Index: src/hg/makeDb/trackDb/trackDb.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.ra,v
retrieving revision 1.571
retrieving revision 1.572
diff -b -B -U 1000000 -r1.571 -r1.572
--- src/hg/makeDb/trackDb/trackDb.ra	28 Dec 2009 23:11:37 -0000	1.571
+++ src/hg/makeDb/trackDb/trackDb.ra	28 Dec 2009 23:29:09 -0000	1.572
@@ -1,4400 +1,4403 @@
 #	"$Id$";
 
 include trackDb.chainNet.ra
 
 # Root trackDb.ra file.  Files from the organism subdirectory and the database sub-sub directory
 # will be layered on.  Organism is something like 'human' and database is something
 # like 'hg18'.  See the README file in this directory for a description of the format.
 #
 
 track mapGenethon
 shortLabel STS Markers
 longLabel Various STS Markers
 group map
 priority 2
 visibility hide
 type bed 5 +
 
 track stsMarker
 shortLabel STS Markers
 longLabel STS Markers on Genetic (blue), FISH (green) and RH (black) Maps
 group map
 priority 3
 visibility dense
 altColor 128,128,255,
 type bed 5 +
 
 track stsMap
 shortLabel STS Markers
 longLabel STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
 group map
 priority 4
 visibility dense
 altColor 128,128,255,
 type bed 5 +
 
 track stsMapMouse
 shortLabel STS Markers
 longLabel STS Markers on Genetic Maps
 group map
 priority 5
 visibility dense
 altColor 128,128,255,
 type bed 5 +
 
 track fishClones
 shortLabel FISH Clones
 longLabel Clones Placed on Cytogenetic Map Using FISH
 group map
 priority 6
 visibility hide
 color 0,150,0,
 type bed 5 +
 
 track genMapDb
 shortLabel GenMapDB Clones
 longLabel GenMapDB BAC Clones 
 group map
 priority 7
 visibility hide
 type bed 6 +
 
 track recombRate
 shortLabel Recomb Rate
 longLabel Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default)
 group map
 priority 8
 visibility hide
 exonArrows off
 type bed 4 +
 
 track ctgPos
 shortLabel Map Contigs
 longLabel Physical Map Contigs
 group map
 priority 9
 visibility hide
 color 150,0,0
 type ctgPos
 
 track gold
 shortLabel Assembly 
 longLabel Assembly from Fragments 
 group map
 priority 10
 visibility hide
 color 150,100,30
 altColor 230,170,40
 type bed 3 +
 
 track gap
 shortLabel Gap
 longLabel Gap Locations
 priority 11
 group map
 visibility dense
 type bed 3 +
 
 track partMrnas
 shortLabel Partially Found mRNAs
 longLabel Partially Found RefSeq and MGC mRNAs
 group map
 priority 12
 visibility hide
 type psl .
 
 track missingHg
 shortLabel Missing Human 
 longLabel Unplaced Human RefSeq Genes Blatted against Mouse Translated
 group map
 priority 13
 visibility hide
 color 0,100,0
 altColor 255,240,200
 type psl .
 
 track clonePos
 priority 14
 shortLabel Coverage
 longLabel Clone Coverage/Fragment Position
 group map
 visibility hide
 altColor 180,180,180 
 type clonePos
 
 track bacEndPairs
 shortLabel BAC End Pairs
 longLabel BAC End Pairs
 group map
 priority 15
 visibility hide
 type bed 6 +
 color 0,0,0
 altColor 80,80,80
 exonArrows off
 
 track bacEndPairsBad
 shortLabel Incorrect BAC End Pairs
 longLabel Orphan, Short and Incorrectly Oriented BAC End Pairs
 group map
 priority 16
 visibility hide
 type bed 6 +
 color 0,0,0
 altColor 90,90,90
 exonArrows off
 
 track bacEndPairsLong
 shortLabel Long BAC End Pairs
 longLabel Long BAC End Pairs
 group map
 priority 17
 visibility hide
 type bed 6 +
 color 0,0,0
 altColor 90,90,90
 exonArrows off
 
 track fosEndPairs
 shortLabel Fosmid End Pairs
 longLabel Fosmid End Pairs
 group map
 priority 18
 visibility hide
 type bed 6 +
 color 0,0,0
 altColor 90,90,90
 exonArrows off
 
 track fosEndPairsBad
 shortLabel Bad Fosmid End Pairs
 longLabel Orphan, Short and Incorrectly Oriented Fosmid End Pairs
 group map
 priority 19
 visibility hide
 type bed 6 +
 color 0,0,0
 altColor 90,90,90
 exonArrows off
 
 track fosEndPairsLong
 shortLabel Long Fosmid End Pairs
 longLabel Long Fosmid End Pairs
 group map
 priority 20
 visibility hide
 type bed 6 +
 color 0,0,0
 altColor 90,90,90
 exonArrows off
 
 track chr18deletions
 shortLabel Chr18 Deletions
 longLabel Chromosome 18 Deletions 
 group map
 priority 21
 visibility hide
 type bed 6 +
 
 track isochores
 shortLabel Isochores
 longLabel GC-Rich (dark) and AT-Rich (light) Isochores
 group map
 priority 22
 visibility hide
 spectrum on
 type bed 4 +
 
 track gcPercent
 shortLabel GC Percent
 longLabel Percentage GC in 20,000-Base Windows
 group map
 priority 23
 visibility hide
 spectrum on
 type bed 4 +
 
 track gcPercentSmall
 shortLabel GC % 100b
 longLabel Percentage GC in 100-Base Windows
 group map
 priority 24
 visibility hide
 spectrum on
 type bed 4 +
 
 track GCwiggle
 shortLabel GC Samples 
 longLabel GC Percent Sample Track (every 20,000 bases)
 group map
 priority 25
 visibility hide
 chromosomes chr22,
 type sample
 
 track pGC
 shortLabel GC Samples 
 longLabel GC Percent Sample Track
 group map
 priority 26
 visibility hide
 type sample
 
 track humanParalog
 shortLabel Human Paralog 
 longLabel Human Paralogs Using Fgenesh++ Gene Predictions
 group map
 priority 28
 visibility hide
 spectrum on
 color 0,100,0
 altColor 255,240,200
 type bed 5 +
 
 track celeraCoverage
 shortLabel WSSD Coverage
 longLabel Regions Assayed for SDD
 group map
 priority 29
 visibility hide
 type bed 4 .
 
 track celeraDupPositive
 shortLabel WSSD Duplication
 longLabel Sequence Identified as Duplicate by High-Depth Celera Reads 
 group map
 priority 30
 visibility hide
 type bed 4 +
 
 track celeraOverlay
 shortLabel WSSD Overlay
 longLabel Celera WGS Assembly Overlay on Public Assembly
 group map
 priority 30.1
 visibility hide
 type bed 4 +
 
 track genomicDups
 shortLabel Duplications
 longLabel Duplications of >1000 Bases Sequence
 group map
 priority 31
 visibility hide
 type bed 6 +
 color 170,0,0
 altColor 160,150,0
 
 track dupes
 shortLabel Duplications
 longLabel Duplications of >98% Identity >1kb
 group map
 priority 32
 visibility dense
 type bed 6 .
 
 track Nregion
 shortLabel N Regions
 longLabel N Regions
 group map
 priority 32.5
 color 150,100,30
 visibility hide
 type bed 4 .
 
 track genieKnown
 shortLabel Known Genes
 longLabel Known Genes (from Full-Length mRNAs)
 group genes
 priority 33
 visibility pack
 color 20,20,170
 type genePred
 
 track knownGene
 shortLabel UCSC Genes
 longLabel UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative Genomics
 group genes
 priority 34
 visibility pack
 color 12,12,120
 type genePred knownGenePep knownGeneMrna
 idXref kgAlias kgID alias
 hgGene on
 hgsid on
 directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s
 baseColorUseCds given
 baseColorDefault genomicCodons
 defaultLinkedTables kgXref
 
 track knownAlt
 shortLabel Alt Events
 longLabel Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
 group genes
 priority 34.2
 visibility hide
 color 90,0,150
 noScoreFilter .
 type bed 6 .
 
 track ccdsGene
 shortLabel CCDS
 longLabel Consensus CDS
 group genes
 priority 34.5
 visibility hide
 color 12,120,12
 type genePred
 baseColorUseCds given
 baseColorDefault genomicCodons
 
 track refGene
 shortLabel RefSeq Genes
 longLabel RefSeq Genes
 group genes
 priority 35
 visibility dense
 color 12,12,120
 type genePred refPep refMrna
 idXref refLink mrnaAcc name
 baseColorUseCds given
 
 track augustus
 shortLabel Augustus
 longLabel Augustus Gene Predictions
 group genes
 priority 51.7
 visibility hide
 color 180,0,0
 type genePred
 
