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Configure Tracks on UCSC Genome Browser: D. erecta May 2011 (Agencourt dere_caf1/DereCAF1)
  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
Assembly Assembly from Fragments
CpG Islands CpG Islands Identified by newcpgreport
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Prediction Tracks    
RefSeq Genes BLAT Alignments of NCBI RefSeq Genes
D. mel Transcripts BLAT Alignment of D. melanogaster Transcripts
D. mel Proteins Spaln Alignment of D. melanogaster Proteins
genBlastG Genes genBlastG Gene Predictions
GeMoMa Genes GeMoMa Gene Predictions
Drosophila RefSeq Transcripts BLAT Alignment of Drosophila RefSeq Transcripts
Potential Frame Shifts Potential Frame Shifts Detected by SPALN2
CDS Mapping TBLASTN Mapping of D. melanogaster CDS
Genscan Genes Genscan Gene Predictions
Geneid Genes Geneid Gene Predictions
Augustus Augustus Gene Predictions
SNAP SNAP Gene Predictions
GlimmerHMM GlimmerHMM Gene Predictions
tRNA Genes Transfer RNA Genes Identified by tRNAscan-SE 2.0
rRNA Genes Ribosomal RNA Genes Identified by RNAmmer
-   Gene Predictions (Species-specific Parameters)    
Augustus Genes (BUSCO) Augustus Gene Predictions with BUSCO Training Set
Geneid Genes (BUSCO) Geneid Gene Predictions with CEGMA Training Set
SNAP Genes (BUSCO) SNAP Gene Predictions with BUSCO Training Set
GlimmerHMM Genes (BUSCO) GlimmerHMM Gene Predictions with BUSCO Training Set
-   Expression and Regulation    
Combined RAMPAGE TSS Combined RAMPAGE Transcription Start Sites
RAMPAGE TSS Read Density RAMPAGE Read Density for Different Developmental Stages
TSRchitect Combined RAMPAGE TSS TSRchitect Combined RAMPAGE Transcription Start Sites
TSRchitect RAMPAGE TSS Read Density TSRchitect RAMPAGE Read Density for Different Developmental Stages
Eye Discs ATAC-Seq ATAC-Seq of D. erecta Eye Discs
-   RNA Seq Tracks    
RNA-Seq Coverage D. erecta RNA-Seq Read Coverage
Splice Junctions Splice Junctions Predicted by regtools using D. erecta RNA-Seq
TransDecoder Transcripts Transcripts and Coding Regions Predicted by TransDecoder
-   Comparative Genomics    
Drosophila Chain/Net Drosophila Genomes, Chain and Net Alignments
D. erecta (DereRS2) Chain D. erecta (Oct. 2018 (The University of Chicago/DereRS2)) Chained Alignments
D. erecta (DereRS2) Net D. erecta (Oct. 2018 (The University of Chicago/DereRS2)) Alignment Net
-   Variation and Repeats    
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust
RepeatMasker Repeating Elements by RepeatMasker
TE Density RepeatMasker Transposon Density (1kb window, 100bp step size)
tantan Simple Repeats Identified by tantan
Tallymer Repetitive Regions Identified by Tallymer
TransposonPSI (Pfam) Pfam Transposon Protein Domains Identified by TransposonPSI
LTRharvest LTR Fragments Identified by LTRharvest