Control track and group visibility more selectively below.
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| GEP Gene Models |
| Gene Models Reconciled by GEP Students |
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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 |
| 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 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 |
| tRNA Genes |
| Transfer RNA Genes Identified by tRNAscan-SE 2.0 |
| rRNA Genes |
| Ribosomal RNA Genes Identified by RNAmmer |
| BUSCO (diptera_odb10) |
| BUSCO Genes from the diptera_odb10 Dataset |
| Pfam Conserved Domains |
| Similarity to Pfam Conserved Domains Identified by RPS-BLAST |
| D. kik Mitochondria |
| Sequence Similarity to D. kikkawai Mitochondria Genome |
| Wolbachia Endosymbionts |
| Megablast Alignments to Wolbachia Endosymbionts |
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| Combined CSHL RAMPAGE TSS |
| Combined CSHL RAMPAGE Transcription Start Sites |
| CSHL RAMPAGE TSS Read Density |
| CSHL RAMPAGE Read Density for Different Developmental Stages |
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| Combined Splice Junctions |
| Combined Splice Junctions for Multiple Developmental Stages |
| RNA-Seq Coverage (Stages) |
| RNA-Seq Coverage for Different Developmental Stages |
| TransDecoder Transcripts |
| Transcripts and Coding Regions Predicted by TransDecoder |
| Trinity Transcripts |
| Transcripts Assembled by Genome-Guided Trinity |
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| 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. kikkawai DkikGB2 Chain |
| D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Chained Alignments |
| D. kikkawai DkikGB2 Net |
| D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Alignment Net |
| D. kikkawai DkikPurged1 Chain |
| D. kikkawai (Dec. 2020 (GEP/DkikPurged1)) Chained Alignments |
| D. kikkawai DkikPurged1 Net |
| D. kikkawai (Dec. 2020 (GEP/DkikPurged1)) 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 |
| EDTA Intact Repeats |
| Intact Repeats Identified by EDTA |
| EDTA TEanno Repeats |
| Intact and Fragmented Repeats Identified by EDTA (TEanno) |
| Octopus Variants |
| Variants Identified by Octopus |
| Inspector Small Errors |
| Small-Scale Errors Identified by Inspector |
| Inspector Structural Errors |
| Structural Errors Identified by Inspector |
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