*   Reference Sequence File: alu-2-repeats.uc
*     Library Sequence File: chrY.NT_087001.1.part1.fa.subset
*
*   Output file format:
*
*   LOCUS1 N1 N2 LOCUS2 M1 M2 F1 F2 F3 L S #
*
*   ... aligned fragments ...
*
*   ... statistics line from original file ...
*
*   where N1,N2,M1,M2 - aligned fragments boundaries
*   F1 - (no. of Matches)/(no. of Matches + no. of Mismatches + no. of Gaps),
*   F2 - (Number of Gaps)/(Number of Mismatches),
*        which is set to 0 if (Number of Mismatches) == 0,
*   F3 - (Number of Mismatches)/(Number of Transitions),
*        which is set to 1 if (Number of Transitions) == 0
*        and to 100 if both numbers == 0,
*   L  - Length of the top sequence fragment,
*   S  - Local Score.
*
*   Local parameters:
*   Margin                              =      150
*   Similarity threshold                =    25.00
*   Similarity threshold to always keep =    35.00
*   Ratio threshold                     =     2.50
*   Relative Similarity threshold       =     0.23
*   Gap Constant D1                     =   1.0100
*   Gap Constant D2                     =   0.9100
*   Mismatch Penalty D3                 =  -0.9000
*   (Gap penalty = -(D1 + D2 * length))