Promoter Chip Tile Mapping to mm8

We mapped all the of the promoter chip tile primer pairs to the mouse genome release mm8 using the program me-PCR with a 'margin' of 1000bp. This large margin means that the primers for a tile may map to a location that places them up to 1000bp closer or further away than we thought they were when we designed the chip. Although the vast majority of tiles mapped uniquely to mm8 under these conditions and with a length very close to the original length, a number of tiles hits multiple locations or did not map at all. When a tile mapped to multiple locations, we have tried to guess, based on the primers, size, number and location of the hits to classify the tile.

The table below represents our current results. The links lead you to a tabular display of the primer pairs and their mapping location. In every case, except 'unhandled condition', we report the location with a margin closest to zero as the primary location, and report any other locations in the rightmost column. In these displays the locations are links to the UCSC genome browser.

There appear to be some miss classifications which suggests that further work may be needed to improve the classification.

Class Number of Tiles Defintion
missed 606 Primer pair did not map to any location.
unique 33698 The primer pair maps to only one location.
dinuc 390 Either one of the primers consists entirely of 'CA' or 'GT' repeats.
repeat tile 71 A primer pair maps to 9 or more places
end repeat 100 A primer pair maps to one chromosome and the beginning or end of (the first) two hits are are the same place.
local duplication 330 A primer pair maps to one chromosome and the range of margins is less than 50 or the total span of the tiles is less than 500KB.
dispersed multi-chromosome duplication 26 A primer pair maps to more than one chromosome but the range of margins is less than 50.
probable-repeat 7 A primer pairs maps to four or more positions and is not classified above.
unhandled-condition 16 The primer pair mappings do not meet any of the definitions above.