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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| Annotation Projects |
| GEP Annotation Projects |
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| Reconciled Gene Models |
| Reconciled GEP Gene Models for D. willistoni |
| RefSeq Genes |
| 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 with RNA-Seq |
| 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 |
| N-SCAN |
| N-SCAN Gene Predictions |
| N-SCAN PASA-EST |
| N-SCAN PASA-EST Gene Predictions |
| Augustus |
| Augustus Gene Predictions |
| Augustus (Protein Hints) |
| Augustus Gene Predictions (D. melanogaster Proteins Hints) |
| GlimmerHMM |
| GlimmerHMM Gene Predictions |
| InterProScan |
| InterPro Signatures Identified by InterProScan |
| tRNA Genes |
| Transfer RNA Genes Identified by tRNAscan-SE 2.0 |
| rRNA Genes |
| Ribosomal RNA Genes Identified by RNAmmer |
| Pfam Conserved Domains |
| Similarity to Pfam Conserved Domains Identified by RPS-BLAST |
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| Eye Discs ATAC-Seq |
| ATAC-Seq of D. willistoni Eye Discs |
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| Combined Splice Junctions |
| Combined Splice Junctions for Multiple Tissues |
| Aggregated RNA-Seq Coverage |
| Aggregated RNA-Seq Coverage |
| RNA-Seq Coverage (Tissues) |
| RNA-Seq Coverage for Different Tissues |
| TransDecoder Transcripts |
| Transcripts and Coding Regions Predicted by TransDecoder |
| Trinity Transcripts |
| Transcripts Assembled by Genome-Guided Trinity |
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| FLNC Iso-Seq Reads |
| Alignments of Full-Length Non-Chimeric (FLNC) Iso-Seq Reads |
| Clustered Iso-Seq Reads |
| Alignments of Clustered Iso-Seq Reads |
| Collapsed Iso-Seq Transcripts |
| Non-redundant Transcripts Derived from Clustered Iso-Seq Reads |
| SQANTI3 QC Transcripts |
| Iso-Seq Transcripts Classified by SQANTI3 QC |
| SQANTI3 Filtered Transcripts |
| Iso-Seq Transcripts Filtered by SQANTI3 Using the Default Rules |
| uLTRA FLNC Iso-Seq Reads |
| uLTRA Alignments of Full-Length Non-Chimeric (FLNC) Iso-Seq Reads |
| uLTRA Collapsed Iso-Seq Transcripts |
| Non-redundant Transcripts Derived from uLTRA Alignments of Iso-Seq Reads |
| TAMA Collapsed Transcripts |
| Iso-Seq Transcripts Assembled by TAMA Collapse |
| StringTie2 Iso-Seq Transcripts |
| Transcripts Assembled by StringTie2 Using PacBio Iso-Seq Reads |
| Scallop-LR Iso-Seq Transcripts |
| Transcripts Assembled by Scallop-LR Using PacBio Iso-Seq Reads |
| TransDecoder Iso-Seq Transcripts |
| Transcripts Predicted by TransDecoder Using PacBio Iso-Seq and Illumina RNA-Seq Reads |
| Filtered TransDecoder Iso-Seq Transcripts |
| Filtered Coding Regions of TransDecoder Iso-Seq Transcripts |
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| Hi-C Matrix |
| Juicer Hi-C Matrix (Adult Female) |
| TAD Domains |
| HiCExplorer TAD Domains |
| TAD Boundaries |
| HiCExplorer TAD Boundaries |
| TAD Insulation Scores |
| HiCExplorer TAD Insulation Scores |
| Hi-C PCA 1 |
| HiCExplorer First Eigenvector from hicPCA |
| Hi-C PCA 2 |
| HiCExplorer Second Eigenvector from hicPCA |
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| D. willistoni Conservation (10 Species) |
| ROAST Alignment and Conservation of Ten Drosophila Genomes |
| Basewise Conservation (phyloP) |
| Basewise Conservation of Ten Drosophila Genomes (phyloP) |
| Basewise Conservation (phastCons) |
| Basewise Conservation of Ten Drosophila Genomes (phastCons) |
| Conserved Elements |
| Conserved Elements Identified by PhastCons (Ten Drosophila Species) |
| ROAST Alignments |
| ROAST Alignments for Ten Drosophila Genomes |
| Drosophila 2-Split Alignments |
| LAST 2-Split, Post-Masked Alignments of Drosophila Genomes |
| D. melanogaster Chain |
| D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Chained Alignments |
| D. melanogaster Net |
| D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Alignment Net |
| D. willistoni DwilCAF1 Chain |
| D. willistoni (May 2011 (JCVI dwil_caf1/DwilCAF1)) Chained Alignments |
| D. willistoni DwilCAF1 Net |
| D. willistoni (May 2011 (JCVI dwil_caf1/DwilCAF1)) 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 |
| TANTAN Tandem |
| Tandem Repeats Identified by TANTAN |
| RepeatModeler |
| Transposons Identified by RepeatModeler |
| TransposonPSI (Pfam) |
| Pfam Transposon Protein Domains Identified by TransposonPSI |
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