Mercurial > repos > jankanis > blast2html
view NCBI Blast reference example.html @ 75:4d2c25baf5a3 py2.6
Fix rounding errors
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Wed, 18 Jun 2014 17:50:32 +0200 |
| parents | 344cd76f6fd2 |
| children |
line wrap: on
line source
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"><head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1"> <meta name="jig" content="ncbitoggler ncbiautocomplete ncbilocalnav ncbigrid ncbipopper"> <meta name="ncbitoggler" content="animation:'none'"> <meta name="ncbipopper" content="animation:'none',closeEvent: 'click',openEvent: 'click',destPosition: 'top right',triggerPosition: 'bottom right'"> <meta name="ncbi_app" content="blast"> <meta name="ncbi_pdid" content="blastresults"> <meta name="ncbi_stat" content="false"> <meta name="ncbi_sessionid" content="8A8E11EE2CABF371_0000SID"> <meta name="ncbi_phid" content="5AAB74D7368F2C81000000000000C9C8"> <script type="text/javascript"> var ncbi_startTime = new Date(); </script> <title>NCBI Blast:Nucleotide Sequence (16 letters)</title> <script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jig.js"></script><link rel="stylesheet" type="text/css" href="NCBI%20Blast%20reference%20example_files/jig.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_002.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_005.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_004.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_004.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery_007.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_003.css"><script type="text/javascript" src="NCBI%20Blast%20reference%20example_files/jquery.js"></script><link type="text/css" rel="stylesheet" href="NCBI%20Blast%20reference%20example_files/jquery_007.css"><script 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align="left" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td align="right" bgcolor="#336699"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img src="NCBI%20Blast%20reference%20example_files/myncbihelpicon.gif" alt="My NCBI help" border="0"></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to sign in" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Sign In]</a> <a href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide" title="Click to register for an account" onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FADJUSTED%5FFOR%5FSHORT%5FQUERY%3Don%26ALIGNMENTS%3D100%26ALIGNMENT%5FVIEW%3DPairwise%26BLAST%5FPROGRAMS%3Dblastn%26CLIENT%3Dweb%26CMD%3DGet%26COMPOSITION%5FBASED%5FSTATISTICS%3D0%26CONFIG%5FDESCR%3D2%2C3%2C4%2C5%2C6%2C7%2C8%26DATABASE%3Dpdb%26DBTYPE%3Dgc%26DEFAULT%5FPROG%3DmegaBlast%26DESCRIPTIONS%3D100%26DYNAMIC%5FFORMAT%3Don%26EQ%5FOP%3DAND%26EXPECT%3D1000%26FORMAT%5FNUM%5FORG%3D1%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dpdb%26GAPCOSTS%3D5%2B2%26GET%5FSEQUENCE%3Don%26HSP%5FRANGE%5FMAX%3D0%26JOB%5FTITLE%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26LAYOUT%3DOneWindow%26LINE%5FLENGTH%3D60%26MASK%5FCHAR%3D2%26MASK%5FCOLOR%3D1%26MATCH%5FSCORES%3D1%2C%2D3%26MAX%5FNUM%5FSEQ%3D100%26NUCL%5FPENALTY%3D%2D2%26NUCL%5FREWARD%3D1%26NUM%5FDIFFS%3D1%26NUM%5FOPTS%5FDIFFS%3D0%26NUM%5FORG%3D1%26NUM%5FOVERVIEW%3D100%26OLD%5FBLAST%3Dfalse%26OLD%5FVIEW%3Dfalse%26PAGE%3DNucleotides%26PAGE%5FTYPE%3DBlastSearch%26PROGRAM%3Dblastn%26QUERY%5FINFO%3DNucleotide%2BSequence%2B%2816%2Bletters%29%26QUERY%5FLENGTH%3D16%26REPEATS%3Drepeat%5F9606%26RID%3DPHWP1JNZ014%26RTOE%3D42%26SEARCH%5FDB%5FSTATUS%3D42%26SELECTED%5FPROG%5FTYPE%3DmegaBlast%26SERVICE%3Dplain%26SHORT%5FQUERY%5FADJUST%3Don%26SHOW%5FLINKOUT%3Don%26SHOW%5FOVERVIEW%3Don%26USER%5FDEFAULT%5FMATCH%5FSCORES%3D0%26USER%5FDEFAULT%5FPROG%5FTYPE%3DmegaBlast%26USER%5FTYPE%3D2%26WORD%5FSIZE%3D7%26%5FPGR%3D1%26%5FPGR%3D1%26db%3Dnucleotide%26stype%3Dnucleotide');return false;">[Register]</a></td></tr></tbody></table></div> </div> <a class="skp" href="#content-wrap">Jump to Page Content</a> <ul id="nav"> <li class="first "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li> <li class="recent "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li> <li class="saved "><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li> <li class="last documentation "> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li> </ul> </div> <div id="content-wrap"> <div id="breadcrumb" class="inlineDiv"> <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/ <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/ <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=">blastn suite</a>/ <strong>Formatting Results - PHWP1JNZ014</strong> </div> <div class="inlineDiv resHeader resPage"> </div> <ul class="print-log-res"><li></li></ul> <!-- CDD info for old design --> <div id="content"> <!--<ul id="msg" class="msg"><li class="info"><p class=""></p><p class=""></p><p class=""></p></li></ul>--> <ul id="msg" class="msg"><li class="info"><p class="info">Your search parameters were adjusted to search for a short input sequence.</p></li></ul> <a href="#" class="resLink resPage" id="searchOptions" submitform="setSavedOptions">Edit and Resubmit</a> <a href="#" class="resLink resPage hidden" id="saveSearchOptions" submitform="saveOptions">Save Search Strategies</a> <span class="reslink resPage">[Sign in above to save your search strategy]</span> <a aria-expanded="false" role="button" aria-disabled="false" id="showFormat" class="resLink resPage resArrowLinkB ui-ncbitoggler jig-ncbitoggler ui-widget" data-ncbitoggler-toggles="FormatForm" href="#"> <span class="ui-ncbitoggler-master-text">Formatting options </span> <span class="ui-icon ui-icon-triangle-1-e"></span> </a> <a aria-expanded="false" role="button" aria-disabled="false" id="showDownload" class="resLink resPage resArrowLinkB jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="FormatDownload" href="#"> <span class="ui-ncbitoggler-master-text">Download</span> <span class="ui-icon ui-icon-triangle-1-e"></span> </a> <span id="hnr"> <a id="ytb" class="ytb " title="External link to YouTube" href="http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq" target="lnkPHWP1JNZ014">How to read this page</a> <a id="brFtp" class="" title="Blast report description" href="ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_NewBLAST.pdf" target="lnkPHWP1JNZ014">Blast report description</a> </span> <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results"> <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden"><input name="ALIGNMENTS" value="100" type="hidden"><input name="ALIGNMENT_VIEW" value="Pairwise" type="hidden"><input name="BLAST_PROGRAMS" value="blastn" type="hidden"><input name="CLIENT" value="web" type="hidden"><input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden"><input name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden"><input name="DATABASE" value="pdb" type="hidden"><input name="DBTYPE" value="gc" type="hidden"><input name="DEFAULT_PROG" value="megaBlast" type="hidden"><input name="DESCRIPTIONS" value="100" type="hidden"><input name="DYNAMIC_FORMAT" value="on" type="hidden"><input name="EQ_OP" value="AND" type="hidden"><input name="EXPECT" value="1000" type="hidden"><input name="FORMAT_NUM_ORG" value="1" type="hidden"><input name="FORMAT_OBJECT" value="Alignment" type="hidden"><input name="FORMAT_TYPE" value="HTML" type="hidden"><input name="FULL_DBNAME" value="pdb" type="hidden"><input name="GAPCOSTS" value="5 2" type="hidden"><input name="GET_SEQUENCE" value="on" type="hidden"><input name="HSP_RANGE_MAX" value="0" type="hidden"><input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="LAYOUT" value="OneWindow" type="hidden"><input name="LINE_LENGTH" value="60" type="hidden"><input name="MASK_CHAR" value="2" type="hidden"><input name="MASK_COLOR" value="1" type="hidden"><input name="MATCH_SCORES" value="1,-3" type="hidden"><input name="MAX_NUM_SEQ" value="100" type="hidden"><input name="NUCL_PENALTY" value="-2" type="hidden"><input name="NUCL_REWARD" value="1" type="hidden"><input name="NUM_DIFFS" value="1" type="hidden"><input name="NUM_OPTS_DIFFS" value="0" type="hidden"><input name="NUM_ORG" value="1" type="hidden"><input name="NUM_OVERVIEW" value="100" type="hidden"><input name="OLD_BLAST" value="false" type="hidden"><input name="OLD_VIEW" value="false" type="hidden"><input name="PAGE" value="Nucleotides" type="hidden"><input name="PAGE_TYPE" value="BlastSearch" type="hidden"><input name="PROGRAM" value="blastn" type="hidden"><input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="QUERY_LENGTH" value="16" type="hidden"><input name="REPEATS" value="repeat_9606" type="hidden"><input name="RID" value="PHWP1JNZ014" type="hidden"><input name="RTOE" value="42" type="hidden"><input name="SEARCH_DB_STATUS" value="43" type="hidden"><input name="SELECTED_PROG_TYPE" value="megaBlast" type="hidden"><input name="SERVICE" value="plain" type="hidden"><input name="SHORT_QUERY_ADJUST" value="on" type="hidden"><input name="SHOW_LINKOUT" value="on" type="hidden"><input name="SHOW_OVERVIEW" value="on" type="hidden"><input name="USER_DEFAULT_MATCH_SCORES" value="0" type="hidden"><input name="USER_DEFAULT_PROG_TYPE" value="megaBlast" type="hidden"><input name="USER_TYPE" value="2" type="hidden"><input name="WORD_SIZE" value="7" type="hidden"><input name="_PGR" value="2" type="hidden"><input name="db" value="nucleotide" type="hidden"><input name="stype" value="nucleotide" type="hidden"> <input name="QUERY_INDEX" value="0" type="hidden"> <input name="_PGR" value="2" type="hidden"> <input id="seqViewUrl" value="http://www.ncbi.nlm.nih.gov/projects/sviewer" type="hidden"> <input name="CMD" value="Get" type="hidden"> </form> <!-- Reformat and downlaod for new design --> <div class="ui-helper-reset" aria-live="assertive"> <form aria-hidden="true" action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="FormatForm" id="FormatForm" class="resbox ui-ncbitoggler-slave ui-ncbitoggler"> <table class="options blastn "> <tbody><tr> <td class="frh" colspan="2"> <div class="fi"> <div class="tb">Formatting options</div> <input id="onPageReformat" src="NCBI%20Blast%20reference%20example_files/reformat.jpg" class="blastbutton" alt="Reformat" mouseovimg="css/images/reformatOver.jpg" mouseoutimg="css/images/reformat.jpg" mousedownimg="css/images/reformatDown.jpg" mouseupimg="css/images/reformatOver.jpg" border="0" type="image"> </div> </td></tr> <tr class="paramSet xgl"> <td class="hd"><label for="FORMAT_OBJECT">Show</label></td> <td> <div class="fi"> <input id="FORMAT_OBJECT" value="Alignment" name="FORMAT_OBJECT" type="hidden"> <label for="FORMAT_TYPE" id="nft">Alignment as</label> <select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defval="HTML"> <option value="HTML" selected="selected">HTML</option> <option value="Text">Plain text</option> </select> <span id="advView" class=""> <span class=""><input name="OLD_VIEW" id="OLD_VIEW" class="cb reset" defval="unchecked" false="" type="checkbox"> <label for="OLD_VIEW">Old View</label></span> </span> <a class="resetAll" id="resetAll">Reset form to defaults</a> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments object formatting help" id="formatHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp1"> These options control formatting of alignments in results pages. The default is HTML, but other formats (including plain text) are available. PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST. The Advanced view option allows the database descriptions to be sorted by various indices in a table. