1)The flanking sequences (500pb) of all repeats from the query genome (stored in our database) will be used to identify allelic regions in the target strain. When the borders of the query repeat are partialy conserved, the coordinates of the variable regions and the number of bases that did not match in 5' and 3' of the repeat will be indicated in the 2 columns surounding the repeat position column. If corresponding region in the target strain contains one or more TRF repeats referenced in our database , the maximal score repeat will be printed in the result table else the table will contain the coordinates and length of the internal fragment defined on the basis of the border's conservation. The results are ordered according to the position in the target strain.
2) To complete the output, some data from the reciproqual comparison are added, showing regions of the query strain that are allelic to repeats identified in the target strain but did not contain any repeats in the query strain.
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