Schema for RepeatModeler - Transposons Identified by RepeatModeler
  Database: DbipGB2    Primary Table: RepeatModeler_LTR Data last updated: 2014-11-20
Big Bed File: /gbdb/DbipGB2/bbi/DbipGB2_LTR.bb
Item Count: 28,525
Format description: RepeatMasker .out record
fieldexampledescription
chromAFFE02000004Genomic sequence name
chromStart148Start in genomic sequence
chromEnd219End in genomic sequence
namernd-5_family-1315Name of repeat
score0always 0 place holder
strand-Relative orientation + or -
swScore239Smith Waterman alignment score
milliDiv25.6Base mismatches in parts per thousand
milliDel0.0Bases deleted in parts per thousand
milliIns4.4Bases inserted in parts per thousand
genoLeft-1145-#bases after match in genomic sequence
repClassLTRClass of repeat
repFamilyPaoFamily of repeat
repStart-3025Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd458End in repeat sequence
repLeft399-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows
 
chromchromStartchromEndnamescorestrandswScoremilliDivmilliDelmilliInsgenoLeftrepClassrepFamilyrepStartrepEndrepLeft
AFFE02000004148219rnd-5_family-13150-23925.60.04.4-1145LTRPao-3025458399

RepeatModeler (RepeatModeler) Track Description
 

Description

This track shows the transposon fragments identified by RepeatMasker using the species-specific RepeatModeler library constructed by the GEP. The consensus sequences produced by RepeatModeler were reclassified using the protocol described in the supplemental methods section.

References

Smit, AFA, Hubley, R. RepeatModeler Open-1.0. http://www.repeatmasker.org. 2008-2010.

Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.