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annotate NCBI Blast reference example.html @ 120:2729c2326235

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Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 31 Jul 2014 16:14:36 +0200
parents 344cd76f6fd2
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1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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2 <html xmlns="http://www.w3.org/1999/xhtml"><head>
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3
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4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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5 <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
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6 <meta name="jig" content="ncbitoggler ncbiautocomplete ncbilocalnav ncbigrid ncbipopper">
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7 <meta name="ncbitoggler" content="animation:'none'">
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8 <meta name="ncbipopper" content="animation:'none',closeEvent: 'click',openEvent: 'click',destPosition: 'top right',triggerPosition: 'bottom right'">
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9
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10 <meta name="ncbi_app" content="blast">
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11 <meta name="ncbi_pdid" content="blastresults">
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12 <meta name="ncbi_stat" content="false">
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13 <meta name="ncbi_sessionid" content="8A8E11EE2CABF371_0000SID">
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14 <meta name="ncbi_phid" content="5AAB74D7368F2C81000000000000C9C8">
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15 <script type="text/javascript"> var ncbi_startTime = new Date(); </script>
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16 <title>NCBI Blast:Nucleotide Sequence (16 letters)</title>
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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">
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18 <script type="text/javascript"> jQuery.getScript("/core/alerts/alerts.js", function() {
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19 galert(['div#header', 'body > *:nth-child(1)'])
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20 });</script>
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21 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/main.css" media="screen">
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22 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/blastRes.css" media="screen">
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23 <!--[if IE]>
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24 <link rel="stylesheet" type="text/css" href="css/descriptionsIE.css" media="screen" />
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25 <![endif]-->
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26 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/print.css" media="print">
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27 <!--[if lte IE 6]>
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28 <link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
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29 <![endif]-->
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30 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/blastReq.css" media="screen">
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31 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/results.css" media="screen">
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32 <link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/dynFormatRes.css" media="screen">
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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>
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36 <body id="type-a" class="noToggleCheck ">
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37 <div id="wrap">
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38 <div id="header">
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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>
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40 </div>
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41 <div id="search">
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42
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43 <div>
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44 <script language="JavaScript" type="text/javascript"><!--
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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>
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46 </div>
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47 <a class="skp" href="#content-wrap">Jump to Page Content</a>
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48 <ul id="nav">
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49 <li class="first "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
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50 <li class="recent "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&amp;RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
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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>
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52 <li class="last documentation "> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>
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53 </ul>
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54 </div>
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55
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56 <div id="content-wrap">
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57
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58 <div id="breadcrumb" class="inlineDiv">
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59 <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
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60 <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome">BLAST</a>/
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61 <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&amp;PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=">blastn suite</a>/
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62 <strong>Formatting Results - PHWP1JNZ014</strong>
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63 </div>
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64 <div class="inlineDiv resHeader resPage">
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65
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66 </div>
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67 <ul class="print-log-res"><li></li></ul>
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68
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69 <!-- CDD info for old design -->
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70
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71
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72
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73
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74
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75
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76
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77
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78 <div id="content">
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79
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80 <!--<ul id="msg" class="msg"><li class="info"><p class=""></p><p class=""></p><p class=""></p></li></ul>-->
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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>
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82 <a href="#" class="resLink resPage" id="searchOptions" submitform="setSavedOptions">Edit and Resubmit</a>
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83 <a href="#" class="resLink resPage hidden" id="saveSearchOptions" submitform="saveOptions">Save Search Strategies</a>
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84 <span class="reslink resPage">[Sign in above to save your search strategy]</span>
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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="#">
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86 <span class="ui-ncbitoggler-master-text">Formatting options </span>
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87 <span class="ui-icon ui-icon-triangle-1-e"></span>
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88 </a>
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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="#">
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90 <span class="ui-ncbitoggler-master-text">Download</span>
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91 <span class="ui-icon ui-icon-triangle-1-e"></span>
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92 </a>
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93 <span id="hnr">
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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>
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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>
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96 </span>
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97 <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
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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">
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99 <input name="QUERY_INDEX" value="0" type="hidden">
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100 <input name="_PGR" value="2" type="hidden">
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101 <input id="seqViewUrl" value="http://www.ncbi.nlm.nih.gov/projects/sviewer" type="hidden">
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102 <input name="CMD" value="Get" type="hidden">
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103 </form>
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104 <!-- Reformat and downlaod for new design -->