 # NSCAN gene predictions from BrentLab
 #   - local trackDb must specify $informant for use in html
 #   - will need to override searchTable entry for non-chrom assemblies
 track nscanGene
 shortLabel N-SCAN
 longLabel N-SCAN Gene Predictions
 group genes
 priority 45.1
 visibility hide
 color 34,139,34
 type genePred nscanPep
 baseColorUseCds given
 baseColorDefault genomicCodons
 informant BUG: INFORMANT DESCRIPTION NOT SET IN TRACK DB FILE
 
 searchTable nscanGene
 searchType genePred
 termRegex chr[0-9a-zA-Z_]+\.[0-9]+\.[0-9]+(\.[0-9a-z]+)?
 searchPriority 50
 
 track rgdEst
 shortLabel RGD EST
 longLabel RGD EST
 group rna
 priority 57.5
 visibility hide
 spectrum on
 color 12,12,120
 type psl est
 url http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=
 
 track rgdGene
 shortLabel RGD Genes
 longLabel Rat Genome Database Curated Genes
 group genes
 priority 35.5
 visibility dense
 color 12,12,120
 type genePred
 url http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=
 
 track rgdSslp
 shortLabel RGD SSLP
 longLabel Rat Genome Database Simple Sequence Length Polymorphisms 
 group varRep
 priority 144.5
 visibility hide
 color 12,12,120
 type bed 4 .
 url http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=
 
 track rgdQtl
 shortLabel RGD QTL
 longLabel $Organism Quantitative Trait Locus from RGD
 group phenDis
 priority 150
 visibility hide
 color 12,12,120
 type bed 4 .
 url http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=
 
 track rgdRatQtl
 shortLabel RGD Rat QTL
 longLabel $o_Organism Quantitative Trait Locus from RGD Coarsely Mapped to $Organism
 group phenDis
 priority 150.001
 visibility hide
 color 12,100,100
 type bed 4 .
 otherDb rn4
 url http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=
 
 track xenoRefGene
 shortLabel Other RefSeq
 longLabel Non-$Organism RefSeq Genes
 group genes
 priority 35.1
 visibility dense
 color 12,12,120
 type genePred xenoRefPep xenoRefMrna
 
 track mgcFullMrna
 shortLabel MGC Genes
 longLabel Mammalian Gene Collection Full ORF mRNAs
 group genes
 priority 36
 visibility hide
 color 34,139,34
 type psl
 baseColorDefault diffCodons
 baseColorUseCds genbank
 baseColorUseSequence genbank
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 
 searchTable mgcFullMrna
 searchType psl
 searchPriority 25
 semiShortCircuit 1
 
 # keep adjacent to MGC
 track orfeomeMrna
 shortLabel ORFeome Clones
 longLabel ORFeome Collaboration Gene Clones
 group genes
 priority 36.1
 visibility hide
 color 34,139,34
 type psl
 baseColorDefault diffCodons
 baseColorUseCds genbank
 baseColorUseSequence genbank
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 
 searchTable orfeomeMrna
 searchType psl
 searchPriority 25
 semiShortCircuit 1
 
 
 track transMap
 superTrack on
 shortLabel TransMap
 longLabel TransMap Alignments
 group genes
 priority 37.001
 
     track transMapAlnUcscGenes
     superTrack transMap pack
     shortLabel TransMap UCSC
     longLabel TransMap UCSC Gene Mappings
     group genes
     type psl
     priority 37.002
     color 0,100,0
     visibility pack
     transMapInfo transMapInfoUcscGenes
     transMapSrc hgFixed.transMapSrcUcscGenes
     transMapGene hgFixed.transMapGeneUcscGenes
     transMapTypeDesc UCSC Gene
     baseColorDefault diffCodons
     baseColorUseCds table hgFixed.transMapGeneUcscGenes
     baseColorUseSequence extFile hgFixed.transMapSeqUcscGenes hgFixed.transMapExtFileUcscGenes
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
 
 searchTable transMapAlnUcscGenes
 searchType psl
 searchMethod prefix
 searchPriority 2.31
 
     track transMapAlnRefSeq
     superTrack transMap pack
     shortLabel TransMap RefGene
     longLabel TransMap RefSeq Gene Mappings
     group genes
     type psl
     priority 37.003
     color 0,100,0
     visibility pack
     transMapInfo transMapInfoRefSeq
     transMapSrc hgFixed.transMapSrcRefSeq
     transMapGene hgFixed.transMapGeneRefSeq
     baseColorDefault diffCodons
     baseColorUseCds table hgFixed.transMapGeneRefSeq
     baseColorUseSequence extFile hgFixed.transMapSeqRefSeq hgFixed.transMapExtFileRefSeq
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
 
 searchTable transMapAlnRefSeq
 searchType psl
 searchMethod prefix
 searchPriority 2.31
 
     track transMapAlnMRna
     superTrack transMap pack
     shortLabel TransMap mRNA
     longLabel TransMap GenBank mRNA Mappings
     group genes
     type psl
     priority 37.004
     color 0,100,0
     visibility pack
     transMapInfo transMapInfoMRna
     transMapSrc hgFixed.transMapSrcMRna
     transMapGene hgFixed.transMapGeneMRna
     baseColorDefault diffCodons
     baseColorUseCds table hgFixed.transMapGeneMRna
     baseColorUseSequence extFile hgFixed.transMapSeqMRna hgFixed.transMapExtFileMRna
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
 
 searchTable transMapAlnMRna
 searchType psl
 searchMethod prefix
 searchPriority 2.31
 
     track transMapAlnSplicedEst
     superTrack transMap hide
     shortLabel TransMap ESTs
     longLabel TransMap Spliced EST Mappings
     group genes
     type psl
     priority 37.005
     color 0,100,0
     visibility hide
     transMapInfo transMapInfoSplicedEst
     transMapSrc hgFixed.transMapSrcSplicedEst
     baseColorDefault none
     baseColorUseSequence extFile hgFixed.transMapSeqSplicedEst hgFixed.transMapExtFileSplicedEst
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
 
 searchTable transMapAlnSplicedEst
 searchType psl
 searchMethod prefix
 searchPriority 2.31
 
 track reconTransMap
 superTrack on
 shortLabel Recon TransMap
 longLabel Reconstruction TransMap Alignments
 group genes
 priority 38.001
 
     track reconTransMapAlnRefSeq
     superTrack reconTransMap pack
     shortLabel Recon TransMap RefGene
     longLabel Reconstruction TransMap RefSeq Gene Mappings
     group genes
     type psl
     priority 38.003
     color 0,100,0
     visibility pack
     transMapInfo reconTransMapInfoRefSeq
     transMapSrc hgFixed.reconTransMapSrcRefSeq
     transMapGene hgFixed.reconTransMapGeneRefSeq
     baseColorDefault diffCodons
     baseColorUseCds table hgFixed.reconTransMapGeneRefSeq
     baseColorUseSequence extFile hgFixed.reconTransMapSeqRefSeq hgFixed.reconTransMapExtFileRefSeq
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
 
 searchTable reconTransMapAlnRefSeq
 searchType psl
 searchMethod prefix
 searchPriority 2.31
 
 track genieAlt
 shortLabel AltGenie
 longLabel Genie Gene Predictions from Affymetrix
 group genes
 priority 39
 visibility dense
 color 125,0,150
 type genePred genieAltPep
 
 track ensGene
 shortLabel Ensembl Genes
 longLabel Ensembl Gene Predictions
 group genes
 priority 40
 visibility hide
 color 150,0,0
 type genePred ensPep
 
 track ensEstGene
 shortLabel Ensembl EST Genes
 longLabel Ensembl EST Gene Predictions
 group genes
 priority 40.5
 visibility hide
 color 150,0,0
 type genePred ensEstPep
 url http://www.ensembl.org/perl/geneview?db=estgene&transcript=$$
 
 track sibGene
 shortLabel SIB Genes
 longLabel Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs 
 group  genes
 priority 41.4
 visibility hide
 color 195,90,0
 type genePred
 url http://www.isrec.isb-sib.ch/cgi-bin/tromer/tromer_quick_search.pl?query_str=$$
 urlLabel SIB link:
 
 track ECgene
 shortLabel ECgene Genes
 longLabel ECgene Gene Predictions with Alt-Splicing
 group genes
 priority 41.5
 visibility hide
 color 155,0,125
 type genePred ECgenePep
 
 track ensEst
 shortLabel Ensembl ESTs
 longLabel $Organism ESTs From Ensembl
 group genes
 priority 42
 visibility hide
 color 175,20,125
 type genePred ensEstPep
 
 track ncbiGenes
 shortLabel NCBI Gene Models
 longLabel $Organism Gene Models from NCBI
 group genes
 priority 43
 visibility hide
 type genePred ncbiPep
 
 track npredGene
 shortLabel NCBI Prediction
 longLabel NCBI Gene Predictions
 group genes
 priority 44
 visibility hide
 color 170,100,0
 type genePred npredPep 
 url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=$$
 
 track twinscan
 shortLabel Twinscan
 longLabel Twinscan Gene Predictions Using Mouse/Human Homology
 group genes
 priority 45
 visibility hide
 color 0,100,100
 type genePred twinscanPep
 
 track ucscFromMouse
 shortLabel UCSC Mm3
 longLabel UCSC Gene Predictions from Known Mouse Genes Mapped to Human
 group genes
 priority 45
 visibility hide
 color 0,100,100
 altColor 0,50,50
 type genePred 
 
 track contrastGene
 shortLabel CONTRAST
 longLabel CONTRAST Gene Predictions
 group genes
 priority 45.2
 visibility hide
 color 34,34,139
 type coloredExon
 
 searchTable contractGene
 searchType bed
 termRegex CONTRAST\..+
 searchPriority 50
 
 track genomeScan
 shortLabel NCBI GenomeScan
 longLabel $Organism GenomeScan Models from NCBI
 group genes
 priority 46
 visibility hide
 type genePred genomeScanPep
 
 track sgpGene
 shortLabel SGP Genes
 longLabel SGP Gene Predictions Using Mouse/Human Homology
 group genes
 priority 47
 visibility hide
 color 0,90,100
 type genePred sgpPep
 
 track softberryGene
 shortLabel Fgenesh++ Genes
 longLabel Fgenesh++ Gene Predictions
 group genes
 priority 48
 visibility hide
 color 0,100,0
 type genePred softberryPep
 
 track geneid
 shortLabel Geneid Genes
 longLabel Geneid Gene Predictions
 group genes
 priority 49
 visibility hide
 color 0,90,100
 type genePred geneidPep
 
 track genscan
 shortLabel Genscan Genes
 longLabel Genscan Gene Predictions
 group genes
 priority 50
 visibility hide
 color 170,100,0
 type genePred genscanPep
 
