hub GCA_015832495.2 genome assembly
shortLabel moose/elk (AALL_1980 2023)
longLabel moose/elk (AALL_1980 2023)/Alces alces/GCA_015832495.2_NRM_Aalces_2_0.fsa genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_015832495.2_NRM_Aalces_2_0.fsa.description.html

genome GCA_015832495.2
taxId 9852
groups groups.txt
description moose/elk (AALL_1980 2023)
twoBitPath GCA_015832495.2.2bit
twoBitBptUrl GCA_015832495.2.2bit.bpt
chromSizes GCA_015832495.2.chrom.sizes.txt
chromAliasBb GCA_015832495.2.chromAlias.bb
organism NRM_Aalces_2_0.fsa May 2023
defaultPos JADEYB020000024.1:44556012-44566012
scientificName Alces alces
htmlPath html/GCA_015832495.2_NRM_Aalces_2_0.fsa.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/015/832/495/GCA_015832495.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/015/832/495/GCA_015832495.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/015/832/495/GCA_015832495.2
liftOver.GCA_007570765.1 liftOver/GCA_015832495.2ToGCA_007570765.1.over.chain.gz
liftOver.GCA_964270355.1 liftOver/GCA_015832495.2ToGCA_964270355.1.over.chain.gz

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_015832495.2_NRM_Aalces_2_0.fsa.assembly.bb
type bigBed 6
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.assembly
searchIndex name
searchTrix ixIxx/GCA_015832495.2_NRM_Aalces_2_0.fsa.assembly.ix
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track gap
longLabel AGP gap
shortLabel Gap (AGP defined)
visibility dense
color 0,0,0
bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.gap.bb
type bigBed 4
group map
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.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_015832495.2_NRM_Aalces_2_0.fsa.gc5Base.bw
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.gapOverlap.bb
    type bigBed 12

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.rmsk.bb
xrefDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.rModel.bb
xrefDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.rModel.align.bb
maxWindowToDraw 5000000
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.simpleRepeat.bb
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.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_015832495.2_NRM_Aalces_2_0.fsa.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_015832495.2_NRM_Aalces_2_0.fsa.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_015832495.2_NRM_Aalces_2_0.fsa.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.windowMasker.bb
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.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_015832495.2_NRM_Aalces_2_0.fsa.allGaps.bb
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.augustus.bb
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.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_015832495.2_NRM_Aalces_2_0.fsa.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_015832495.2_NRM_Aalces_2_0.fsa.xenoRefGene.ix
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.xenoRefGene

track GCA_015832495.2_NRM_Aalces_2_0.fsaChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_015832495.2_NRM_Aalces_2_0.fsa
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=GCA_964270355.1 s001=GCA_007570765.1
subGroup3 chainType chain_type c00=chain c01=syntenic c02=reciprocal_best c03=lift_over c04=chain_align c05=syntenic_align c06=reciprocal_align c07=lift_over_align
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=chainType dimensionY=species
sortOrder species=+ view=+ chainType=+
configurable on
html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet

    track GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNet
    spectrum on

    track GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNet
    spectrum on

    track GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNet
    spectrum on

    track GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNet
    spectrum on

        track chainGCA_964270355.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel GCA_964270355.1 Chain
        longLabel GCA_964270355.1/GCA_964270355.1_Elg.assembly.v.1.0 (2024-09-28) Chained Alignments
        type bigChain GCA_964270355.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainGCA_964270355.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainGCA_964270355.1Link.bb
        otherDb GCA_964270355.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 4.728

        track chainSynGCA_964270355.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel GCA_964270355.1 synChain
        longLabel GCA_964270355.1/GCA_964270355.1_Elg.assembly.v.1.0 (2024-09-28) Chained Alignments
        type bigChain GCA_964270355.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainSynGCA_964270355.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainSynGCA_964270355.1Link.bb
        otherDb GCA_964270355.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 4.728

        track chainRBestGCA_964270355.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel GCA_964270355.1 rbChain
        longLabel GCA_964270355.1/GCA_964270355.1_Elg.assembly.v.1.0 (2024-09-28) Chained Alignments
        type bigChain GCA_964270355.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainRBestGCA_964270355.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainRBestGCA_964270355.1Link.bb
        otherDb GCA_964270355.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 4.728

        track chainLiftOverGCA_964270355.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel GCA_964270355.1 loChain
        longLabel GCA_964270355.1/GCA_964270355.1_Elg.assembly.v.1.0 (2024-09-28) Chained Alignments
        type bigChain GCA_964270355.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainLiftOverGCA_964270355.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainLiftOverGCA_964270355.1Link.bb
        otherDb GCA_964270355.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 4.728

        track chainGCA_007570765.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel GCA_007570765.1 Chain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainGCA_007570765.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 5.759

        track chainSynGCA_007570765.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel GCA_007570765.1 synChain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainSynGCA_007570765.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainSynGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 5.759

        track chainRBestGCA_007570765.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel GCA_007570765.1 rbChain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainRBestGCA_007570765.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainRBestGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 5.759

        track chainLiftOverGCA_007570765.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel GCA_007570765.1 loChain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainLiftOverGCA_007570765.1.bb
        linkDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainLiftOverGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 5.759

    track GCA_015832495.2_NRM_Aalces_2_0.fsaMafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_015832495.2_NRM_Aalces_2_0.fsaChainNet

        track netGCA_964270355.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaMafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel GCA_964270355.1 mafNet
        longLabel GCA_964270355.1/GCA_964270355.1_Elg.assembly.v.1.0 (2024-09-28) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_964270355.1.net.bb
        summary bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_964270355.1.net.summary.bb
        speciesOrder GCA_964270355.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 4.728

        track synNetGCA_964270355.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaMafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel GCA_964270355.1 synNet
        longLabel GCA_964270355.1/GCA_964270355.1_Elg.assembly.v.1.0 (2024-09-28) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_964270355.1.synNet.bb
        summary bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_964270355.1.synNet.summary.bb
        speciesOrder GCA_964270355.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 4.728

        track rbestNetGCA_964270355.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaMafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel GCA_964270355.1 rbestNet
        longLabel GCA_964270355.1/GCA_964270355.1_Elg.assembly.v.1.0 (2024-09-28) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_964270355.1.rbestNet.bb
        summary bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_964270355.1.rbestNet.summary.bb
        speciesOrder GCA_964270355.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 4.728

        track netGCA_007570765.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaMafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel GCA_007570765.1 mafNet
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_007570765.1.net.bb
        summary bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_007570765.1.net.summary.bb
        speciesOrder GCA_007570765.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 5.759

        track synNetGCA_007570765.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaMafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel GCA_007570765.1 synNet
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_007570765.1.synNet.bb
        summary bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_007570765.1.synNet.summary.bb
        speciesOrder GCA_007570765.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 5.759

        track rbestNetGCA_007570765.1
        parent GCA_015832495.2_NRM_Aalces_2_0.fsaMafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel GCA_007570765.1 rbestNet
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_007570765.1.rbestNet.bb
        summary bbi/GCA_015832495.2_NRM_Aalces_2_0.fsa.GCA_007570765.1.rbestNet.summary.bb
        speciesOrder GCA_007570765.1
        html html/GCA_015832495.2_NRM_Aalces_2_0.fsa.chainNet
        priority 5.759