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105 <div class="ui-helper-reset" aria-live="assertive">
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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">
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107 <table class="options blastn ">
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108 <tbody><tr>
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109 <td class="frh" colspan="2">
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110 <div class="fi">
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111 <div class="tb">Formatting options</div>
31
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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
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113 </div>
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114 </td></tr>
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115 <tr class="paramSet xgl">
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116 <td class="hd"><label for="FORMAT_OBJECT">Show</label></td>
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117 <td>
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118 <div class="fi">
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119 <input id="FORMAT_OBJECT" value="Alignment" name="FORMAT_OBJECT" type="hidden">
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120 <label for="FORMAT_TYPE" id="nft">Alignment as</label>
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121 <select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defval="HTML">
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122 <option value="HTML" selected="selected">HTML</option>
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123 <option value="Text">Plain text</option>
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124
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125 </select>
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126
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127 <span id="advView" class="">
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128 <span class=""><input name="OLD_VIEW" id="OLD_VIEW" class="cb reset" defval="unchecked" false="" type="checkbox">
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129 <label for="OLD_VIEW">Old View</label></span>
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130 </span>
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131 <a class="resetAll" id="resetAll">Reset form to defaults</a>
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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>
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133 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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134 <div class="ui-helper-reset" aria-live="assertive">
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135 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp1">
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136 These options control formatting of alignments in results pages. The
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137 default is HTML, but other formats (including plain text) are available.
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138 PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
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139 The Advanced view option allows the database descriptions to be sorted by various indices in a table.
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140 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a>
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141 </p>
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142 </div><!-- ARIA -->
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143 </div>
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144 </td>
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145 </tr>
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146
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147 <tr class="odd paramSet">
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148 <td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td>
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149 <td>
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150 <div class="fi">
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151 <select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defval="Pairwise" class="reset">
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152 <option value="Pairwise" selected="selected">Pairwise</option>
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153 <option value="PairwiseWithIdentities">Pairwise with dots for identities</option>
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154 <option value="QueryAnchored">Query-anchored with dots for identities</option>
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155 <option value="QueryAnchoredNoIdentities">Query-anchored with letters for identities</option>
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156 <option value="FlatQueryAnchored">Flat query-anchored with dots for identities</option>
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157 <option value="FlatQueryAnchoredNoIdentities">Flat query-anchored with letters for identities</option>
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158
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159 </select>
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160
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161
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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>
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163 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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164 <div class="ui-helper-reset" aria-live="assertive">
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165 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp2">
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166 Choose how to view alignments.
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167 The default "pairwise" view shows how each subject sequence aligns
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168 individually to the query sequence. The "query-anchored" view shows how
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169 all subject sequences align to the query sequence. For each view type,
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170 you can choose to show "identities" (matching residues) as letters or
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171 dots.
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172 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a>
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173 </p>
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174 </div><!-- ARIA -->
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175 </div>
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176 </td>
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177 </tr>
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178
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179 <tr class="paramSet">
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180 <td class="hd"><label>Display</label></td>
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181 <td class="cb">
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182 <div class="fi">
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183 <input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" class="cb reset" defval="checked" checked="checked" type="checkbox">
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184 <label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label>
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185
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186 <span class="hidden" id="shl">
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187 <input name="SHOW_LINKOUT" id="SHOW_LINKOUT" class="cb reset" defval="checked" checked="checked" type="checkbox">
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188 <label class="rb" for="SHOW_LINKOUT">Linkout</label>
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189 </span>
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190 <span class="hidden" id="gts">
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191 <input name="GET_SEQUENCE" id="GET_SEQUENCE" class="cb reset" defval="checked" checked="checked" type="checkbox">
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192 <label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label>
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193 </span>
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194
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195 <input name="NCBI_GI" id="NCBI_GI" class="cb reset" defval="unchecked" type="checkbox">
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196 <label class="rb" for="NCBI_GI">NCBI-gi</label>
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197 <span id="scf">
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198 <input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" class="cb reset blastn" defval="unchecked" type="checkbox">
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199 <label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label>
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200 </span>
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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>
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202 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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203 <div class="ui-helper-reset" aria-live="assertive">
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204 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp3">
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205 <li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query.
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206 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a>
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207 </li>
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208 <li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases.
