tr class="psiBlast odd paramSet xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	405 <td class="hd"><label>Format for</label></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	406 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	407 <div class="fi">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	408 <input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" class="cb psiBlast" type="checkbox">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	409 <label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	410 <label for="I_THRESH">with inclusion threshold:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	411 <input name="I_THRESH" id="I_THRESH" size="10" defval="0.005" type="text">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	412 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	413 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	414 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	415 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp9">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	416 <li>Format for PSI-BLAST: The Position-Specific Iterated BLAST
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	417 (PSI-BLAST) program performs iterative searches with a protein query,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	418 in which sequences found in one round of search are used to build a
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	419 custom score model for the next round.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	420 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	421 </li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	422 <li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	423 by PSI-BLAST to create the PSSM on the next iteration.</li>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	424 </ul>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	425 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	426 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	427 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	428 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	429 </tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	430
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	431
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	432 <input name="ViewReport" value="ViewReport" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	433 <input name="REFORMAT_REPORT" value="shown" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	434 <input name="RID" value="PHWP1JNZ014" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	435 <input name="CDD_RID" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	436 <input name="CDD_SEARCH_STATE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	437
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	438 <input name="STEP_NUMBER" value="" id="stepNumber" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	439 <input name="CMD" value="Get" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	440 <input name="FORMAT_EQ_OP" value="AND" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	441 <input name="RESULTS_PAGE_TARGET" id="resPageTarget" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	442 <!-- <input name="QUERY_INFO" type="hidden" value="Nucleotide Sequence (16 letters)" /> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	443 <!-- <input name="ENTREZ_QUERY" type="hidden" value="" /> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	444 <input name="QUERY_INDEX" value="0" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	445 <input name="NUM_QUERIES" value="1" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	446 <input name="PHI_PTTRN_INDEX" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	447 <input id="cfcDsSave" name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	448 <!-- Those params are set in the template (blastn.dat, blastp.dat etc. -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	449 <input name="BLAST_PROGRAMS" value="blastn" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	450 <input name="PAGE" value="Nucleotides" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	451 <input name="PROGRAM" value="blastn" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	452 <input name="MEGABLAST" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	453 <input name="RUN_PSIBLAST" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	454 <input name="BLAST_SPEC" id="blastSpec" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	455
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	456
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	457 <input name="QUERY" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	458 <input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	459 <input name="QUERY_TO" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	460 <input name="QUERY_FROM" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	461 <input name="EQ_TEXT" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	462 <input name="ORGN" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	463 <input name="EQ_MENU" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	464 <input name="ORG_EXCLUDE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	465 <input name="PHI_PATTERN" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	466 <input name="EXPECT" value="1000" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	467 <input name="DATABASE" value="pdb" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	468 <input name="DB_GROUP" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	469 <input name="SUBGROUP_NAME" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	470
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	471 <input name="GENETIC_CODE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	472 <input name="WORD_SIZE" value="7" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	473 <input name="MATCH_SCORES" value="1,-3" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	474 <input name="MATRIX_NAME" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	475 <input name="GAPCOSTS" value="5 2" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	476 <input name="MAX_NUM_SEQ" id="maxNumSeq" value="100" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	477 <input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	478 <input name="NEWWIN" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	479 <input name="SHORT_QUERY_ADJUST" value="on" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	480 <input name="FILTER" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	481 <input name="REPEATS" value="repeat_9606" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	482 <input name="ID_FOR_PSSM" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	483 <input name="EXCLUDE_MODELS" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	484 <input name="EXCLUDE_SEQ_UNCULT" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	485 <input name="WP_PROTEINS" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	486 <input name="SEQ_FROM_TYPE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	487 <input name="ENTREZ_QUERY_PRESET" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	488 <input name="ENTREZ_QUERY_PRESET_EXCL" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	489 <input name="NUM_ORG" value="1" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	490
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	491 <!-- PSSM -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	492 <input name="LCASE_MASK" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	493 <input name="TEMPLATE_TYPE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	494 <input name="TEMPLATE_LENGTH" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	495 <input name="I_THRESH" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	496 <input name="PSI_PSEUDOCOUNT" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	497 <input name="DI_THRESH" id="diThresh" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	498 <input name="HSP_RANGE_MAX" value="0" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	499
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	500
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	501
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	502 <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	503 <input name="MIXED_QUERIES" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	504 <input name="MIXED_DATABASE" id="mixedDb" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	505 <input name="BUILD_NAME" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	506 <input name="ORG_DBS" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	507
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	508 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	509 </div> <!-- aria -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	510 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	511 <form aria-hidden="true" name="FormatDownload" id="FormatDownload" class="resbox ui-ncbitoggler-slave ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	512 <table class="options dwnl ">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	513 <tbody><tr><td class="frh" colspan="6"><div class="tb">Download</div></td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	514 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	515 <td id="tdal">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	516 <div class="dnHeader">Alignment</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	517 <div class="dnLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	518 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	519 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	520 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	521 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	522 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	523 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	524 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	525 <td class="dnl xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	526 <div class="dnHeader">Search Strategies</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	527 <div class="dnLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	528 <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on&RID=PHWP1JNZ014&DOWNLOAD_OPTIONS=true">ASN.1</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	529 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	530 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	531 <td class="dnl hidden" id="dnPSSMPar">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	532 <div class="dnHeader">PssmWithParameters</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	533 <div class="dnLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	534 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	535 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	536 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	537 <td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	538 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	539 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	540 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	541 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	542 </tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	543 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	544 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp11">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	545 The Download link provides BLAST output that may be used as input to
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	546 another program.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	547 This includes parseable formats such as the tabular report or XML as
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	548 well as the Search Strategy files read by the BLAST+ applications.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	549 More details on the parseable (XML, tabular, and ASN.1) reports can be
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	550 found at
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	551 <a href="http://www.ncbi.nlm.nih.gov/books/NBK21097/" target="helpWin">http://www.ncbi.nlm.nih.gov/books/NBK21097/</a><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	552 <br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	553 The following formats are offered under the Alignment section:<br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	554 1). "Text". Non-HTML standard BLAST report.<br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	555
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	556 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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	557
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	558 3). "ASN.1" Alignment. This is the alignment written out in Abstract Syntax Notation 1.<br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	559
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	560 4). "Hit Table(text)". The tabular report as text.<br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	561
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	562 5). "Hit Table(csv)". The tabular report ready for import into spread-sheet programs like Excel.<br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	563 <br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	564 The following report is offered under the Search Strategy section:<br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	565
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	566 1). "ASN.1" Search Strategy. A record of the parameters, query, and
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	567 database used in the search. This file can be used to start a
