I am using Blast command line. The query (length 9) is ADZTZZETK, but when blasted against database sequence, it gives alignment of length 8 (ADZTZZET:ADZTZZET). It means that last, 9th, character of query sequence, K, is mis-matched with database sequence. However I still want to get the 9th mis-matched character of database sequence. Could someone tell me which option I should use in command line blast for that?
Unfortunately, I don't think you can get the full query or subject sequence from BLAST. If you look under the outfmt options in the command-line documentation the closest option is sseq, which says Aligned part of subject sequence. If you can download the database in FASTA format, then you can parse that file separately and get the subject sequence.