Team:Heidelberg/Modeling/miBSdesigner

From 2010.igem.org

(Difference between revisions)
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div.wrapper {width: 260px; height: 650px; margin:auto; text-align:center;}
div.wrapper {width: 260px; height: 650px; margin:auto; text-align:center;}
div.wrapper2 {margin:auto; height: 750px; text-align:left; }
div.wrapper2 {margin:auto; height: 750px; text-align:left; }
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div.title {text-indent:30px;}
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div.title {text-indent:5px;}
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div.option {text-indent:50px; white-space:pre-wrap;}
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div.option {text-indent:15px; white-space:pre-wrap;}
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div.optionl {text-indent:15px; white-space:pre-wrap; float:left;}
div.optionr {display:inline; white-space:pre-wrap; margin-right: 45px; float:right;}
div.optionr {display:inline; white-space:pre-wrap; margin-right: 45px; float:right;}
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div.suboption {text-indent:25px;}
div.clear {clear: both;}
div.clear {clear: both;}
div.reswrap2 {padding:5px; width: 240px; margin:auto; text-align:left; display:none; font-size:12pt;}
div.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;}
</style>
</style>
</head>
</head>
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<br>
<br>
<br>
<br>
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<div class="title">
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<table>
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<span style="font-size: 17.0px; font-weight:bold;">
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<tr height=120px>
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Seed sequence (1-8) </span></div>
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<td width=320px>
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<div class="option"><SELECT name="seed" onchange="chMd1()" disabled="disabled">
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<div class="title">
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                <OPTION value="0">
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<span style="font-size: 17.0px; font-weight:bold;">
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<OPTION value="6mer">6mer                (2-7 paired)
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Seed sequence (1-8) </span></div>
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<OPTION value="7merA1">7merA1          (1-7 paired)
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<div class="option"><SELECT name="seed" onchange="chMd1()" disabled="disabled">
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<OPTION value="7merm8">7merm8          (2-8 paired)
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<OPTION value="0">
-
<OPTION value="8mer">8mer                (1-8 paired)
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<OPTION value="6mer">6mer                (2-7 paired)
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<OPTION value="custom">Custom
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<OPTION value="7merA1">7merA1          (1-7 paired)
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</SELECT></div>
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<OPTION value="7merm8">7merm8          (2-8 paired)
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<div class="suboption">
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<OPTION value="8mer">8mer                (1-8 paired)
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<span style="font-size: 15.0px;"> Customized </span>
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<OPTION value="custom">Custom
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<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MISMATCH </span>
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</SELECT></div>
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<span style="font-size: 15.0px;">position</span></div>
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<div class="suboption">
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<div class="suboption">
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<span style="font-size: 15.0px;"> Customized </span>
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<input type="text" id="mis" size="30" disabled="disabled" value="2"/>
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<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MISMATCH </span>
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</div>
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<span style="font-size: 15.0px;">position</span></div>
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<br>
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<div class="suboption">
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<div class="title">
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<input type="text" id="mis" size="29" disabled="disabled" value="2"/>
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<span style="font-size: 17.0px; font-weight:bold;">
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</div>
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Supplementary region </span></div>
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</td>
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<div class="option"><SELECT name="comp" onchange="chMd2()" disabled="disabled">
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<td>
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                <OPTION value="0">
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<div class="title">
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<OPTION value="3">3                  (14-16 paired)
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<span style="font-size: 17.0px; font-weight:bold;">
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<OPTION value="4">4                  (13-16 paired)
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Supplementary region </span></div>
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<OPTION value="5">5                  (13-17 paired)
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<div class="option"><SELECT name="comp" onchange="chMd2()" disabled="disabled">
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<OPTION value="6">6                  (13-18 paired)
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<OPTION value="0">
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<OPTION value="7">7                  (13-19 paired)
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<OPTION value="3">3                  (14-16 paired)
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<OPTION value="8">8                  (13-20 paired)
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<OPTION value="4">4                  (13-16 paired)
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<OPTION value="total">Total            (13-22 paired)
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<OPTION value="5">5                  (13-17 paired)
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<OPTION value="custom">Custom  
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<OPTION value="6">6                  (13-18 paired)
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</SELECT></div>
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<OPTION value="7">7                  (13-19 paired)
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<div class="suboption">
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<OPTION value="8">8                  (13-20 paired)
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<span style="font-size: 15.0px;"> Customized </span>
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<OPTION value="total">Total            (13-22 paired)
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<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MATCH </span>
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<OPTION value="custom">Custom  
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<span style="font-size: 15.0px;">positions (input numbers from 9 to 22)</span></div>
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</SELECT></div>
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<div class="suboption">
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<div class="suboption">
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<input type="text" id="match" size="30" disabled="disabled" value="10, 15, 16, 17, 18, 19, 20"/></div>
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<span style="font-size: 15.0px;"> Customized </span>
-
<br>
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<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MATCH </span>
-
<br>
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<span style="font-size: 15.0px;">positions</span></div>
 +
<div class="suboption">
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<input type="text" id="match" size="29" disabled="disabled" value="10, 15, 16, 17, 18, 19, 20"/>
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</div>
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</td>
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</tr>
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<tr>
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<td>
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<div class="title">
<div class="title">
<span style="font-size: 17.0px; font-weight:bold;">
<span style="font-size: 17.0px; font-weight:bold;">
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<div class="clear">
<div class="clear">
<div class="optionl"><input name="AU" value="9" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 9</span></div>
<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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<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><br>
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<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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<br>
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</td>
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<td style="vertical-align:top;">
<div class="title"><span style="font-size: 17.0px; font-weight:bold;">Sticky ends for integration in plasmid: </span></div>
<div class="title"><span style="font-size: 17.0px; font-weight:bold;">Sticky ends for integration in plasmid: </span></div>
<div class="option">  <SELECT id="stickyends" name="stickyends" onchange="chMd3()">
<div class="option">  <SELECT id="stickyends" name="stickyends" onchange="chMd3()">
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<OPTION value="custom">Custom sequence
<OPTION value="custom">Custom sequence
</SELECT></div>
</SELECT></div>
-
<div class="option"><span style="font-size: 15.0px;">     Customized:   5'</span><input type="text" id="end5" size="15" disabled="disabled"/>         <span style="font-size: 15.0px;">3'</span><input type="text" id="end3" size="15" disabled="disabled"/>
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<div class="option"><span style="font-size: 15.0px;">Customized:</span>
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<span style="font-size: 15.0px;">5'&nbsp;&nbsp;</span><input type="text" id="end5" size="15" disabled="disabled"/>
 +
<span style="font-size: 15.0px;">3'&nbsp;&nbsp;</span><input type="text" id="end3" size="15" disabled="disabled"/>
</div>
</div>
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</td>
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</tr>
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</table>
 +
<br>
<center>
<center>
<input value="      Get your Binding Site!      " type="button" onclick="SBS(seqIn)">
<input value="      Get your Binding Site!      " type="button" onclick="SBS(seqIn)">
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</center>
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</center>
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<br>
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</div>
</div>
</form>
</form>
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<br>
 
</body>
</body>
<script type="text/javascript" src="http://2010.igem.org/wiki/images/3/3a/Very_final_code_miBS_HD2010.txt"> </script>
<script type="text/javascript" src="http://2010.igem.org/wiki/images/3/3a/Very_final_code_miBS_HD2010.txt"> </script>

Revision as of 08:00, 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 0
A in position 1
A in position 8
A in position 9
A in position 10
Sticky ends for integration in plasmid:
Customized: 5'   3'  









Name of primer 1


Sequence of primer 1


Name of primer 2


Sequence of primer 2