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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 signatures for shared ancesstory or OCCUPIED loci in the comparative genome. Complete alignment of the repeat overhangs contiguously with their respective flanks and the separation between the flanks within 100 base range of the transposon length in the main genome. From left to right - Pink line - upstream flank, blue arrows - Target site duplication sequence, Green line - repeat sequence, dotted lines- poly (A) tails, orange line - downstream flank. 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.