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a> </p> </div><!-- ARIA --> </div> </td> </tr> <tr class="odd paramSet"> <td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td> <td> <div class="fi"> <select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defval="Pairwise" class="reset"> <option value="Pairwise" selected="selected">Pairwise</option> <option value="PairwiseWithIdentities">Pairwise with dots for identities</option> <option value="QueryAnchored">Query-anchored with dots for identities</option> <option value="QueryAnchoredNoIdentities">Query-anchored with letters for identities</option> <option value="FlatQueryAnchored">Flat query-anchored with dots for identities</option> <option value="FlatQueryAnchoredNoIdentities">Flat query-anchored with letters for identities</option> </select> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments view options help" id="alnViewHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp2"> Choose how to view alignments. The default "pairwise" view shows how each subject sequence aligns individually to the query sequence. The "query-anchored" view shows how all subject sequences align to the query sequence. For each view type, you can choose to show "identities" (matching residues) as letters or dots. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a> </p> </div><!-- ARIA --> </div> </td> </tr> <tr class="paramSet"> <td class="hd"><label>Display</label></td> <td class="cb"> <div class="fi"> <input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" class="cb reset" defval="checked" checked="checked" type="checkbox"> <label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label> <span class="hidden" id="shl"> <input name="SHOW_LINKOUT" id="SHOW_LINKOUT" class="cb reset" defval="checked" checked="checked" type="checkbox"> <label class="rb" for="SHOW_LINKOUT">Linkout</label> </span> <span class="hidden" id="gts"> <input name="GET_SEQUENCE" id="GET_SEQUENCE" class="cb reset" defval="checked" checked="checked" type="checkbox"> <label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label> </span> <input name="NCBI_GI" id="NCBI_GI" class="cb reset" defval="unchecked" type="checkbox"> <label class="rb" for="NCBI_GI">NCBI-gi</label> <span id="scf"> <input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" class="cb reset blastn" defval="unchecked" type="checkbox"> <label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label> </span> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments display options help" id="displayHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp3"> <li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a> </li> <li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin">more...</a> </li> <li>Sequence Retrieval: Show buttons to download matching sequences. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin">more...</a> </li> <li>NCBI-gi: Show NCBI gi identifiers. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin">more...</a> </li> <li>CDS feature: Show annotated coding region and translation. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin">more...</a> </li></ul> </div><!-- ARIA --> </div> </td> </tr> <tr class="paramSet odd xgl"> <td class="hd"><label>Masking</label></td> <td> <div class="fi"> <label for="MASK_CHAR"> Character: </label> <select name="MASK_CHAR" id="MASK_CHAR" class="reset" defval="2"> <option value="0">X for protein, n for nucleotide</option> <option value="2" selected="selected">Lower Case</option> </select> <label for="MASK_COLOR"> Color:</label> <select name="MASK_COLOR" id="MASK_COLOR" class="reset" defval="1"> <option value="0">Black </option> <option value="1" selected="selected">Grey </option> <option value="2">Red </option> </select> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Alignments masking help" id="maskingHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp4"> <li>Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein). </li> <li>Masking Color: Display masked sequence regions in the given color.</li> </ul> </div><!-- ARIA --> </div> </td> </tr> <tr id="lr" class="paramSet xgl"> <td class="hd"><label>Limit results</label></td> <td> <div class="fi"> <label for="FRM_DESCRIPTIONS">Descriptions:</label> <select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defval="100"> <option value="10">10</option> <option value="50">50</option> <option value="100" selected="selected">100</option> </select> <label for="FRM_NUM_OVERVIEW">Graphical overview:</label> <select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defval="100"> <option value="0">0</option> <option value="10">10</option> <option value="50">50</option> <option value="100" selected="selected">100</option> </select> <span class="hidden" id="frmAln"> <label for="FRM_ALIGNMENTS">Alignments:</label> <select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defval="100"> <option value="0">0</option> <option value="10">10</option> <option value="50">50</option> <option value="100" selected="selected">100</option> </select> </span> <label for="FRM_LINE_LENGTH">Line length:</label> <select name="LINE_LENGTH" id="FRM_LINE_LENGTH" class="reset" defval="60"> <option value="60" selected="selected">60</option> <option value="90">90</option> <option value="120">120</option> <option value="150">150</option> </select> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit number of descriptions/alignments help" id="numHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp5"> <li>Descriptions: Show short descriptions for up to the given number of sequences.</li> <li>Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.</li> <li>Line lenghth: ....</li> </ul> </div><!-- ARIA --> </div> </td> </tr> <tr class="paramSet odd xgl "> <td class="hd"></td> <td> <div class=""> <label for="qorganism">Organism</label> <span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br> <input role="textbox" aria-autocomplete="list" aria-haspopup="true" title="Use up and down arrows to choose an item from the autocomplete." name="FORMAT_ORGANISM" size="55" id="qorganism" value="Enter organism name or id--completions will be suggested" data-jigconfig="dictionary:'taxids_sg'" autocomplete="off" class="jig-ncbiautocomplete reset orgHint" type="text"> <input name="FORMAT_ORG_EXCLUDE" class="oExclR cb" id="orgExcl" type="checkbox"> <input value="1" name="FORMAT_NUM_ORG" id="numOrg" type="hidden"> <label for="orgExcl" class="right">Exclude</label> <a href="#" title="Add organism" id="addOrg"><img src="NCBI%20Blast%20reference%20example_files/addOrg.jpg" id="addOrgIm" alt="Add organism" mouseovimg="css/images/addOrgOver.jpg" mouseoutimg="css/images/addOrg.jpg" mousedownimg="css/images/addOrgDown.jpg" mouseupimg="css/images/addOrgOver.jpg" border="0"></a> <div id="orgs"> </div> <div class="fi"> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by organism help" id="organismHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp6"> Show only sequences from the given organism. </p> </div><!-- ARIA --> </div> </div> </td> </tr> <tr class="paramSet xgl "> <td class="hd"></td> <td> <div class="fi"> <label for="FORMAT_EQ_TEXT">Entrez query:</label> <input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" class="reset" type="text"> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by Entrez query help" id="entrezHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp7"> Show only those sequences that match the given Entrez query. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#limit_result" target="helpWin" title="Additional limit results by Entrez query help">more...</a> </p> </div><!-- ARIA --> </div> </td> </tr> <tr class="paramSet odd xgl"> <td class="hd"></td> <td> <div class="fi"> <label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" class="reset" type="text"> <label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" class="reset" type="text"> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by expect value range help" id="expectHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp8"> Show only sequences with expect values in the given range. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect_range" target="helpWin" title="Additional limit results by expect value range help">more...</a> </p> </div><!-- ARIA --> </div> </td> </tr> <tr class="paramSet xgl"> <td class="hd"></td> <td> <div class="fi"> <label for="PERC_IDENT_LOW">Percent Identity Min:</label> <input name="PERC_IDENT_LOW" id="PERC_IDENT_LOW" size="10" class="reset" type="text"> <label for="PERC_IDENT_HIGH">Percent Identity Max:</label> <input name="PERC_IDENT_HIGH" id="PERC_IDENT_HIGH" size="10" class="reset" type="text"> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Limit results by percent identity range help" id="percIdentHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp10"> Show only sequences with percent identity values in the given range. </p> </div><!-- ARIA --> </div> </td> </tr> <tr class="psiBlast odd paramSet xgl"> <td class="hd"><label>Format for</label></td> <td> <div class="fi"> <input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" class="cb psiBlast" type="checkbox"> <label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label> <label for="I_THRESH">with inclusion threshold:</label> <input name="I_THRESH" id="I_THRESH" size="10" defval="0.005" type="text"> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="PSI BLAST formatting help" id="psiHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> <div class="ui-helper-reset" aria-live="assertive"> <ul aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp9"> <li>Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query, in which sequences found in one round of search are used to build a custom score model for the next round. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a> </li> <li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.</li> </ul> </div><!-- ARIA --> </div> </td> </tr> </tbody></table> <input name="ViewReport" value="ViewReport" type="hidden"> <input name="REFORMAT_REPORT" value="shown" type="hidden"> <input name="RID" value="PHWP1JNZ014" type="hidden"> <input name="CDD_RID" value="" type="hidden"> <input name="CDD_SEARCH_STATE" value="" type="hidden"> <input name="STEP_NUMBER" value="" id="stepNumber" type="hidden"> <input name="CMD" value="Get" type="hidden"> <input name="FORMAT_EQ_OP" value="AND" type="hidden"> <input name="RESULTS_PAGE_TARGET" id="resPageTarget" value="" type="hidden"> <!