http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&feed=atom&action=history
Team:HokkaidoU Japan/Shuffling Kit/Primer Designer - Revision history
2024-03-28T11:29:27Z
Revision history for this page on the wiki
MediaWiki 1.16.5
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=359500&oldid=prev
TaKeZo at 02:50, 29 October 2013
2013-10-29T02:50:12Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h1 id="common-header-title">Maestro E.coli</h1></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h1 id="common-header-title">Maestro <ins class="diffchange diffchange-inline"><span class="italic"></ins>E. coli<ins class="diffchange diffchange-inline"></span></ins></h1></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2 id="common-header-subtitle">Shuffling Kit</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2 id="common-header-subtitle">Shuffling Kit</h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img id="common-header-img" src="https://static.igem.org/mediawiki/2013/e/ea/HokkaidoU2013_Maestro_Header.png"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img id="common-header-img" src="https://static.igem.org/mediawiki/2013/e/ea/HokkaidoU2013_Maestro_Header.png"></div></td></tr>
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TaKeZo
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=350862&oldid=prev
Barao at 19:56, 28 October 2013
2013-10-28T19:56:20Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h1 id="common-header-title">Maestro E.coli</h1></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h1 id="common-header-title">Maestro E.coli</h1></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h2 id="common-header-subtitle"><del class="diffchange diffchange-inline">Optimization </del>Kit</h2></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h2 id="common-header-subtitle"><ins class="diffchange diffchange-inline">Shuffling </ins>Kit</h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img id="common-header-img" src="https://static.igem.org/mediawiki/2013/e/ea/HokkaidoU2013_Maestro_Header.png"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img id="common-header-img" src="https://static.igem.org/mediawiki/2013/e/ea/HokkaidoU2013_Maestro_Header.png"></div></td></tr>
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Barao
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=347242&oldid=prev
TaKeZo at 15:26, 28 October 2013
2013-10-28T15:26:44Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><a href="https://2013.igem.org/Team:HokkaidoU_Japan/<del class="diffchange diffchange-inline">Optimization</del>/How_To_Use"><div class="arrow-div"></div><span>How To Use</span></a></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><a href="https://2013.igem.org/Team:HokkaidoU_Japan/<ins class="diffchange diffchange-inline">Shuffling_Kit</ins>/How_To_Use"><div class="arrow-div"></div><span>How To Use</span></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><a href="https://2013.igem.org/Team:HokkaidoU_Japan/<del class="diffchange diffchange-inline">Optimization</del>/Examples"><div class="arrow-div"></div><span>Examples</span></a></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><a href="https://2013.igem.org/Team:HokkaidoU_Japan/<ins class="diffchange diffchange-inline">Shuffling_Kit</ins>/Examples"><div class="arrow-div"></div><span>Examples</span></a></div></td></tr>
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TaKeZo
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=346912&oldid=prev
TaKeZo: moved Team:HokkaidoU Japan/Optimization/Primer Designer to Team:HokkaidoU Japan/Shuffling Kit/Primer Designer
2013-10-28T15:00:54Z
<p>moved <a href="/Team:HokkaidoU_Japan/Optimization/Primer_Designer" class="mw-redirect" title="Team:HokkaidoU Japan/Optimization/Primer Designer">Team:HokkaidoU Japan/Optimization/Primer Designer</a> to <a href="/Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer" title="Team:HokkaidoU Japan/Shuffling Kit/Primer Designer">Team:HokkaidoU Japan/Shuffling Kit/Primer Designer</a></p>
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<td colspan='1' style="background-color: white; color:black;">Revision as of 15:00, 28 October 2013</td>
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TaKeZo
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=324407&oldid=prev
TaKeZo at 13:12, 22 October 2013
