I'm trying to align some sequences that have large deletion (~150bp) using command line blastn.
Size of subject is 266bp and query size is about 115bp. Blastn can align the query either to 5' end or 3' end of the subject but it cannot align the query as a single alignment with large gap. I tried to change gap opening and gap extension penalty to 0 but it wasn't helpful. Does anyone have an idea how to run blastn to get a single alignment with large gap? Below is my code and example sequences.
blastn -db ~/data/raw/GSKOampliconNGS/IntronGSgene.fa -query test.fa -out test_results.out -max_hsps 1 -gapopen 0 -gapextend 0 \ subject - ttggccttattctaaaggtcaacatgttctttctagtgggaattccaaataggaccctgtgaaggaatccgcatgggagatcatctctgggtggcccgtttcatcttgcatcgagtatgtgaagactttggggtaatagcaacctttgaccccaagcccattcctgggaactggaatggtgcaggctgccataccaactttagcaccaaggccatgcgggaggagaatggtctgaagtaagtagcttcctctggagccatctttat \ query - ATAAAGATGGCTCCAGAGGAAGCTACTTACTTCAGACCATTCTCCTCCCGGATTCCTTCACAGGGTCCTATTTGGAATTCCCACTAGAAAGAACATGTTGACCTTTAGAATAAGGCCAA