I'm using this blastn command to find identity between a number of sequences. This is the command:
blastn -query IAM_O_DNA_0001_0001.txt -subject IAM_O_DNA_0001_0001.txt -outfmt 10 -max_target_seqs 100000 1>BLAST_O_0001_0001.txt
I'm basically blasting the same file against itself. The file contains 10 sequences each with 5842792 nucleotides. I'm expecting the output to be something like this:
and since there are 10 sequences, it should be 100 lines (10 X 10). But the actual output is like this (first 6 lines):
1,1,100.00,5842792,0,0,1,5842792,1,5842792,0.0,1.079e+007 1,1,100.00,5629,0,0,2608960,2614588,2401317,2395689,0.0,10395 1,1,100.00,5629,0,0,2395689,2401317,2614588,2608960,0.0,10395 1,1,99.69,5214,14,2,3593811,3599023,1890756,1885544,0.0,9539 1,1,99.69,5214,14,2,1885544,1890756,3599023,3593811,0.0,9539 1,1,99.83,4594,8,0,5108830,5113423,1876943,1881536,0.0,8440
with thousands of lines. I'm not sure what's happening. The program works for smaller sequences (same number of sequence, less nucleotides). Any suggestions as to why this is happening and how to fix it?