Genomic sequence has introns in it which are sometimes quite large. Try
to "large gap" algorithm in assembly options in the sequencher. That
should get sequencher to expect large gaps introduced by introns.
Also there is a EST2genome program available for this kind of stuff from
>> In an attempt to find the genomic sequences for the cDNA of my interest I
> pulled out a bunch of WGS trace sequences. I used SEQUENCHER to assemble
> these trace sequences (against my cDNA sequence) only to find out that most
> of the best hits (BLAST) didn't form 'contigs' with my cDNA sequence. I'm
> not sure if it's a function of my sequences or of SEQUENCHER. Can anyone
> help me in this regard? (I hope I stated my problem clearly enough).
>> Thanks a lot for all the help.