2013-10-22T13:12:45Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>5. Now, repeat previous step for remaining fragments included in the target plasmid.</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>5. Now, repeat previous step for remaining fragments included in the target plasmid.</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><script type="text/javascript"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><script type="text/javascript"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>(function(){var n,f,e,h,d,a,j,g,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return q};n=function(o){var q,p;q=k(o);p=c(o);return(1000*q/(-10.8+p+1.987*-15.89495209964411))-273.15+16.6*-1.3010299956639813};d=function(p){var r,o,q;if(n(p.slice(0,35))<60){alert("Sequence is too short.");return false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(<del class="diffchange diffchange-inline">o</del>){if(/GGTCTC/.test(<del class="diffchange diffchange-inline">o</del>)||/GGTCTC/.test(m(<del class="diffchange diffchange-inline">o</del>))){alert(<del class="diffchange 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diffchange-inline">else{</del>if(/GCGGCCGC/.test(<del class="diffchange diffchange-inline">o</del>)||/GCGGCCGC/.test(m(<del class="diffchange diffchange-inline">o</del>))){alert(<del class="diffchange diffchange-inline">"</del>This sequence contains NotI cutting site<del class="diffchange diffchange-inline">.</del>");<del class="diffchange diffchange-inline">return </del>false}<del class="diffchange diffchange-inline">else{</del>if(/ACTAGT/.test(<del class="diffchange diffchange-inline">o</del>)||/ACTAGT/.test(m(<del class="diffchange diffchange-inline">o</del>))){alert(<del class="diffchange diffchange-inline">"</del>This sequence contains SpeI cutting site<del class="diffchange diffchange-inline">.</del>");<del class="diffchange diffchange-inline">return </del>false}<del class="diffchange diffchange-inline">else{</del>if(/TCTAGA/.test(<del class="diffchange diffchange-inline">o</del>)||/TCTAGA/.test(m(<del class="diffchange diffchange-inline">o</del>))){alert(<del class="diffchange diffchange-inline">"</del>This sequence contains XbaI cutting site<del class="diffchange diffchange-inline">.</del>");<del class="diffchange diffchange-inline">return </del>false}<del class="diffchange diffchange-inline">else{</del>return <del class="diffchange diffchange-inline">true}}}}}}</del>};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join(""<del class="diffchange diffchange-inline">);console.log(e(u));console.log(e(s));console.log(e(t));console.log(f(u));console.log(f(s));console.log(f(t)</del>);o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return 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false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(<ins class="diffchange diffchange-inline">p</ins>){<ins class="diffchange diffchange-inline">var o;o=true;</ins>if(/GGTCTC/.test(<ins class="diffchange diffchange-inline">p</ins>)||/GGTCTC/.test(m(<ins class="diffchange diffchange-inline">p</ins>))){alert(<ins class="diffchange diffchange-inline">'</ins>This sequence contains BsaI cutting site "<ins class="diffchange diffchange-inline">GGTCTC" or "GAGACC".\r\nYou can just ignore this alert, if unnecessary.'</ins>);<ins class="diffchange diffchange-inline">o=</ins>false}if(/GAATTC/.test(<ins class="diffchange diffchange-inline">p</ins>)||/GAATTC/.test(m(<ins class="diffchange diffchange-inline">p</ins>))){alert(<ins class="diffchange diffchange-inline">'</ins>This sequence contains EcoRI cutting site "<ins class="diffchange diffchange-inline">GAATTC".\r\nYou can just ignore this alert, if unnecessary.'</ins>);<ins class="diffchange diffchange-inline">o=</ins>false}if(/CTGCAG/.test(<ins class="diffchange diffchange-inline">p</ins>)||/CTGCAG/.test(m(<ins class="diffchange diffchange-inline">p</ins>))){alert(<ins class="diffchange diffchange-inline">'</ins>This sequence contains PstI cutting site "<ins class="diffchange diffchange-inline">CTGCAG".\r\nYou can just ignore this alert, if unnecessary.'</ins>);<ins class="diffchange diffchange-inline">o=</ins>false}if(/GCGGCCGC/.test(<ins class="diffchange diffchange-inline">p</ins>)||/GCGGCCGC/.test(m(<ins class="diffchange diffchange-inline">p</ins>))){alert(<ins class="diffchange diffchange-inline">'</ins>This sequence contains NotI cutting site "<ins class="diffchange diffchange-inline">GCGGCCGC".\r\nYou can just ignore this alert, if unnecessary.'</ins>);<ins class="diffchange diffchange-inline">o=</ins>false}if(/ACTAGT/.test(<ins class="diffchange diffchange-inline">p</ins>)||/ACTAGT/.test(m(<ins class="diffchange diffchange-inline">p</ins>))){alert(<ins class="diffchange diffchange-inline">'</ins>This sequence contains SpeI cutting site "<ins class="diffchange diffchange-inline">ACTAGT".\r\nYou can just ignore this alert, if unnecessary.'</ins>);<ins class="diffchange diffchange-inline">o=</ins>false}if(/TCTAGA/.test(<ins class="diffchange diffchange-inline">p</ins>)||/TCTAGA/.test(m(<ins class="diffchange diffchange-inline">p</ins>))){alert(<ins class="diffchange diffchange-inline">'</ins>This sequence contains XbaI cutting site "<ins class="diffchange diffchange-inline">TCTAGA".\r\nYou can just ignore this alert, if unnecessary.'