[Mauve-users] Unexpected alignment result

[Christine J. <chr...@gm...>]

Hey there,

I aligned two Tuberculosis genomes with progressiveMauve with default
paramaters and got a puzzling result. (see below -I did not include the
sequence of the first block, as it is very long and not part of the problem)

I expect the sequences of the second and the last block to be aligned in
one single block as their sequences are almost the same... What could be
the reason for such a behaviour?

Thanks a lot,
Christine



#FormatVersion Mauve1
#Sequence1File GCF_000153685.2_ASM15368v2_genomic.fna
#Sequence1Format        FastA
#Sequence2File  GCF_001545055.1_ASM154505v1_genomic.fna
#Sequence2Format        FastA

> 1:103-4408223 + GCF_000153685.2_ASM15368v2_genomic.fna
....
> 2:2-4426387 + GCF_001545055.1_ASM154505v1_genomic.fna
...
=
> 1:1-102 + GCF_000153685.2_ASM15368v2_genomic.fna
TTTGTGGATAGCCATGTGGACAGTTCACCTGCCCACAACAACGGTTGTAGCTCGACCCGGAACCAAGACCCGGAACTAACGAGAACCAGGGAGATACGTCGT
=
> 1:4408224-4408224 + GCF_000153685.2_ASM15368v2_genomic.fna
A
=
> 2:1-1 + GCF_001545055.1_ASM154505v1_genomic.fna
T
=
> 2:4426388-4426489 + GCF_001545055.1_ASM154505v1_genomic.fna
ATTTGTGGATAGCCATGTGGACAGTTCACCTGCCCACAACAACGGTTGTAGCTCGACCCGGAACCAAGACCCGGAACTAACGAGAACCAGGGAGATACGTCG