 track genscanExtra
 shortLabel Genscan Extra
 longLabel Genscan Extra (Suboptimal) Exon Predictions 
 group genes
 priority 51
 visibility hide
 color 180,90,0
 type bed 6 .
 chromosomes chr22,
 
 track rnaGene
 shortLabel RNA Genes
 longLabel Non-coding RNA Genes (dark) and Pseudogenes (light)
 group genes
 priority 52
 visibility hide
 color 170,80,0
 altColor 230,180,130
 type bed 6 +
 
 track superfamily
 shortLabel Superfamily
 longLabel Superfamily/SCOP: Proteins Having Homologs with Known Structure/Function
 group genes
 priority 53
 visibility hide
 color 150,0,0
 type bed 4 +
 url http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/cgi-bin/gene.cgi?genome=
 
 track exonWalk
 shortLabel ExonWalk
 longLabel ExonWalk Alt-Splicing Transcripts
 color 23,58,58
 group genes
 priority 72
 visibility hide
 type genePred
 
 track exonWalk2
 shortLabel ExonWalk2
 longLabel ExonWalk Alt-Splicing Transcripts - take 2
 color 23,58,58
 group genes
 priority 72.01
 visibility hide
 type genePred
 
 track exonWalkRna
 shortLabel ExonWalkRna
 longLabel ExonWalk Alt-Splicing Transcripts mRNA only, no orthology
 color 23,58,58
 group genes
 priority 72.02
 visibility hide
 type genePred
 
 track exonWalkRnaNoCds
 shortLabel ExonWalkRnaNoCds
 longLabel Exonwalk on Rna only, no orthology, no CDS mapping
 color 23,58,58
 group genes
 priority 72.03
 visibility hide
 type bed 12
 
 track mrna
 shortLabel $Organism mRNAs
 longLabel $Organism mRNAs from GenBank 
 group rna
 priority 54
 visibility pack
 type psl .
 baseColorUseCds genbank
 baseColorUseSequence genbank
 baseColorDefault diffCodons
 showDiffBasesAllScales .
 indelDoubleInsert on
 indelQueryInsert on
 indelPolyA on
 
 track tightMrna
 shortLabel Tight mRNAS
 longLabel Tightly Filtered $Organism mRNAs from GenBank
 group rna
 priority 55
 visibility hide
 spectrum on
 type psl .
 baseColorUseCds genbank
 baseColorUseSequence genbank
 baseColorDefault diffCodons
 showDiffBasesAllScales .
 indelDoubleInsert on
 indelQueryInsert on
 indelPolyA on
 
 track intronEst
 shortLabel Spliced ESTs
 longLabel $Organism ESTs That Have Been Spliced
 group rna
 priority 56
 visibility dense
 spectrum on
 intronGap 30
 type psl est
 baseColorUseSequence genbank
 showDiffBasesAllScales .
 indelDoubleInsert on
 indelQueryInsert on
 maxItems 300
 
 track est
 shortLabel $Organism ESTs
 longLabel $Organism ESTs Including Unspliced
 group rna
 priority 57
 visibility hide
 spectrum on
 intronGap 30
 type psl est
 baseColorUseSequence genbank
 indelDoubleInsert on
 indelQueryInsert on
 maxItems 300
 
 track interPro
 shortLabel InterPro
 longLabel InterPro Domains
 group genes
 priority 34.6
 visibility hide
 color 12,12,120
 type bed 4
 
 track protBlat
 shortLabel Protein BLAT
 longLabel Protein Blatted Against Genome
 group genes
 priority 37
 visibility hide
 color 0,100,0
 altColor 255,240,200
 type psl protein
 
 track tightEst
 shortLabel Tight ESTs
 longLabel Tightly Filtered $Organism ESTs Including Unspliced
 group rna
 priority 58
 visibility hide
 spectrum on
 type psl est
 baseColorUseSequence genbank
 indelDoubleInsert on
 indelQueryInsert on
 
 track xenoMrna
 shortLabel Other mRNAs
 longLabel Non-$Organism mRNAs from GenBank
 group rna
 priority 63
 visibility hide
 spectrum on
 type psl xeno
 baseColorUseCds genbank
 baseColorUseSequence genbank
 showDiffBasesAllScales .
 indelDoubleInsert on
 indelQueryInsert on
 
 track xenoBestMrna
 shortLabel Other Best mRNAs
 longLabel Non-$Organism mRNAs from GenBank Best in Genome Alignments
 group rna
 priority 64
 visibility hide
 spectrum on
 type psl xeno
 baseColorUseCds genbank
 baseColorUseSequence genbank
 showDiffBasesAllScales .
 indelDoubleInsert on
 indelQueryInsert on
 
 track xenoEst
 shortLabel Other ESTs
 longLabel Non-$Organism ESTs from GenBank 
 group rna
 priority 65
 visibility hide
 spectrum on
 type psl xeno
 baseColorUseSequence genbank
 indelDoubleInsert on
 indelQueryInsert on
 url http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$
 
 track anyCovBed
 shortLabel mRNA/EST/Pseud
 longLabel Blastz Alignments of GenBank mRNA Including Pseudogenes and All ESTs
 group rna
 priority 66
 visibility hide
 color 170,128,128
 type bed 3 .
 
 track anyMrnaCov
 shortLabel mRNA/Pseud
 longLabel Blastz Alignments of GenBank mRNA Including Pseudogenes
 group rna
 priority 67
 visibility hide
 color 170,128,128
 type bed 3 .
 
 track tigrGeneIndex
 shortLabel TIGR Gene Index
 longLabel Alignment of TIGR Gene Index TCs Against the $Organism Genome
 group rna
 priority 68
 visibility hide
 color 100,0,0
 type genePred
 autoTranslate 0
 url http://www.tigr.org/tigr-scripts/tgi/tc_report.pl?$$
 
 track uniGene_2
 shortLabel UniGene
 longLabel UniGene Alignments and SAGE Info
 group rna
 priority 69
 visibility hide
 spectrum on
 type bed 12 .
 
 track uniGene_3
 shortLabel UniGene
 longLabel UniGene Alignments
 group rna
 priority 69
 visibility hide
 url http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=
 spectrum on
 type psl
 
 track orthoIntrons
 shortLabel orthoIntrons
 longLabel Bed version of AltGraphX Mapped Inrons from Mouse
 group rna
 color 107,74,34,
 priority 72.2
 visibility hide
 type bed 12 .
 
 track uniGene
 shortLabel UniGene
 longLabel UniGene Alignments and SAGE Info
 group rna
 priority 70
 visibility hide
 type psl . 
 
 track rnaCluster
 shortLabel Gene Bounds 
 longLabel Gene Boundaries as Defined by RNA and Spliced EST Clusters
 group rna
 priority 71
 visibility hide
 color 200,0,50
 type bed 12 .
 
 track genieBounds
 shortLabel Clone Bounds 
 longLabel Clone Boundaries from EST Mate Pairs
 group rna
 priority 72
 visibility hide
 color 178,34,34
 type bed 9 .
 
 track agxMapped
 shortLabel agxMapped
 longLabel Condensed version of AltGraphX Mapped from Mouse
 group rna
 color 153,26,42,
 priority 72.1
 visibility hide
 type bed 12 .
 
 track altGraph
 shortLabel AltGraph
 longLabel AltGraph
 group rna
 priority 73
 visibility hide
 type psl .
 
 track sibTxGraph
 shortLabel SIB Alt-Splicing
 longLabel Alternative Splicing Graph from Swiss Institute of Bioinformatics 
 group rna
 priority 74.5
 visibility hide
 type altGraphX
 url http://www.isrec.isb-sib.ch/cgi-bin/tromer/tromergraph2draw.pl?species=H.+sapiens&tromer=$$
 urlLabel SIB link:
 idInUrlSql select name from sibTxGraph where id=%s
 
 track sibAltEvents
 shortLabel SIB Alt Events
 longLabel Alt-Splicing, Alternative Promoters, Alternative Poly-A etc from SIB
 group rna
 priority 74.6
 visibility hide
 type bed 6 .
 
 track cgapSage
 shortLabel CGAP SAGE
 longLabel CGAP Long SAGE
 group rna
 priority 200.1
 visibility hide
 type bed 8 +
 
 track miRNA
 shortLabel miRNA
 longLabel MicroRNAs from miRBase
 group genes
 priority 63
 visibility hide
 useScore 1
 color 255,64,64
 type bed 8 .
 url http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$$ 
 urlLabel miRBase:
 
 track allenBrainAli
 shortLabel Allen Brain
 longLabel Allen Brain Atlas Probes
 group regulation
 priority 80
 visibility hide
 color 50,0,100
 type psl .
 
 track cpgIsland
 shortLabel CpG Islands
 longLabel CpG Islands (Islands < 300 Bases are Light Green)
 group regulation
 priority 90
 visibility hide
 color 0,100,0
 altColor 128,228,128
 type bed 4 +
 
 track cpgIslandExt
 shortLabel CpG Islands
 longLabel CpG Islands (Islands < 300 Bases are Light Green)
 group regulation
 priority 90
 visibility hide
 color 0,100,0
 altColor 128,228,128
 type bed 4 +
 
 track cpgIslandGgfAndyMasked
 shortLabel CpG Islands (AL)
 longLabel CpG Islands - Andy Law, masked sequence (Islands < 300 Bases are Light Green)
 group regulation
 priority 90.001
 visibility hide
 color 0,100,0
 altColor 128,228,128
 type bed 4 +
 
 track cpgIslandGgfAndy
 shortLabel CpG Islands (AL)
 longLabel CpG Islands - Andy Law (Islands < 300 Bases are Light Green)
 group regulation
 priority 90.01
 visibility hide
 color 0,100,0
 altColor 128,228,128
 type bed 4 +
 
 track firstEF
 shortLabel FirstEF 
 longLabel FirstEF: First-Exon and Promoter Prediction
 group regulation
 priority 90.1
 visibility hide
 spectrum on
 type bed 6 .
 scoreMin 500
 scoreMax 1000
 url http://rulai.cshl.org/tools/FirstEF/Readme/README.html
 
 track softPromoter
 shortLabel TSSW Promoters
 longLabel TSSW Promoter Predictions
 group regulation
 priority 90.2
 visibility hide
 color 0,100,0
 type bed 5 +
 
 track transfacHit
 shortLabel Transfac Hits 
 longLabel Transfac Transcription Factor Binding Sites Near Transcription Start
 group regulation
 priority 91
 visibility hide
 spectrum on
 type bed 6 .
 
