I have aligned a 5k sequence to a reference sequence longer than 5k. The Blast alignment report shows alignment not from the start position of the reference but from bases from where alignment starts. I want an alignment report where reference which does not match to the consensus is also mentioned in the report.
For example (Desired Output);
Query ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ AGCTTGGCCC ATTGCATACG TTGTATCCAT Reference AAACGAGCTC TGCTTTTATA GGCGCCCACC AGCTTGGCCC ATTGCATACG TTGTATCCAT Query ~~~~~~~~~~ ~~~~~~~~~ Reference AATTAAGCGC GCAACGATG
Blast only reports bases which are aligned. Example:
Query AGCTTGGCCC ATTGCATACG TTGTATCCAT Reference AGCTTGGCCC ATTGCATACG TTGTATCCAT
I can only use BLAST to do this.
How can I obtain such alignment report using Blast?
Thanks in advance!!!