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	568 stand-alone BLAST search, see
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	569 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	570 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	571 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	572 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	573 </div> <!-- aria -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	574 <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" name="overview0">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	575 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	576 <input name="CMD" value="Get" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	577 <p id="qb"><!--
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	578 QBlastInfoBegin
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	579 Status=READY
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	580 QBlastInfoEnd
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	581 --></p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	582 <div id="page">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	583
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	584 <div id="summary" class="">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	585 <div id="ht"></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	586 <h1>Nucleotide Sequence (16 letters) <span id="hdTitle" class="shownInl"></span></h1>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	587 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	588 <div id="multipleSeqs" class="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	589 <label for="queryList">Results for:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	590 <select id="queryList" name="queryList">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	591 <option value="0" selected="selected" class="">lcl\|59987 None(16bp)</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	592 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	593 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	594 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	595 </div><!--/#multipleSeqs"-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	596
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	597 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	598 <p aria-hidden="true" id="queryInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	599 Your BLAST job specified more than one input sequence.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	600 This box lets you choose which input sequence to show BLAST results for.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	601 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	602 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	603 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	604 <div id="summarylists">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	605 <dl>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	606 <dt>RID</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	607 <dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	608 <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)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	609 </dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	610 </dl>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	611 <div id="querysummary">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	612 <dl>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	613 <dt>Query ID</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	614 <dd class="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	615 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	616 </dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	617 <dd class="">lcl\|59987</dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	618 <dt>Description</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	619 <dd>None</dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	620 <dt>Molecule type</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	621 <dd>nucleic acid</dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	622 <dt>Query Length</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	623 <dd>16</dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	624 </dl>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	625 </div><!--/#querysummary-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	626
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	627 <div id="dbsummary">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	628 <dl>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	629 <dt> </dt><dd> </dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	630 <dt>Database Name</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	631 <dd>pdb</dd>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	632 <dt>Description</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	633 <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 ---->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	634 <dt class="xgl">Program</dt>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	635 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	636 </dl>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	637 </div><!--/#dbsummary-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	638 </div><!--/#summarylists -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	639 <br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	640 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	641 <div aria-hidden="true" id="dbDetails" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	642 <!-- multiple databases or subjects table -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	643 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	644 </div> <!-- aria end -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	645 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	646 <div aria-hidden="true" id="refInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	647 <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9254694&dopt=Citation">Reference </a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	648 <div>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	649 Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	650 "Gapped BLAST and PSI-BLAST: a new generation of protein database search
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	651 programs", Nucleic Acids Res. 25:3389-3402.</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	652 </div> <!-- refInfo -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	653 </div> <!-- aria end -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	654
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	655 <div id="seealso">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	656 <label>Other reports:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	657 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	658 <span class="xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	659 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	660 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	661
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	662
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	663
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	664 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	665 </div> <!-- seealso -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	666
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	667 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	668 <div aria-hidden="true" id="resStat" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	669 <table id="params" class="dbInfo">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	670 <caption>Search Parameters</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	671 <tbody><tr><th><div>Search parameter name</div></th><th><div>Search parameter value</div></th></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	672 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	673 </tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	674 <table id="dbStat" class="dbInfo">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	675 <caption>Database</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	676 <tbody><tr><th><div>Database parameter name</div></th><th><div>Database parameter value</div></th></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	677 <tr><td>Posted date</td><td>Apr 29, 2014 3:14 AM</td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	678 <tr><td>Number of letters</td><td>885,284</td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	679 <tr><td>Number of sequences</td><td>8,975</td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	680 <tr><td>Entrez query</td><td>none</td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	681 </tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	682
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	683 <table id="Kappa" class="dbInfo show xgl">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	684 <caption>Karlin-Altschul statistics</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	685 <tbody><tr><th><div>Params</div></th><th><div>Ungapped</div></th><th><div>Gapped</div></th></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	686 <tr><td>Lambda</td><td>1.37406</td><td>1.37406</td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	687 <tr><td>K</td><td>0.710603</td><td>0.710603</td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	688 <tr><td>H</td><td>1.30725</td><td>1.30725</td></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	689
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	690 </tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	691
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	692
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	693 <table class="dbInfo show">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	694 <caption>Results Statistics</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	695 <tbody><tr><th><div>Results Statistics parameter name</div></th><th><div>Results Statistics parameter value</div></th></tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	696 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	697 </tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	698 <!-- Results statistics -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	699 </div> <!-- resStat -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	700 </div> <!-- aria end -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	701 </div><!--/#summary-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	702 </div><!--/#page-->
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	703 <iframe id="RSIFrameDesc" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="NCBI%20Blast%20reference%20example_files/plinkcgi.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	704
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	705 <div id="grView" class="hidden shown">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	706 <h2 class="resArr">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	707 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	708 <span class="ui-ncbitoggler-master-text">Graphic Summary</span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	709 <span class="ui-icon ui-icon-plus-minus-big-open"></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	710 </a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	711 </h2>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	712 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	713 <div aria-hidden="false" id="graphicInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	714
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	715
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	716 <div id="graphic" class="hidden shown">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	717 <h3>Distribution of 45 Blast Hits on the Query Sequence
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	718 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	719 <span class="ui-icon ui-icon-triangle-1-e"></span></a></h3>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	720 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	721 <p aria-hidden="true" id="ovrInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	722 An overview of the database sequences aligned to the query sequence is
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	723 shown. The score of each alignment is indicated by one of five
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	724 different colors, which divides the range of scores into five groups.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	725 Multiple alignments on the same database sequence are connected
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	726 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,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	727 <span class="hl">clicking</span> on a hit sequence takes the user to the associated alignments.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	728 New:
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	729 This graphic is an overview of database sequences aligned to the query sequence.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	730 Alignments are color-coded by score, within one of five score ranges.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	731 Multiple alignments on the same database sequence are connected by a dashed line.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	732 <span class="hl">Mousing</span> over an alignment shows the alignment definition and score in the box at the top.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	733 <span class="hl">Clicking</span> an alignment displays the alignment detail.
