Schema for RepeatModeler - Transposons Identified by RepeatModeler
  Database: DsuzGB1    Primary Table: RepeatModeler_Unknown Data last updated: 2014-11-20
Big Bed File: /gbdb/DsuzGB1/bbi/DsuzGB1_Unknown.bb
Item Count: 107,465
Format description: RepeatMasker .out record
fieldexampledescription
chromAWUT01012676Genomic sequence name
chromStart65011Start in genomic sequence
chromEnd65382End in genomic sequence
namernd-1_family-172Name of repeat
score0always 0 place holder
strand+Relative orientation + or -
swScore2187Smith Waterman alignment score
milliDiv6.3Base mismatches in parts per thousand
milliDel8.6Bases deleted in parts per thousand
milliIns1.8Bases inserted in parts per thousand
genoLeft-29213-#bases after match in genomic sequence
repClassUnknownClass of repeat
repFamilyUnknownFamily of repeat
repStart1Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd396End in repeat sequence
repLeft-10-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows
 
chromchromStartchromEndnamescorestrandswScoremilliDivmilliDelmilliInsgenoLeftrepClassrepFamilyrepStartrepEndrepLeft
AWUT010126766501165382rnd-1_family-1720+21876.38.61.8-29213UnknownUnknown1396-10
AWUT010126766575865808rnd-1_family-7090+2308.30.04.2-28787UnknownUnknown148-81
AWUT010126766583066325rnd-1_family-3920+18825.72.31.6-28270UnknownUnknown12950
AWUT010126766632066488rnd-3_family-60-14311.80.00.0-28107UnknownUnknown-18898731
AWUT010126767003370347rnd-1_family-1720+15379.90.610.1-24248UnknownUnknown117403-3
AWUT010126767031770369rnd-5_family-46810+2291.911.51.8-24226UnknownUnknown561-2
AWUT010126767372673770rnd-5_family-10150-15839.79.12.4-20825UnknownUnknown-471929636
AWUT010126767657576899rnd-5_family-10070-22787.44.90.3-17696UnknownUnknown-495943605
AWUT010126767935979530rnd-1_family-2960-11625.88.80.0-15065UnknownUnknown-59411226
AWUT010126767952579610rnd-1_family-980-33817.91.21.2-14985UnknownUnknown-44812642

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.