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209 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin">more...</a>
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210 </li>
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211 <li>Sequence Retrieval: Show buttons to download matching sequences.
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212 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin">more...</a>
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213 </li>
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214 <li>NCBI-gi: Show NCBI gi identifiers.
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215 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin">more...</a>
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216 </li>
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217 <li>CDS feature: Show annotated coding region and translation.
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218 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin">more...</a>
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219 </li></ul>
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220 </div><!-- ARIA -->
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221 </div>
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222 </td>
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223 </tr>
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224
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225
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226 <tr class="paramSet odd xgl">
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227 <td class="hd"><label>Masking</label></td>
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228 <td>
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229 <div class="fi">
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230 <label for="MASK_CHAR"> Character: </label>
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231 <select name="MASK_CHAR" id="MASK_CHAR" class="reset" defval="2">
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232 <option value="0">X for protein, n for nucleotide</option>
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233 <option value="2" selected="selected">Lower Case</option>
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234 </select>
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235 <label for="MASK_COLOR"> Color:</label>
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236 <select name="MASK_COLOR" id="MASK_COLOR" class="reset" defval="1">
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237 <option value="0">Black
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238 </option>
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239
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240 <option value="1" selected="selected">Grey
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241 </option>
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242
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243 <option value="2">Red
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244 </option>
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245
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246 </select>
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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>
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248 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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249 <div class="ui-helper-reset" aria-live="assertive">
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250 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp4">
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251 <li>Masking Character: Display masked (filtered) sequence regions as
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252 lower-case or as specific letters (N for nucleotide, P for protein).
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253 </li>
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254 <li>Masking Color: Display masked sequence regions in the given color.</li>
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255 </ul>
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256 </div><!-- ARIA -->
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257 </div>
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258 </td>
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259 </tr>
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260
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261
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262 <tr id="lr" class="paramSet xgl">
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263 <td class="hd"><label>Limit results</label></td>
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264 <td>
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265 <div class="fi">
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266 <label for="FRM_DESCRIPTIONS">Descriptions:</label>
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267 <select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defval="100">
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268
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269 <option value="10">10</option>
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270 <option value="50">50</option>
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271 <option value="100" selected="selected">100</option>
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272
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273
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274
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275
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276
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277
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278 </select>
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279
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280 <label for="FRM_NUM_OVERVIEW">Graphical overview:</label>
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281 <select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defval="100">
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282 <option value="0">0</option>
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283 <option value="10">10</option>
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284 <option value="50">50</option>
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285 <option value="100" selected="selected">100</option>
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286
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287
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288
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289 </select>
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290 <span class="hidden" id="frmAln">
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291 <label for="FRM_ALIGNMENTS">Alignments:</label>
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292 <select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defval="100">
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293 <option value="0">0</option>
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294 <option value="10">10</option>
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295 <option value="50">50</option>
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296 <option value="100" selected="selected">100</option>
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297
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298
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299
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300
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301
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302
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303 </select>
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304 </span>
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305 <label for="FRM_LINE_LENGTH">Line length:</label>
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306 <select name="LINE_LENGTH" id="FRM_LINE_LENGTH" class="reset" defval="60">
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307 <option value="60" selected="selected">60</option>
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308 <option value="90">90</option>
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309 <option value="120">120</option>
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310 <option value="150">150</option>
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311 </select>
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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>
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313 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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314 <div class="ui-helper-reset" aria-live="assertive">
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315 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp5">
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316 <li>Descriptions: Show short descriptions for up to the given number of sequences.</li>
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317 <li>Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.</li>
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318 <li>Line lenghth: ....</li>
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319 </ul>
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320 </div><!-- ARIA -->
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321 </div>
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322 </td>
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323 </tr>
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324
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325 <tr class="paramSet odd xgl ">
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326 <td class="hd"></td>
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327 <td>
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328 <div class="">
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329 <label for="qorganism">Organism</label>
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330 <span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br>
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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">
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332 <input name="FORMAT_ORG_EXCLUDE" class="oExclR cb" id="orgExcl" type="checkbox">
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333 <input value="1" name="FORMAT_NUM_ORG" id="numOrg" type="hidden">
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334 <label for="orgExcl" class="right">Exclude</label>
31
344cd76f6fd2 rename NCBI reference example
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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
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336 <div id="orgs">
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337
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338 </div>
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339 <div class="fi">
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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>
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341 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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342 <div class="ui-helper-reset" aria-live="assertive">
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343 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp6">
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344 Show only sequences from the given organism.
