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Upload the XtAtoh7.maf file ( or another acceptable alignment format ) and click Next ...

For this demo you already need the XtAtoh7.maf multiple alignment file from demo (a). Another example.maf file is also available on the ConTra help page in the description of Step1. Upload the XtAtoh7.maf file ( or another acceptable alignment format ) and click Next.

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Upload the XtAtoh7.maf file ( or another acceptable alignment format ) and click Next ...

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  1. For this demo youalreadyneed the XtAtoh7.maf multiple alignment file from demo (a). Anotherexample.maf file is alsoavailableon the ConTra help page in the description of Step1.

  2. Upload the XtAtoh7.maf file (oranotheracceptablealignmentformat) and click Next...

  3. Uploadingyourown multiple alignment file willskip steps 2 and 3 (transcript and sequence part selection) and shows step 4 forselecting the stringency and positionweight matrices (PWMs). For the XtAtoh7 example click on TRANSFAC...

  4. Select the PWM fordetectingEboxes and click the Run ConTrabutton...

  5. Threealignmentblocks have been analyzed and are shownon the result page. In the secondblockon the preview figuretwoconserved sites are shown. Click on the To resultpage link to see the details or use the .fc and .fasta file to view the results in Jalview and createan image.

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