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	734 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	735 </div><!-- ARIA -->
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	736 <center><input name="defline" size="85" value="Mouse-over to show defline and scores, click to show alignments" type="text"><table bordercolordark="#0000FF" bordercolorlight="#0000FF" border="1" cellpadding="10" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	737 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/score.gif" height="40" width="500"></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	738 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	739 <table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/query_no_scale.gif" height="10" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	740 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="51"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	741 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	742 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	743 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	744 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	745 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	746 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	747 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	748 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	749 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	750 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	751 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	752 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	753 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	754 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	755 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	756 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/3.gif" height="13" width="10"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	757 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	758 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/6.gif" height="13" width="10"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	759 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	760 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/9.gif" height="13" width="10"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	761 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="73"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	762 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	763 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/2.gif" height="13" width="10"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	764 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="73"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	765 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	766 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/5.gif" height="13" width="10"></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	767 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	768 <br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	769 <td align="LEFT" valign="CENTER"><a href="#557804451" onclick='DisplayAlignFromGraphics("557804451",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J5A_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	770 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	771 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	772 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	773 <td align="LEFT" valign="CENTER"><a href="#557804395" onclick='DisplayAlignFromGraphics("557804395",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J58_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	774 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	775 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	776 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	777 <td align="LEFT" valign="CENTER"><a href="#557804339" onclick='DisplayAlignFromGraphics("557804339",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J56_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	778 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	779 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	780 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	781 <td align="LEFT" valign="CENTER"><a href="#557804283" onclick='DisplayAlignFromGraphics("557804283",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J54_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	782 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	783 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	784 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	785 <td align="LEFT" valign="CENTER"><a href="#557804227" onclick='DisplayAlignFromGraphics("557804227",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J52_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	786 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	787 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	788 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	789 <td align="LEFT" valign="CENTER"><a href="#557804195" onclick='DisplayAlignFromGraphics("557804195",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J51_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	790 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	791 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	792 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	793 <td align="LEFT" valign="CENTER"><a href="#557804163" onclick='DisplayAlignFromGraphics("557804163",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J50_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	794 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	795 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	796 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	797 <td align="LEFT" valign="CENTER"><a href="#557804083" onclick='DisplayAlignFromGraphics("557804083",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J4X_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	798 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	799 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	800 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	801 <td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="250"></a></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	802 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	803 <td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	804 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	805 <td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	806 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	807 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	808 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	809 <td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 14" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=14 E=1.9e+02'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="219"></a></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	810 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	811 <td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="155"></a></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	812 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	813 <td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	814 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	815 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	816 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	817 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="94"></td>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	818 <td align="LEFT" valign="CENTER"><a href="#357380483" onclick='DisplayAlignFromGraphics("357380483",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J0O_8 Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex .. S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="281"></a></td>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	819 </tr></tbody></table>
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	820 <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	821 </td></tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	822 </center><hr>
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bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	827 <!--HITMATRIX_VIEW - only for bl2seq -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	828
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	829 <div id="dscrView" class="hidden shown">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	830 <h2 class="resArr">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	831 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	832 <span class="ui-ncbitoggler-master-text">Descriptions</span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	833 <span class="ui-icon ui-icon-plus-minus-big-open"></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	834 </a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	835 </h2>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	836 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	837 <div aria-hidden="false" id="descrInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	838 <!-- legend to links to other resources -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	839 <a name="sort_mark"></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	840
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	841
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	842 <div id="debug">, Reading indexes 1-5, displaying indexes 1-5</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	843 <input id="Rid" value="PHWP1JNZ014" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	844 <input id="useAlignDB" name="useAlignDB" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	845 <input id="dbType" value="GenBank" type="hidden"><!-- Indicates genbank, etc -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	846 <input id="serviceType" value="plain" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	847 <input id="clientType" value="web" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	848 <input id="currQuery" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	849 <input id="minDispAlnLen" value="2000" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	850 <input id="maxDispAlnLen" value="20000" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	851 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	852 <div id="descriptions" class="blRes">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	853 <!--<pre> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	854 <div class="cap">Sequences producing significant alignments:</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	855 <a id="shcl" href="#" onclick="showAllCol(event,this)" class="shcl hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	856 Show all columns <span class="accsb"> of the table presenting sequences producing significant alignments </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	857 </a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	858 <span id="cntDesc">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	859 <span>Select:<a href="#" id="cntSelA" sel="all">All</a><a href="#" id="cntSelN" sel="n">None</a></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	860 <span>Selected:<span id="slcNum">0</span></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	861 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	862
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	863 <div id="descTblCtrl" class="cnf">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	864 <a href="#alignInfo" id="alnNav" class="toolsCtr alnNav" title="Go to alignments"><span>Alignments</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	865 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	866
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	867 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	868 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	869 <div class=""><input name="dwn" id="dwFSTAl" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl">FASTA (aligned sequences)</label></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	870 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	871 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	872 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	873 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	874 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	875 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	876 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	877 <button class="cfg" id="dw_cont">Continue</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	878 <button class="cfg cnc">Cancel</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	879 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	880 </div> <!-- dsDownload -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	881
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	882
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	883
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	884
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	885
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	886 <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 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	887 <a href="#" class="toolsCtr " minslct="1" view="graph" title="See graphic representation for selected sequences" disabled="disabled">Graphics</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	888 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	889 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	890
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	891 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	892
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	893 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	894 <div class="tl">Available columns</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	895 <input checked="checked" id="chkDs" value="2" type="checkbox"><label class="shownInl" for="chkDs">Description</label><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	896 <input checked="checked" id="chkMS" value="3" type="checkbox"><label class="shownInl" for="chkMs">Max Score</label><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	897 <input checked="checked" id="chkTS" value="4" type="checkbox"><label class="shownInl" for="chkTs">Total Score</label><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	898 <input checked="checked" id="chkCov" value="5" type="checkbox"><label class="shownInl" for="chkCov">Coverage</label><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	899 <input checked="checked" id="chkEval" value="6" type="checkbox"><label class="shownInl" for="chkEval">E-value</label><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	900 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	901 <input checked="checked" id="chkAcc" value="8" type="checkbox"><label class="shownInl" for="chkAcc">Accession</label><br>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	902 <button class="cfg rdf" id="dscRsDf">Restore Defaults</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	903 <button class="cfg" id="dscOk">Ok</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	904 <button class="cfg cnc" id="dscCnc">Cancel</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	905 </div> <!-- dsConfig -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	906
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	907 <input id="cfcDsInf" defval="2,3,4,5,6,7,8" value="2,3,4,5,6,7,8" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	908 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	909 <div class="ui-ncbigrid-outer-div caption-exists">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	910 <div class="ui-ncbigrid-inner-div">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	911 <table id="dscTable" class="jig-ncbigrid ui-ncbigrid" data-jigconfig="" cellpadding="0" cellspacing="0">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	912 <caption class="hdnHeader">Sequences producing significant alignments:</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	913 <thead>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	914 <tr class="first">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	915 <th class="c0" id="c0"><span>Select for downloading or viewing reports</span></th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	916 <th class="dflnDth c2" id="c2">Description</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	917 <th class=" c3" id="c3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	918
