[Bioperl-l] help with BLAST

[Crook, R.]

Hi,
I'm a newbie to this site so please be gentle!!
I'm using blastn and remoteblast to find human LINEs and its not working as I'd expect.  I'm using the stardard code to get the acc and start of each match but the matches aren't as I expect.  They have been fragmented so even when the subject matches with itself it divides into three parts.  I could write a long complex prog to find the real start but I think this would be difficult as the many of the sequences will have two LINEs in them.  Does anyone know a way round the matching.

I hope thats clear to you.  

Becca
Leicester Uni.