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Figure 8 | BMC Bioinformatics

Figure 8

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 8

Alignment signatures for Insertion-mediated deletion with exclusive mobilization of the transposon. Insertion-mediated deletion results in replacement of original sequence by the transposon without the duplication of target site. On alignment at the orthologous locus in the comparative genome, no match is found for the repeat overhangs (represented by oblique green lines) and the upstream and downstream flanks are separated by a sequence stretch representing the original sequence lost upon insertion of the repeat in the main genome. Ancestral locus - from left to right - Pink line - 5' flank, turquoise line - sequence lost on L1 insertion, orange line - 3' flank. DS QFC - downstream sequence query first coordinate, DS SFC - downstream sequence subject first coordinate, 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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