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_009819655.1_bSylAtr1.pri.assembly.bb
type bigBed 6
html html/GCA_009819655.1_bSylAtr1.pri.assembly
searchIndex name
searchTrix ixIxx/GCA_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.pri.gc5Base.bw
html html/GCA_009819655.1_bSylAtr1.pri.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_009819655.1_bSylAtr1.pri.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.pri.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.pri.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rmsk.Other.bb

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rModel.bb
xrefDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rModel.align.bb
maxWindowToDraw 5000000
html html/GCA_009819655.1_bSylAtr1.pri.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.simpleRepeat.bb
html html/GCA_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.pri.windowMasker.bb
html html/GCA_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.pri.allGaps.bb
html html/GCA_009819655.1_bSylAtr1.pri.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.augustus.bb
html html/GCA_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.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_009819655.1_bSylAtr1.pri.xenoRefGene.ix
html html/GCA_009819655.1_bSylAtr1.pri.xenoRefGene

track GCA_009819655.1_bSylAtr1.priChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain and Net alignments to target sequence: GCA_009819655.1_bSylAtr1.pri
subGroup1 view Views chain=Chains net=Nets
subGroup2 species Species s000=taeGut1 s001=taeGut2
subGroup3 clade Clade c00=human
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=clade dimensionY=species
sortOrder species=+ view=+ clade=+
configurable on
html html/GCA_009819655.1_bSylAtr1.pri.chainNet

    track GCA_009819655.1_bSylAtr1.priChainNetViewchain
    shortLabel  Chains
    view chain
    visibility pack
    subTrack GCA_009819655.1_bSylAtr1.priChainNet
    spectrum on

        track chainTaeGut1
        subTrack GCA_009819655.1_bSylAtr1.priChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel taeGut1 Chain
        longLabel taeGut1 (Jul. 2008) Chained Alignments
        type bigChain taeGut1
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut1.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut1Link.bb
        otherDb taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 1

        track chainSynTaeGut1
        subTrack GCA_009819655.1_bSylAtr1.priChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel taeGut1 synChain
        longLabel taeGut1 (Jul. 2008) Syntenic Chained Alignments
        type bigChain taeGut1
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut1.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut1Link.bb
        otherDb taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 2

        track chainRBestTaeGut1
        subTrack GCA_009819655.1_bSylAtr1.priChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel taeGut1 rbChain
        longLabel taeGut1 (Jul. 2008) Reciprocal Best Chained Alignments
        type bigChain taeGut1
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut1.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut1Link.bb
        otherDb taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 3

        track chainTaeGut2
        subTrack GCA_009819655.1_bSylAtr1.priChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel taeGut2 Chain
        longLabel taeGut2 (Feb. 2013) Chained Alignments
        type bigChain taeGut2
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut2.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut2Link.bb
        otherDb taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 4

        track chainSynTaeGut2
        subTrack GCA_009819655.1_bSylAtr1.priChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel taeGut2 synChain
        longLabel taeGut2 (Feb. 2013) Syntenic Chained Alignments
        type bigChain taeGut2
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut2.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut2Link.bb
        otherDb taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 5

        track chainRBestTaeGut2
        subTrack GCA_009819655.1_bSylAtr1.priChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel taeGut2 rbChain
        longLabel taeGut2 (Feb. 2013) Reciprocal Best Chained Alignments
        type bigChain taeGut2
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut2.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut2Link.bb
        otherDb taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 6

    track GCA_009819655.1_bSylAtr1.priMafNetViewnet
    shortLabel Nets
    view net
    visibility dense
    subTrack GCA_009819655.1_bSylAtr1.priChainNet

        track synNetTaeGut1
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel taeGut1 synNet
        longLabel taeGut1 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.synNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.synNet.summary.bb
        speciesOrder taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 1

        track rbestNetTaeGut1
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel taeGut1 rbestNet
        longLabel taeGut1 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.rbestNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.rbestNet.summary.bb
        speciesOrder taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 2

        track synNetTaeGut2
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel taeGut2 synNet
        longLabel taeGut2 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.synNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.synNet.summary.bb
        speciesOrder taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 3

        track rbestNetTaeGut2
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel taeGut2 rbestNet
        longLabel taeGut2 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.rbestNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.rbestNet.summary.bb
        speciesOrder taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 4

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