Understanding Mauve Contig MOver Alignment Result

[chariko]

Hi,
I have used Mauve Contig mover to reorder 20 contigs into just one using a reference genome file. When running Mauve Contig Mover, I obtain 2 alignment folders and when I look through the Alignment2 file I obtain various files. The one I do not understand is the one called alignment. It looks like:

#FormatVersion Mauve1
#Sequence1File reference.gb
#Sequence1Format GenBank
#Annotation1File reference.gb
#Annotation1Format GenBank
#Sequence2File 20_contigs.fasta
#Sequence2Format FastA
#BackboneFile alignment2.bbcols

> 1:1-46592 + ..alignment2/reference.gb
acgtgcc--tcg....
> 2:643-45360 +alignment2/20_contigs.fasta
ttt---cgttaacca...
> 1:46633-47274 + ../alignment2/reference.gb
tgtacga
> 2:1-642 + alignment2/20_contigs.fasta
cgggc
> 1:46593-46632 + ../alignment2/reference.gb
cgggc
> 2:45361-47649 + alignment2/20_contigs.fasta


Which one is my unique contig? the ones whose fasta header ended in reference or in 20_contigs?

Any suggestion is really appreciated.