Schema for RepeatModeler - Transposons Identified by RepeatModeler
  Database: DbiaGB2    Primary Table: RepeatModeler_Unknown Data last updated: 2014-11-20
Big Bed File: /gbdb/DbiaGB2/bbi/DbiaGB2_Unknown.bb
Item Count: 66,650
Format description: RepeatMasker .out record
fieldexampledescription
chromAFFD02000006Genomic sequence name
chromStart0Start in genomic sequence
chromEnd52End in genomic sequence
namernd-1_family-460Name of repeat
score0always 0 place holder
strand-Relative orientation + or -
swScore422Smith Waterman alignment score
milliDiv1.9Base mismatches in parts per thousand
milliDel0.0Bases deleted in parts per thousand
milliIns0.0Bases inserted in parts per thousand
genoLeft-1070-#bases after match in genomic sequence
repClassUnknownClass of repeat
repFamilyUnknownFamily of repeat
repStart-455Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd53End in repeat sequence
repLeft2-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows
 
chromchromStartchromEndnamescorestrandswScoremilliDivmilliDelmilliInsgenoLeftrepClassrepFamilyrepStartrepEndrepLeft
AFFD02000006052rnd-1_family-4600-4221.90.00.0-1070UnknownUnknown-455532
AFFD0200000624342rnd-1_family-5530-22992.910.13.2-780UnknownUnknown03413
AFFD020000063451122rnd-5_family-14340-36138.29.30.10UnknownUnknown06992

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.