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. 2010 Dec 26;11:609. doi: 10.1186/1471-2105-11-609

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Copyright ©2010 Singh and Mishra; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<url>http://creativecommons.org/licenses/by/2.0</url>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Alignment signature for CAN (canonical transposition). Query1 and Query2 show an overlap in the region of target site duplication at the orthologous empty locus, while the repeat overhangs do not align (represented by oblique green lines) and DSQFC is < 71 or A and AT score > 0.65 or 0.90 respectively. 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, orange line - downstream flank. DSQFC - downstream sequence query first coordinate, DSSFC - 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.