Example of a repeat map, and graphical representation. Name contains locus names of submitted query sequences (first column) and library sequences (fourth column). Repbase names are hyperlinked to their sequences in web-based Censor. From/To contains beginning/end positions of reported fragments on their corresponding sequence. Dir indicates orientation ('d' for direct, 'c' for complementary) of repeat fragment. Column Sim contains the similarity between 2 aligned fragments, calculated as described in the text. Pos is roughly the ratio of positive matches (bases that produce positive scores in the alignment matrix) to alignment length. This ratio is calculated the same way as we calculate similarity (see main text), with positive_count instead of match_count. This information is particularly useful for estimating the quality of protein alignments. Score is the alignment score obtained from BLAST.