-- <input name="QUERY_INFO" type="hidden" value="Nucleotide Sequence (16 letters)" /> --> <!-- <input name="ENTREZ_QUERY" type="hidden" value="" /> --> <input name="QUERY_INDEX" value="0" type="hidden"> <input name="NUM_QUERIES" value="1" type="hidden"> <input name="PHI_PTTRN_INDEX" value="" type="hidden"> <input id="cfcDsSave" name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden"> <!-- Those params are set in the template (blastn.dat, blastp.dat etc. --> <input name="BLAST_PROGRAMS" value="blastn" type="hidden"> <input name="PAGE" value="Nucleotides" type="hidden"> <input name="PROGRAM" value="blastn" type="hidden"> <input name="MEGABLAST" value="" type="hidden"> <input name="RUN_PSIBLAST" value="" type="hidden"> <input name="BLAST_SPEC" id="blastSpec" value="" type="hidden"> <input name="QUERY" value="" type="hidden"> <input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden"> <input name="QUERY_TO" value="" type="hidden"> <input name="QUERY_FROM" value="" type="hidden"> <input name="EQ_TEXT" value="" type="hidden"> <input name="ORGN" value="" type="hidden"> <input name="EQ_MENU" value="" type="hidden"> <input name="ORG_EXCLUDE" value="" type="hidden"> <input name="PHI_PATTERN" value="" type="hidden"> <input name="EXPECT" value="1000" type="hidden"> <input name="DATABASE" value="pdb" type="hidden"> <input name="DB_GROUP" value="" type="hidden"> <input name="SUBGROUP_NAME" value="" type="hidden"> <input name="GENETIC_CODE" value="" type="hidden"> <input name="WORD_SIZE" value="7" type="hidden"> <input name="MATCH_SCORES" value="1,-3" type="hidden"> <input name="MATRIX_NAME" value="" type="hidden"> <input name="GAPCOSTS" value="5 2" type="hidden"> <input name="MAX_NUM_SEQ" id="maxNumSeq" value="100" type="hidden"> <input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden"> <input name="NEWWIN" value="" type="hidden"> <input name="SHORT_QUERY_ADJUST" value="on" type="hidden"> <input name="FILTER" value="" type="hidden"> <input name="REPEATS" value="repeat_9606" type="hidden"> <input name="ID_FOR_PSSM" value="" type="hidden"> <input name="EXCLUDE_MODELS" value="" type="hidden"> <input name="EXCLUDE_SEQ_UNCULT" value="" type="hidden"> <input name="WP_PROTEINS" value="" type="hidden"> <input name="SEQ_FROM_TYPE" value="" type="hidden"> <input name="ENTREZ_QUERY_PRESET" value="" type="hidden"> <input name="ENTREZ_QUERY_PRESET_EXCL" value="" type="hidden"> <input name="NUM_ORG" value="1" type="hidden"> <!-- PSSM --> <input name="LCASE_MASK" value="" type="hidden"> <input name="TEMPLATE_TYPE" value="" type="hidden"> <input name="TEMPLATE_LENGTH" value="" type="hidden"> <input name="I_THRESH" value="" type="hidden"> <input name="PSI_PSEUDOCOUNT" value="" type="hidden"> <input name="DI_THRESH" id="diThresh" value="" type="hidden"> <input name="HSP_RANGE_MAX" value="0" type="hidden"> <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden"> <input name="MIXED_QUERIES" value="" type="hidden"> <input name="MIXED_DATABASE" id="mixedDb" value="" type="hidden"> <input name="BUILD_NAME" value="" type="hidden"> <input name="ORG_DBS" value="" type="hidden"> </form> </div> <!-- aria --> <div class="ui-helper-reset" aria-live="assertive"> <form aria-hidden="true" name="FormatDownload" id="FormatDownload" class="resbox ui-ncbitoggler-slave ui-ncbitoggler"> <table class="options dwnl "> <tbody><tr><td class="frh" colspan="6"><div class="tb">Download</div></td></tr> <tr> <td id="tdal"> <div class="dnHeader">Alignment</div> <div class="dnLinks"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&ALIGNMENTS=100&CMD=Get">Text</a> <a class="xgl" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get">XML</a> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=Alignment&CMD=Get">ASN.1</a> <a id="hitText" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get">Hit Table(text)</a> <a id="hitCvs" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=CSV&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get">Hit Table(csv)</a> </div> </td> <td class="dnl xgl"> <div class="dnHeader">Search Strategies</div> <div class="dnLinks"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on&RID=PHWP1JNZ014&DOWNLOAD_OPTIONS=true">ASN.1</a> </div> </td> <td class="dnl hidden" id="dnPSSMPar"> <div class="dnHeader">PssmWithParameters</div> <div class="dnLinks"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=PSSM_Scoremat&CMD=Get">ASN.1</a> </div> </td> <td> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Download help" data-ncbitoggler-toggles="hlp11" id="dnHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> </td> </tr> </tbody></table> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler" id="hlp11"> The Download link provides BLAST output that may be used as input to another program. This includes parseable formats such as the tabular report or XML as well as the Search Strategy files read by the BLAST+ applications. More details on the parseable (XML, tabular, and ASN.1) reports can be found at <a href="http://www.ncbi.nlm.nih.gov/books/NBK21097/" target="helpWin">http://www.ncbi.nlm.nih.gov/books/NBK21097/</a><br> <br> The following formats are offered under the Alignment section:<br> 1). "Text". Non-HTML standard BLAST report.<br> 2). "XML". XML report based upon the DTD at <a href="http://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd" target="helpWin">http://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd</a><br> 3). "ASN.1" Alignment. This is the alignment written out in Abstract Syntax Notation 1.<br> 4). "Hit Table(text)". The tabular report as text.<br> 5). "Hit Table(csv)". The tabular report ready for import into spread-sheet programs like Excel.<br> <br> The following report is offered under the Search Strategy section:<br> 1). "ASN.1" Search Strategy. A record of the parameters, query, and database used in the search. This file can be used to start a stand-alone BLAST search, see <a href="http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra" target="helpWin">http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra</a> </p> </div><!-- ARIA --> </form> </div> <!-- aria --> <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" name="overview0"> <input name="ADJUSTED_FOR_SHORT_QUERY" value="on" type="hidden"><input name="ALIGNMENTS" value="100" type="hidden"><input name="ALIGNMENT_VIEW" value="Pairwise" type="hidden"><input name="BLAST_PROGRAMS" value="blastn" type="hidden"><input name="CLIENT" value="web" type="hidden"><input name="COMPOSITION_BASED_STATISTICS" value="0" type="hidden"><input name="CONFIG_DESCR" value="2,3,4,5,6,7,8" type="hidden"><input name="DATABASE" value="pdb" type="hidden"><input name="DBTYPE" value="gc" type="hidden"><input name="DEFAULT_PROG" value="megaBlast" type="hidden"><input name="DESCRIPTIONS" value="100" type="hidden"><input name="DYNAMIC_FORMAT" value="on" type="hidden"><input name="EQ_OP" value="AND" type="hidden"><input name="EXPECT" value="1000" type="hidden"><input name="FORMAT_NUM_ORG" value="1" type="hidden"><input name="FORMAT_OBJECT" value="Alignment" type="hidden"><input name="FORMAT_TYPE" value="HTML" type="hidden"><input name="FULL_DBNAME" value="pdb" type="hidden"><input name="GAPCOSTS" value="5 2" type="hidden"><input name="GET_SEQUENCE" value="on" type="hidden"><input name="HSP_RANGE_MAX" value="0" type="hidden"><input name="JOB_TITLE" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="LAYOUT" value="OneWindow" type="hidden"><input name="LINE_LENGTH" value="60" type="hidden"><input name="MASK_CHAR" value="2" type="hidden"><input name="MASK_COLOR" value="1" type="hidden"><input name="MATCH_SCORES" value="1,-3" type="hidden"><input name="MAX_NUM_SEQ" value="100" type="hidden"><input name="NUCL_PENALTY" value="-2" type="hidden"><input name="NUCL_REWARD" value="1" type="hidden"><input name="NUM_DIFFS" value="1" type="hidden"><input name="NUM_OPTS_DIFFS" value="0" type="hidden"><input name="NUM_ORG" value="1" type="hidden"><input name="NUM_OVERVIEW" value="100" type="hidden"><input name="OLD_BLAST" value="false" type="hidden"><input name="OLD_VIEW" value="false" type="hidden"><input name="PAGE" value="Nucleotides" type="hidden"><input name="PAGE_TYPE" value="BlastSearch" type="hidden"><input name="PROGRAM" value="blastn" type="hidden"><input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden"><input name="QUERY_LENGTH" value="16" type="hidden"><input name="REPEATS" value="repeat_9606" type="hidden"><input name="RID" value="PHWP1JNZ014" type="hidden"><input name="RTOE" value="42" type="hidden"><input name="SEARCH_DB_STATUS" value="43" type="hidden"><input name="SELECTED_PROG_TYPE" value="megaBlast" type="hidden"><input name="SERVICE" value="plain" type="hidden"><input name="SHORT_QUERY_ADJUST" value="on" type="hidden"><input name="SHOW_LINKOUT" value="on" type="hidden"><input name="SHOW_OVERVIEW" value="on" type="hidden"><input name="USER_DEFAULT_MATCH_SCORES" value="0" type="hidden"><input name="USER_DEFAULT_PROG_TYPE" value="megaBlast" type="hidden"><input name="USER_TYPE" value="2" type="hidden"><input name="WORD_SIZE" value="7" type="hidden"><input name="_PGR" value="2" type="hidden"><input name="db" value="nucleotide" type="hidden"><input name="stype" value="nucleotide" type="hidden"> <input name="CMD" value="Get" type="hidden"> <p id="qb"><!-- QBlastInfoBegin Status=READY QBlastInfoEnd --></p> <div id="page"> <div id="summary" class=""> <div id="ht"></div> <h1>Nucleotide Sequence (16 letters) <span id="hdTitle" class="shownInl"></span></h1> <div> <div id="multipleSeqs" class="hidden"> <label for="queryList">Results for:</label> <select id="queryList" name="queryList"> <option value="0" selected="selected" class="">lcl|59987 None(16bp)</option> </select> <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="queryInfo" title="Multiple quries help" id="queryHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a> </div><!--/#multipleSeqs"--> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" id="queryInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> Your BLAST job specified more than one input sequence. This box lets you choose which input sequence to show BLAST results for. </p> </div><!-- ARIA --> </div> <div id="summarylists"> <dl> <dt>RID</dt> <dd> <a title="BLAST search request ID" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014">PHWP1JNZ014</a> (Expires on 05-07 22:33 pm) </dd> </dl> <div id="querysummary"> <dl> <dt>Query ID</dt> <dd class="hidden"> <a title="Find query in Entrez" href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=nucleotide&term=59987&dopt=GenBank" target="lnkPHWP1JNZ014">lcl|59987</a> </dd> <dd class="">lcl|59987</dd> <dt>Description</dt> <dd>None</dd> <dt>Molecule type</dt> <dd>nucleic acid</dd> <dt>Query Length</dt> <dd>16</dd> </dl> </div><!