Schema for RepeatModeler - Transposons Identified by RepeatModeler
  Database: DbiaGB2    Primary Table: RepeatModeler_RC Data last updated: 2014-11-20
Big Bed File: /gbdb/DbiaGB2/bbi/DbiaGB2_RC.bb
Item Count: 16,467
Format description: RepeatMasker .out record
fieldexampledescription
chromAFFD02000007Genomic sequence name
chromStart1Start in genomic sequence
chromEnd17End in genomic sequence
namernd-5_family-697Name of repeat
score0always 0 place holder
strand-Relative orientation + or -
swScore613Smith Waterman alignment score
milliDiv21.9Base mismatches in parts per thousand
milliDel14.6Bases deleted in parts per thousand
milliIns3.6Bases inserted in parts per thousand
genoLeft-2370-#bases after match in genomic sequence
repClassRCClass of repeat
repFamilyHelitronFamily of repeat
repStart-474Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd715End in repeat sequence
repLeft692-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows
 
chromchromStartchromEndnamescorestrandswScoremilliDivmilliDelmilliInsgenoLeftrepClassrepFamilyrepStartrepEndrepLeft
AFFD02000007117rnd-5_family-6970-61321.914.63.6-2370RCHelitron-474715692
AFFD02000007140321rnd-5_family-6970-61321.914.63.6-2066RCHelitron-474691400
AFFD02000007141448rnd-2_family-60+108916.73.614.4-1939RCHelitron5528290
AFFD0200000718982062rnd-1_family-100+89211.00.32.1-325RCHelitron1142-1
AFFD0200000720932387rnd-5_family-6970-157910.218.40.30RCHelitron-77441569

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.