</ins>);<ins class="diffchange diffchange-inline">o=</ins>false}return <ins class="diffchange diffchange-inline">o</ins>};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return $("#not-conform").show()}});$('[name="cds-number"]').val("3");$('[name="cds-number"]').change(function(){switch($(this).val()){case"1":$(".hide-1").hide();$(".hide-2").hide();$(".disable-1").attr("disabled","disabled");return $(".disable-2").attr("disabled","disabled");case"2":$(".hide-1").show();$(".hide-2").hide();$(".disable-1").removeAttr("disabled");return $(".disable-2").attr("disabled","disabled");case"3":$(".hide-1").show();$(".hide-2").show();$(".disable-1").removeAttr("disabled");return $(".disable-2").removeAttr("disabled")}});$('[name="part-beginning"]').change(function(){return l()});return $('[name="part-end"]').change(function(){return l()})})}).call(this);</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></script></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></script></div></td></tr>
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</table>
TaKeZo
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=324366&oldid=prev
TaKeZo at 12:41, 22 October 2013
2013-10-22T12:41:49Z
<p></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 12:41, 22 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 142:</td>
<td colspan="2" class="diff-lineno">Line 142:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>5. Now, repeat previous step for remaining fragments included in the target plasmid.</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>5. Now, repeat previous step for remaining fragments included in the target plasmid.</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><script type="text/javascript"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><script type="text/javascript"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>(function(){var n,f,e,h,d,a,j,g,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return q};n=function(o){var q,p;q=k(o);p=c(o);return(1000*q/(-10.8+p+1.987*-15.89495209964411))-273.15+16.6*-1.3010299956639813};d=function(p){var r,o,q;if(n(p.slice(0,35))<60){alert("Sequence is too short.");return false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){alert("This sequence contains BsaI cutting site.");return false}else{if(/GAATTC/.test(o)||/GAATTC/.test(m(o))){alert("This sequence contains EcoRI cutting site.");return false}else{if(/CTGCAG/.test(o)||/CTGCAG/.test(m(o))){alert("This sequence contains PstI cutting site.");return false}else{if(/GCGGCCGC/.test(o)||/GCGGCCGC/.test(m(o))){alert("This sequence contains NotI cutting site.");return false}else{if(/ACTAGT/.test(o)||/ACTAGT/.test(m(o))){alert("This sequence contains SpeI cutting site.");return false}else{if(/TCTAGA/.test(o)||/TCTAGA/.test(m(o))){alert("This sequence contains XbaI cutting site.");return false}else{return true}}}}}}};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");console.log(<del class="diffchange diffchange-inline">check_bsa_site</del>(u));console.log(<del class="diffchange diffchange-inline">check_bsa_site</del>(s));console.log(<del class="diffchange diffchange-inline">check_bsa_site</del>(t));console.log(f(u));console.log(f(s));console.log(f(t));o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return $("#not-conform").show()}});$('[name="cds-number"]').val("3");$('[name="cds-number"]').change(function(){switch($(this).val()){case"1":$(".hide-1").hide();$(".hide-2").hide();$(".disable-1").attr("disabled","disabled");return $(".disable-2").attr("disabled","disabled");case"2":$(".hide-1").show();$(".hide-2").hide();$(".disable-1").removeAttr("disabled");return $(".disable-2").attr("disabled","disabled");case"3":$(".hide-1").show();$(".hide-2").show();$(".disable-1").removeAttr("disabled");return $(".disable-2").removeAttr("disabled")}});$('[name="part-beginning"]').change(function(){return l()});return $('[name="part-end"]').change(function(){return l()})})}).call(this);</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>(function(){var n,f,e,h,d,a,j,g,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return q};n=function(o){var q,p;q=k(o);p=c(o);return(1000*q/(-10.8+p+1.987*-15.89495209964411))-273.15+16.6*-1.3010299956639813};d=function(p){var r,o,q;if(n(p.slice(0,35))<60){alert("Sequence is too short.");return false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){alert("This sequence contains BsaI cutting site.");return false}else{if(/GAATTC/.test(o)||/GAATTC/.test(m(o))){alert("This sequence contains EcoRI cutting site.");return false}else{if(/CTGCAG/.test(o)||/CTGCAG/.test(m(o))){alert("This sequence contains PstI cutting site.");return false}else{if(/GCGGCCGC/.test(o)||/GCGGCCGC/.test(m(o))){alert("This sequence contains NotI cutting site.");return false}else{if(/ACTAGT/.test(o)||/ACTAGT/.test(m(o))){alert("This sequence contains SpeI cutting site.");return false}else{if(/TCTAGA/.test(o)||/TCTAGA/.test(m(o))){alert("This sequence contains XbaI cutting site.");return false}else{return true}}}}}}};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");console.log(<ins class="diffchange diffchange-inline">e</ins>(u));console.log(<ins class="diffchange diffchange-inline">e</ins>(s));console.log(<ins class="diffchange diffchange-inline">e</ins>(t));console.log(f(u));console.log(f(s));console.log(f(t));o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return 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</table>
