I am trying to find the optimal local alignment score of a short sequence (50bp) to a reference bacterial genome of several Mbp. When I use Biopython Align module, I always get the score equal to the length of the shorter (query) sequence. For example, with alignxx function:

('--G------------------A-----------TC-G-G-G------AC-G---C--C----G--G-------T---TG-C-GA----AT---A--CA-C----AG-G--------T----------TT---AT-G----TG-C-T-----G------G--------AC--G--A-A----A-A----A----C-A----------------A---T--C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------', 'CGGTGCCCTCCTCCGCGGCGTACACCCCGCGCGTCCGCGCGGGCGCGACTGATACAGCTTACGCCGGCGCGACTGCCTGTCCGAGTCGATCGCATACATCTGTTAGCGCGGCAGGGTGAACGCGGCGTTCGCATCGCCGATGGCGTACTACGCCTCCCGGGGGCCGCACACGTGACATCGGACAGGCGAGGTTCCACCGGGCCCCGCTCCGGAGCCTGGCGCGAGTGAATGCCATACCTTATATAAACTCAGTCCGCCCAGAACTATGGGTATGGAACCCGGCGGTATAGGGCACTCGCCCACCCATTGTCCTGAACTGCTGCTGAACATTGCGCGATTATGGTTGATACCGCGGATACCTCAGCGCGCTCTGCGACGCGCCCTGAGGACCCGACCGCCACTTAAGCATAGGCCGCCAGAAGAGCGCCGCTCCTAGGTGCGGCCGCGGAGACTAGGGCGGCCTTGAGACCGGAAATGCAAGGACCTGGGCAACCAACTTACCCCTTCGCTAGTGCTGAGCTACGGCGGATAAGAACGTCAATAGGCGAATAGAGTCTCCGCACCCATCGCCCTCTGAGGTTTGGAGGGCGGCCAAAGATACTGGGCAGGACCCCCGCATCCCAAGGTAGTCTGGTTCGGGACCAGCCTATCGAACAGTTCGAAATACGGAGCGGGACAAACGAAGCATCGCGCGTACCGTGTCCCGGACGCGGTGCGGACCTCGCCCGCACTTGCTTCCCGTGAACACGGAGCGGTCCCGCCCGTAGGGATCATATCGTCCCAAGGGACAGCCATAGCCCGCCTCCTCCTATGGTGCTGAGAAGCCCGGGGGCCCCCAGCAGCCTCTCCGCGGACCGAGGATGAGAGGAACACGCTCTACCGAGGCACAGTACCCTGGTTTTGTTCCAGCAATCCCCTTCCACGGCGCTATCTTGCTTAGGTGCGGTGAGAATAATGTCCGACTCCCGTTCCCGGGGATTTGGCGGTGCGGCCCAGTAT', 54.0, 0, 999)

The local alignment seems to give correct values (similar to editor distance) if the two sequences are comparable in size.

1. Why are the gaps in one of the sequence not counted? Can I set a parameter to alleviate that?
2. Is the editor distance a good approximation to the alignment score (taking into account it doesn't handle reverse complements)?

Thanks!