 track eponine
 shortLabel Eponine TSS
 longLabel Eponine Predicted Transcription Start Sites
 group regulation
 priority 91.9
 visibility hide
 color 0,100,100
 type bed 4 +
 
 track triangleSelf
 shortLabel Golden Triangle  
 longLabel Golden Triangle Possible Transcription Factor Binding Sites
 group regulation
 priority 92
 visibility hide
 spectrum on
 type bed 6 .
 
 track nibbImageProbes
 shortLabel NIBB Frog Images
 longLabel Xenopus Laevis In Situ mRNA Probes from NIBB
 group regulation
 priority 92
 visibility hide
 color 50,0,100
 type psl xeno
 
 track esRegGeneToMotif
 shortLabel Reg. Module 
 longLabel Eran Segal Regulatory Module
 group regulation
 priority 93
 visibility dense
 spectrum on
 noScoreFilter .
 type bed 6 +
 exonArrows off
 
 track triangle
 shortLabel Golden Extra
 longLabel Golden Triangle Motif Matching Sites Near Transcription Start
 group regulation
 priority 94
 visibility hide
 spectrum on
 type bed 6 .
 
 track transfac
 shortLabel Transfac Hits
 longLabel Transfac Hits
 group regulation
 priority 95
 visibility hide
 color 12,12,120
 type genePred refPep refMrna
 
 track transfacRatios
 shortLabel Transfac Ratios
 longLabel Transfac Likelihood Ratios
 group regulation
 priority 96
 visibility hide
 color 12,12,120
 type bed 6 .
 
 track psuReg
 shortLabel Known Regulatory 
 longLabel Functional Regulatory Elements Compiled by Penn State 
 group regulation
 priority 97
 visibility hide
 color 30,130,210
 type bed 4 .
 
 track oreganno
 shortLabel ORegAnno
 longLabel Regulatory elements from ORegAnno
 group regulation
 priority 98
 visibility hide
 color 102,102,0
 type bed 4 +
 
 track rosetta
 shortLabel Rosetta
 longLabel Rosetta Experimental Confirmation of Chr22 Exons
 group regulation
 priority 88
 visibility hide
 chromosomes chr22,
 type bed 15 +
 
 track exoFish
 shortLabel Exofish Ecores
 longLabel Exofish Tetraodon/Human Evolutionarily Conserved Regions
 group compGeno
 priority 111
 visibility dense
 color 0,60,120
 altColor 200,220,255
 spectrum on
 type bed 5 .
 
 track blatFish
 shortLabel Tetraodon Blat
 longLabel Tetraodon nigroviridis Translated Blat Alignments
 group compGeno
 priority 112
 visibility dense
 color 0,60,120
 altColor 200,220,255
 spectrum on
 type psl xeno
 
 track blatFugu
 shortLabel Fugu Blat
 longLabel Takifugu rubripes Translated Blat Alignments
 group compGeno
 priority 150
 visibility hide
 color 0,60,120
 altColor 200,220,255
 spectrum on
 type psl xeno
 
 track blatFr1
 shortLabel Fugu Blat
 longLabel $o_Organism ($o_date/$o_db) Translated Blat Alignments
 group compGeno
 priority 139.7
 visibility hide
 color 0,60,120
 altColor 200,220,255
 spectrum on
 type psl xeno fr1
 otherDb fr1
 colorChromDefault off
 
 track blatCi1
 shortLabel Squirt Blat
 longLabel Ciona intestinalis Translated Blat Alignments
 group compGeno
 priority 135
 visibility hide
 color 0,60,120
 altColor 200,220,255
 spectrum on
 type psl xeno 
 
 track blatTetra
 shortLabel Tetra Blat
 longLabel Tetraodon nigroviridis Translated Blat Alignments
 group compGeno
 priority 114
 visibility dense
 color 0,60,120
 altColor 200,220,255
 spectrum on
 type psl xeno
 
 track tet_waba
 shortLabel Tetraodon
 longLabel Tetraodon nigroviridis Homologies
 group compGeno
 priority 115
 visibility hide
 color 50,100,200
 altColor 85,170,225
 
 track blatChicken
 shortLabel Chicken Blat
 longLabel Chicken Translated Blat Alignments
 group compGeno
 priority 116
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type psl xeno
 
 track HMRConservation
 shortLabel HMRConservation
 longLabel Mouse/Human/Rat Evolutionary Conservation Score
 group compGeno
 color 100,50,0
 altColor 175,150,128
 priority 110
 visibility hide
 type sample 0 .466217
 
 track syntenyHuman
 shortLabel Human Synteny
 longLabel Human/Mouse Synteny Using Blastz Single Coverage (100k window)
 group compGeno
 priority 127
 visibility hide
 color 0,100,0
 altColor 255,240,200
 type bed 4 +
 
 track ratChain
 shortLabel $o_Organism Chain 
 longLabel Chained Rat/$Organism Alignments
 group compGeno
 priority 133
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain rn2
 otherDb rn2
 
 track ratNet
 shortLabel Rat Net
 longLabel Rat/$Organism Alignment Net
 group compGeno
 priority 171
 visibility hide
 spectrum on
 type netAlign rn2 ratChain
 otherDb rn2
 
 track mouseSyn
 shortLabel NCBI Synteny
 longLabel Corresponding Chromosome in Mouse (NCBI)
 group compGeno
 priority 137
 visibility hide
 color 120,70,30
 altColor 0,0,0
 type bed 4 +
 
 shortLabel Rat Synteny
 longLabel Human/Rat Synteny Using Blastz Single Coverage (100,000-base window)
 group compGeno
 priority 138
 visibility hide
 color 0,100,0
 altColor 255,240,200
 type bed 4 .
 
 track mouseSynWhd
 shortLabel Mouse Synteny
 longLabel Whitehead Corresponding Chromosome in Mouse (300k window)
 group compGeno
 priority 139
 visibility hide
 color 120,70,30
 altColor 0,0,0
 type bed 6 +
 
 track syntenyRat
 shortLabel Rat Synteny
 longLabel $Organism/Rat Synteny Using Blastz Single Coverage (100k window)
 group compGeno
 priority 140
 visibility hide
 color 0,100,0
 altColor 255,240,200
 type bed 4 +
 
 track blatChimpWashu
 shortLabel Chimp Blat - WashU
 longLabel Chimp Blat Alignments - WashU
 group compGeno
 priority 141
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type psl xeno
 
 track chimp
 shortLabel Chimp
 longLabel Chimp Sample Track
 group compGeno
 priority 142
 visibility hide
 chromosomes chr7,
 color 100,50,0
 altColor 0,0,255
 type sample
 
 # Affy Exon supertrack
         track affyAllExonSuper
         superTrack on
         shortLabel Affy Exon
         longLabel Affymetrix All Exon Microarrays
         group regulation
         priority 0
 
 track affyExonTissues
 shortLabel Affy Exon Tissues
 longLabel Affymetrix Exon Array 1.0: Normal Tissues
 superTrack affyAllExonSuper dense
 group regulation
 priority 1.0
 visibility full
 type expRatio
 expScale 3.0
 expStep 0.5
 expTable affyExonTissuesExps
 groupings affyExonTissuesGroups
 
 track affyAllExonProbes
 shortLabel Affy Exon Probes
 longLabel Affymetrix Exon Array 1.0: Probesets
 superTrack affyAllExonSuper dense
 group regulation
 priority 2.0
 visibility pack
 spectrum on
 useScore 1
 exonArrows on
 type bed 6 .
 
 track snp130
 shortLabel SNPs (130)
 longLabel Simple Nucleotide Polymorphisms (dbSNP build 130)
 group varRep
 priority 100.094
 visibility dense 
 url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
 urlLabel dbSNP: 
 defaultGeneTracks knownGene
 maxWindowToDraw 10000000
 type bed 6 +
 
 track snp129
 shortLabel SNPs (129)
 longLabel Simple Nucleotide Polymorphisms (dbSNP build 129)
 group varRep
 priority 100.095
 visibility dense 
 url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
 urlLabel dbSNP: 
 defaultGeneTracks knownGene
 maxWindowToDraw 10000000
 type bed 6 +
 
 track snp128
 shortLabel SNPs (128)
 longLabel Simple Nucleotide Polymorphisms (dbSNP build 128) 
 group varRep
 priority 100.096
 visibility dense 
 url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
 urlLabel dbSNP: 
 maxWindowToDraw 10000000
 type bed 6 +
 
 track snp127
 shortLabel SNPs (127)
 longLabel Simple Nucleotide Polymorphisms (dbSNP build 127) 
 group varRep
 priority 100.097
 visibility dense 
 url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
 urlLabel dbSNP: 
 maxWindowToDraw 10000000
 type bed 6 +
 
 track snp126
 shortLabel SNPs (126)
 longLabel Simple Nucleotide Polymorphisms (dbSNP build 126) 
 group varRep
 priority 100.098
 visibility dense 
 url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
 urlLabel dbSNP: 
 maxWindowToDraw 10000000
 type bed 6 +
 
 track snp125
 shortLabel SNPs 
 longLabel Simple Nucleotide Polymorphisms (dbSNP build 125) 
 group varRep
 priority 100.099
 visibility dense 
 url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
 urlLabel dbSNP: 
 maxWindowToDraw 10000000
 type bed 6 +
 
 track snp
 shortLabel SNPs
 longLabel Simple Nucleotide Polymorphisms (SNPs)
 group varRep
 priority 100
 visibility dense
 type bed 6 +
 
 track snpMap
 shortLabel SNPs
 longLabel Simple Nucleotide Polymorphisms (SNPs)
 group varRep
 priority 100
 visibility hide
 type bed 4 .
 