--/#querysummary--> <div id="dbsummary"> <dl> <dt> </dt><dd> </dd> <dt>Database Name</dt> <dd>pdb</dd> <dt>Description</dt> <dd>PDB nucleotide database <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="See multiple databases detailed information" class="jtg resArrowLinkB hidden jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="dbDetails" id="showDetails"><span class="ui-ncbitoggler-master-text">See details</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd> <!-- -- Database or subject info ----> <dt class="xgl">Program</dt> <dd class="xgl">BLASTN 2.2.29+ <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="How to cite BLAST in publications" class="resArrowLinkB hidden shown jig-ncbitoggler ui-ncbitoggler jtg ui-widget" data-ncbitoggler-toggles="refInfo" id="showRefs"><span class="ui-ncbitoggler-master-text">Citation</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd> </dl> </div><!--/#dbsummary--> </div><!--/#summarylists --> <br> <div class="ui-helper-reset" aria-live="assertive"> <div aria-hidden="true" id="dbDetails" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> <!-- multiple databases or subjects table --> </div> </div> <!-- aria end --> <div class="ui-helper-reset" aria-live="assertive"> <div aria-hidden="true" id="refInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9254694&dopt=Citation">Reference </a> <div>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</div> </div> <!-- refInfo --> </div> <!-- aria end --> <div id="seealso"> <label>Other reports:</label> <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="Show statistics" class="resArrowLinkB jtg jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="resStat" id="showStat"><span class="ui-ncbitoggler-master-text">Search Summary</span><span class="ui-icon ui-icon-triangle-1-e"></span></a> <span class="xgl"> <a id="tax" class="hidden shown" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=PHWP1JNZ014&FORMAT_OBJECT=TaxBlast&NCBI_GI=off&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_BLOCK_ON_RESPAGE=Top&MASK_COLOR=1&MASK_CHAR=2" target="lnkPHWP1JNZ014" title="See results arranged by taxonomy">[Taxonomy reports]</a> <a href="http://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&blastRID=PHWP1JNZ014&queryID=lcl%7C59987&entrezLim=&ex=&exl=&exh=&ns=100" class="" id="TreeViewlcl|59987" onclick="ViewTree('TreeViewlcl|59987');return false;" target="lnkPHWP1JNZ014" title="See a distance tree of these pairwise comparisons">[Distance tree of results]</a> </span> </div> <!-- seealso --> <div class="ui-helper-reset" aria-live="assertive"> <div aria-hidden="true" id="resStat" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> <table id="params" class="dbInfo"> <caption>Search Parameters</caption> <tbody><tr><th><div>Search parameter name</div></th><th><div>Search parameter value</div></th></tr> <tr><td>Program</td><td>blastn</td></tr><tr><td>Word size</td><td>7</td></tr><tr><td>Expect value</td><td>1000</td></tr><tr><td>Hitlist size</td><td>100</td></tr><tr><td>Match/Mismatch scores</td><td>1,-3</td></tr><tr><td>Gapcosts</td><td>5,2</td></tr><tr><td>Filter string </td><td>F</td></tr><tr><td>Genetic Code</td><td>1</td></tr> </tbody></table> <table id="dbStat" class="dbInfo"> <caption>Database</caption> <tbody><tr><th><div>Database parameter name</div></th><th><div>Database parameter value</div></th></tr> <tr><td>Posted date</td><td>Apr 29, 2014 3:14 AM</td></tr> <tr><td>Number of letters</td><td>885,284</td></tr> <tr><td>Number of sequences</td><td>8,975</td></tr> <tr><td>Entrez query</td><td>none</td></tr> </tbody></table> <table id="Kappa" class="dbInfo show xgl"> <caption>Karlin-Altschul statistics</caption> <tbody><tr><th><div>Params</div></th><th><div>Ungapped</div></th><th><div>Gapped</div></th></tr> <tr><td>Lambda</td><td>1.37406</td><td>1.37406</td></tr> <tr><td>K</td><td>0.710603</td><td>0.710603</td></tr> <tr><td>H</td><td>1.30725</td><td>1.30725</td></tr> </tbody></table> <table class="dbInfo show"> <caption>Results Statistics</caption> <tbody><tr><th><div>Results Statistics parameter name</div></th><th><div>Results Statistics parameter value</div></th></tr> <tr><td>Length adjustment</td><td> 11</td></tr><tr><td>Effective length of query</td><td> 5</td></tr><tr><td>Effective length of database</td><td> 786559</td></tr><tr><td>Effective search space</td><td> 3932795</td></tr><tr><td>Effective search space used</td><td> 3932795</td></tr> </tbody></table> <!-- Results statistics --> </div> <!-- resStat --> </div> <!-- aria end --> </div><!--/#summary--> </div><!--/#page--> <iframe id="RSIFrameDesc" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="NCBI%20Blast%20reference%20example_files/plinkcgi.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe> <div id="grView" class="hidden shown"> <h2 class="resArr"> <a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showGraphic" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="graphicInfo" title="Show/hide Graphic Summary"> <span class="ui-ncbitoggler-master-text">Graphic Summary</span> <span class="ui-icon ui-icon-plus-minus-big-open"></span> </a> </h2> <div class="ui-helper-reset" aria-live="assertive"> <div aria-hidden="false" id="graphicInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler"> <div id="graphic" class="hidden shown"> <h3>Distribution of 45 Blast Hits on the Query Sequence <a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Graphic summary help" id="grHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> <span class="ui-icon ui-icon-triangle-1-e"></span></a></h3> <div class="ui-helper-reset" aria-live="assertive"> <p aria-hidden="true" id="ovrInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five different colors, which divides the range of scores into five groups. Multiple alignments on the same database sequence are connected by a striped line. <span class="hl">Mousing over</span> a hit sequence causes the definition and score to be shown in the window at the top, <span class="hl">clicking</span> on a hit sequence takes the user to the associated alignments. New: This graphic is an overview of database sequences aligned to the query sequence. Alignments are color-coded by score, within one of five score ranges. Multiple alignments on the same database sequence are connected by a dashed line. <span class="hl">Mousing</span> over an alignment shows the alignment definition and score in the box at the top. <span class="hl">Clicking</span> an alignment displays the alignment detail. </p> </div><!-- ARIA --> <center><input name="defline" size="85" value="Mouse-over to show defline and scores, click to show alignments" type="text"><table bordercolordark="#0000FF" bordercolorlight="#0000FF" border="1" cellpadding="10" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/score.gif" height="40" width="500"></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/query_no_scale.gif" height="10" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="51"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="91"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/scale.gif" height="10" width="2"></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/3.gif" height="13" width="10"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/6.gif" height="13" width="10"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="83"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/9.gif" height="13" width="10"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="73"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/2.gif" height="13" width="10"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="73"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/1.gif" height="13" width="10"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/5.gif" height="13" width="10"></td> </tr></tbody></table> <br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804451" onclick='DisplayAlignFromGraphics("557804451",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J5A_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804395" onclick='DisplayAlignFromGraphics("557804395",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J58_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804339" onclick='DisplayAlignFromGraphics("557804339",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J56_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804283" onclick='DisplayAlignFromGraphics("557804283",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J54_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804227" onclick='DisplayAlignFromGraphics("557804227",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J52_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804195" onclick='DisplayAlignFromGraphics("557804195",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J51_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804163" onclick='DisplayAlignFromGraphics("557804163",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J50_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#557804083" onclick='DisplayAlignFromGraphics("557804083",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J4X_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="500"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="250"></a></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td> <td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td> <td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. Sapiens 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 14" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=14 E=1.9e+02'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="219"></a></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td> <td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="155"></a></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/black.gif" height="6" width="1"></td> <td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=16 E=47'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="124"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="50"></td> <td align="LEFT" valign="CENTER"><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="94"></td> <td align="LEFT" valign="CENTER"><a href="#357380483" onclick='DisplayAlignFromGraphics("357380483",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J0O_8 Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex .. S=18 E=12'" src="NCBI%20Blast%20reference%20example_files/black.gif" height="4" border="0" width="281"></a></td> </tr></tbody></table> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="NCBI%20Blast%20reference%20example_files/white.gif" height="4" width="550"></td></tr></tbody></table> </td></tr></tbody></table> </center><hr> </div><!--/#graphic--> </div><!-- graphicInfo --> </div><!-- ARIA --> </div> <!