## Description

This track shows the number of species aligned to the human genome in the ENCODE regions in which the alignment does not contain a gap at a particular human base position. The multiple species alignments, which were generated by the programs MAVID, MLAGAN and TBA (v2), are taken from the Sep. 2005 ENCODE MSA freeze.

This track, which complements the MSA Alignment Agreement track (Align Agree), is useful for distinguishing between agreements in which both programs align the human base to the same base in another species and those instances in which both align the human base to a gap in the other species.

## Display Conventions and Configuration

This annotation follows the display conventions for composite tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

## Methods

See the description page for the Align Agree track for a discussion of the methods used to generate these data.

## Credits

The agreement tracks were generated by Lior Pachter and Ariel Schwartz of UC Berkeley.

## References

Schwartz AS, Myers EW, Pachter L. Alignment metric accuracy. Submitted. 2007.