Schema for RepeatModeler - Transposons Identified by RepeatModeler
  Database: DeugGB2    Primary Table: RepeatModeler_DNA Data last updated: 2014-11-20
Big Bed File: /gbdb/DeugGB2/bbi/DeugGB2_DNA.bb
Item Count: 10,952
Format description: RepeatMasker .out record
fieldexampledescription
chromAFPQ02000018Genomic sequence name
chromStart0Start in genomic sequence
chromEnd69End in genomic sequence
namernd-1_family-117Name of repeat
score0always 0 place holder
strand-Relative orientation + or -
swScore537Smith Waterman alignment score
milliDiv4.4Base mismatches in parts per thousand
milliDel0.0Bases deleted in parts per thousand
milliIns1.5Bases inserted in parts per thousand
genoLeft-1861-#bases after match in genomic sequence
repClassDNAClass of repeat
repFamilyMaverickFamily of repeat
repStart-344Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd495End in repeat sequence
repLeft428-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows
 
chromchromStartchromEndnamescorestrandswScoremilliDivmilliDelmilliInsgenoLeftrepClassrepFamilyrepStartrepEndrepLeft
AFPQ02000018069rnd-1_family-1170-5374.40.01.5-1861DNAMaverick-344495428
AFPQ0200001868242rnd-1_family-1170-14132.96.30.0-1688DNAMaverick-338501317
AFPQ02000018241287rnd-1_family-850-2317.02.26.8-1643DNAMaverick-236958915
AFPQ02000018272811rnd-1_family-850-39904.82.80.4-1119DNAMaverick-6425521
AFPQ020000187671930rnd-1_family-1130+56147.61.20.00DNAMaverick17530

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.