BTOP an other trail to explore

Instead of dealing with the alignment, one can just parse the BTOP if provided in the output.

"The “Blast trace-back operations” (BTOP) string describes the alignment produced by BLAST. This string is similar to the CIGAR string produced in SAM format, but there are important differences. BTOP is a more flexible format that lists not only the aligned region but also matches and mismatches. BTOP operations consist of 1.) a number with a count of matching letters, 2.) two letters showing a mismatch (e.g., “AG” means A was replaced by G), or 3.) a dash (“-“) and a letter showing a gap. The box below shows a blastn run first with BTOP output and then the same run with the BLAST report showing the alignments."

Ex : 
btop = 7AG39
Query  1   ACGTCCGAGACGCGAGCAGCGAGCAGCAGAGCGACGAGCAGCGACGA  47
           ||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct  47  ACGTCCGGGACGCGAGCAGCGAGCAGCAGAGCGACGAGCAGCGACGA  93

btop = 7A-39
Query  1   ACGTCCGAGACGCGAGCAGCGAGCAGCAGAGCGACGAGCAGCGACGA  47
           ||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct  1   ACGTCCG-GACGCGAGCAGCGAGCAGCAGAGCGACGAGCAGCGACGA  46

Khalid,