 track genomicSuperDups
 shortLabel Segmental Dups
 longLabel Duplications of >1000 Bases of Non-RepeatMasked Sequence
 group varRep
 priority 146
 visibility hide
 type bed 6 .
 noScoreFilter .
 
 track lineageMutations
 shortLabel LineageMutations
 longLabel Lineage Specific Mutations
 group varRep
 priority 147
 altColor 0,160,0
 visibility hide
 type sample
 
 track rmsk
 shortLabel RepeatMasker
 longLabel Repeating Elements by RepeatMasker
 group varRep
 priority 149.1
 visibility dense
 spectrum on
 type rmsk
 maxWindowToDraw 10000000
 canPack off
 
 track nestedRepeats
 shortLabel Interrupted Rpts
 longLabel Fragments of Interrupted Repeats Joined by RepeatMasker ID
 group varRep
 priority 149.11
 visibility hide
 useScore 1
 type bed 12 +
 
 track rmskCensor
 shortLabel CENSOR Repeats
 longLabel Repeating Elements by CENSOR and RepBase 11.6 (Giri Ihstitute)
 group varRep
 priority 149.2
 visibility hide
 spectrum on
 type rmsk
 canPack off
 
 track rmskRM327
 shortLabel RepMask 3.2.7
 longLabel Repeating Elements by RepeatMasker version 3.2.7
 group varRep
 priority 149.105
 visibility hide
 spectrum on
 type rmsk
 canPack off
 
 track nestedRepeatsRM327
 shortLabel Intr Rpts 3.2.7
 longLabel Fragments of Interrupted Repeats Joined by RepeatMasker ID (RM version 3.2.7)
 group varRep
 priority 149.115
 visibility hide
 useScore 1
 type bed 12 +
 
 track reconRepeat
 shortLabel Recon Repeats
 longLabel Repeats Determined with Recon
 group varRep
 priority 149.2
 visibility hide
 type bed 4 +
 
 track windowmasker
 shortLabel WindowMasker
 longLabel Genomic Intervals Masked by WindowMasker
 group varRep
 priority 149.25
 visibility hide
 type bed 3
 
 track windowmaskerSdust
 shortLabel WM + SDust
 longLabel Genomic Intervals Masked by WindowMasker + SDust
 group varRep
 priority 149.26
 visibility hide
 type bed 3
 
 track simpleRepeat
 shortLabel Simple Repeats
 longLabel Simple Tandem Repeats by TRF
 group varRep
 priority 149.3
 visibility hide
 type bed 4 +
 
 track microsat
 shortLabel Microsatellite
 longLabel Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
 group varRep
 priority 149.4
 visibility hide
 type bed 4 
 
 track blastzSelfUnmasked
 shortLabel Self Unmasked
 longLabel Blastz Self Join without Repeats Masked (tandem repeats masked)
 group x
 priority 159
 visibility hide
 spectrum on
 type psl xeno
 
 track olly25
 shortLabel Cross-hyb3 25
 longLabel Cross-hybridization Counts for Off-by-3 25-mers 
 group x
 priority 148.5
 visibility hide
 type sample 0 5 0.199
 
 track olly2
 shortLabel Cross-hyb2 25
 longLabel Cross-hybridization for Off-by-2 25-mers 
 group x
 priority 148.6
 visibility hide
 type sample 0 5 0.199
 
 track gpcr
 shortLabel Gpcr
 longLabel Gpcr from softberry and Rachel Karchin's HMM
 group x
 priority 149
 visibility hide
 type genePred
 
 track loweProbes
 shortLabel Lowe's Probes
 longLabel Candidate Oligos for Stanford Microarray
 group x
 priority 151
 visibility hide
 chromosomes chr22,
 type bed 6 .
 
 track exoMouse
 shortLabel Exonerate Mouse
 longLabel Mouse/Human Evolutionarily Conserved Regions (Exonerate)
 group x
 priority 152
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type bed 6 +
 
 track mouseOrtho
 shortLabel Mouse Ortholog
 longLabel Mouse Orthology Using Fgenesh++ Gene Predictions
 group x
 priority 157
 visibility hide
 color 0,100,0
 altColor 255,240,200
 type bed 5 +
 
 track mouseOrthoSeed
 shortLabel Tight Ortholog
 longLabel Tight Mouse Orthology Using Fgenesh++ Gene Predictions (only reciprocal best)
 group x
 priority 158
 visibility hide
 spectrum on
 color 0,100,0
 altColor 255,240,200
 type bed 5 +
 
 track ancientR
 shortLabel Ancient Repeats
 longLabel Human/Mouse Ancient Repeats
 group x
 priority 163
 visibility hide
 spectrum on
 type bed 12 .
 
 track quality
 shortLabel Quality Scores
 longLabel $Organism Sequencing Quality Scores
 group map
 priority 23.6
 visibility hide
 autoScale Off
 maxHeightPixels 128:36:16
 graphTypeDefault Bar
 windowingFunction Mean
 gridDefault OFF
 color 0,128,255
 altColor 255,128,0
 spanList 1,1024
 type wig 0 100 
 
 track gc5Base
 shortLabel GC Percent
 longLabel GC Percent in 5-Base Windows
 group map
 priority 23.5
 visibility hide
 autoScale Off
 maxHeightPixels 128:36:16
 graphTypeDefault Bar
 gridDefault OFF
 windowingFunction Mean
 color 0,0,0
 altColor 128,128,128
 viewLimits 30:70
 spanList 5
 type wig 0 100 
 
 track ensemblGeneScaffold
 shortLabel Ensembl Assembly
 longLabel Ensembl Gene Scaffold assembly
 group map
 priority 26
 visibility hide
 color 0,0,0
 useScore 1
 type bed 6 +
 
 track blatHg16KG
 shortLabel Human knownGene BLAT
 longLabel Human knownGene BLAT
 group compGeno
 priority 142
 visibility hide
 colorChromDefault off
 type psl protein
 
+# release beta until composite chainBraFlo1 track becomes the default
 track chainBraFlo1
+release beta
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 137
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrixHeader A, C, G, T
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 spectrum on
 type chain braFlo1
 otherDb braFlo1
 
 track netBraFlo1
+release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 138
 visibility hide
 spectrum on
 type netAlign braFlo1 chainBraFlo1
 otherDb braFlo1
 
 track blastDm2FB
 shortLabel D. mel. Proteins (dm2)
 longLabel D. melanogaster Proteins (dm2) Mapped by Chained tBLASTn
 group genes
 priority 200
 visibility dense
 colorChromDefault off
 type psl protein
 pred dm2.blastFBPep01
 blastRef dm2.blastFBRef01
 url http://flybase.bio.indiana.edu/.bin/fbidq.html?
 
 track blastDm1FB
 shortLabel D. mel. Proteins
 longLabel D. melanogaster Proteins (dm1) Mapped by Chained tBLASTn
 group genes
 priority 201
 visibility dense
 colorChromDefault off
 type psl protein
 pred dm1.blastFBPep00
 blastRef dm1.blastFBRef00
 url http://flybase.bio.indiana.edu/.bin/fbidq.html?
 
 track blastHg16KG
 shortLabel Human Proteins
 longLabel Human Proteins (hg16) Mapped by Chained tBLASTn
 group genes
 priority 250.4
 visibility hide
 colorChromDefault off
 type psl protein
 pred hg16.blastKGPep00
 blastRef hg16.blastKGRef00
 
 track chainDm1
 release beta
 shortLabel D. mel. Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 133
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain dm1
 otherDb dm1
 
 track netDm1
 release beta
 shortLabel D. mel. Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 134
 visibility dense
 spectrum on
 type netAlign dm1 chainDm1
 otherDb dm1
 
 track chainDm1
 release alpha
 shortLabel (dm1) D. mel. Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 133.91
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain dm1
 otherDb dm1
 
 track netDm1
 release alpha
 shortLabel (dm1) D. mel. Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 133.92
 visibility dense
 spectrum on
 type netAlign dm1 chainDm1
 otherDb dm1
 
 track chainDm2
 shortLabel D. mel. Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 133.81
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain dm2
 otherDb dm2
 
 track netDm2
 shortLabel D. mel. Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 133.82
 visibility hide
 spectrum on
 type netAlign dm2 chainDm2
 otherDb dm2
 
 # release alpha: $o_db in shortLabel
 track chainDm3
 shortLabel ($o_db) D. mel. Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 133.71
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain dm3
 otherDb dm3
 release alpha
 
 # release alpha: $o_db in shortLabel
 track netDm3
 shortLabel ($o_db) D. mel. Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 133.72
 visibility hide
 spectrum on
 type netAlign dm3 chainDm3
 otherDb dm3
 release alpha
 
 # release beta: no $o_db in shortLabel
 track chainDm3
 shortLabel D. mel. Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 133.71
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain dm3
 otherDb dm3
 release beta
 
 # release beta: no $o_db in shortLabel
 track netDm3
 shortLabel D. mel. Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 133.72
 visibility hide
 spectrum on
 type netAlign dm3 chainDm3
 otherDb dm3
 release beta
 