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345 </p>
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346 </div><!-- ARIA -->
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347 </div>
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348 </div>
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349 </td>
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350 </tr>
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351
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352 <tr class="paramSet xgl ">
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353 <td class="hd"></td>
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354 <td>
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355 <div class="fi">
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356 <label for="FORMAT_EQ_TEXT">Entrez query:</label>
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357 <input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" class="reset" type="text">
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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>
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359 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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360 <div class="ui-helper-reset" aria-live="assertive">
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361 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp7">
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362 Show only those sequences that match the given Entrez query.
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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>
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364 </p>
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365 </div><!-- ARIA -->
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366 </div>
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367 </td>
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368 </tr>
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369
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370
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371 <tr class="paramSet odd xgl">
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372 <td class="hd"></td>
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373 <td>
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374 <div class="fi">
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375 <label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" class="reset" type="text">
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376 <label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" class="reset" type="text">
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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>
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378 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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379 <div class="ui-helper-reset" aria-live="assertive">
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380 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp8">
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381 Show only sequences with expect values in the given range.
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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>
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383 </p>
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384 </div><!-- ARIA -->
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385 </div>
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386 </td>
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387 </tr>
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388 <tr class="paramSet xgl">
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389 <td class="hd"></td>
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390 <td>
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391 <div class="fi">
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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">
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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">
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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>
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395 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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396 <div class="ui-helper-reset" aria-live="assertive">
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397 <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp10">
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398 Show only sequences with percent identity values in the given range.
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399 </p>
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400 </div><!-- ARIA -->
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401 </div>
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402 </td>
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403 </tr>
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404 <tr class="psiBlast odd paramSet xgl">
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405 <td class="hd"><label>Format for</label></td>
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406 <td>
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407 <div class="fi">
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408 <input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" class="cb psiBlast" type="checkbox">
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409 <label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label>
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410 <label for="I_THRESH">with inclusion threshold:</label>
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411 <input name="I_THRESH" id="I_THRESH" size="10" defval="0.005" type="text">
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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>
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413 <span class="ui-icon ui-icon-triangle-1-e"></span></a>
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414 <div class="ui-helper-reset" aria-live="assertive">
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415 <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp9">
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416 <li>Format for PSI-BLAST: The Position-Specific Iterated BLAST
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417 (PSI-BLAST) program performs iterative searches with a protein query,
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418 in which sequences found in one round of search are used to build a
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419 custom score model for the next round.
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420 <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a>
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421 </li>
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422 <li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used
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423 by PSI-BLAST to create the PSSM on the next iteration.</li>
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424 </ul>
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425 </div><!-- ARIA -->
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426 </div>
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427 </td>
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428 </tr>
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429 </tbody></table>
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430
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431
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432 <input name="ViewReport" value="ViewReport" type="hidden">
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433 <input name="REFORMAT_REPORT" value="shown" type="hidden">
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434 <input name="RID" value="PHWP1JNZ014" type="hidden">
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435 <input name="CDD_RID" value="" type="hidden">
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436 <input name="CDD_SEARCH_STATE" value="" type="hidden">
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437
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438 <input name="STEP_NUMBER" value="" id="stepNumber" type="hidden">
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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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;DESCRIPTIONS=100&amp;ALIGNMENTS=100&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=XML&amp;FORMAT_OBJECT=Alignment&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=Alignment&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=CSV&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;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&amp;RECENT_RESULTS=on&amp;RID=PHWP1JNZ014&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=PSSM_Scoremat&amp;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>
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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&amp;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&amp;db=nucleotide&amp;term=59987&amp;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&amp;cmd=Retrieve&amp;list_uids=9254694&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_OBJECT=TaxBlast&amp;NCBI_GI=off&amp;DESCRIPTIONS=100&amp;ALIGNMENTS=100&amp;FORMAT_BLOCK_ON_RESPAGE=Top&amp;MASK_COLOR=1&amp;MASK_CHAR=2" target="lnkPHWP1JNZ014" title="See results arranged by taxonomy">[Taxonomy reports]</a>
