Fig. 6

Seed alignment examples from raw Dfam 3.3 entries. A) ERV1 (LTR) (DR0086957.1; Eulemur macaco (black lemur)). The red bracket indicates a group of sequences differing in length and divergence patterns. 506 sequences contribute to the seed alignment for this 503 bp model. B) L1 sequence (DR0215804.1; Phyllostomus discolor (pale spear-nosed bat)). The red brackets indicate two groups of sequences that differ in their 5′ alignment. One thousand one hundred eighty-six sequences contribute to the seed alignment for this 7353 bp model. Each sequence is represented by a single row (sorted by start position) where the color gradient indicates alignment quality (red = low; blue = high) over 10 bp non-overlapping windows. The solid green shape over the two seed alignments indicate the coverage along the model consensus sequence. Note: the two panels differ in scale