Hello, I run the mummer command for a pairwaise alignment
mummer -s -mum refer.txt query.txt > refer_query.align
The result is:
> query
1450 9370 21
gaggttgcagtgagctgagat
2122 9771 21
caaaaaaaaaaaaaaaaaaaa
3296 9570 26
gaggtcaggagatcgagaccatcctg
3318 9243 20
cctgaccaacatggtgaaac
3428 9353 30
cttgaacctgggaggcagaggttgcagtga
3461 9386 20
gagatcatgccactgcactc
3502 9773 20
aaaaaaaaaaaaaaaaaaag
My question is the result seems only display the matched strings in the query sequence. Can we also show the ones in the reference sequence?
If you are interested in variants, you can try dnadiff from MUMmer.