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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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Misannotation because of sequencing gaps. Since a certain amount of sequence information at the orthologous locus is missing and substituted by approximate number of Ns, only partial matches for the upstream and downstream sequences are obtained resulting in false annotation by RISCI. 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.