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 |
Restr Enzymes |
| Restriction Enzymes from REBASE |
Short Match |
| Perfect Matches to Short Sequence () |
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GEP V1 projects |
| Mapping GEP Version 1 Projects to New Assembly |
D. biarmipes v1 Chain |
| Version 1 D. biarmipes (March 2012 (BCM-HGSC)) Chained Alignments |
D. biarmipes v1 Net |
| Version 1 D. biarmipes (March 2012 (BCM-HGSC)) Alignment Net |
D. biarmipes v1 Difference |
| Difference with D. biarmipes Version 1 Assembly |
Finishing Projects |
| GEP Sequence Improvement Projects |
Assembly Problems |
| Assembly Problems Identified by Consed bamscape |
Read Coverage |
| Genomic Read Coverage |
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D. mel Transcripts |
| Spaln Alignment of D. melanogaster Transcripts |
D. mel Proteins |
| Spaln Alignment of D. melanogaster Proteins |
Sim4cc D. mel Transcripts |
| Sim4cc Alignment of D. melanogaster Transcripts |
MAKER Proteins |
| Spaln Alignment of Proteins Predicted by MAKER |
MAKER Transcripts |
| Spaln Alignment of Transcripts Predicted by MAKER |
CDS Mapping |
| BLASTX Mapping of Coding DNA Sequences |
D. mel. TBLASTN Proteins |
| Initial TBLASTN mapping of D. melanogaster proteins |
Potential Frame Shifts |
| Potential Frame Shifts Detected by SPALN2 |
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modENCODE RNA-Seq Coverage |
| modENCODE D. biarmipes RNA-Seq Coverage |
modENCODE TopHat Junctions |
| Junctions predicted by TopHat using modENCODE D. biarmipes RNA-Seq |
modENCODE Cufflinks Transcripts |
| modENCODE D. biarmipes Cufflinks Transcripts |
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Promoter Predictions |
| Core Promoters predicted by EP3 |
Core Promoter Motifs |
| Similarity to Drosophila Core Promoter Motifs Identified by Patser |
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Conservation |
| 7 Drosophila Species Multiz Alignments & phastCons Scores |
Most Conserved |
| PhastCons Conserved Elements (7 Drosophila Species) |
(dm3) D. mel. Chain |
| D. melanogaster (Apr. 2006) Chained Alignments |
(dm3) D. mel. Net |
| D. melanogaster (Apr. 2006) Alignment Net |
D. ere. Chain |
| D. erecta (Feb. 2006 (CAF1)) Chained Alignments |
D. ere. Net |
| D. erecta (Feb. 2006 (CAF1)) Alignment Net |
D. fic. Chain |
| D. ficusphila (Mar. 2013 (WGS / Dfic_2.0)) Chained Alignments |
D. fic. Net |
| D. ficusphila (Mar. 2013 (WGS / Dfic_2.0)) Alignment Net |
D. eug. Chain |
| D. eugracilis (Mar. 2013 (WGS / Deug_2.0)) Chained Alignments |
D. eug. Net |
| D. eugracilis (Mar. 2013 (WGS / Deug_2.0)) Alignment Net |
D. tak. Chain |
| D. takahashii (Mar. 2013 (WGS / Dtak_2.0)) Chained Alignments |
D. tak. Net |
| D. takahashii (Mar. 2013 (WGS / Dtak_2.0)) Alignment Net |
D. ana. Chain |
| D. ananassae (Feb. 2006 (CAF1)) Chained Alignments |
D. ana. Net |
| D. ananassae (Feb. 2006 (CAF1)) Alignment Net |
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Repeat Density |
| Repeat Density (1kb window, 0.5kb overlap) |
RepeatMasker |
| Repeating Elements by RepeatMasker |
Simple Repeats |
| Simple Tandem Repeats by TRF |
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