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Configure Tracks on UCSC Genome Browser: D. mojavensis Apr. 2014 (GEP/DmojImproved)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Mapping and Sequencing Tracks    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
Melting Temp. Melting Temperature Estimated by dan
GEP Fosmids Fosmid Projects Improved by the GEP
Assembly Notes GEP Sequence Improvement Notes
-   Genes and Gene Prediction Tracks    
GEP Genes GEP Gene Annotations
GLEAN-R Genes FlyBase GLEAN-R Gene Predictions
GLEAN-R Gene Density FlyBase GLEAN-R Gene Density (1kb window, 0.5kb overlap)
D. mel Proteins Spaln Alignment of D. melanogaster Proteins
Potential Frame Shifts Potential Frame Shifts Detected by SPALN2
GLEAN-R Alignments Alignment of GLEAN-R Predictions from Other Drosophila species
D. mojavensis ESTs Alignment of D. mojavensis ESTs from GenBank
Non-coding RNAs FlyBase Non-coding RNAs
D. mel Non-coding RNAs FASTA alignment of D. melanoagster Non-coding RNAs
-   RNA Seq Tracks    
modENCODE RNA-Seq Coverage modENCODE RNA-Seq Coverage
modENCODE TopHat Junctions Junctions predicted by TopHat using modENCODE RNA-Seq
modENCODE TrueSight Junctions Junctions predicted by TrueSight using modENCODE RNA-Seq
modENCODE Cufflinks Transcripts Transcripts assembled by Cufflinks
modENCODE CEM Transcripts Transcripts assembled by CEM
D. mojavensis Assembled Proteins Assembled Proteins from modENCODE D. mojavensis RNA-Seq
D. virilis Assembled Transcripts Assembled Transcripts from modENCODE D. virilis RNA-Seq
D. virilis Assembled Proteins Assembled Proteins from modENCODE D. virilis RNA-Seq
D. virilis Unmapped Proteins Assembled Unmapped Proteins from modENCODE D. virilis RNA-Seq
Head Tissues RNA-Seq Coverage modENCODE Head Tissues RNA-Seq Coverage
Head Tissues TopHat Junctions Junctions predicted by TopHat using modENCODE RNA-Seq from Head Tissues
Head Tissues Cufflinks Transcripts Cufflinks Transcripts using modENCODE RNA-Seq from Head Tissues
Head Tissues CEM Transcripts CEM Transcripts using modENCODE RNA-Seq from Head Tissues
Unmapped modENCODE RNA-Seq Assembled Unmapped modENCODE RNA-Seq Reads
-   Comparative Genomics    
Drosophila Conservation Drosophila Multiz Alignments & phastCons Scores
Conserved Elements PhastCons Conserved Elements with Different Parameters
DmojWGS Chain DmojWGS (DmojWGS) Chained Alignments
DmojWGS Net DmojWGS (DmojWGS) Alignment Net
D. mojavensis CAF1 Difference Difference with D. mojavensis CAF1 Assembly
D. melanogaster Chain D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Chained Alignments
D. melanogaster Net D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Alignment Net
D. yakuba Chain D. yakuba (Feb. 2006 (CAF1/DyakWGS)) Chained Alignments
D. yakuba Net D. yakuba (Feb. 2006 (CAF1/DyakWGS)) Alignment Net
D. erecta Chain D. erecta (Feb. 2006 (CAF1/DereWGS)) Chained Alignments
D. erecta Net D. erecta (Feb. 2006 (CAF1/DereWGS)) Alignment Net
D. virilis Chain D. virilis (Feb. 2006 (CAF1/DvirWGS)) Chained Alignments
D. virilis Net D. virilis (Feb. 2006 (CAF1/DvirWGS)) Alignment Net
D. grimshawi Chain D. grimshawi (Apr. 2014 (GEP/DgriImproved)) Chained Alignments
D. grimshawi Net D. grimshawi (Apr. 2014 (GEP/DgriImproved)) Alignment Net
-   Variation and Repeats    
TransposonPSI Transposons Fragments Identified by TransposonPSI
RepBase Repeats RepeatMasker using RepBase Drosophila Repeat Library
Combined Repeats RepeatMasker using Combined Custom Repeat Libraries
LTRharvest LTR Fragments Identified by LTRharvest
LTR_Finder LTR Fragments Identified by LTR_Finder
BLASTN | RECON | MAP Repeats RepeatMasker using BLASTN | RECON | MAP Repeat Library
ReAS Repeats RepeatMasker using ReAS Repeat Library
RepeatModeler Classified RepeatMasker using Classified RepeatModeler Repeat Library
DCBLAST | Grouper | MAP Repeats RepeatMasker using DCBLAST | Grouper | MAP Repeat Library
PALS | PILER-DF | MUSCLE Repeats RepeatMasker using PALS | PILER-DF | MUSCLE Repeat Library
Tallymer | CD-HIT Repeats RepeatMasker using Tallymer | CD-HIT Repeat Library
Repeat Density Repeat Density (1kb window, 0.5kb overlap)
WindowMasker Repetitive Regions Identified by WindowMasker
TANTAN Simple Repeats Identified by TANTAN
Tallymer Repetitive Regions Identified by Tallymer
TRF Density Tandem Repeats Density (1kb window, 0.5kb overlap)
Repseek Repetitive Regions Identified by Repseek
Inverted Repeats Inverted Repeats Identified by Inverted Repeats Finder
PHOBOS Repeats Tandem Repeats Identified by PHOBOS
mReps Repeats Tandem Repeats Identified by mReps
Repfind Repeats Repeats Identified by Repfind
RepeatMasker Repeating Elements by RepeatMasker
Simple Repeats Simple Tandem Repeats by TRF