Most splits are relatively simple to determine because mismatches are consistent across columns. An example of this is the following, where three columns contain mismatches:
seq1 ...AA G CTGG C TCCG C TA...
seq2 ...AA G CTGG C TCCG C TA...
seq3 ...AA G CTGG C TCCG C TA...
seq4 ...AA A CTGG T TCCG A TA...
seq5 ...AA A CTGG T TCCG A TA...
seq6 ...AA A CTGG T TCCG A TA...
In this case, SeqMan Pro will suggest a split that puts sequences 1 through 3 in one contig and 4 through 6 in another. Although most splits are of this straightforward type, the case below is more difficult:
seq1 ...AA G CTGG C TCCG C TA...
seq2 ...AA G CTGG C TCCG C TA...
seq3 ...AA G CTGG C TCCG C TA...
seq4 ...AA A CTGG C TCCG A TA...
seq5 ...AA A CTGG T TCCG A TA...
seq6 ...AA A CTGG T TCCG A TA...
Mismatches in the first and the third mismatched columns indicate that sequences 1 through 3 should be in one new contig and 4 through 6 in another. However, the mismatches in the second mismatched column indicate that sequences 1 through 4 should be in one new contig and 5 and 6 in another. Rather than splitting the contig into multiple contigs to resolve the inconsistency (in this case, sequences 1 through 3 in one contig, 4 in another, and 5 and 6 in another), SeqMan Pro will suggest a split that is consistent with the majority of the mismatched columns.