STS Markers Track Settings
STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps   (All Mapping and Sequencing tracks)

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Data last updated: 2009-05-06


This track shows locations of Sequence Tagged Site (STS) markers along the draft assembly. These markers have been mapped using either genetic mapping (Genethon, Marshfield, and deCODE maps), radiation hybridization mapping (Stanford, Whitehead RH, and GeneMap99 maps) or YAC mapping (the Whitehead YAC map) techniques. Since August 2001, this track no longer displays fluorescent in situ hybridization (FISH) clones, which are now displayed in a separate track.

Genetic map markers are shown in blue; radiation hybrid map markers are shown in black. When a marker maps to multiple positions in the genome, it is shown in a lighter color.


Positions of STS markers are determined using both full sequences and primer information. Full sequences are aligned using blat, while isPCR (Jim Kent) and ePCR are used to find locations using primer information. Both sets of placements are combined to give final positions. In nearly all cases, full sequence and primer-based locations are in agreement, but in cases of disagreement, full sequence positions are used. Sequence and primer information for the markers were obtained from the primary sites for each of the maps, and from UniSTS.

Using the Filter

The track filter can be used to change the color or include/exclude a set of map data within the track. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter:

  • In the pulldown menu, select the map whose data you would like to highlight or exclude in the display. By default, the "All Genetic" option is selected.
  • Choose the color or display characteristic that will be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display data from the map selected in the pulldown list. If "include" is selected, the browser will display only data from the selected map.

When you have finished configuring the filter, click the Submit button.


This track was designed and implemented by Terry Furey. Many thanks to the researchers who worked on these maps, and to Greg Schuler, Arek Kasprzyk, Wonhee Jang, and Sanja Rogic for helping process the data. Additional data on the individual maps can be found at the following links: