![]() ![]() Select the sequence list containing the raw sequence data from the mitochondrial DNA control region. Double-click on the list to open it in a new window. In the General tab to the right of the sequence view, choose to display Colors according to Quality. This will highlight the base calls according to the quality of the sequence at that base – the darker the blue, the lower the quality. ![]() When zoomed out you won’t see the individual bases or chromatogram peaks, but there will be a graph visible giving an indication of sequence quality. If you scroll down the sequences you’ll see that the sequence quality decreases dramatically at the end of each sequence. Zoom in to at least 50% to see what the chromatograms look like in good vs poor quality regions. One of the sequences (CLG3) has no sequence, indicating the sequencing reaction failed so delete this one from the list. Sequence SRE1 has only a short stretch of good quality sequence before the sequence becomes unreadable so delete this one as well. Save the edited sequence list and close the window. Trim the poor quality bases off the ends of the sequences by clicking Annotate and Predict→Trim Ends. Choose to “Remove new trimmed regions from sequences” and set the Error probability limit to 0.01, as shown in the screenshot below. Click OK and then Save once the trimming is finished.įrom here it is more efficient to finish cleaning up and editing the sequences once they are aligned. Select the sequence list (Cyanistes CR sequences) again and click Align/Assemble→Multiple Align.
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June 2023
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