TaKeZo
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=321652&oldid=prev
Nousan at 07:15, 19 October 2013
2013-10-19T07:15:57Z
<p></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 07:15, 19 October 2013</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><link href='http://fonts.googleapis.com/css?family=Inconsolata' rel='stylesheet' type='text/css'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><link href='http://fonts.googleapis.com/css?family=Inconsolata' rel='stylesheet' type='text/css'></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h1><del class="diffchange diffchange-inline">POK-ROK </del>Primer Designer</h1></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h1>Primer Designer <ins class="diffchange diffchange-inline">for Maestro</ins></h1></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>1. First, you have to decide whether or not you conform to our default overhang set.</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>1. First, you have to decide whether or not you conform to our default overhang set.</h3></div></td></tr>
</table>
Nousan
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=241921&oldid=prev
Kenta at 03:51, 28 September 2013
2013-09-28T03:51:00Z
<p></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 03:51, 28 September 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 41:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> CDS(s) included.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> CDS(s) included.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h3>3. Then, please select the region to where your <del class="diffchange diffchange-inline">flagment </del>correspond in target plasmid.</h3></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h3>3. Then, please select the region to where your <ins class="diffchange diffchange-inline">fragment </ins>correspond in target plasmid.</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div id="plasmid-map"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div id="plasmid-map"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div id="plasmid-0"> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div id="plasmid-0"> </div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="form-group"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="form-group"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <label for="part-beginning"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <label for="part-beginning"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Beginning of the <del class="diffchange diffchange-inline">flagment</del>:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Beginning of the <ins class="diffchange diffchange-inline">fragment</ins>:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </label></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </label></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <select name="part-beginning" class="form-control monospace"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <select name="part-beginning" class="form-control monospace"></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="form-group"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="form-group"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <label for="part-end"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <label for="part-end"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> End of the <del class="diffchange diffchange-inline">flagment</del>:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> End of the <ins class="diffchange diffchange-inline">fragment</ins>:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </label></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </label></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <select name="part-end" class="form-control monospace"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <select name="part-end" class="form-control monospace"></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h3>4. Okey, now we are ready to go. Enter your <del class="diffchange diffchange-inline">flagment</del>'s sequence, and press "Calculate"!</h3></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h3>4. Okey, now we are ready to go. Enter your <ins class="diffchange diffchange-inline">fragment</ins>'s sequence, and press "Calculate"!