--HITMATRIX_VIEW - only for bl2seq --> <div id="dscrView" class="hidden shown"> <h2 class="resArr"> <a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showDescr" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="descrInfo" title="Show/hide Descriptions"> <span class="ui-ncbitoggler-master-text">Descriptions</span> <span class="ui-icon ui-icon-plus-minus-big-open"></span> </a> </h2> <div class="ui-helper-reset" aria-live="assertive"> <div aria-hidden="false" id="descrInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler"> <!-- legend to links to other resources --> <a name="sort_mark"></a> <div id="debug">, Reading indexes 1-5, displaying indexes 1-5</div> <input id="Rid" value="PHWP1JNZ014" type="hidden"> <input id="useAlignDB" name="useAlignDB" value="" type="hidden"> <input id="dbType" value="GenBank" type="hidden"><!-- Indicates genbank, etc --> <input id="serviceType" value="plain" type="hidden"> <input id="clientType" value="web" type="hidden"> <input id="currQuery" value="" type="hidden"> <input id="minDispAlnLen" value="2000" type="hidden"> <input id="maxDispAlnLen" value="20000" type="hidden"> <div class="hidden" id="dynHspTmpl"><div class="alnParLinks moreHsps" id="@moreHspsID@"><a class="gbd toolsCtr navNext" title="Load matches @segs@ out of @totalHSP@ for @accs@" onmouseover="scan(this)" ref="range=@segs@&currseq=@alnSeqGi@" onclick="ReadNextHSPSet(@argstring@);"><span>Load next set</span></a><a class="gbd toolsCtr navPrev" title="Go to previous match #@aln_prev_num@ for @accs@" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a></div></div> <div id="descriptions" class="blRes"> <!--<pre> --> <div class="cap">Sequences producing significant alignments:</div> <a id="shcl" href="#" onclick="showAllCol(event,this)" class="shcl hidden"> Show all columns <span class="accsb"> of the table presenting sequences producing significant alignments </span> </a> <span id="cntDesc"> <span>Select:<a href="#" id="cntSelA" sel="all">All</a><a href="#" id="cntSelN" sel="n">None</a></span> <span>Selected:<span id="slcNum">0</span></span> </span> <div id="descTblCtrl" class="cnf"> <a href="#alignInfo" id="alnNav" class="toolsCtr alnNav" title="Go to alignments"><span>Alignments</span></a> <a aria-haspopup="true" aria-expanded="false" role="button" href="#dsDownload" minslct="1" class="jig-ncbipopper toolsCtr dnld dialog " data-jigconfig="hasArrow:'true',arrowDirection:'top'" id="dscDwnld" disabled="disabled" title="Download information for selected sequences"><span>Download</span></a> <div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsDownload" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> <div class=""><input name="dwn" checked="checked" id="dwFST" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST">FASTA (complete sequence)</label></div> <div class=""><input name="dwn" id="dwFSTAl" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl">FASTA (aligned sequences)</label></div> <div class=""><input name="dwn" id="dwGenBank" getgi="on" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class=" shownInl" for="dwGenBank">GenBank (complete sequence)</label></div> <div><input name="dwn" id="dwHitText" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get" type="radio"><label class="shownInl" for="dwHitText">Hit Table (text)</label></div> <div><input name="dwn" id="dwHitCsv" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=CSV&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get" type="radio"><label class="shownInl" for="dwHitCsv">Hit Table (CSV)</label></div> <div><input name="dwn" id="dwText" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwText">Text</label></div> <div><input name="dwn" id="dwXML" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwXML">XML</label></div> <div><input name="dwn" id="dwASN" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwASN">ASN.1</label></div> <div> <button class="cfg" id="dw_cont">Continue</button> <button class="cfg cnc">Cancel</button> </div> </div> <!-- dsDownload --> <a href="#" class="toolsCtr" minslct="1" view="dflt" frm="submitterTop" seqlist="selSeqs" title="See genbank report for selected sequences" disabled="disabled">GenBank</a> <!-- genbank or Traces --> <a href="#" class="toolsCtr " minslct="1" view="graph" title="See graphic representation for selected sequences" disabled="disabled">Graphics</a> <a href="#" class="toolsCtr hidden shown" view="tree" minslct="1" frm="sbmtTreeView" seqlist="selSeqsTr" disabled="disabled" title="See a distance tree of pairwise comparisons for the selected sequences">Distance tree of results</a> <a href="#" class="toolsCtr hidden " view="dflt" minslct="2" frm="sbmtMultiAln" seqlist="selSeqsMl" disabled="disabled" title="See multple alignment of query and target sequences for the selected sequences with expect value better than 0.001">Multiple alignment</a> <a aria-haspopup="true" aria-expanded="false" role="button" class="jig-ncbipopper button_config" title="Show/hide columns" id="button_config" href="#dsConfig"><span class="accsb">Show/hide columns of the table presenting sequences producing significant alignments </span></a> <div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsConfig" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> <div class="tl">Available columns</div> <input checked="checked" id="chkDs" value="2" type="checkbox"><label class="shownInl" for="chkDs">Description</label><br> <input checked="checked" id="chkMS" value="3" type="checkbox"><label class="shownInl" for="chkMs">Max Score</label><br> <input checked="checked" id="chkTS" value="4" type="checkbox"><label class="shownInl" for="chkTs">Total Score</label><br> <input checked="checked" id="chkCov" value="5" type="checkbox"><label class="shownInl" for="chkCov">Coverage</label><br> <input checked="checked" id="chkEval" value="6" type="checkbox"><label class="shownInl" for="chkEval">E-value</label><br> <input checked="checked" id="chkIdnt" value="7" type="checkbox"><label class="shownInl" for="chkIdnt"><span class="">Ident</span><span class="hidden">N</span></label><br> <input checked="checked" id="chkAcc" value="8" type="checkbox"><label class="shownInl" for="chkAcc">Accession</label><br> <button class="cfg rdf" id="dscRsDf">Restore Defaults</button> <button class="cfg" id="dscOk">Ok</button> <button class="cfg cnc" id="dscCnc">Cancel</button> </div> <!-- dsConfig --> <input id="cfcDsInf" defval="2,3,4,5,6,7,8" value="2,3,4,5,6,7,8" type="hidden"> </div> <div class="ui-ncbigrid-outer-div caption-exists"> <div class="ui-ncbigrid-inner-div"> <table id="dscTable" class="jig-ncbigrid ui-ncbigrid" data-jigconfig="" cellpadding="0" cellspacing="0"> <caption class="hdnHeader">Sequences producing significant alignments:</caption> <thead> <tr class="first"> <th class="c0" id="c0"><span>Select for downloading or viewing reports</span></th> <th class="dflnDth c2" id="c2">Description</th> <th class=" c3" id="c3"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=1&HSP_SORT=1" class="dcs" title="Sort by max score">Max score</a> </th> <th class=" c4" id="c4"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=2&HSP_SORT=1" class="dcs" title="Sort by total score">Total score</a> </th> <th class=" c5" id="c5"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=4&HSP_SORT=0" class="dcs" title="Sort by query coverage">Query cover</a> </th> <th class="sel c6" id="c6"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=0&HSP_SORT=0" class="dcs" title="Sort by E value">E value</a> </th> <th class="c7" id="c7"> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&DISPLAY_SORT=3&HSP_SORT=3" class="dcs" title="Sort by ident">Ident</a> </th> <th class="c1" id="c8">Accession</th> </tr> </thead> <tbody> <tr id="dtr_557804451" ind="1" class="odd dflLnk"> <td class="l c0"><span class="ind">1</span><input id="chk_1" class="cb" name="getSeqGi" value="557804451" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_1" class="accsb">Select seq pdb|3J5A|A</label></td> <td class="lim l c2"> <div class="lim n"> <a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="1" accs="pdb|3J5A|A" seqfsta="gi|557804451" gi="557804451" seqid="557804451" id="deflnDesc_1" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804451">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nucltop&blast_rank=1&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J5A_A">3J5A_A</a> </td> </tr><tr id="dtr_557804395" ind="2" class="even dflLnk"> <td class="l c0"><span class="ind">2</span><input id="chk_2" class="cb" name="getSeqGi" value="557804395" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_2" class="accsb">Select seq pdb|3J58|A</label></td> <td class="lim l c2"> <div class="lim n"> <a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="2" accs="pdb|3J58|A" seqfsta="gi|557804395" gi="557804395" seqid="557804395" id="deflnDesc_2" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804395">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nucltop&blast_rank=2&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J58_A">3J58_A</a> </td> </tr><tr id="dtr_557804339" ind="3" class="odd dflLnk"> <td class="l c0"><span class="ind">3</span><input id="chk_3" class="cb" name="getSeqGi" value="557804339" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_3" class="accsb">Select seq pdb|3J56|A</label></td> <td class="lim l c2"> <div class="lim n"> <a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="3" accs="pdb|3J56|A" seqfsta="gi|557804339" gi="557804339" seqid="557804339" id="deflnDesc_3" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804339">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nucltop&blast_rank=3&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J56_A">3J56_A</a> </td> </tr><tr id="dtr_557804283" ind="4" class="even dflLnk"> <td class="l c0"><span class="ind">4</span><input id="chk_4" class="cb" name="getSeqGi" value="557804283" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_4" class="accsb">Select seq pdb|3J54|A</label></td> <td class="lim l c2"> <div class="lim n"> <a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="4" accs="pdb|3J54|A" seqfsta="gi|557804283" gi="557804283" seqid="557804283" id="deflnDesc_4" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804283">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nucltop&blast_rank=4&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J54_A">3J54_A</a> </td> </tr><tr id="dtr_557804227" ind="5" class="odd dflLnk"> <td class="l c0"><span class="ind">5</span><input id="chk_5" class="cb" name="getSeqGi" value="557804227" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_5" class="accsb">Select seq pdb|3J52|A</label></td> <td class="lim l c2"> <div class="lim n"> <a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="5" accs="pdb|3J52|A" seqfsta="gi|557804227" gi="557804227" seqid="557804227" id="deflnDesc_5" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804227">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nucltop&blast_rank=5&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J52_A">3J52_A</a> </td> </tr><tr