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	919 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	920 </th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	921 <th class=" c4" id="c4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	922 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	923 </th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	924 <th class=" c5" id="c5">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	925 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	926 </th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	927 <th class="sel c6" id="c6">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	928 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	929 </th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	930 <th class="c7" id="c7">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	931 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	932 </th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	933
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	934 <th class="c1" id="c8">Accession</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	935 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	936 </thead>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	937 <tbody>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	938 <tr id="dtr_557804451" ind="1" class="odd dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	939 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	940 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	941 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	942 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	943 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	944 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	945 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	946 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	947 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	948 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	949 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	950 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	951 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	952 </tr><tr id="dtr_557804395" ind="2" class="even dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	953 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	954 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	955 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	956 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	957 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	958 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	959 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	960 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	961 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	962 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	963 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	964 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	965 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	966 </tr><tr id="dtr_557804339" ind="3" class="odd dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	967 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	968 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	969 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	970 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	971 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	972 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	973 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	974 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	975 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	976 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	977 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	978 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	979 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	980 </tr><tr id="dtr_557804283" ind="4" class="even dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	981 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	982 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	983 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	984 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	985 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	986 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	987 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	988 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	989 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	990 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	991 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	992 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	993 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	994 </tr><tr id="dtr_557804227" ind="5" class="odd dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	995 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	996 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	997 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	998 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	999 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1000 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1001 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1002 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1003 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1004 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1005 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1006 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1007 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1008 </tr><tr id="dtr_557804195" ind="6" class="even dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1009 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1010 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1011 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1012 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1013 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1014 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1015 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1016 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1017 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1018 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1019 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1020 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1021 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1022 </tr><tr id="dtr_557804163" ind="7" class="odd dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1023 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1024 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1025 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1026 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1027 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1028 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1029 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1030 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1031 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1032 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1033 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1034 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1035 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1036 </tr><tr id="dtr_557804083" ind="8" class="even dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1037 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1038 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1039 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1040 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1041 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1042 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1043 <td class="c3">32.2</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1044 <td class="c4">77.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1045 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1046 <td class="c6">8e-04</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1047 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1048 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1049 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1050 </tr><tr id="dtr_485601478" ind="9" class="odd dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1051 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1052 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1053 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1054 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1055 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1056 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1057 <td class="c3">18.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1058 <td class="c4"> 128</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1059 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1060 <td class="c6"> 12</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1061 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1062 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1063 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1064 </tr><tr id="dtr_485601474" ind="10" class="even dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1065 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1066 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1067 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1068 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1069 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1070 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1071 <td class="c3">18.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1072 <td class="c4">63.4</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1073 <td class="c5">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1074 <td class="c6"> 12</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1075 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1076 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1077 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1078 </tr><tr id="dtr_357380483" ind="11" class="odd dflLnk">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1079 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1080 <td class="lim l c2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1081 <div class="lim n">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1082 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1083 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1084 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1085 <td class="c3">18.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1086 <td class="c4">18.3</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1087 <td class="c5">56%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1088 <td class="c6"> 12</td><td class="c7">100%</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1089 <td class="c1 l lim">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1090 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1091 </td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1092 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1093 </tbody>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1094 </table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1095 </div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1096 <!--</pre> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1097 </div><!--/#descriptions-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1098 </div><!-- descrInfo -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1099 </div><!--ARIA-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1100 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1101 </form><!-- this is the end tag for the <form in blastcgi templates -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1102 <form id="dwdlSubmit" action="" method="post" class="getseq">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1103 <input name="" value="" id="selDnSeqs" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1104 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1105 <form class="getseq" method="post" seqsform="getSeqAlignment1" action="http://www.ncbi.nlm.nih.gov/sites/entrez" target="lnkPHWP1JNZ014" id="submitterTop">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1106 <input name="db" value="Nucleotide" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1107 <input id="selSeqs" name="term" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1108 <input name="doptcmdl" value="docsum" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1109 <input name="cmd" value="search" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1110 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1111 <form class="getseq" method="get" action="http://www.ncbi.nlm.nih.gov/projects/sviewer/" target="lnkPHWP1JNZ014" id="sbmtGraphics">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1112 <input id="ridParam" value="PHWP1JNZ014" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1113 <input id="seqViewParams" name="RID" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1114 <input name="appname" value="ncbiblast" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1115 <input name="link_loc" value="fromDescr" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1116 <input name="tracks" value="[key:sequence_track,ShowLabel:true]" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1117 <input name="id" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1118 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1119 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1120 <input id="selSeqsTr" name="sequenceSet" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1121 <input id="scrWidth" name="screenWidth" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1122 <input id="scrHeight" name="screenHeight" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1123 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1124 <form class="getseq" method="post" action="?CMD=submit&blastRID=PHWP1JNZ014&queryID=lcl\|59987&numSeqs=100" id="sbmtMultiAln" target="lnkPHWP1JNZ014">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1125 <input id="selSeqsMl" name="sequenceSet" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1126 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1127 <form class="getseq" enctype="text/plain" method="post" action="http://blast.ncbi.nlm.nih.gov/blast/SEQDUMP/seqdump.cgi" id="sbmtFASTA">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1128 <input name="RID" value="PHWP1JNZ014" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1129 <input name="DATABASE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1130 <input name="ALIGNDB_BATCH_ID" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1131 <input name="ALIGNDB_MASTER_ALIAS" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1132 <input name="ALIGNDB_CGI_HOST" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1133 <input name="ALIGNDB_CGI_PATH" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1134 <input name="SERVICE_TYPE" value="plain" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1135 <input name="DBTYPE" value="nucl" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1136 <input name="DOWNLOAD_TYPE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1137 <input name="ALIGN_SEQ_LIST" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1138 </form><!-- used in redesign -->
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	1139 <iframe id="RSIFrameAln" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="NCBI%20Blast%20reference%20example_files/plinkcgi_002.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1140 <div id="alignView" class=" ">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1141 <h2 class="resArr">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1142 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1143 <span class="ui-ncbitoggler-master-text">Alignments</span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1144 <span class="ui-icon ui-icon-plus-minus-big-open"></span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1145 </a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1146 </h2>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1147