 # release beta until composite chainNetFr1 track becomes the default
 track chainFr1
 release beta
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 140
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain fr1
 otherDb fr1
 
 track netFr1
 release beta
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 140.1
 visibility hide
 spectrum on
 type netAlign fr1 chainFr1
 otherDb fr1
 
 # release beta until composite chainNetFr2 track becomes the default
 track chainFr2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 139.8
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 spectrum on
 type chain fr2
 otherDb fr2
 
 # release beta until composite chainNetFr2 track becomes the default
 track netFr2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 139.9
 visibility hide
 spectrum on
 type netAlign fr2 chainFr2
 otherDb fr2
 
 # release beta until composite chainNetTetNig1 track becomes the default
 track chainTetNig1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 150
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain tetNig1
 otherDb tetNig1
 
 track netTetNig1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 150.1
 visibility hide
 spectrum on
 type netAlign tetNig1 chainTetNig1
 otherDb tetNig1
 
 # release beta until composite danRer5 tracks become the default
 track chainDanRer5
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 159.1
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain danRer5
 otherDb danRer5
 
 track netDanRer5
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 159.2
 visibility hide
 spectrum on
 type netAlign danRer5 chainDanRer5
 otherDb danRer5
 
 # release beta until composite danRer4 tracks become the default
 track chainDanRer4
 release beta
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 159.3
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain danRer4
 otherDb danRer4
 
 track netDanRer4
 release beta
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 159.4
 visibility hide
 spectrum on
 type netAlign danRer4 chainDanRer4
 otherDb danRer4
 
 # release beta until composite danRer3 tracks become the default
 track chainDanRer3
 release beta
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 160
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain danRer3
 otherDb danRer3
 
 # release beta until composite danRer3 tracks become the default
 track netDanRer3
 release beta
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 160.1
 visibility hide
 spectrum on
 type netAlign danRer3 chainDanRer3
 otherDb danRer3
 
 # release beta until composite danRer2 tracks become the default
 track chainDanRer2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 160.3
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain danRer2
 otherDb danRer2
 
 # release beta until composite danRer2 tracks become the default
 track netDanRer2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 160.4
 visibility hide
 spectrum on
 type netAlign danRer2 chainDanRer2
 otherDb danRer2
 
 # release beta until composite danRer1 tracks become the default
 track chainDanRer1
 release beta
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 160
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain danRer1
 otherDb danRer1
 
 # release beta until composite petMar1 tracks become the default
 track chainPetMar1
 release beta
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 138.8
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 spectrum on
 type chain petMar1
 otherDb petMar1
 
 track netPetMar1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 138.9
 visibility hide
 spectrum on
 type netAlign petMar1 chainPetMar1
 otherDb petMar1
 
 # release beta until composite oryLat2 tracks become the default
 track chainOryLat2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 165.49
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 spectrum on
 type chain oryLat2
 otherDb oryLat2
 
 # release beta until composite oryLat2 tracks become the default
 track netOryLat2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 165.50
 visibility hide
 spectrum on
 type netAlign oryLat2 chainOryLat2
 otherDb oryLat2
 
 # release beta until composite oryLat1 tracks become the default
 #	at which point all this should be removed
 track chainOryLat1
 release beta
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 165.49
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 spectrum on
 type chain oryLat1
 otherDb oryLat1
 
 track netOryLat1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 165.50
 visibility hide
 spectrum on
 type netAlign oryLat1 chainOryLat1
 otherDb oryLat1
 
 # release beta until composite gasAcu1 tracks become the default
 track chainGasAcu1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 165.51
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 spectrum on
 type chain gasAcu1
 otherDb gasAcu1
 
 # release beta until composite gasAcu1 tracks become the default
 track netGasAcu1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 165.52
 visibility hide
 spectrum on
 type netAlign gasAcu1 chainGasAcu1
 otherDb gasAcu1
 
 # release beta until composite anoCar1 tracks become the default
 track chainAnoCar1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 167
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain anoCar1
 otherDb anoCar1
 
 track netAnoCar1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 167.1
 visibility hide
 spectrum on
 type netAlign anoCar1 chainAnoCar1
 otherDb anoCar1
 
 # release beta until composite chainNetXenTro1 track becomes the default
 track chainXenTro1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 170.2
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain xenTro1
 otherDb xenTro1
 
 track netXenTro1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 170.3
 visibility hide
 spectrum on
 type netAlign xenTro1 chainXenTro1
 otherDb xenTro1
 
 # release beta until composite chainNetXenTro1 track becomes the default
 track chainXenTro2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 170
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain xenTro2
 otherDb xenTro2
 
 track netXenTro2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 170.1
 visibility hide
 spectrum on
 type netAlign xenTro2 chainXenTro2
 otherDb xenTro2
 
 # release beta until galGal2 individual chain/net tracks phased out
 track chainGalGal2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 180
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain galGal2
 otherDb galGal2
 
 track netGalGal2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 180.1
 visibility hide
 spectrum on
 type netAlign galGal2 chainGalGal2
 otherDb galGal2
 
 track chainGalGal3
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 181
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain galGal3
 otherDb galGal3
 
 track netGalGal3
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 181.1
 visibility hide
 spectrum on
 type netAlign galGal3 chainGalGal3
 otherDb galGal3
 
 # release alpha: $o_db in shortLabel
 track chainTaeGut1
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 179
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain taeGut1
 otherDb taeGut1
 release alpha
 
 # release beta: $o_Organism in shortLabel
 track chainTaeGut1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 179
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain taeGut1
 otherDb taeGut1
 release beta
 
 # release alpha: $o_db in shortLabel
 track netTaeGut1
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 179.1
 visibility hide
 spectrum on
 type netAlign taeGut1 chainTaeGut1
 otherDb taeGut1
 release alpha
 
 # release beta: $o_Organism in shortLabel
 track netTaeGut1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 179.1
 visibility hide
 spectrum on
 type netAlign taeGut1 chainTaeGut1
 otherDb taeGut1
 release beta
 
 # release beta until ornAna1 individual chain/net tracks phased out
 track chainOrnAna1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 185
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain ornAna1
 otherDb ornAna1
 
 # release beta until ornAna1 individual chain/net tracks phased out
 track netOrnAna1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 185.1
 visibility hide
 spectrum on
 type netAlign ornAna1 chainOrnAna1
 otherDb ornAna1
 
 track chainMacEug1
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 190
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain macEug1
 otherDb macEug1
 
 track netMacEug1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 190.1
 visibility hide
 spectrum on
 type netAlign macEug1 chainMacEug1
 otherDb macEug1
 
 track chainMonDom4
 release beta
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 190
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain monDom4
 otherDb monDom4
 
 track netMonDom4
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 190.1
 visibility hide
 spectrum on
 type netAlign monDom4 chainMonDom4
 otherDb monDom4
 
 track chainMonDom2
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 190
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain monDom2
 otherDb monDom2
 
 track netMonDom2
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 190.1
 visibility hide
 spectrum on
 type netAlign monDom2 chainMonDom2
 otherDb monDom2
 
 # release beta until composite chainNetMonDom1 track becomes the default
 track chainMonDom1
 release beta
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 190
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain monDom1
 otherDb monDom1
 
 track netMonDom1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 190.1
 visibility hide
 spectrum on
 type netAlign monDom1 chainMonDom1
 otherDb monDom1
 
 # release beta until composite chainNetRn3 track becomes the default
 track chainRn3
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 200
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain rn3
 otherDb rn3
 
 track netRn3
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 200.1
 visibility hide 
 spectrum on
 type netAlign rn3 chainRn3
 otherDb rn3
 
 # release beta until composite chainNetRn4 track becomes the default
 track chainRn4
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 200
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain rn4
 otherDb rn4
 
 # release beta until composite chainNetRn4 track becomes the default
 track netRn4
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 200.1
 visibility hide 
 spectrum on
 type netAlign rn4 chainRn4
 otherDb rn4
 
 track chainMm3
 shortLabel $o_db Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 210
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain mm3
 otherDb mm3
 
 track chainMm4
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 210
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain mm4
 otherDb mm4
 
 track chainMm5
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 210
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain mm5
 otherDb mm5
 
 track netMm5
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 210.1
 visibility hide
 spectrum on
 type netAlign mm5 chainMm5
 otherDb mm5
 
 # release beta until composite chainNetMm6 track becomes the default
 track chainMm6
 release beta
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 210
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain mm6
 otherDb mm6
 
 track netMm6
 release beta
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 210.1
 visibility hide
 spectrum on
 type netAlign mm6 chainMm6
 otherDb mm6
 
 # release beta until composite chainNetMm9 track becomes the default
 track chainMm9
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 209
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 spectrum on
 type chain mm9
 otherDb mm9
 
 track netMm9
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 209.1
 visibility hide
 spectrum on
 type netAlign mm9 chainMm9
 otherDb mm9
 
 # release beta until composite chainNetMm8 track becomes the default
 track chainMm8
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 210
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 spectrum on
 type chain mm8
 otherDb mm8
 
 track netMm8
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 210.1
 visibility hide
 spectrum on
 type netAlign mm8 chainMm8
 otherDb mm8
 
 # release beta until composite chainNetMm7 track becomes the default
 track chainMm7
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 210
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain mm7
 otherDb mm7
 
 track netMm7
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 210.1
 visibility hide
 spectrum on
 type netAlign mm7 chainMm7
 otherDb mm7
 
 track chainSorAra1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 256.26
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain sorAra1
 otherDb sorAra1
 
 track netSorAra1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 256.27
 visibility hide
 spectrum on
 type netAlign sorAra1 chainSorAra1
 otherDb sorAra1
 
 track chainEriEur1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 256.28
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain eriEur1
 otherDb eriEur1
 
 track netEriEur1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 256.29
 visibility hide
 spectrum on
 type netAlign eriEur1 chainEriEur1
 otherDb eriEur1
 