id="dtr_557804195" ind="6" class="even dflLnk"> <td class="l c0"><span class="ind">6</span><input id="chk_6" class="cb" name="getSeqGi" value="557804195" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_6" class="accsb">Select seq pdb|3J51|A</label></td> <td class="lim l c2"> <div class="lim n"> <a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="6" accs="pdb|3J51|A" seqfsta="gi|557804195" gi="557804195" seqid="557804195" id="deflnDesc_6" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804195">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804195?report=genbank&log$=nucltop&blast_rank=6&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J51_A">3J51_A</a> </td> </tr><tr id="dtr_557804163" ind="7" class="odd dflLnk"> <td class="l c0"><span class="ind">7</span><input id="chk_7" class="cb" name="getSeqGi" value="557804163" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_7" class="accsb">Select seq pdb|3J50|A</label></td> <td class="lim l c2"> <div class="lim n"> <a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="7" accs="pdb|3J50|A" seqfsta="gi|557804163" gi="557804163" seqid="557804163" id="deflnDesc_7" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804163">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804163?report=genbank&log$=nucltop&blast_rank=7&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J50_A">3J50_A</a> </td> </tr><tr id="dtr_557804083" ind="8" class="even dflLnk"> <td class="l c0"><span class="ind">8</span><input id="chk_8" class="cb" name="getSeqGi" value="557804083" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_8" class="accsb">Select seq pdb|3J4X|A</label></td> <td class="lim l c2"> <div class="lim n"> <a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="8" accs="pdb|3J4X|A" seqfsta="gi|557804083" gi="557804083" seqid="557804083" id="deflnDesc_8" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804083">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)</a> </div> </td> <td class="c3">32.2</td> <td class="c4">77.3</td> <td class="c5">100%</td> <td class="c6">8e-04</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804083?report=genbank&log$=nucltop&blast_rank=8&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J4X_A">3J4X_A</a> </td> </tr><tr id="dtr_485601478" ind="9" class="odd dflLnk"> <td class="l c0"><span class="ind">9</span><input id="chk_9" class="cb" name="getSeqGi" value="485601478" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_9" class="accsb">Select seq pdb|3J3F|5</label></td> <td class="lim l c2"> <div class="lim n"> <a title="Go to alignment for Chain 5, Structure Of The H. Sapiens 60s Rrna" class="deflnDesc" hsp="8" len="63" ind="9" accs="pdb|3J3F|5" seqfsta="gi|485601478" gi="485601478" seqid="485601478" id="deflnDesc_9" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601478">Chain 5, Structure Of The H. Sapiens 60s Rrna</a> </div> </td> <td class="c3">18.3</td> <td class="c4"> 128</td> <td class="c5">100%</td> <td class="c6"> 12</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601478?report=genbank&log$=nucltop&blast_rank=9&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3F_5">3J3F_5</a> </td> </tr><tr id="dtr_485601474" ind="10" class="even dflLnk"> <td class="l c0"><span class="ind">10</span><input id="chk_10" class="cb" name="getSeqGi" value="485601474" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_10" class="accsb">Select seq pdb|3J3E|5</label></td> <td class="lim l c2"> <div class="lim n"> <a title="Go to alignment for Chain 5, Structure Of The D. Melanogaster 60s Rrna" class="deflnDesc" hsp="4" len="31" ind="10" accs="pdb|3J3E|5" seqfsta="gi|485601474" gi="485601474" seqid="485601474" id="deflnDesc_10" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601474">Chain 5, Structure Of The D. Melanogaster 60s Rrna</a> </div> </td> <td class="c3">18.3</td> <td class="c4">63.4</td> <td class="c5">100%</td> <td class="c6"> 12</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601474?report=genbank&log$=nucltop&blast_rank=10&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3E_5">3J3E_5</a> </td> </tr><tr id="dtr_357380483" ind="11" class="odd dflLnk"> <td class="l c0"><span class="ind">11</span><input id="chk_11" class="cb" name="getSeqGi" value="357380483" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_11" class="accsb">Select seq pdb|3J0O|8</label></td> <td class="lim l c2"> <div class="lim n"> <a title="Go to alignment for Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2" class="deflnDesc" hsp="1" len="9" ind="11" accs="pdb|3J0O|8" seqfsta="gi|357380483" gi="357380483" seqid="357380483" id="deflnDesc_11" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_357380483">Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2</a> </div> </td> <td class="c3">18.3</td> <td class="c4">18.3</td> <td class="c5">56%</td> <td class="c6"> 12</td><td class="c7">100%</td> <td class="c1 l lim"> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/357380483?report=genbank&log$=nucltop&blast_rank=11&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J0O_8">3J0O_8</a> </td> </tr> </tbody> </table> </div></div> <!--</pre> --> </div><!--/#descriptions--> </div><!-- descrInfo --> </div><!--ARIA--> </div> </form><!-- this is the end tag for the <form in blastcgi templates --> <form id="dwdlSubmit" action="" method="post" class="getseq"> <input name="" value="" id="selDnSeqs" type="hidden"> </form> <form class="getseq" method="post" seqsform="getSeqAlignment1" action="http://www.ncbi.nlm.nih.gov/sites/entrez" target="lnkPHWP1JNZ014" id="submitterTop"> <input name="db" value="Nucleotide" type="hidden"> <input id="selSeqs" name="term" value="" type="hidden"> <input name="doptcmdl" value="docsum" type="hidden"> <input name="cmd" value="search" type="hidden"> </form> <form class="getseq" method="get" action="http://www.ncbi.nlm.nih.gov/projects/sviewer/" target="lnkPHWP1JNZ014" id="sbmtGraphics"> <input id="ridParam" value="PHWP1JNZ014" type="hidden"> <input id="seqViewParams" name="RID" value="" type="hidden"> <input name="appname" value="ncbiblast" type="hidden"> <input name="link_loc" value="fromDescr" type="hidden"> <input name="tracks" value="[key:sequence_track,ShowLabel:true]" type="hidden"> <input name="id" value="" type="hidden"> </form> <form class="getseq" method="post" action="http://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&blastRID=PHWP1JNZ014&queryID=lcl|59987&entrezLim=&ex=&exl=&exh=&ns=100" id="sbmtTreeView" target="lnkPHWP1JNZ014"> <input id="selSeqsTr" name="sequenceSet" value="" type="hidden"> <input id="scrWidth" name="screenWidth" value="" type="hidden"> <input id="scrHeight" name="screenHeight" value="" type="hidden"> </form> <form class="getseq" method="post" action="?CMD=submit&blastRID=PHWP1JNZ014&queryID=lcl|59987&numSeqs=100" id="sbmtMultiAln" target="lnkPHWP1JNZ014"> <input id="selSeqsMl" name="sequenceSet" value="" type="hidden"> </form> <form class="getseq" enctype="text/plain" method="post" action="http://blast.ncbi.nlm.nih.gov/blast/SEQDUMP/seqdump.cgi" id="sbmtFASTA"> <input name="RID" value="PHWP1JNZ014" type="hidden"> <input name="DATABASE" value="" type="hidden"> <input name="ALIGNDB_BATCH_ID" value="" type="hidden"> <input name="ALIGNDB_MASTER_ALIAS" value="" type="hidden"> <input name="ALIGNDB_CGI_HOST" value="" type="hidden"> <input name="ALIGNDB_CGI_PATH" value="" type="hidden"> <input name="SERVICE_TYPE" value="plain" type="hidden"> <input name="DBTYPE" value="nucl" type="hidden"> <input name="DOWNLOAD_TYPE" value="" type="hidden"> <input name="ALIGN_SEQ_LIST" value="" type="hidden"> </form><!-- used in redesign --> <iframe id="RSIFrameAln" class="ifrm shown" name="RSIFrame" noresize="noresize" border="0" cellspacing="0" scrolling="no" marginwidth="0" marginheight="0" src="NCBI%20Blast%20reference%20example_files/plinkcgi_002.html" title="Primer-BLAST ad" frameborder="0" align="middle"></iframe> <div id="alignView" class=" "> <h2 class="resArr"> <a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showAlign" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="alignInfo" title="Show/hide Alignments"> <span class="ui-ncbitoggler-master-text">Alignments</span> <span class="ui-icon ui-icon-plus-minus-big-open"></span> </a> </h2> <div class="ui-helper-reset" aria-live="assertive"> <div aria-hidden="false" id="alignInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler"> <div id="alignments" class="blRes"> <span id="alnStart"></span><div seqlist="gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227" indexes="1-5" id="alnShow_1" class="alnMsg"><div class="alnMsgS hidden" id="alnMsg_1">Loading alignment...<span class="db"> for sequences gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227 Reading indexes 1-5</span></div><div id="alnShowReal_1" class="alnMsgR"><form name="getSeqAlignment1"> <div class="alnHdr cnf" id="alnHdr_557804451" seqid="557804451" accs="pdb|3J5A|A"> <a name="557804451"></a> <a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804451" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804451" title="Download information for pdb|3J5A|A"><span>Download</span></a> <div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804451" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> <div><input seqfsta="gi|557804451" name="dwn_557804451" checked="checked" id="dwFST_557804451" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804451">FASTA (complete sequence)</label></div> <div><input seqfsta="gi|557804451" name="dwn_557804451" id="dwFSTAl_557804451" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804451">FASTA (aligned sequences)</label></div> <div class=""><input name="dwn_557804451" id="dwGenBank_557804451" getgi="557804451" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804451">GenBank (complete sequence)</label></div> <div> <button class="cfg" id="dw_cont_557804451">Continue</button> <button class="cfg cnc">Cancel</button> </div> </div> <!-- dsDownload --> <span class="csLinks" id="csLinks_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics">Graphics</a></span> <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> <select id="sa_557804451" onchange="SortHSPAlnSel(event,this)"> <option selected="selected" value="0">E value</option> <option value="1"> Score</option> <option value="3">Percent identity</option> <option value="2">Query start position</option> <option value="4">Subject start position</option> </select> </div> <span class="alnSeqLinks"> <a title="Go to next alignment for pdb|3J58|A" class="gbd toolsCtr navNext" ref="ordinalpos=1&currseq=557804451" id="alnNxt_557804451" onclick="goToNextAlign('dtr_557804451',true);"><span>Next</span></a> <a disabled="disabled" class="gbd toolsCtr navPrev" ref="ordinalpos=1&currseq=557804451" id="alnPrv_557804451" onclick="goToNextAlign('dtr_557804451',false);"><span>Previous</span></a> <a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J5A|A" id="alnDsc_557804451" onclick="goToDefLine('dtr_557804451');" href="#dtr_557804451"><span>Descriptions</span></a> </span> </div> <div class="oneSeqAln" id="aln_557804451"> <div id="dln_557804451"> <div class="dlfRow"> Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit) <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J5A|A">pdb|3J5A|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> </div> </div> <div class="relInf" id="relInf_557804451"><label>Related Information</label></div> <!