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1148 <div class="ui-helper-reset" aria-live="assertive">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1149 <div aria-hidden="false" id="alignInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1150 <div id="alignments" class="blRes">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1151 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1152 <div class="alnHdr cnf" id="alnHdr_557804451" seqid="557804451" accs="pdb\|3J5A\|A">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1153 <a name="557804451"></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1154 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1155 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1156 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1157 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1158 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1159 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1160 <button class="cfg" id="dw_cont_557804451">Continue</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1161 <button class="cfg cnc">Cancel</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1162 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1163 </div> <!-- dsDownload -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1164 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1165
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1166 <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1167 <select id="sa_557804451" onchange="SortHSPAlnSel(event,this)">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1168 <option selected="selected" value="0">E value</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1169 <option value="1"> Score</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1170 <option value="3">Percent identity</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1171 <option value="2">Query start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1172 <option value="4">Subject start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1173 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1174 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1175 <span class="alnSeqLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1176 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1177 <a disabled="disabled" class="gbd toolsCtr navPrev" ref="ordinalpos=1&currseq=557804451" id="alnPrv_557804451" onclick="goToNextAlign('dtr_557804451',false);"><span>Previous</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1178 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1179 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1180 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1181 <div class="oneSeqAln" id="aln_557804451">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1182 <div id="dln_557804451">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1183 <div class="dlfRow">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1184 Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1185 <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb\|3J5A\|A">pdb\|3J5A\|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1186 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1187 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1188 <div class="relInf" id="relInf_557804451"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1189 <!--
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1190 <pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1191 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1192 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1193 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1194 <div class="alnAll" id="alnAll_557804451"><div id="hd_557804451_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1195 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1196 <span id="hsp557804451_1" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1197 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1198 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1199 <a class="gbd toolsCtr navBack hidden" href="#hsp557804451_1" title="Go to first match for pdb\|3J5A\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1200 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1201 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1202 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1203 <caption class="hdnHeader">Alignment statistics for match #1</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1204 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1205 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1206 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1207 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1208 <td>32.2 bits(16)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1209 <td>8e-04<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1210 <td>16/16(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1211 <td>0/16(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1212 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1213 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1214 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1215 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1216 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1217 <div id="ar_557804451_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1218 <pre>Query 1 CGTCCGTCGTGAAGAG 16
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1219 \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1220 Sbjct 961 CGTCCGTCGTGAAGAG 976
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1221
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1222
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1223 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1224 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1225 <div id="hd_557804451_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1226 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1227 <span id="hsp557804451_2" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1228 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1229 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1230 <a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb\|3J5A\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1231 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1232 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1233 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1234 <caption class="hdnHeader">Alignment statistics for match #2</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1235 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1236 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1237 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1238 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1239 <td>16.4 bits(8)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1240 <td> 47<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1241 <td>8/8(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1242 <td>0/8(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1243 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1244 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1245 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1246 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1247 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1248 <div id="ar_557804451_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1249 <pre>Query 5 CGTCGTGA 12
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1250 \|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1251 Sbjct 2591 CGTCGTGA 2598
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1252
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1253
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1254 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1255 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1256 <div id="hd_557804451_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1257 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1258 <span id="hsp557804451_3" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1259 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1260 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1261 <a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb\|3J5A\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1262 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1263 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1264 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1265 <caption class="hdnHeader">Alignment statistics for match #3</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1266 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1267 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1268 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1269 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1270 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1271 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1272 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1273 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1274 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1275 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1276 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1277 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1278 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1279 <div id="ar_557804451_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1280 <pre>Query 7 TCGTGAA 13
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1281 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1282 Sbjct 839 TCGTGAA 845
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1283
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1284
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1285 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1286 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1287 <div id="hd_557804451_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1288 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1289 <span id="hsp557804451_4" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1290 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1291 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1292 <a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb\|3J5A\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1293 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1294 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1295 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1296 <caption class="hdnHeader">Alignment statistics for match #4</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1297 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1298 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1299 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1300 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1301 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1302 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1303 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1304 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1305 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1306 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1307 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1308 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1309 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1310 <div id="ar_557804451_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1311 <pre>Query 9 GTGAAGA 15
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1312 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1313 Sbjct 2027 GTGAAGA 2033
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1314
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1315
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1316 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1317 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1318 </div> <!-- alnAll_557804451 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1319 </div> <!-- aln_557804451 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1320 <div class="alnHdr cnf" id="alnHdr_557804395" seqid="557804395" accs="pdb\|3J58\|A">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1321 <a name="557804395"></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1322 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1323 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1324 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1325 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1326 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1327 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1328 <button class="cfg" id="dw_cont_557804395">Continue</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1329 <button class="cfg cnc">Cancel</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1330 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1331 </div> <!-- dsDownload -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1332 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1333
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1334 <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1335 <select id="sa_557804395" onchange="SortHSPAlnSel(event,this)">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1336 <option selected="selected" value="0">E value</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1337 <option value="1"> Score</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1338 <option value="3">Percent identity</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1339 <option value="2">Query start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1340 <option value="4">Subject start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1341 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1342 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1343 <span class="alnSeqLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1344 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1345 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1346 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1347 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1348 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1349 <div class="oneSeqAln" id="aln_557804395">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1350 <div id="dln_557804395">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1351 <div class="dlfRow">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1352 Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1353 <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb\|3J58\|A">pdb\|3J58\|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1354 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1355 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1356 <div class="relInf" id="relInf_557804395"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1357 <!--
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1358 <pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1359 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1360 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1361 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1362 <div class="alnAll" id="alnAll_557804395"><div id="hd_557804395_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1363 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1364 <span id="hsp557804395_1" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1365 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1366 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1367 <a class="gbd toolsCtr navBack hidden" href="#hsp557804395_1" title="Go to first match for pdb\|3J58\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1368 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1369 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1370 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1371 <caption class="hdnHeader">Alignment statistics for match #1</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1372 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1373 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1374 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1375 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1376 <td>32.2 bits(16)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1377 <td>8e-04<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1378 <td>16/16(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1379 <td>0/16(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1380 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1381 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1382 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1383 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1384 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1385 <div id="ar_557804395_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1386 <pre>Query 1 CGTCCGTCGTGAAGAG 16
