Distances between matching characters at corresponding positions are listed as distance, number at that distance, percentage of all matches. ACGTcount is percentage of each nucleotide in the repeat sequence. Consensus sequence is shown by itself. Weights for match, mismatch and indels. These parameters are for Smith-Waterman style local alignment using wraparound dynamic programming.
Lower weights allow alignments with more mismatches and indels.
A 3 is more permissive and a 7 less permissive of these types of alignments choices. Minimum Alignment Score. The alignment score must meet or exceed this value for the repeat to be reported. Maximum Period Size. The period size must be no larger than this value for the repeat to be reported.