Blast Display Non-Matching Ends Of Sequence

Question

[W Langdon]

Is it possible for blastn to show the parts of the database which do not match? Eg if I ask blastn for matches to a 36 base pair sequence and it finds a human DNA sequence which matches 27 bases of 30, by default, it shows me the 30 (including 3 mis-matches) but does not show me the six bases which do not match. Eg:

 Score = 36.2 bits (18),  Expect = 6.6
 Identities = 27/30 (90%), Gaps = 0/30 (0%)
 Strand=Plus/Minus

Query  1         CTTCTTGTTTTAGCTCTCCTAATGTAAACA  30
                 |||||||||| ||||||| || ||||||||
Sbjct  98391026  CTTCTTGTTTCAGCTCTCATACTGTAAACA  98390997

Can I tell it to show the reference sequence 98390997-6 to 98390997-1 ???

Thank you Bill

Answer 1

[Jeremy Leipzig]

BLAST stands for Basic Local Alignment Search Tool

If you want a global alignment or glocal/semi-global alignment (i.e. full query sequence) then there are options for that:[?] http://en.wikipedia.org/wiki/List_of_sequence_alignment_software