</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div id="not-conform"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div id="not-conform"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h3>2. Please enter overhangs and <del class="diffchange diffchange-inline">flagment</del>'s sequence, and press "Calculate"</h3></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h3>2. Please enter overhangs and <ins class="diffchange diffchange-inline">fragment</ins>'s sequence, and press "Calculate"</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="form-group"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="form-group"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <label for="sequence"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <label for="sequence"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline">Flagment </del>sequence:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <ins class="diffchange diffchange-inline">Fragment </ins>sequence:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </label></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </label></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <textarea class="form-control monospace" type="text" name="sequence"></textarea><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <textarea class="form-control monospace" type="text" name="sequence"></textarea><br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </dl></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </dl></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h3>5. Now, repeat previous step for remaining <del class="diffchange diffchange-inline">flagments </del>included in the target plasmid.</h3></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h3>5. Now, repeat previous step for remaining <ins class="diffchange diffchange-inline">fragments </ins>included in the target plasmid.</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><script type="text/javascript"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><script type="text/javascript"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>(function(){var n,f,e,h,d,a,j,g,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return 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false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){alert("This sequence contains BsaI cutting site.");return false}else{if(/GAATTC/.test(o)||/GAATTC/.test(m(o))){alert("This sequence contains EcoRI cutting site.");return false}else{if(/CTGCAG/.test(o)||/CTGCAG/.test(m(o))){alert("This sequence contains PstI cutting site.");return false}else{if(/GCGGCCGC/.test(o)||/GCGGCCGC/.test(m(o))){alert("This sequence contains NotI cutting site.");return false}else{if(/ACTAGT/.test(o)||/ACTAGT/.test(m(o))){alert("This sequence contains SpeI cutting site.");return false}else{if(/TCTAGA/.test(o)||/TCTAGA/.test(m(o))){alert("This sequence contains XbaI cutting site.");return false}else{return true}}}}}}};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");console.log(check_bsa_site(u));console.log(check_bsa_site(s));console.log(check_bsa_site(t));console.log(f(u));console.log(f(s));console.log(f(t));o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return $("#not-conform").show()}});$('[name="cds-number"]').val("3");$('[name="cds-number"]').change(function(){switch($(this).val()){case"1":$(".hide-1").hide();$(".hide-2").hide();$(".disable-1").attr("disabled","disabled");return $(".disable-2").attr("disabled","disabled");case"2":$(".hide-1").show();$(".hide-2").hide();$(".disable-1").removeAttr("disabled");return $(".disable-2").attr("disabled","disabled");case"3":$(".hide-1").show();$(".hide-2").show();$(".disable-1").removeAttr("disabled");return $(".disable-2").removeAttr("disabled")}});$('[name="part-beginning"]').change(function(){return l()});return $('[name="part-end"]').change(function(){return l()})})}).call(this);</div></td></tr>
</table>
Kenta
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=230021&oldid=prev
TaKeZo at 00:28, 28 September 2013
2013-09-28T00:28:23Z
<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 00:28, 28 September 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 144:</td>
<td colspan="2" class="diff-lineno">Line 144:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>(function(){var n,f,e,h,d,a,j,g,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return q};n=function(o){var q,p;q=k(o);p=c(o);return(1000*q/(-10.8+p+1.987*-15.89495209964411))-273.15+16.6*-1.3010299956639813};d=function(p){var r,o,q;if(n(p.slice(0,35))<60){alert("Sequence is too short.");return false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){alert("This sequence contains BsaI cutting site.");return false}else{if(/GAATTC/.test(o)||/GAATTC/.test(m(o))){alert("This sequence contains EcoRI cutting site.");return false}else{if(/CTGCAG/.test(o)||/CTGCAG/.test(m(o))){alert("This sequence contains PstI cutting site.");return false}else{if(/GCGGCCGC/.test(o)||/GCGGCCGC/.test(m(o))){alert("This sequence contains NotI cutting site.");return false}else{if(/ACTAGT/.test(o)||/ACTAGT/.test(m(o))){alert("This sequence contains SpeI cutting site.");return false}else{if(/TCTAGA/.test(o)||/TCTAGA/.test(m(o))){alert("This