track assembly_
url http://www.ncbi.nlm.nih.gov/nuccore/$$
type bigBed 6
longLabel Assembly
urlLabel NCBI Nucleotide database
color 150,100,30
altColor 230,170,40
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.assembly.bb
priority 10
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/assembly
group map
shortLabel Assembly
visibility pack
colorByStrand 150,100,30 230,170,40

track gap_
type bigBed 4
longLabel Gap
color 0,0,0
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.gap.bb
priority 11
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/gap
group map
shortLabel Gap
visibility dense

track gc5Base_
type bigWig 0 100
longLabel GC Percent in 5-Base Windows
viewLimits 30:70
autoScale Off
color 0,0,0
altColor 128,128,128
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.gc5Base.bw
priority 23.5
graphTypeDefault Bar
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/gc5Base
gridDefault OFF
group map
maxHeightPixels 128:36:16
windowingFunction Mean
shortLabel GC Percent
visibility full

track simpleRepeat_
type bigBed 4 +
longLabel Simple Tandem Repeats by TRF
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.simpleRepeat.bb
priority 149.3
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/simpleRepeat
group varRep
shortLabel Simple Repeats
visibility dense

track genscan_
type bigBed 12 .
longLabel Genscan Gene Predictions
color 170,100,0
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.genscan.bb
priority 50
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/genscan
group genes
shortLabel Genscan Genes
visibility pack

track cpgIslandComposite
shortLabel compLabel
longLabel compLabel
compositeTrack on
subGroup1 view Views cpgIslandView

    track cpgIslandViewTrack
    view cpgIslandView
    parent cpgIslandComposite
    type bigBed
    shortLabel viewLabel
    longLabel viewLabel

        track cpgIslandExt_
        parent cpgIslandView
        type bigBed 4 +
        longLabel CpG Islands (Islands < 300 Bases are Light Green)
        color 0,100,0
        altColor 128,228,128
        bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.cpgIslandExt.bb
        priority 90
        html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/cpgIslandExt
        group regulation
        shortLabel CpG Islands
        visibility pack
        subGroups view=cpgIslandView

track repeatMasker_
noInherit on
type bed 3 .
longLabel Repeating Elements by RepeatMasker
priority 149.1
compositeTrack on
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/repeatMasker
group varRep
shortLabel RepeatMasker
visibility dense

track repeatMaskerRNA_
type bigBed 6 +
longLabel RNA Repeating Elements by RepeatMasker
parent repeatMasker_
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.rmsk.RNA.bb
priority 1
maxWindowToDraw 10000000
spectrum on
shortLabel RNA
colorByStrand 50,50,150 150,50,50

track repeatMaskerSimple_
type bigBed 6 +
longLabel Simple Repeating Elements by RepeatMasker
parent repeatMasker_
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.rmsk.Simple.bb
priority 2
maxWindowToDraw 10000000
spectrum on
shortLabel Simple
colorByStrand 50,50,150 150,50,50

track repeatMaskerLowComplexity_
type bigBed 6 +
longLabel Low Complexity Repeating Elements by RepeatMasker
parent repeatMasker_
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.rmsk.LowComplexity.bb
priority 3
maxWindowToDraw 10000000
spectrum on
shortLabel Low Complexity
colorByStrand 50,50,150 150,50,50

track repeatMaskerOther_
type bigBed 6 +
longLabel Other Repeating Elements by RepeatMasker
parent repeatMasker_
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.rmsk.Other.bb
priority 4
maxWindowToDraw 10000000
spectrum on
shortLabel Other
colorByStrand 50,50,150 150,50,50

track windowMasker
type bigBed 3 .
longLabel Genomic Intervals Masked by WindowMasker + SDust
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/ricCom1.windowMasker.bb
priority 149.26
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/windowMasker
group varRep
shortLabel WM + SDust
visibility dense

track lastzAraTha1
type bigBed 12 .
longLabel lastz chain to araTha1
bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/bbi/lastzRicCom1ToAraTha1.bb
priority 150
group compGeno
shortLabel lastz araTha1
visibility dense