Team:Heidelberg/Modeling/miBSdesigner

From 2010.igem.org

(Difference between revisions)
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.reswrap2 {padding:5px; width: 240px; margin:auto; text-align:left; display:none; font-size:12pt;}
.variaresult {font-size: 12pt; color: #11526f; font-weight: bold;}
.variaresult {font-size: 12pt; color: #11526f; font-weight: bold;}
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td {vertical-align:top;}
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<div class="t1">
<div class="t1">
Construction of microRNA binding sites </div><br><br>
Construction of microRNA binding sites </div><br><br>
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<span style="font-size: 17.0px;">Sequence name </span>
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<div class="largetext">
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<br>
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Sequence name<br>
<input type="text" name="name" id="name" size="40" value="hsa-miR122"/><br>
<input type="text" name="name" id="name" size="40" value="hsa-miR122"/><br>
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<span style="font-size: 17.0px;">microRNA Sequence ( 5' -> 3')</span><br>
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microRNA Sequence ( 5' -> 3')<br>
<input type="text" name="mir" id="mir" size="40" value="UCAGUUUACUAGUGCCAUUUGU"/><br>
<input type="text" name="mir" id="mir" size="40" value="UCAGUUUACUAGUGCCAUUUGU"/><br>
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<span style="font-size: 17.0px;">
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Spacer (inert sequence)<br>
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Spacer (inert sequence) </span><br>
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<input type="text" name="spacer" id="spacer" size="40" value="TTATATTTTATGACA"/>
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<input type="text" name="spacer" id="spacer" size="40" value="TTATATTTTATGACA"/></center>
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</div></center>
<br><br>
<br><br>
 +
<div class="largetext">
<input name="quality" value="perfect" onchange="chMd()" checked="checked" type="radio">
<input name="quality" value="perfect" onchange="chMd()" checked="checked" type="radio">
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<span style="font-size: 17.0px;">
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Perfect Binding Site<br>
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Perfect Binding Site </span>
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-
<br>
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<input name="quality" value="bulge" onchange="chMd()" type="radio">
<input name="quality" value="bulge" onchange="chMd()" type="radio">
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<span style="font-size: 17.0px;">
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Imperfect Binding Site with 4 nt bulge (9-12)<br>
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Imperfect Binding Site with 4 nt bulge (9-12) </span>
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-
<br>
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<input name="quality" value="personal" onchange="chMd()" type="radio">
<input name="quality" value="personal" onchange="chMd()" type="radio">
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<span style="font-size: 17.0px;">
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Personalized Binding Site  
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Personalized Binding Site </span>
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</div>
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<br>
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<br>
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<br>
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<table>
<table>
<tr height=120px>
<tr height=120px>
<td width=320px>
<td width=320px>
<div class="title">
<div class="title">
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<span style="font-size: 17.0px; font-weight:bold;">
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Seed sequence (1-8)</div>
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Seed sequence (1-8) </span></div>
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<div class="option"><SELECT name="seed" onchange="chMd1()" disabled="disabled">
<div class="option"><SELECT name="seed" onchange="chMd1()" disabled="disabled">
<OPTION value="0">
<OPTION value="0">
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</SELECT></div>
</SELECT></div>
<div class="suboption">
<div class="suboption">
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<span style="font-size: 15.0px;"> Customized </span>
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Customized <span style="color:#11526f; font-weight:bold;">MISMATCH</span> position
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<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MISMATCH </span>
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<span style="font-size: 15.0px;">position</span></div>
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<div class="suboption">
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<input type="text" id="mis" size="29" disabled="disabled" value="2"/>
<input type="text" id="mis" size="29" disabled="disabled" value="2"/>
</div>
</div>
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<td>
<td>
<div class="title">
<div class="title">
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<span style="font-size: 17.0px; font-weight:bold;">
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Supplementary region</div>
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Supplementary region </span></div>
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<div class="option"><SELECT name="comp" onchange="chMd2()" disabled="disabled">
<div class="option"><SELECT name="comp" onchange="chMd2()" disabled="disabled">
<OPTION value="0">
<OPTION value="0">
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</SELECT></div>
</SELECT></div>
<div class="suboption">
<div class="suboption">
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<span style="font-size: 15.0px;"> Customized </span>
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Customized <span style="color: #11526f; font-weight:bold;">MATCH</span> positions
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<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MATCH </span>
