low optimal alignment score for almost identical sequences

[bing-jian]

Not sure why sometimes the alignment function returns very low optimal alignment score for almost identical sequences and hence no alignment is returned (query_begin == query_end in the result).
Example:
In [211]: align_func = ssw_aligner.local_pairwise_align_ssw
In [212]: o = align_func(seq1[0:10], seq1[1:11])
In [213]: o
Out[213]:
{
'optimal_alignment_score': 2,
'suboptimal_alignment_score': 0,
'query_begin': 9,
'query_end': 9,
'target_begin': 8,
'target_end_optimal': 8,
'target_end_suboptimal': 0,
'cigar': '1M',
'query_sequence': 'bbbbbbbbBT',
'target_sequence': 'bbbbbbbBTT'
}