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1387 \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1388 Sbjct 961 CGTCCGTCGTGAAGAG 976
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1389
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1390
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1391 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1392 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1393 <div id="hd_557804395_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1394 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1395 <span id="hsp557804395_2" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1396 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1397 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1398 <a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb\|3J58\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1399 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1400 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1401 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1402 <caption class="hdnHeader">Alignment statistics for match #2</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1403 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1404 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1405 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1406 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1407 <td>16.4 bits(8)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1408 <td> 47<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1409 <td>8/8(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1410 <td>0/8(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1411 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1412 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1413 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1414 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1415 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1416 <div id="ar_557804395_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1417 <pre>Query 5 CGTCGTGA 12
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1418 \|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1419 Sbjct 2591 CGTCGTGA 2598
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1420
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1421
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1422 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1423 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1424 <div id="hd_557804395_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1425 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1426 <span id="hsp557804395_3" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1427 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1428 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1429 <a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb\|3J58\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1430 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1431 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1432 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1433 <caption class="hdnHeader">Alignment statistics for match #3</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1434 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1435 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1436 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1437 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1438 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1439 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1440 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1441 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1442 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1443 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1444 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1445 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1446 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1447 <div id="ar_557804395_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1448 <pre>Query 7 TCGTGAA 13
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1449 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1450 Sbjct 839 TCGTGAA 845
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1451
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1452
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1453 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1454 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1455 <div id="hd_557804395_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1456 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1457 <span id="hsp557804395_4" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1458 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1459 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1460 <a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb\|3J58\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1461 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1462 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1463 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1464 <caption class="hdnHeader">Alignment statistics for match #4</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1465 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1466 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1467 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1468 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1469 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1470 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1471 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1472 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1473 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1474 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1475 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1476 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1477 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1478 <div id="ar_557804395_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1479 <pre>Query 9 GTGAAGA 15
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1480 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1481 Sbjct 2027 GTGAAGA 2033
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1482
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1483
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1484 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1485 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1486 </div> <!-- alnAll_557804395 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1487 </div> <!-- aln_557804395 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1488 <div class="alnHdr cnf" id="alnHdr_557804339" seqid="557804339" accs="pdb\|3J56\|A">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1489 <a name="557804339"></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1490 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1491 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1492 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1493 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1494 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1495 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1496 <button class="cfg" id="dw_cont_557804339">Continue</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1497 <button class="cfg cnc">Cancel</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1498 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1499 </div> <!-- dsDownload -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1500 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1501
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1502 <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1503 <select id="sa_557804339" onchange="SortHSPAlnSel(event,this)">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1504 <option selected="selected" value="0">E value</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1505 <option value="1"> Score</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1506 <option value="3">Percent identity</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1507 <option value="2">Query start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1508 <option value="4">Subject start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1509 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1510 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1511 <span class="alnSeqLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1512 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1513 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1514 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1515 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1516 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1517 <div class="oneSeqAln" id="aln_557804339">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1518 <div id="dln_557804339">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1519 <div class="dlfRow">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1520 Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1521 <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb\|3J56\|A">pdb\|3J56\|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1522 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1523 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1524 <div class="relInf" id="relInf_557804339"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1525 <!--
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1526 <pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1527 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1528 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1529 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1530 <div class="alnAll" id="alnAll_557804339"><div id="hd_557804339_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1531 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1532 <span id="hsp557804339_1" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1533 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1534 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1535 <a class="gbd toolsCtr navBack hidden" href="#hsp557804339_1" title="Go to first match for pdb\|3J56\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1536 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1537 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1538 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1539 <caption class="hdnHeader">Alignment statistics for match #1</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1540 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1541 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1542 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1543 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1544 <td>32.2 bits(16)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1545 <td>8e-04<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1546 <td>16/16(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1547 <td>0/16(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1548 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1549 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1550 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1551 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1552 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1553 <div id="ar_557804339_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1554 <pre>Query 1 CGTCCGTCGTGAAGAG 16
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1555 \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1556 Sbjct 961 CGTCCGTCGTGAAGAG 976
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1557
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1558
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1559 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1560 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1561 <div id="hd_557804339_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1562 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1563 <span id="hsp557804339_2" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1564 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1565 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1566 <a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb\|3J56\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1567 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1568 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1569 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1570 <caption class="hdnHeader">Alignment statistics for match #2</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1571 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1572 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1573 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1574 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1575 <td>16.4 bits(8)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1576 <td> 47<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1577 <td>8/8(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1578 <td>0/8(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1579 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1580 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1581 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1582 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1583 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1584 <div id="ar_557804339_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1585 <pre>Query 5 CGTCGTGA 12
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1586 \|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1587 Sbjct 2591 CGTCGTGA 2598
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1588
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1589
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1590 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1591 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1592 <div id="hd_557804339_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1593 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1594 <span id="hsp557804339_3" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1595 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1596 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1597 <a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb\|3J56\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1598 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1599 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1600 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1601 <caption class="hdnHeader">Alignment statistics for match #3</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1602 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1603 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1604 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1605 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1606 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1607 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1608 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1609 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1610 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1611 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1612 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1613 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1614 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1615 <div id="ar_557804339_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1616 <pre>Query 7 TCGTGAA 13
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1617 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1618 Sbjct 839 TCGTGAA 845
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1619
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1620
