hub GCF_000392375.2 genome assembly
shortLabel Clostridium tyrobutyricum ATCC 25755 (DSM 2637 JCM 11008 2013 Univ. Cattolica del Sacro Cuore)
longLabel Clostridium tyrobutyricum ATCC 25755 (DSM 2637 JCM 11008 2013 Univ. Cattolica del Sacro Cuore)/Clostridium tyrobutyricum DSM 2637 = ATCC 25755 = JCM 11008/GCF_000392375.2_ASM39237v2 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_000392375.2_ASM39237v2.description.html

genome GCF_000392375.2
taxId 1121342
groups groups.txt
description Clostridium tyrobutyricum ATCC 25755 (DSM 2637 JCM 11008 2013 Univ. Cattolica del Sacro Cuore)
twoBitPath GCF_000392375.2.2bit
twoBitBptUrl GCF_000392375.2.2bit.bpt
chromSizes GCF_000392375.2.chrom.sizes.txt
chromAliasBb GCF_000392375.2.chromAlias.bb
organism ASM39237v2 May 2013
defaultPos NZ_ARYO01000149.1:45796-55796
scientificName Clostridium tyrobutyricum DSM 2637 = ATCC 25755 = JCM 11008
htmlPath html/GCF_000392375.2_ASM39237v2.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/392/375/GCF_000392375.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/392/375/GCF_000392375.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/392/375/GCF_000392375.2

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/GCF_000392375.2_ASM39237v2.assembly.bb
type bigBed 6
html html/GCF_000392375.2_ASM39237v2.assembly
searchIndex name
searchTrix ixIxx/GCF_000392375.2_ASM39237v2.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/GCF_000392375.2_ASM39237v2.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/GCF_000392375.2_ASM39237v2.gc5Base.bw
html html/GCF_000392375.2_ASM39237v2.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000392375.2_ASM39237v2.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_000392375.2_ASM39237v2.tandemDups.bb
    type bigBed 12

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000392375.2_ASM39237v2.simpleRepeat.bb
html html/GCF_000392375.2_ASM39237v2.simpleRepeat

track ncbiGene
longLabel NCBI gene predictions
shortLabel NCBI Genes
visibility pack
color 0,80,150
altColor 150,80,0
colorByStrand 0,80,150 150,80,0
bigDataUrl bbi/GCF_000392375.2_ASM39237v2.ncbiGene.bb
type bigGenePred
html html/GCF_000392375.2_ASM39237v2.ncbiGene
searchIndex name
searchTrix ixIxx/GCF_000392375.2_ASM39237v2.ncbiGene.ix
url https://www.ncbi.nlm.nih.gov/gene/?term=$$
urlLabel Entrez gene:
labelFields geneName,geneName2
defaultLabelFields geneName2
group genes

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/GCF_000392375.2_ASM39237v2.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/GCF_000392375.2_ASM39237v2.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/GCF_000392375.2_ASM39237v2.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000392375.2_ASM39237v2.windowMasker.bb
html html/GCF_000392375.2_ASM39237v2.windowMasker