 # release beta until composite chainNetBosTau4 track becomes the default
 track chainBosTau4
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 256.291
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 chainMinScore 3000
 chainLinearGap medium
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain bosTau4
 otherDb bosTau4
 
 track netBosTau4
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 256.292
 visibility hide
 spectrum on
 type netAlign bosTau4 chainBosTau4
 otherDb bosTau4
 
 # release beta until composite chainNetBosTau3 track becomes the default
 track chainBosTau3
 release beta
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 256.3
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain bosTau3
 otherDb bosTau3
 
 track netBosTau3
 release beta
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 256.4
 visibility hide
 spectrum on
 type netAlign bosTau3 chainBosTau3
 otherDb bosTau3
 
 # release beta until composite chainNetBosTau2 track becomes the default
 track chainBosTau2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 220
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 chainMinScore 3000
 chainLinearGap medium
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain bosTau2
 otherDb bosTau2
 
 track netBosTau2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 220.1
 visibility hide
 spectrum on
 type netAlign bosTau2 chainBosTau2
 otherDb bosTau2
 
 track chainBosTau1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 220
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain bosTau1
 otherDb bosTau1
 
 track netBosTau1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 220.1
 visibility hide
 spectrum on
 type netAlign bosTau1 chainBosTau1
 otherDb bosTau1
 
 track chainCanFam2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 230 
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain canFam2
 otherDb canFam2
 
 # release beta until composite chainNetFelCat3 track becomes the default
 track chainFelCat3
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 230 
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 chainMinScore 3000
 chainLinearGap medium
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain felCat3
 otherDb felCat3
 
 track chainTupBel1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments 
 group compGeno
 priority 272
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain tupBel1
 otherDb tupBel1
 
 track netTupBel1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 272.2
 visibility hide
 spectrum on
 type netAlign tupBel1 chainTupBel1
 otherDb tupBel1
 
 track chainOtoGar1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 274
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain otoGar1
 otherDb otoGar1
 
 track chainOtoGar1Best
 shortLabel $o_Organism Best Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments Recip Best
 group compGeno
 priority 274.1
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain otoGar1
 otherDb otoGar1
 
 track netOtoGar1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 274.2
 visibility hide
 spectrum on
 type netAlign otoGar1 chainOtoGar1
 otherDb otoGar1
 
 track chainCanHg12
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 200 
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain canHg12
 otherDb canHg12
 
 track chainBorEut13
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 200 
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain borEut13
 otherDb borEut13
 
 # release beta until composite chainNetFelCat3 track becomes the default
 track netFelCat3
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 230.1
 visibility hide
 spectrum on
 type netAlign felCat3 chainFelCat3
 otherDb felCat3
 
 track netCanFam2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 230.1
 visibility hide
 spectrum on
 type netAlign canFam2 chainCanFam2
 otherDb canFam2
 
 track chainCanFam1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 230
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain canFam1
 otherDb canFam1
 
 track netCanFam1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 230.1
 visibility hide
 spectrum on
 type netAlign canFam1 chainCanFam1
 otherDb canFam1
 
 # release beta until composite chainNetCavPor3 track becomes the default
 track chainCavPor3
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 198
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 spectrum on
 type chain cavPor3
 otherDb cavPor3
 
 track netCavPor3
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 198.1
 visibility hide
 spectrum on
 type netAlign cavPor3 chainCavPor3
 otherDb cavPor3
 
 # release beta until composite chainNetCavPor2 track becomes the default
 track chainCavPor2
 release beta
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 198.2
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain cavPor2
 otherDb cavPor2
 
 track netCavPor2
 release beta
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 198.3
 visibility hide
 spectrum on
 type netAlign cavPor2 chainCavPor2
 otherDb cavPor2
 
 track chainOryCun1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 197
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 spectrum on
 type chain oryCun1
 otherDb oryCun1
 
 track netOryCun1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 197.1
 visibility hide
 spectrum on
 type netAlign oryCun1 chainoryCun1
 otherDb oryCun1
 
 # release beta until composite chainNetPanTro1 track becomes the default
 track chainPanTro1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 240
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain panTro1
 otherDb panTro1
 
 track netPanTro1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 240.1
 visibility hide
 spectrum on
 type netAlign panTro1 chainPanTro1
 otherDb panTro1
 
 # release beta until composite chainNetPanTro2 track becomes the default
 track chainPanTro2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 240
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrixHeader A, C, G, T
 spectrum on
 type chain panTro2
 otherDb panTro2
 
 track netPanTro2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 240.1
 visibility hide
 spectrum on
 type netAlign panTro2 chainPanTro2
 otherDb panTro2
 
 track chainGorGor1
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 287
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain gorGor1
 otherDb gorGor1
 
 track netGorGor1
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 287.1
 visibility hide
 spectrum on
 type netAlign gorGor1 chainGorGor1
 otherDb gorGor1
 
 track chainPonAbe2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 285
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain ponAbe2
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb ponAbe2
 
 track netPonAbe2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 285.1
 visibility hide
 spectrum on
 type netAlign ponAbe2 chainPonAbe2
 otherDb ponAbe2
 
 track chainPonAbe1
 shortLabel $o_db Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 241
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain ponAbe1
 otherDb ponAbe1
 
 track netPonAbe1
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 241.1
 visibility hide
 spectrum on
 type netAlign ponAbe1 chainPonAbe1
 otherDb ponAbe1
 
 track chainHg15
 shortLabel $o_Organism Chain Hg15
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 250
 visibility dense
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain hg15
 otherDb hg15
 
 track chainHg16
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 250
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain hg16
 otherDb hg16
 
 track chainHg17
 release beta
 shortLabel $o_db Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 250
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain hg17
 otherDb hg17
 
 track netHg17
 release beta
 shortLabel $o_db Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 250.1
 visibility dense
 spectrum on
 type netAlign hg17 chainHg17
 otherDb hg17
 
 track chainHg18
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 250
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 spectrum on
 type chain hg18
 otherDb hg18
 
 track netHg18
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 250.1
 visibility dense
 spectrum on
 type netAlign hg18 chainHg18
 otherDb hg18
 
 track chainRheMac2
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 257.1
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain rheMac2
 otherDb rheMac2
 
 track netRheMac2
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 257.2
 visibility hide
 spectrum on
 type netAlign rheMac2 chainRheMac2
 otherDb rheMac2
 
 # release beta until composite chainNetCalJac1 track becomes the default
 track chainCalJac1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 278
 visibility hide
 color 100,50,0
 altColor 255,240,200
 matrixHeader A, C, G, T
 spectrum on
 type chain calJac1
 otherDb calJac1
 
 track netCalJac1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 278.1
 visibility hide
 spectrum on
 type netAlign calJac1 chainCalJac1
 otherDb calJac1
 
 # release beta until equCab2 phased in
 track chainEquCab1
 release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 235
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 type chain equCab1
 otherDb equCab1
 
 # release beta until equCab2 phased in
 track netEquCab1
 release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 235.1
 visibility hide
 spectrum on
 type netAlign equCab1 chainEquCab1
 otherDb equCab1
 
 track chainCi2
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 209
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain ci2
 otherDb ci2
 
 track netCi2
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 209.1
 visibility hide
 spectrum on
 type netAlign ci2 chainCi2 
 otherDb ci2
 
 track chainStrPur2
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 209.2
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 type chain strPur2
 otherDb strPur2
 
 track netStrPur2
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 209.3
 visibility hide
 spectrum on
 type netAlign strPur2 chainStrPur2
 otherDb strPur2
 
 track blastSacCer1SG
 shortLabel Yeast Proteins
 longLabel  Yeast Proteins from SGD Mapped by Chained tBLASTn
 group genes
 priority 200
 visibility hide
 colorChromDefault off
 type psl protein
 pred sacCer1.blastSGPep00
 blastRef sacCer1.blastSGRef00
 url http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=
 
 track chainMm3XSingle
 shortLabel Mm3X Best Recip
 longLabel  Mm3X  Best Reciprocal (best w/no overlap)
 group x
 priority 300
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain mm3X
 otherDb mm3X
 
 track chainMm2XSingle
 shortLabel  Mm2X Best Recip
 longLabel  Mm2X Best Reciprocal (best w/no overlap)
 group x
 priority 301
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain mm2X
 otherDb mm2X
 
 track blastHg17KG
 shortLabel Hg17  Proteins
 longLabel Hg17 Proteins Mapped by Chained tBLASTn
 group genes
 priority 250.3
 visibility pack
 colorChromDefault off
 type psl protein
 pred hg17.blastKGPep01
 blastRef hg17.blastKGRef01
 
 track blastHg18KG
 shortLabel Human Proteins
 longLabel Human Proteins Mapped by Chained tBLASTn
 group genes
 priority 250.2
 visibility pack
 colorChromDefault off
 type psl protein
 pred hg18.blastKGPep04
 blastRef hg18.blastKGRef04
 
 track BRout
 shortLabel BRout
 longLabel  BRout
 group x
 spectrum on
 priority 128
 visibility hide
 type psl xeno
 
 track tblastHg16
 shortLabel tblastHg16
 longLabel  tblastHg16 
 group x
 spectrum on
 priority 128
 visibility hide
 type psl xeno
 
 track chainHg16ProtEx
 shortLabel chainHg16ProtEx
 longLabel chainHg16ProtEx
 group x
 priority 302
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain hg16
 otherDb hg16
 
 track chainHg16MergeEx
 shortLabel chainHg16MergeEx
 longLabel chainHg16MergeEx
 group x
 priority 303
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain hg16
 otherDb hg16
 
 track chainDm1MergeEx
 shortLabel chainDm1MergeEx
 longLabel chainDm1MergeEx
 group x
 priority 304
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain dm1
 otherDb dm1
 
 track blastzBestMm3X
 shortLabel Mm3X Best
 longLabel Mm3X Blastz Best-in-Genome Alignments
 group x
 priority 200.8
 visibility hide
 spectrum on
 type psl xeno mm3X
 otherDb mm3X
 
 track blastzBestMm2X
 shortLabel Mm2X Best
 longLabel Mm2X Blastz Best-in-Genome Alignments
 group x
 priority 201.8
 visibility hide
 spectrum on
 type psl xeno mm2X
 otherDb mm2X
 
 track phastConsElements
 shortLabel Most Conserved
 longLabel PhastCons Conserved Elements
 group compGeno
 priority 105
 visibility hide
 exonArrows off
 showTopScorers 200
 type bed 5 .
 