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1621 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1622 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1623 <div id="hd_557804339_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1624 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1625 <span id="hsp557804339_4" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1626 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1627 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1628 <a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb\|3J56\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1629 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1630 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1631 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1632 <caption class="hdnHeader">Alignment statistics for match #4</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1633 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1634 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1635 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1636 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1637 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1638 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1639 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1640 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1641 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1642 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1643 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1644 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1645 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1646 <div id="ar_557804339_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1647 <pre>Query 9 GTGAAGA 15
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1648 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1649 Sbjct 2027 GTGAAGA 2033
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1650
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1651
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1652 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1653 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1654 </div> <!-- alnAll_557804339 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1655 </div> <!-- aln_557804339 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1656 <div class="alnHdr cnf" id="alnHdr_557804283" seqid="557804283" accs="pdb\|3J54\|A">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1657 <a name="557804283"></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1658 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1659 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1660 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1661 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1662 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1663 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1664 <button class="cfg" id="dw_cont_557804283">Continue</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1665 <button class="cfg cnc">Cancel</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1666 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1667 </div> <!-- dsDownload -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1668 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1669
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1670 <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1671 <select id="sa_557804283" onchange="SortHSPAlnSel(event,this)">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1672 <option selected="selected" value="0">E value</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1673 <option value="1"> Score</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1674 <option value="3">Percent identity</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1675 <option value="2">Query start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1676 <option value="4">Subject start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1677 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1678 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1679 <span class="alnSeqLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1680 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1681 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1682 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1683 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1684 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1685 <div class="oneSeqAln" id="aln_557804283">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1686 <div id="dln_557804283">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1687 <div class="dlfRow">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1688 Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1689 <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb\|3J54\|A">pdb\|3J54\|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1690 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1691 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1692 <div class="relInf" id="relInf_557804283"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1693 <!--
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1694 <pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1695 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1696 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1697 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1698 <div class="alnAll" id="alnAll_557804283"><div id="hd_557804283_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1699 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1700 <span id="hsp557804283_1" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1701 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1702 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1703 <a class="gbd toolsCtr navBack hidden" href="#hsp557804283_1" title="Go to first match for pdb\|3J54\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1704 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1705 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1706 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1707 <caption class="hdnHeader">Alignment statistics for match #1</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1708 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1709 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1710 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1711 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1712 <td>32.2 bits(16)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1713 <td>8e-04<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1714 <td>16/16(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1715 <td>0/16(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1716 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1717 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1718 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1719 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1720 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1721 <div id="ar_557804283_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1722 <pre>Query 1 CGTCCGTCGTGAAGAG 16
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1723 \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1724 Sbjct 961 CGTCCGTCGTGAAGAG 976
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1725
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1726
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1727 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1728 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1729 <div id="hd_557804283_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1730 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1731 <span id="hsp557804283_2" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1732 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1733 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1734 <a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb\|3J54\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1735 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1736 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1737 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1738 <caption class="hdnHeader">Alignment statistics for match #2</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1739 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1740 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1741 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1742 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1743 <td>16.4 bits(8)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1744 <td> 47<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1745 <td>8/8(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1746 <td>0/8(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1747 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1748 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1749 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1750 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1751 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1752 <div id="ar_557804283_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1753 <pre>Query 5 CGTCGTGA 12
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1754 \|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1755 Sbjct 2591 CGTCGTGA 2598
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1756
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1757
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1758 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1759 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1760 <div id="hd_557804283_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1761 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1762 <span id="hsp557804283_3" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1763 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1764 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1765 <a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb\|3J54\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1766 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1767 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1768 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1769 <caption class="hdnHeader">Alignment statistics for match #3</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1770 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1771 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1772 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1773 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1774 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1775 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1776 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1777 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1778 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1779 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1780 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1781 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1782 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1783 <div id="ar_557804283_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1784 <pre>Query 7 TCGTGAA 13
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1785 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1786 Sbjct 839 TCGTGAA 845
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1787
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1788
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1789 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1790 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1791 <div id="hd_557804283_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1792 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1793 <span id="hsp557804283_4" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1794 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1795 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1796 <a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb\|3J54\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1797 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1798 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1799 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1800 <caption class="hdnHeader">Alignment statistics for match #4</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1801 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1802 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1803 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1804 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1805 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1806 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1807 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1808 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1809 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1810 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1811 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1812 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1813 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1814 <div id="ar_557804283_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1815 <pre>Query 9 GTGAAGA 15
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1816 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1817 Sbjct 2027 GTGAAGA 2033
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1818
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1819
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1820 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1821 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1822 </div> <!-- alnAll_557804283 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1823 </div> <!-- aln_557804283 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1824 <div class="alnHdr cnf" id="alnHdr_557804227" seqid="557804227" accs="pdb\|3J52\|A">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1825 <a name="557804227"></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1826 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1827 <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">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1828 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1829 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1830 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1831 <div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1832 <button class="cfg" id="dw_cont_557804227">Continue</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1833 <button class="cfg cnc">Cancel</button>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1834 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1835 </div> <!-- dsDownload -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1836 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1837
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1838 <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1839 <select id="sa_557804227" onchange="SortHSPAlnSel(event,this)">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1840 <option selected="selected" value="0">E value</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1841 <option value="1"> Score</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1842 <option value="3">Percent identity</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1843 <option value="2">Query start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1844 <option value="4">Subject start position</option>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1845 </select>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1846 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1847 <span class="alnSeqLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1848 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1849 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1850 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1851 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1852 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1853 <div class="oneSeqAln" id="aln_557804227">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1854 <div id="dln_557804227">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1855 <div class="dlfRow">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1856 Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1857 <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb\|3J52\|A">pdb\|3J52\|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1858 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1859 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1860 <div class="relInf" id="relInf_557804227"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1861 <!--
