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Alignments in the contig editor

Tim Cutts timc at chiark.greenend.org.uk
Thu May 18 07:48:00 EST 2000

I've just been observing some odd behaviour in the contig editor of the
1999.1 release (haven't had time to get the new version yet!)

In one particular contig, the textual alignment of the reads looks
absolutely fine, but when I open the traces for some reads, they are not
aligned with each other.

I'm not particularly knowledgeable about this aspect of gap4, and would
be very grateful if someone could suggest reasons why this might be the
case, and what can be done about it?

Thanks in advance...


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