Schema for RepeatModeler - Transposons Identified by RepeatModeler
  Database: DrhoGB2    Primary Table: RepeatModeler_LTR Data last updated: 2014-11-20
Big Bed File: /gbdb/DrhoGB2/bbi/DrhoGB2_LTR.bb
Item Count: 42,551
Format description: RepeatMasker .out record
fieldexampledescription
chromAFPP02000077Genomic sequence name
chromStart0Start in genomic sequence
chromEnd185End in genomic sequence
namernd-1_family-651Name of repeat
score0always 0 place holder
strand+Relative orientation + or -
swScore1426Smith Waterman alignment score
milliDiv4.3Base mismatches in parts per thousand
milliDel0.0Bases deleted in parts per thousand
milliIns0.0Bases inserted in parts per thousand
genoLeft-1883-#bases after match in genomic sequence
repClassLTRClass of repeat
repFamilyGypsyFamily of repeat
repStart627Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd811End in repeat sequence
repLeft0-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows
 
chromchromStartchromEndnamescorestrandswScoremilliDivmilliDelmilliInsgenoLeftrepClassrepFamilyrepStartrepEndrepLeft
AFPP020000770185rnd-1_family-6510+14264.30.00.0-1883LTRGypsy6278110
AFPP02000077186399rnd-5_family-2710+17600.90.00.0-1669LTRGypsy1213-238
AFPP0200007712231326rnd-5_family-2710+8221.00.00.0-742LTRGypsy209311-140
AFPP0200007713251593rnd-1_family-1150+16447.21.00.4-475LTRPao4686610

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.