sequence contains XbaI cutting site.");return false}else{return true}}}}}}};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");console.log(check_bsa_site(u));console.log(check_bsa_site(s));console.log(check_bsa_site(t));console.log(f(u));console.log(f(s));console.log(f(t));o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return $("#not-conform").show()}});$('[name="cds-number"]').val("3");$('[name="cds-number"]').change(function(){switch($(this).val()){case"1":$(".hide-1").hide();$(".hide-2").hide();$(".disable-1").attr("disabled","disabled");return $(".disable-2").attr("disabled","disabled");case"2":$(".hide-1").show();$(".hide-2").hide();$(".disable-1").removeAttr("disabled");return $(".disable-2").attr("disabled","disabled");case"3":$(".hide-1").show();$(".hide-2").show();$(".disable-1").removeAttr("disabled");return $(".disable-2").removeAttr("disabled")}});$('[name="part-beginning"]').change(function(){return l()});return $('[name="part-end"]').change(function(){return l()})})}).call(this);</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>(function(){var n,f,e,h,d,a,j,g,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return q};n=function(o){var q,p;q=k(o);p=c(o);return(1000*q/(-10.8+p+1.987*-15.89495209964411))-273.15+16.6*-1.3010299956639813};d=function(p){var r,o,q;if(n(p.slice(0,35))<60){alert("Sequence is too short.");return false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){alert("This sequence contains BsaI cutting site.");return false}else{if(/GAATTC/.test(o)||/GAATTC/.test(m(o))){alert("This sequence contains EcoRI cutting site.");return false}else{if(/CTGCAG/.test(o)||/CTGCAG/.test(m(o))){alert("This sequence contains PstI cutting site.");return false}else{if(/GCGGCCGC/.test(o)||/GCGGCCGC/.test(m(o))){alert("This sequence contains NotI cutting site.");return false}else{if(/ACTAGT/.test(o)||/ACTAGT/.test(m(o))){alert("This sequence contains SpeI cutting site.");return false}else{if(/TCTAGA/.test(o)||/TCTAGA/.test(m(o))){alert("This sequence contains XbaI cutting site.");return false}else{return true}}}}}}};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");console.log(check_bsa_site(u));console.log(check_bsa_site(s));console.log(check_bsa_site(t));console.log(f(u));console.log(f(s));console.log(f(t));o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return $("#not-conform").show()}});$('[name="cds-number"]').val("3");$('[name="cds-number"]').change(function(){switch($(this).val()){case"1":$(".hide-1").hide();$(".hide-2").hide();$(".disable-1").attr("disabled","disabled");return $(".disable-2").attr("disabled","disabled");case"2":$(".hide-1").show();$(".hide-2").hide();$(".disable-1").removeAttr("disabled");return $(".disable-2").attr("disabled","disabled");case"3":$(".hide-1").show();$(".hide-2").show();$(".disable-1").removeAttr("disabled");return $(".disable-2").removeAttr("disabled")}});$('[name="part-beginning"]').change(function(){return l()});return $('[name="part-end"]').change(function(){return l()})})}).call(this);</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></script></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></script></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><div id="prev-page"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><a href="https://2013.igem.org/Team:HokkaidoU_Japan/Optimization/How_To_Use"><div class="arrow-div"></div><span>How To Use</span></a></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></div></ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><div id="next-page"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><a href="https://2013.igem.org/Team:HokkaidoU_Japan/Optimization/Examples"><div class="arrow-div"></div><span>Examples</span></a></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></div></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- end contents / begin footer --></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- end contents / begin footer --></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td></tr>
</table>
TaKeZo
http://2013.igem.org/wiki/index.php?title=Team:HokkaidoU_Japan/Shuffling_Kit/Primer_Designer&diff=209501&oldid=prev
TaKeZo at 15:12, 27 September 2013
2013-09-27T15:12:48Z
<p></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:12, 27 September 2013</td>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h1><del class="diffchange diffchange-inline">GGA </del>Primer Designer</h1></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h1><ins class="diffchange diffchange-inline">POK-ROK </ins>Primer Designer</h1></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>1. First, you have to decide whether or not you conform to our default overhang set.</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>1. First, you have to decide whether or not you conform to our default overhang set.</h3></div></td></tr>
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