-- <pre> <@aln_gene_info@> </pre> --> <div class="alnAll" id="alnAll_557804451"><div id="hd_557804451_1"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> <span id="hsp557804451_1" class="alnParLinks"> <a init="on" class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack hidden" href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #1</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>32.2 bits(16)</td> <td>8e-04<span class="sumN ">()</span></td> <td>16/16(100%)</td> <td>0/16(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804451_1"> <pre>Query 1 CGTCCGTCGTGAAGAG 16 |||||||||||||||| Sbjct 961 CGTCCGTCGTGAAGAG 976 </pre> </div> <div id="hd_557804451_2"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> <span id="hsp557804451_2" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #2</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>16.4 bits(8)</td> <td> 47<span class="sumN ">()</span></td> <td>8/8(100%)</td> <td>0/8(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804451_2"> <pre>Query 5 CGTCGTGA 12 |||||||| Sbjct 2591 CGTCGTGA 2598 </pre> </div> <div id="hd_557804451_3"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> <span id="hsp557804451_3" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #3</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804451_3"> <pre>Query 7 TCGTGAA 13 ||||||| Sbjct 839 TCGTGAA 845 </pre> </div> <div id="hd_557804451_4"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> <span id="hsp557804451_4" class="alnParLinks"> <a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #4</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804451_4"> <pre>Query 9 GTGAAGA 15 ||||||| Sbjct 2027 GTGAAGA 2033 </pre> </div> </div> <!-- alnAll_557804451 --> </div> <!-- aln_557804451 --> <div class="alnHdr cnf" id="alnHdr_557804395" seqid="557804395" accs="pdb|3J58|A"> <a name="557804395"></a> <a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804395" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804395" title="Download information for pdb|3J58|A"><span>Download</span></a> <div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804395" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> <div><input seqfsta="gi|557804395" name="dwn_557804395" checked="checked" id="dwFST_557804395" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804395">FASTA (complete sequence)</label></div> <div><input seqfsta="gi|557804395" name="dwn_557804395" id="dwFSTAl_557804395" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804395">FASTA (aligned sequences)</label></div> <div class=""><input name="dwn_557804395" id="dwGenBank_557804395" getgi="557804395" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804395">GenBank (complete sequence)</label></div> <div> <button class="cfg" id="dw_cont_557804395">Continue</button> <button class="cfg cnc">Cancel</button> </div> </div> <!-- dsDownload --> <span class="csLinks" id="csLinks_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics">Graphics</a></span> <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> <select id="sa_557804395" onchange="SortHSPAlnSel(event,this)"> <option selected="selected" value="0">E value</option> <option value="1"> Score</option> <option value="3">Percent identity</option> <option value="2">Query start position</option> <option value="4">Subject start position</option> </select> </div> <span class="alnSeqLinks"> <a title="Go to next alignment for pdb|3J56|A" class="gbd toolsCtr navNext" ref="ordinalpos=2&currseq=557804395" id="alnNxt_557804395" onclick="goToNextAlign('dtr_557804395',true);"><span>Next</span></a> <a title="Go to previous alignment for pdb|3J5A|A" class="gbd toolsCtr navPrev" ref="ordinalpos=2&currseq=557804395" id="alnPrv_557804395" onclick="goToNextAlign('dtr_557804395',false);"><span>Previous</span></a> <a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J58|A" id="alnDsc_557804395" onclick="goToDefLine('dtr_557804395');" href="#dtr_557804395"><span>Descriptions</span></a> </span> </div> <div class="oneSeqAln" id="aln_557804395"> <div id="dln_557804395"> <div class="dlfRow"> Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit) <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J58|A">pdb|3J58|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> </div> </div> <div class="relInf" id="relInf_557804395"><label>Related Information</label></div> <!-- <pre> <@aln_gene_info@> </pre> --> <div class="alnAll" id="alnAll_557804395"><div id="hd_557804395_1"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> <span id="hsp557804395_1" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack hidden" href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #1</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>32.2 bits(16)</td> <td>8e-04<span class="sumN ">()</span></td> <td>16/16(100%)</td> <td>0/16(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804395_1"> <pre>Query 1 CGTCCGTCGTGAAGAG 16 |||||||||||||||| Sbjct 961 CGTCCGTCGTGAAGAG 976 </pre> </div> <div id="hd_557804395_2"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> <span id="hsp557804395_2" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #2</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>16.4 bits(8)</td> <td> 47<span class="sumN ">()</span></td> <td>8/8(100%)</td> <td>0/8(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804395_2"> <pre>Query 5 CGTCGTGA 12 |||||||| Sbjct 2591 CGTCGTGA 2598 </pre> </div> <div id="hd_557804395_3"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> <span id="hsp557804395_3" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #3</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804395_3"> <pre>Query 7 TCGTGAA 13 ||||||| Sbjct 839 TCGTGAA 845 </pre> </div> <div id="hd_557804395_4"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> <span id="hsp557804395_4" class="alnParLinks"> <a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #4</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804395_4"> <pre>Query 9 GTGAAGA 15 ||||||| Sbjct 2027 GTGAAGA 2033 </pre> </div> </div> <!-- alnAll_557804395 --> </div> <!-- aln_557804395 --> <div class="alnHdr cnf" id="alnHdr_557804339" seqid="557804339" accs="pdb|3J56|A"> <a name="557804339"></a> <a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804339" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804339" title="Download information for pdb|3J56|A"><span>Download</span></a> <div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804339" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> <div><input seqfsta="gi|557804339" name="dwn_557804339" checked="checked" id="dwFST_557804339" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804339">FASTA (complete sequence)</label></div> <div><input seqfsta="gi|557804339" name="dwn_557804339" id="dwFSTAl_557804339" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804339">FASTA (aligned sequences)</label></div> <div class=""><input name="dwn_557804339" id="dwGenBank_557804339" getgi="557804339" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804339">GenBank (complete sequence)</label></div> <div> <button class="cfg" id="dw_cont_557804339">Continue</button> <button class="cfg cnc">Cancel</button> </div> </div> <!-- dsDownload --> <span class="csLinks" id="csLinks_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics">Graphics</a></span> <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> <select id="sa_557804339" onchange="SortHSPAlnSel(event,this)"> <option selected="selected" value="0">E value</option> <option value="1"> Score</option> <option value="3">Percent identity</option> <option value="2">Query start position</option> <option value="4">Subject start position</option> </select> </div> <span class="alnSeqLinks"> <a title="Go to next alignment for pdb|3J54|A" class="gbd toolsCtr navNext" ref="ordinalpos=3&currseq=557804339" id="alnNxt_557804339" onclick="goToNextAlign('dtr_557804339',true);"><span>Next</span></a> <a title="Go to previous alignment for pdb|3J58|A" class="gbd toolsCtr navPrev" ref="ordinalpos=3&currseq=557804339" id="alnPrv_557804339" onclick="goToNextAlign('dtr_557804339',false);"><span>Previous</span></a> <a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J56|A" id="alnDsc_557804339" onclick="goToDefLine('dtr_557804339');" href="#dtr_557804339"><span>Descriptions</span></a> </span> </div> <div class="oneSeqAln" id="aln_557804339"> <div id="dln_557804339"> <div class="dlfRow"> Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit) <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J56|A">pdb|3J56|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> </div> </div> <div class="relInf" id="relInf_557804339"><label>Related Information</label></div> <!-- <pre> <@aln_gene_info@> </pre> --> <div class="alnAll" id="alnAll_557804339"><div id="hd_557804339_1"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> <span id="hsp557804339_1" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack hidden" href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #1</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>32.2 bits(16)</td> <td>8e-04<span class="sumN ">()</span></td> <td>16/16(100%)</td> <td>0/16(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804339_1"> <pre>Query 1 CGTCCGTCGTGAAGAG 16 |||||||||||||||| Sbjct 961 CGTCCGTCGTGAAGAG 976 </pre> </div> <div id="hd_557804339_2"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> <span id="hsp557804339_2" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #2</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>16.4 bits(8)</td> <td> 47<span class="sumN ">()</span></td> <td>8/8(100%)</td> <td>0/8(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804339_2"> <pre>Query 5 CGTCGTGA 12 |||||||| Sbjct 2591 CGTCGTGA 2598 </pre> </div> <div id="hd_557804339_3"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> <span id="hsp557804339_3" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #3</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804339_3"> <pre>Query 7 TCGTGAA 13 ||||||| Sbjct 839 TCGTGAA 845 </pre> </div> <div id="hd_557804339_4"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> <span id="hsp557804339_4" class="alnParLinks"> <a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #4</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804339_4"> <pre>Query 9 GTGAAGA 15 ||||||| Sbjct 2027 GTGAAGA 2033 </pre> </div> </div> <!