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1862 <pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1863 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1864 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1865 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1866 <div class="alnAll" id="alnAll_557804227"><div id="hd_557804227_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1867 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1868 <span id="hsp557804227_1" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1869 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1870 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1871 <a class="gbd toolsCtr navBack hidden" href="#hsp557804227_1" title="Go to first match for pdb\|3J52\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1872 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1873 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1874 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1875 <caption class="hdnHeader">Alignment statistics for match #1</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1876 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1877 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1878 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1879 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1880 <td>32.2 bits(16)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1881 <td>8e-04<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1882 <td>16/16(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1883 <td>0/16(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1884 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1885 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1886 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1887 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1888 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1889 <div id="ar_557804227_1">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1890 <pre>Query 1 CGTCCGTCGTGAAGAG 16
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1891 \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1892 Sbjct 961 CGTCCGTCGTGAAGAG 976
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1893
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1894
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1895 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1896 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1897 <div id="hd_557804227_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1898 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1899 <span id="hsp557804227_2" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1900 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1901 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1902 <a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb\|3J52\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1903 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1904 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1905 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1906 <caption class="hdnHeader">Alignment statistics for match #2</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1907 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1908 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1909 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1910 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1911 <td>16.4 bits(8)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1912 <td> 47<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1913 <td>8/8(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1914 <td>0/8(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1915 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1916 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1917 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1918 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1919 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1920 <div id="ar_557804227_2">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1921 <pre>Query 5 CGTCGTGA 12
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1922 \|\|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1923 Sbjct 2591 CGTCGTGA 2598
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1924
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1925
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1926 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1927 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1928 <div id="hd_557804227_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1929 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1930 <span id="hsp557804227_3" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1931 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1932 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1933 <a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb\|3J52\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1934 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1935 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1936 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1937 <caption class="hdnHeader">Alignment statistics for match #3</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1938 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1939 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1940 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1941 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1942 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1943 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1944 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1945 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1946 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1947 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1948 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1949 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1950 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1951 <div id="ar_557804227_3">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1952 <pre>Query 7 TCGTGAA 13
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1953 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1954 Sbjct 839 TCGTGAA 845
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1955
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1956
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1957 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1958 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1959 <div id="hd_557804227_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1960 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1961 <span id="hsp557804227_4" class="alnParLinks">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1962 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1963 <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>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1964 <a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb\|3J52\|A"><span>First Match</span></a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1965 </span>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1966 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1967 <table class="alnParams">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1968 <caption class="hdnHeader">Alignment statistics for match #4</caption>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1969 <tbody><tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1970 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1971 </tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1972 <tr>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1973 <td>14.4 bits(7)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1974 <td> 186<span class="sumN ">()</span></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1975 <td>7/7(100%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1976 <td>0/7(0%)</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1977 <td>Plus/Plus</td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1978 <td class="aln_frame "></td>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1979 </tr></tbody></table>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1980 <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1981 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1982 <div id="ar_557804227_4">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1983 <pre>Query 9 GTGAAGA 15
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1984 \|\|\|\|\|\|\|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1985 Sbjct 2027 GTGAAGA 2033
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1986
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1987
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1988 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1989 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1990 </div> <!-- alnAll_557804227 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1991 </div> <!-- aln_557804227 -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1992 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1993
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1994 </div></div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1995 <pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1996 </pre>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1997 </div><!--/#alignments-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1998 </div><!-- alignInfo -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1999 </div><!--ARIA-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2000
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2001 </div><!-- alignView -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2002 <form><!-- this is the start tag for the </form in blastcgi templates - needs to be changed-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2003 <!-- not used - verify -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2004 <!-- not used - verify -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2005
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2006
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2007 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2008 </div><!-- /#content -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2009 <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="reformat" id="reformat">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2010 <input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2011 <input name="ENTREZ_QUERY" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2012 <input name="CDD_RID" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2013 <input name="CDD_SEARCH_STATE" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2014 <input name="RID" value="PHWP1JNZ014" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2015 <input name="STEP_NUMBER" value="" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2016 <input name="CMD" value="Web" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2017 <input name="PAGE_TYPE" value="BlastFormatting" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2018
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2019 <!-- TO DO: test all of those changes -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2020 <!-- Psi blast params PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2021 <!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2022 <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2023 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2024
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2025 <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="setSavedOptions" id="setSavedOptions">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2026 <input name="PAGE_TYPE" value="BlastSearch" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2027 <input name="VIEW_SEARCH" value="true" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2028 <input name="CMD" value="Web" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2029 <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2030 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2031
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2032 <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="saveOptions" id="saveOptions">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2033 <input name="SAVE" value="true" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2034 <input name="CMD" value="GetSaved" type="hidden">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2035 <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from formatter> -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2036 </form>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2037 </div><!-- /#content-wrap -->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2038
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2039
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2040 <div id="footer">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2041 <div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2042 <p id="orgns">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2043 <a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2044 <a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2045 <a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2046 <a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2047 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2048
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2049 <p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2050 <a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html" title="NCBI intellectual property statement">Copyright</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2051 <a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer" title="About liability, endorsements, external links, pop-up advertisements">Disclaimer</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2052 <a href="http://www.nlm.nih.gov/privacy.html" title="NLM privacy policy">Privacy</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2053 <a href="http://www.nlm.nih.gov/accessibility.html" title="About using NCBI resources with assistive technology">Accessibility</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2054 <a href="http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html" title="How to get help, submit data, or provide feedback">Contact</a> \|
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2055 <a href="mailto:blast-help@ncbi.nlm.nih.gov" title="How to get help, submit data, or provide feedback">Send feedback</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2056 </p>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2057 </div>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2058 </div><!--/#wrap-->
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2059
31 344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2060 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/utils.js"></script>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2061 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/toggle.js"></script>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2062 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/remote_data_provider.js"></script>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2063 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/results.js"></script><link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/firefox-descriptions.css" media="screen">
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2064 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/blast.js"></script>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2065 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/format.js"></script>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2066 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/formatRes.js"></script>
344cd76f6fd2 rename NCBI reference example Jan Kanis <jan.code@jankanis.nl> parents: 0 diff changeset	2067 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/InstrumentPageStarterJS.js"></script>
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2068
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2069
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2070
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2071 <div class="ui-ncbiautocomplete-holder shadow" aria-live="assertive"><ul class="ui-ncbiautocomplete-options" role="listbox" aria-activedescendant=""></ul><div class="ui-ncbiautocomplete-actions shadow"><a href="#" class="ui-ncbiautocomplete-link-pref">Preferences</a><a href="#" class="ui-ncbiautocomplete-link-off">Turn off</a></div></div><ul class="print-log"><li></li></ul></body></html>

Mercurial > repos > jankanis > blast2html

annotate NCBI Blast reference example.html @ 51:b15a20c2372a