1. 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.

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

3. Uploading your own multiple alignment file will skip steps 2 and 3 (transcript and sequence part selection) and shows step 4 for selecting the stringency and position weight matrices (PWMs). For the XtAtoh7 example click on TRANSFAC... Uploading your own multiple alignment file will skip steps 2 and 3 (transcript and sequence part selection) and shows step 4 for selecting the stringency and position weight matrices (PWMs). For the XtAtoh7 example click on TRANSFAC...

4. Select the PWM for detecting Eboxes and click the Run ConTra button...

5. Three alignment blocks have been analyzed and are shown on the result page. In the second block on the preview figure two conserved 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 create an image. Three alignment blocks have been analyzed and are shown on the result page. In the second block on the preview figure two conserved 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 create an image.