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Figure 6 | BMC Bioinformatics

Figure 6

From: RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

Figure 6

Alignment signatures for PAC and PTS. Query 1 aligns at the orthologous empty locus starting from the TSD upwards. Likwise, Query 2 aligns from the TSD, downwards. The region of Query 2 preceding the TSD (represented by oblique line), which does not find a contiguous match, consists of the 3' repeat overhang and the misannotated poly A tail or the transduced flank depending on the A and AT scores. From left to right - Pink line - upstream flank, blue arrows and line-target site duplication sequence, green line - repeat sequence, dotted lines- poly (A) tails, dark pink line - transduced flank, orange line - downstream flank. DSQFC- downstream sequence query first coordinate, DSSFC - downstream sequence subject first coordinate, PTS - putative transduced sequence, Query1 - 5' or upstream flank with 50 bp repeat overhang, Query2 - 3' or downstream flank with 50 bp repeat overhang, RM - RepeatMasker start and end coordinates, USSLC - upstream sequence subject last coordinate.

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BMC Bioinformatics

ISSN: 1471-2105

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