Primer BLAST result - only part of sequence is aligned
0
0
Entering edit mode
3.8 years ago
AfinaM ▴ 30

Hi all,

I have a list of primer sequence from this one company and I want to check which primer is the most suitable to sequence my sample (an isolate from an animal).

I BLAST the reverse primer and from the result, eventhough its query cover is 100% and per identity 100%, the number of matches is a bit weird. It only aligns to one part of the primer and not the whole primer

From my understanding, the primer should matches/aligns perfectly to the genome sequence to be able to use it, is this right? I am attaching the BLAST result below.

pic

Can anyone suggest what should I do next? I am thinking to use primer BLAST instead and BLAST each primer to check.

BLAST primer • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 1988 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6