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&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl%7C59987&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;ns=100" class="" id="TreeViewlcl|59987" onclick="ViewTree('TreeViewlcl|59987');return false;" target="lnkPHWP1JNZ014" title="See a distance tree of these pairwise comparisons">[Distance tree of results]</a>
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>
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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
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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>
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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>
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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
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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>
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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
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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
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parents:
diff changeset
697 </tbody></table>
bad241dc701f add example input blast xml and output html page
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parents:
diff changeset
698 <!-- Results statistics -->
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parents:
diff changeset
699 </div> <!-- resStat -->
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parents:
diff changeset
700 </div> <!-- aria end -->
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
701 </div><!--/#summary-->
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parents:
diff changeset
702 </div><!--/#page-->
31
344cd76f6fd2 rename NCBI reference example
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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
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
704
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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">
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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
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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
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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
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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
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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
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parents:
diff changeset
735 </div><!-- ARIA -->
31
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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>
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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
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parents:
diff changeset
738 </tr></tbody></table>
31
344cd76f6fd2 rename NCBI reference example
Jan Kanis <jan.code@jankanis.nl>
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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>
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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>
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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
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diff changeset
748 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td>
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Jan Kanis <jan.code@jankanis.nl>
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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>
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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
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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
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diff changeset
752 </tr></tbody></table>
31
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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
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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
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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
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diff changeset
756 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/3.gif" height="13" width="10"></td>
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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
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758 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/6.gif" height="13" width="10"></td>
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759 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td>
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760 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/9.gif" height="13" width="10"></td>
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761 <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="73"></td>
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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
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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
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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
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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
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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
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diff changeset
767 </tr></tbody></table>
31
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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
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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
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diff changeset
770 </tr></tbody></table>
31
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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>
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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
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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
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774 </tr></tbody></table>
31
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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
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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
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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
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778 </tr></tbody></table>
31
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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
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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
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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>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
823 </div><!--/#graphic-->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
824 </div><!-- graphicInfo -->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
825 </div><!-- ARIA -->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
826 </div>
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@&amp;currseq=@alnSeqGi@" onclick="ReadNextHSPSet(@argstring@);"><span>Load next set</span></a><a class="gbd toolsCtr navPrev" title="Go to previous match #@aln_prev_num@ for @accs@" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a></div></div>
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&amp;rettype=gb&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get" type="radio"><label class="shownInl" for="dwHitText">Hit Table (text)</label></div>
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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=CSV&amp;FORMAT_OBJECT=Alignment&amp;ALIGNMENT_VIEW=Tabular&amp;CMD=Get" type="radio"><label class="shownInl" for="dwHitCsv">Hit Table (CSV)</label></div>
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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=Text&amp;FORMAT_OBJECT=Alignment&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=XML&amp;FORMAT_OBJECT=Alignment&amp;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&amp;RID=PHWP1JNZ014&amp;FORMAT_TYPE=ASN.1&amp;FORMAT_OBJECT=Alignment&amp;CMD=Get" type="radio"><label class="shownInl" for="dwASN">ASN.1</label></div>
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&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=1&amp;HSP_SORT=1" class="dcs" title="Sort by max score">Max score</a>
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&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=2&amp;HSP_SORT=1" class="dcs" title="Sort by total score">Total score</a>
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&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=4&amp;HSP_SORT=0" class="dcs" title="Sort by query coverage">Query cover</a>
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&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;OLD_VIEW=false&amp;DISPLAY_SORT=0&amp;HSP_SORT=0" class="dcs" title="Sort by E value">E value</a>
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&amp;ALIGNMENTS=100&amp;ALIGNMENT_VIEW=Pairwise&amp;DATABASE_SORT=0&amp;DESCRIPTIONS=100&amp;DYNAMIC_FORMAT=on&amp;FIRST_QUERY_NUM=0&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_PAGE_TARGET=&amp;FORMAT_TYPE=HTML&amp;GET_SEQUENCE=yes&amp;I_THRESH=&amp;LINE_LENGTH=60&amp;MASK_CHAR=2&amp;MASK_COLOR=1&amp;NUM_OVERVIEW=100&amp;OLD_BLAST=false&amp;PAGE=Nucleotides&amp;QUERY_INDEX=0&amp;QUERY_NUMBER=0&amp;RESULTS_PAGE_TARGET=&amp;RID=PHWP1JNZ014&amp;SHOW_LINKOUT=yes&amp;SHOW_OVERVIEW=yes&amp;STEP_NUMBER=&amp;WORD_SIZE=7&amp;DISPLAY_SORT=3&amp;HSP_SORT=3" class="dcs" title="Sort by ident">Ident</a>