-- alnAll_557804339 --> </div> <!-- aln_557804339 --> <div class="alnHdr cnf" id="alnHdr_557804283" seqid="557804283" accs="pdb|3J54|A"> <a name="557804283"></a> <a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804283" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804283" title="Download information for pdb|3J54|A"><span>Download</span></a> <div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804283" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> <div><input seqfsta="gi|557804283" name="dwn_557804283" checked="checked" id="dwFST_557804283" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804283">FASTA (complete sequence)</label></div> <div><input seqfsta="gi|557804283" name="dwn_557804283" id="dwFSTAl_557804283" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804283">FASTA (aligned sequences)</label></div> <div class=""><input name="dwn_557804283" id="dwGenBank_557804283" getgi="557804283" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804283">GenBank (complete sequence)</label></div> <div> <button class="cfg" id="dw_cont_557804283">Continue</button> <button class="cfg cnc">Cancel</button> </div> </div> <!-- dsDownload --> <span class="csLinks" id="csLinks_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics">Graphics</a></span> <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> <select id="sa_557804283" onchange="SortHSPAlnSel(event,this)"> <option selected="selected" value="0">E value</option> <option value="1"> Score</option> <option value="3">Percent identity</option> <option value="2">Query start position</option> <option value="4">Subject start position</option> </select> </div> <span class="alnSeqLinks"> <a title="Go to next alignment for pdb|3J52|A" class="gbd toolsCtr navNext" ref="ordinalpos=4&currseq=557804283" id="alnNxt_557804283" onclick="goToNextAlign('dtr_557804283',true);"><span>Next</span></a> <a title="Go to previous alignment for pdb|3J56|A" class="gbd toolsCtr navPrev" ref="ordinalpos=4&currseq=557804283" id="alnPrv_557804283" onclick="goToNextAlign('dtr_557804283',false);"><span>Previous</span></a> <a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J54|A" id="alnDsc_557804283" onclick="goToDefLine('dtr_557804283');" href="#dtr_557804283"><span>Descriptions</span></a> </span> </div> <div class="oneSeqAln" id="aln_557804283"> <div id="dln_557804283"> <div class="dlfRow"> Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit) <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J54|A">pdb|3J54|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> </div> </div> <div class="relInf" id="relInf_557804283"><label>Related Information</label></div> <!-- <pre> <@aln_gene_info@> </pre> --> <div class="alnAll" id="alnAll_557804283"><div id="hd_557804283_1"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> <span id="hsp557804283_1" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack hidden" href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #1</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>32.2 bits(16)</td> <td>8e-04<span class="sumN ">()</span></td> <td>16/16(100%)</td> <td>0/16(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804283_1"> <pre>Query 1 CGTCCGTCGTGAAGAG 16 |||||||||||||||| Sbjct 961 CGTCCGTCGTGAAGAG 976 </pre> </div> <div id="hd_557804283_2"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> <span id="hsp557804283_2" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #2</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>16.4 bits(8)</td> <td> 47<span class="sumN ">()</span></td> <td>8/8(100%)</td> <td>0/8(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804283_2"> <pre>Query 5 CGTCGTGA 12 |||||||| Sbjct 2591 CGTCGTGA 2598 </pre> </div> <div id="hd_557804283_3"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> <span id="hsp557804283_3" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #3</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804283_3"> <pre>Query 7 TCGTGAA 13 ||||||| Sbjct 839 TCGTGAA 845 </pre> </div> <div id="hd_557804283_4"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> <span id="hsp557804283_4" class="alnParLinks"> <a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #4</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804283_4"> <pre>Query 9 GTGAAGA 15 ||||||| Sbjct 2027 GTGAAGA 2033 </pre> </div> </div> <!-- alnAll_557804283 --> </div> <!-- aln_557804283 --> <div class="alnHdr cnf" id="alnHdr_557804227" seqid="557804227" accs="pdb|3J52|A"> <a name="557804227"></a> <a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804227" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804227" title="Download information for pdb|3J52|A"><span>Download</span></a> <div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804227" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> <div><input seqfsta="gi|557804227" name="dwn_557804227" checked="checked" id="dwFST_557804227" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804227">FASTA (complete sequence)</label></div> <div><input seqfsta="gi|557804227" name="dwn_557804227" id="dwFSTAl_557804227" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804227">FASTA (aligned sequences)</label></div> <div class=""><input name="dwn_557804227" id="dwGenBank_557804227" getgi="557804227" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804227">GenBank (complete sequence)</label></div> <div> <button class="cfg" id="dw_cont_557804227">Continue</button> <button class="cfg cnc">Cancel</button> </div> </div> <!-- dsDownload --> <span class="csLinks" id="csLinks_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics">Graphics</a></span> <div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> <select id="sa_557804227" onchange="SortHSPAlnSel(event,this)"> <option selected="selected" value="0">E value</option> <option value="1"> Score</option> <option value="3">Percent identity</option> <option value="2">Query start position</option> <option value="4">Subject start position</option> </select> </div> <span class="alnSeqLinks"> <a title="Go to next alignment for pdb|3J51|A" class="gbd toolsCtr navNext" ref="ordinalpos=5&currseq=557804227" id="alnNxt_557804227" onclick="goToNextAlign('dtr_557804227',true);"><span>Next</span></a> <a title="Go to previous alignment for pdb|3J54|A" class="gbd toolsCtr navPrev" ref="ordinalpos=5&currseq=557804227" id="alnPrv_557804227" onclick="goToNextAlign('dtr_557804227',false);"><span>Previous</span></a> <a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J52|A" id="alnDsc_557804227" onclick="goToDefLine('dtr_557804227');" href="#dtr_557804227"><span>Descriptions</span></a> </span> </div> <div class="oneSeqAln" id="aln_557804227"> <div id="dln_557804227"> <div class="dlfRow"> Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit) <div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J52|A">pdb|3J52|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> </div> </div> <div class="relInf" id="relInf_557804227"><label>Related Information</label></div> <!-- <pre> <@aln_gene_info@> </pre> --> <div class="alnAll" id="alnAll_557804227"><div id="hd_557804227_1"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> <span id="hsp557804227_1" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack hidden" href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #1</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>32.2 bits(16)</td> <td>8e-04<span class="sumN ">()</span></td> <td>16/16(100%)</td> <td>0/16(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804227_1"> <pre>Query 1 CGTCCGTCGTGAAGAG 16 |||||||||||||||| Sbjct 961 CGTCCGTCGTGAAGAG 976 </pre> </div> <div id="hd_557804227_2"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> <span id="hsp557804227_2" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #2</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>16.4 bits(8)</td> <td> 47<span class="sumN ">()</span></td> <td>8/8(100%)</td> <td>0/8(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804227_2"> <pre>Query 5 CGTCGTGA 12 |||||||| Sbjct 2591 CGTCGTGA 2598 </pre> </div> <div id="hd_557804227_3"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> <span id="hsp557804227_3" class="alnParLinks"> <a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #3</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804227_3"> <pre>Query 7 TCGTGAA 13 ||||||| Sbjct 839 TCGTGAA 845 </pre> </div> <div id="hd_557804227_4"> <div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> <span id="hsp557804227_4" class="alnParLinks"> <a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> <a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> <a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> </span> </div> <table class="alnParams"> <caption class="hdnHeader">Alignment statistics for match #4</caption> <tbody><tr> <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> </tr> <tr> <td>14.4 bits(7)</td> <td> 186<span class="sumN ">()</span></td> <td>7/7(100%)</td> <td>0/7(0%)</td> <td>Plus/Plus</td> <td class="aln_frame "></td> </tr></tbody></table> <div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> </div> <div id="ar_557804227_4"> <pre>Query 9 GTGAAGA 15 ||||||| Sbjct 2027 GTGAAGA 2033 </pre> </div> </div> <!-- alnAll_557804227 --> </div> <!-- aln_557804227 --> </form> </div></div> <pre> </pre> </div><!--/#alignments--> </div><!-- alignInfo --> </div><!--ARIA--> </div><!-- alignView --> <form><!-- this is the start tag for the </form in blastcgi templates - needs to be changed--> <!-- not used - verify --> <!-- not used - verify --> </form> </div><!-- /#content --> <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="reformat" id="reformat"> <input name="QUERY_INFO" value="Nucleotide Sequence (16 letters)" type="hidden"> <input name="ENTREZ_QUERY" value="" type="hidden"> <input name="CDD_RID" value="" type="hidden"> <input name="CDD_SEARCH_STATE" value="" type="hidden"> <input name="RID" value="PHWP1JNZ014" type="hidden"> <input name="STEP_NUMBER" value="" type="hidden"> <input name="CMD" value="Web" type="hidden"> <input name="PAGE_TYPE" value="BlastFormatting" type="hidden"> <!-- TO DO: test all of those changes --> <!-- Psi blast params PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> --> <!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> --> <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> --> </form> <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="setSavedOptions" id="setSavedOptions"> <input name="PAGE_TYPE" value="BlastSearch" type="hidden"> <input name="VIEW_SEARCH" value="true" type="hidden"> <input name="CMD" value="Web" type="hidden"> <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> --> </form> 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