The 10 sequence characters before and after a repeat are shown. Symbol - indicates an insertion or deletion. Statistics refers to the matches, mismatches and indels overall between adjacent copies in the sequence, not between the sequence and the consensus pattern. 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.