hub GCA_014839835.1 genome assembly shortLabel downy woodpecker (bDryPub1 primary hap 2020) longLabel downy woodpecker (bDryPub1 primary hap 2020)/Dryobates pubescens/GCA_014839835.1_bDryPub1.pri genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_014839835.1_bDryPub1.pri.description.html genome GCA_014839835.1 taxId 118200 groups groups.txt description downy woodpecker (bDryPub1 primary hap 2020) twoBitPath GCA_014839835.1.2bit twoBitBptUrl GCA_014839835.1.2bit.bpt chromSizes GCA_014839835.1.chrom.sizes.txt chromAliasBb GCA_014839835.1.chromAlias.bb chromAuthority ucsc organism bDryPub1.pri Oct. 2020 defaultPos CM026039.1:46719108-46729108 scientificName Dryobates pubescens htmlPath html/GCA_014839835.1_bDryPub1.pri.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/014/839/835/GCA_014839835.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/014/839/835/GCA_014839835.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/014/839/835/GCA_014839835.1 track assembly longLabel Assembly shortLabel Assembly visibility pack colorByStrand 150,100,30 230,170,40 color 150,100,30 altColor 230,170,40 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.assembly.bb type bigBed 6 html html/GCA_014839835.1_bDryPub1.pri.assembly searchIndex name searchTrix ixIxx/GCA_014839835.1_bDryPub1.pri.assembly.ix url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: group map track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.cytoBand.bb track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility full autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 viewLimits 30:70 type bigWig 0 100 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.gc5Base.bw html html/GCA_014839835.1_bDryPub1.pri.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_014839835.1_bDryPub1.pri.tanDups track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.tandemDups.bb type bigBed 12 track repeatMasker compositeTrack on shortLabel RepeatMasker longLabel Repeating Elements by RepeatMasker group varRep visibility dense type bigBed 6 + colorByStrand 50,50,150 150,50,50 maxWindowToDraw 10000000 spectrum on html html/GCA_014839835.1_bDryPub1.pri.repeatMasker track repeatMaskerSINE parent repeatMasker shortLabel SINE longLabel SINE Repeating Elements by RepeatMasker type bigBed 6 + priority 1 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.SINE.bb track repeatMaskerLINE parent repeatMasker shortLabel LINE longLabel LINE Repeating Elements by RepeatMasker type bigBed 6 + priority 2 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.LINE.bb track repeatMaskerLTR parent repeatMasker shortLabel LTR longLabel LTR Repeating Elements by RepeatMasker type bigBed 6 + priority 3 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.LTR.bb track repeatMaskerDNA parent repeatMasker shortLabel DNA longLabel DNA Repeating Elements by RepeatMasker type bigBed 6 + priority 4 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.DNA.bb track repeatMaskerSimple parent repeatMasker shortLabel Simple longLabel Simple Repeating Elements by RepeatMasker type bigBed 6 + priority 5 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.Simple.bb track repeatMaskerLowComplexity parent repeatMasker shortLabel Low Complexity longLabel Low Complexity Repeating Elements by RepeatMasker type bigBed 6 + priority 6 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.Low_complexity.bb track repeatMaskerSatellite parent repeatMasker shortLabel Satellite longLabel Satellite Repeating Elements by RepeatMasker type bigBed 6 + priority 7 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.Satellite.bb track repeatMaskerRNA parent repeatMasker shortLabel RNA longLabel RNA Repeating Elements by RepeatMasker type bigBed 6 + priority 8 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.RNA.bb track repeatMaskerOther parent repeatMasker shortLabel Other longLabel Other Repeating Elements by RepeatMasker type bigBed 6 + priority 9 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rmsk.Other.bb track repeatModeler shortLabel RepeatModeler longLabel RepeatModeler Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rModel.bb xrefDataUrl bbi/GCA_014839835.1_bDryPub1.pri.rModel.align.bb maxWindowToDraw 5000000 html html/GCA_014839835.1_bDryPub1.pri.repeatModeler track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.simpleRepeat.bb html html/GCA_014839835.1_bDryPub1.pri.simpleRepeat track cpgIslands compositeTrack on shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility pack type bigBed 4 + html html/GCA_014839835.1_bDryPub1.pri.cpgIslands track cpgIslandExt parent cpgIslands off shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) type bigBed 4 + priority 1 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.cpgIslandExt.bb track cpgIslandExtUnmasked parent cpgIslands on shortLabel Unmasked CpG longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green) type bigBed 4 + priority 2 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.windowMasker.bb html html/GCA_014839835.1_bDryPub1.pri.windowMasker track allGaps shortLabel All Gaps longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps group map visibility dense type bigBed 3 bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.allGaps.bb html html/GCA_014839835.1_bDryPub1.pri.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.augustus.bb html html/GCA_014839835.1_bDryPub1.pri.augustus track xenoRefGene shortLabel RefSeq mRNAs longLabel RefSeq mRNAs mapped to this assembly group rna visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_014839835.1_bDryPub1.pri.xenoRefGene.bb url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: labelFields name,geneName,geneName2 defaultLabelFields geneName searchIndex name searchTrix ixIxx/GCA_014839835.1_bDryPub1.pri.xenoRefGene.ix html html/GCA_014839835.1_bDryPub1.pri.xenoRefGene track HLTOGAannotvGalGal6v1 bigDataUrl bbi/HLTOGAannotVsGalGal6v1.bb shortLabel TOGA vs. galGal6 longLabel TOGA annotations using chicken/galGal6 as reference group genes visibility pack itemRgb on type bigBed 12 searchIndex name searchTrix ixIxx/HLTOGAannotVsGalGal6v1.ix html html/TOGAannotation