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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| 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 |
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| 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 |
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| 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 |
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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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