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<span style="font-size: 15.0px;">positions</span></div>
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<div class="suboption">
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<input type="text" id="match" size="29" disabled="disabled" value="10, 15, 16, 17, 18, 19, 20"/>
<input type="text" id="match" size="29" disabled="disabled" value="10, 15, 16, 17, 18, 19, 20"/>
</div>
</div>
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<tr>
<tr>
<td>
<td>
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<div class="title">
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<div class="title">
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Modify AU content</div>
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<span style="font-size: 17.0px; font-weight:bold;">
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<table>
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Modify AU content </span>
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<tr>
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</div>
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<td width=130px>
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<div class="optionl"><input name="AU" value="-1" type="checkbox"><span style="font-size: 15.0px;">A in position -1</span></div>
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<input name="AU" value="-1" type="checkbox">A in position -1<br>
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<div class="optionr"><input name="AU" value="0" type="checkbox"><span style="font-size: 15.0px;">A in position 0  </span></div>
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<input name="AU" value="1" disabled="disabled" type="checkbox">A in position 1<br>
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<div class="clear">
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<input name="AU" value="9" disabled="disabled" type="checkbox">A in position 9<br>
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<div class="optionl"><input name="AU" value="1" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 1</span></div>
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</td>
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<div class="optionr"><input name="AU" value="8" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 8  </span></div></div>
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<td>
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<div class="clear">
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<input name="AU" value="0" type="checkbox">A in position 0<br>
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<div class="optionl"><input name="AU" value="9" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 9</span></div>
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<input name="AU" value="8" disabled="disabled" type="checkbox">A in position 8<br>
-
<div class="optionr"><input name="AU" value="10" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 10</span></div></div>
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<input name="AU" value="10" disabled="disabled" type="checkbox">A in position 10<br>
 +
</td>
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</tr>
 +
</table>
</td>
</td>
<td style="vertical-align:top;">
<td style="vertical-align:top;">
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<div class="title"><span style="font-size: 17.0px; font-weight:bold;">Sticky ends for integration in plasmid: </span></div>
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<div class="title">Sticky ends for integration into plasmid</div>
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<div class="option">   <SELECT id="stickyends" name="stickyends" onchange="chMd3()">
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<div class="option"><SELECT id="stickyends" name="stickyends" onchange="chMd3()">
<OPTION SELECTED value="none">None
<OPTION SELECTED value="none">None
<OPTION value="BBB">Biobricks Standard RFC-12
<OPTION value="BBB">Biobricks Standard RFC-12
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<OPTION value="custom">Custom sequence
<OPTION value="custom">Custom sequence
</SELECT></div>
</SELECT></div>
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<div class="option"><span style="font-size: 15.0px;">Customized:</span>
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<div class="suboption">Customized:<br>
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<span style="font-size: 15.0px;">5'&nbsp;&nbsp;</span><input type="text" id="end5" size="15" disabled="disabled"/>
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5'&nbsp;&nbsp;<input type="text" id="end5" size="15" disabled="disabled"/><br>
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<span style="font-size: 15.0px;">3'&nbsp;&nbsp;</span><input type="text" id="end3" size="15" disabled="disabled"/>
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3'&nbsp;&nbsp;<input type="text" id="end3" size="15" disabled="disabled"/>
</div>
</div>
</td>
</td>
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<div class="wrapper"><br>
<div class="wrapper"><br>
<img style="border-width: 0px;" src="https://static.igem.org/mediawiki/2010/c/c0/MiBSdesigner.png" width="260" height="147" />
<img style="border-width: 0px;" src="https://static.igem.org/mediawiki/2010/c/c0/MiBSdesigner.png" width="260" height="147" />
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<br><br><br><br>
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<br><br>
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<br><br><br>
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<div class="reswrap2" id="resultdiv">
<div class="reswrap2" id="resultdiv">
<div class="variaresult">Name of primer 1</div>
<div class="variaresult">Name of primer 1</div>

Revision as of 09:15, 26 October 2010

BS designer for miRNA
Construction of microRNA binding sites


Sequence name

microRNA Sequence ( 5' -> 3')

Spacer (inert sequence)


Perfect Binding Site
Imperfect Binding Site with 4 nt bulge (9-12)
Personalized Binding Site

Seed sequence (1-8)
Customized MISMATCH position
Supplementary region
Customized MATCH positions
Modify AU content
A in position -1
A in position 1
A in position 9
 A in position 0
A in position 8
A in position 10
Sticky ends for integration into plasmid
Customized:
5'  
3'  




Name of primer 1


Sequence of primer 1


Name of primer 2


Sequence of primer 2

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