Control track and group visibility more selectively below.
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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 () |
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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 |
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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 |
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Eye Discs ATAC-Seq |
| ATAC-Seq of D. simulans Eye Discs |
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RNA-Seq Coverage |
| D. simulans RNA-Seq Read Coverage |
Splice Junctions |
| Splice Junctions Predicted by regtools using D. simulans RNA-Seq |
TransDecoder Transcripts |
| Transcripts and Coding Regions Predicted by TransDecoder |
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Drosophila Chain/Net |
| Drosophila Genomes, Chain and Net Alignments |
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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 |
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