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&amp;log$=nucltop&amp;blast_rank=1&amp;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&amp;log$=nucltop&amp;blast_rank=2&amp;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&amp;log$=nucltop&amp;blast_rank=3&amp;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&amp;log$=nucltop&amp;blast_rank=4&amp;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&amp;log$=nucltop&amp;blast_rank=5&amp;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&amp;log$=nucltop&amp;blast_rank=6&amp;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&amp;log$=nucltop&amp;blast_rank=7&amp;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&amp;log$=nucltop&amp;blast_rank=8&amp;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&amp;log$=nucltop&amp;blast_rank=9&amp;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&amp;log$=nucltop&amp;blast_rank=10&amp;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&amp;log$=nucltop&amp;blast_rank=11&amp;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&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl|59987&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;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&amp;blastRID=PHWP1JNZ014&amp;queryID=lcl|59987&amp;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&amp;rettype=gb&amp;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&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics">Graphics</a></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J5A|A">pdb|3J5A|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1186 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1187 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1188 <div class="relInf" id="relInf_557804451"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1189 <!--
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1190 <pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1191 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1192 </pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1193 -->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1194 <div class="alnAll" id="alnAll_557804451"><div id="hd_557804451_1">
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1195 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=1&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&amp;rid=PHWP1JNZ014[557804451]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;rettype=gb&amp;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&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics">Graphics</a></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J58|A">pdb|3J58|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1354 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1355 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1356 <div class="relInf" id="relInf_557804395"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1357 <!--
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1358 <pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1359 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1360 </pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1361 -->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1362 <div class="alnAll" id="alnAll_557804395"><div id="hd_557804395_1">
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1363 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=2&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&amp;rid=PHWP1JNZ014[557804395]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;rettype=gb&amp;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&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics">Graphics</a></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J56|A">pdb|3J56|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1522 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1523 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1524 <div class="relInf" id="relInf_557804339"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1525 <!--
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1526 <pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1527 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1528 </pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1529 -->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1530 <div class="alnAll" id="alnAll_557804339"><div id="hd_557804339_1">
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1531 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=3&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&amp;rid=PHWP1JNZ014[557804339]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;rettype=gb&amp;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&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics">Graphics</a></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J54|A">pdb|3J54|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1690 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1691 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1692 <div class="relInf" id="relInf_557804283"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1693 <!--
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1694 <pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1695 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1696 </pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1697 -->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1698 <div class="alnAll" id="alnAll_557804283"><div id="hd_557804283_1">
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1699 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=4&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&amp;rid=PHWP1JNZ014[557804283]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;rettype=gb&amp;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&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=752:2685&amp;appname=ncbiblast&amp;link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics">Graphics</a></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J52|A">pdb|3J52|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1858 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1859 </div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1860 <div class="relInf" id="relInf_557804227"><label>Related Information</label></div>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1861 <!--
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1862 <pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1863 <@aln_gene_info@>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1864 </pre>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1865 -->
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1866 <div class="alnAll" id="alnAll_557804227"><div id="hd_557804227_1">
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1867 <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=961&amp;to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=961:976&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=2591&amp;to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2591:2598&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=839&amp;to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=839:845&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span>
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&amp;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&amp;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&amp;log$=nuclalign&amp;blast_rank=5&amp;RID=PHWP1JNZ014&amp;from=2027&amp;to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&amp;rid=PHWP1JNZ014[557804227]&amp;tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&amp;v=2027:2033&amp;appname=ncbiblast&amp;link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span>
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&amp;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&amp;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> |
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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> |
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2055 <a href="mailto:blast-help@ncbi.nlm.nih.gov" title="How to get help, submit data, or provide feedback">Send feedback</a>
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2056 </p>
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2057 </div>
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2058 </div><!--/#wrap-->
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2059
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2060 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/utils.js"></script>
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2061 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/toggle.js"></script>
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2062 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/remote_data_provider.js"></script>
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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">
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2064 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/blast.js"></script>
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2065 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/format.js"></script>
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2066 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/formatRes.js"></script>
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2067 <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/InstrumentPageStarterJS.js"></script>
0
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2068
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2069
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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>