 track phastConsElementsPaper
 shortLabel Most Cons. (Std)
 longLabel PhastCons Conserved Elements, Standardized Across Species
 group compGeno
 priority 105.1
 visibility hide
 exonArrows off
 useScore 1
 showTopScorers 200
 type bed 5 .
 
 track encodeRegionsLiftOver
 shortLabel liftOver Regions
 longLabel liftOver ENCODE Region Orthologs (Freeze 3)
 group encode
 priority 170.1
 color 0,200,0
 visibility hide
 type bed 4 .
 
 track encodeRegionsMercator
 shortLabel Mercator Regions
 longLabel Mercator ENCODE Region Orthologs (Freeze 3)
 group encode
 priority 170.2
 color 0,0,200
 visibility hide
 type bed 4 .
 
 track encodeRegionsMercatorMerged
 shortLabel Mercator Regions
 longLabel Merged Mercator ENCODE Region Orthologs (Freeze 3)
 group encode
 priority 170.3
 color 0,0,200
 visibility hide
 type bed 4 .
 
 track encodeRegionsConsensus
 shortLabel ENCODE Region Consensus
 longLabel Consensus Orthology of ENCODE Regions from LiftOver and Mercator (Freeze 3)
 group encode
 priority 170.4
 color 150,100,30
 visibility hide
 type bed 4 .
 
 
 track phastConsTopPaper
 shortLabel phastCons HCE
 longLabel PhastCons Highly Conserved Elements (HCEs)
 group compGeno
 priority 109.25
 visibility hide
 color 0,100,0
 type bed 5 .
 
 
 searchTable ctgPos
 searchMethod exact
 shortCircuit 1
 termRegex (ctg|NT_|NG_|NC_)[0-9]+
 query select chrom,chromStart,chromEnd,contig from %s where contig like '%s'
 searchPriority 5
 
 searchTable cytoBand
 searchMethod exact
 searchType cytoBand
 shortCircuit 1
 termRegex (x|y|[1-9][0-9]?)(p|q)[0-9]+(\.[0-9]+)?
 searchPriority 6
 padding 500000
 
 searchTable clonePos
 searchMethod exact
 searchType bed
 shortCircuit 1
 termRegex [a-z]+_?[0-9]+\.[0-9]+
 searchPriority 7
 
 searchName clonePosNoVers
 searchTable clonePos
 searchMethod prefix
 shortCircuit 1
 termRegex [a-z][a-z0-9]_?[0-9]+
 query select chrom,chromStart,chromEnd,name from %s where name like '%s.%%'
 dontCheck [a-z][a-z0-9]_?[0-9]+\.[0-9]+
 searchPriority 7
 
 searchTable gold
 searchMethod exact
 searchType gold
 shortCircuit 1
 termRegex [abuz].[0-9]+(\.[0-9]+)?
 searchPriority 8
 
 searchName knownGeneAcc
 searchTable knownGene
 searchMethod exact
 searchType knownGene
 shortCircuit 1
 semiShortCircuit 1
 termRegex (uc[0-9]{3}[a-z]{3}(\.[0-9]+)?|N(M|R)_[0-9]{6}[0-9]*|[a-z][a-z0-9][0-9]{4}[0-9]*)
 searchPriority 9
 
 searchName refGeneAcc
 searchTable refGene
 searchMethod exact
 searchType genePred
 semiShortCircuit 1
 termRegex N(M|R)_[0-9]{6}[0-9]*
 searchPriority 9.5
 
 searchName mrnaAcc
 searchTable all_mrna
 searchMethod prefix
 searchType mrnaAcc
 shortCircuit 1
 semiShortCircuit 1
 termRegex [a-z][a-z0-9][0-9]+
 searchPriority 10
 
 searchName stsMapAliasMrnaAcc
 searchTable stsMap
 searchType bed
 shortCircuit 1
 semiShortCircuit 1
 xrefTable stsAlias
 xrefQuery select trueName,alias from %s where alias like '%s'
 searchBoth on
 termRegex [a-z][a-z0-9][0-9]+
 dontCheck [^[:space:]]+
 searchDescription Alias of STS Marker
 searchPriority 11
 padding 100000
 
 searchTable encodeRegions
 searchMethod prefix
 searchType bed
 shortCircuit 1
 termRegex EN[rm][0-9]+(_[0-9]+)?
 searchPriority 11
 
 searchTable encodeRegionsConsensus
 searchMethod prefix
 searchType bed
 shortCircuit 1
 termRegex EN[rm][0-9]+(_[0-9]+)?
 searchPriority 11
 
 searchName snpMapShort
 searchTable snpMap
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)
 dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?)
 searchPriority 12.999
 padding 250
 
 searchName snpShort
 searchTable snp
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)
 dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?)
 searchPriority 12.998
 padding 250
 
 searchTable snp125
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex ([0-9]+|rs[0-9]+)
 searchPriority 12.997
 padding 250
 
 searchTable snp126
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 12.996
 padding 250
 
 searchTable snp127
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 12.995
 padding 250
 
 searchTable snp128
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 12.994
 padding 250
 
 searchTable snp129
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 12.993
 padding 250
 
 searchTable snp130
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 12.992
 padding 250
 
 searchTable ensGene
 searchType genePred
 shortCircuit 1
 termRegex ENS([A-Z]{3})?T[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchName ensDotPrefix
 searchTable ensGene
 query select chrom,txStart,txEnd,name from %s where name like '%s.%%'
 shortCircuit 1
 termRegex ENS([A-Z]{3})?T[0-9]+
 dontCheck ENS([A-Z]{3})?T[0-9]+\.[0-9]+
 searchPriority 50
 
 searchName ensGeneGtpGene
 searchTable ensGene
 searchType genePred
 searchMethod prefix
 shortCircuit 1
 xrefTable ensGtp
 xrefQuery select transcript,gene from %s where gene like '%s%%'
 termRegex ENS([A-Z]{3})?G[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchName ensGeneGtpProtein
 searchTable ensGene
 searchType genePred
 searchMethod prefix
 shortCircuit 1
 xrefTable ensGtp
 xrefQuery select transcript,protein from %s where protein like '%s%%'
 termRegex ENS([A-Z]{3})?P[0-9]+(\.[0-9]+)?
 
 searchTable ensEstGene
 searchType genePred
 shortCircuit 1
 searchMethod prefix
 termRegex ENSESTT[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchName ensEstGeneGtpGene
 searchTable ensEstGene
 searchType genePred
 searchMethod prefix
 shortCircuit 1
 xrefTable ensEstGtp
 xrefQuery select transcript,gene from %s where gene like '%s%%'
 termRegex ENSESTG[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchName ensEstGeneGtpProtein
 searchTable ensEstGene
 searchType genePred
 searchMethod prefix
 shortCircuit 1
 xrefTable ensEstGtp
 xrefQuery select transcript,protein from %s where protein like '%s%%'
 termRegex ENSESTP[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchTable knownGene
 searchType knownGene
 searchPriority 1
 
 searchName refLink
 searchTable refGene
 searchType refGene
 searchPriority 2
 grepIndex genbankGrep/refLink.mrnaAccProduct
 
 searchTable xenoRefGene
 searchType refGene
 searchPriority 2.1
 grepIndex refLinkGrep/refLink.mrnaAccProduct
 
 searchTable retroMrnaInfo
 searchType bed
 searchMethod prefix
 searchPriority 3.5
 
 searchName retroMrnaInfoRefSeq
 searchTable retroMrnaInfo
 query select chrom, chromStart,chromEnd, refSeq from %s where refSeq = '%s'
 xrefTable refLink
 xrefQuery select mrnaAcc, name from %s where name like '%s%%'
 searchPriority 3.51
 
 searchTable pseudoGeneLink
 query select chrom, chromStart,chromEnd, refSeq from %s where refSeq = '%s'
 xrefTable refLink
 xrefQuery select mrnaAcc, name from %s where name like '%s%%'
 searchPriority 2.5
 
 searchName pseudoGeneUniProt
 searchTable pseudoGeneLink
 query select chrom, chromStart,chromEnd, kgName from %s where kgName = '%s'
 xrefTable kgXref
 xrefQuery select kgID, spDisplayID from %s where spDisplayID = '%s'
 searchPriority 2.6
 
 searchTable pseudoYaleEncode
 searchType genePred
 searchMethod exact
 searchPriority 4
 
 searchTable pseudoHavana
 searchType genePred
 searchMethod exact
 searchPriority 4
 
 searchTable pseudoGIS
 searchType genePred
 searchMethod exact
 searchPriority 4
 
 searchTable superfamily
 searchType bed
 searchMethod fuzzy
 xrefTable sfDescription
 xrefQuery select name,description from %s where description like '%%%s%%'
 searchDescription Description of Superfamily Protein
 searchPriority 6
 padding 100
 
 searchTable fishClones
 searchMethod exact
 searchType bed
 termRegex (RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+
 searchPriority 7
 
 searchTable bacEndPairs
 searchMethod exact
 searchType bed
 termRegex ([[:alnum:]_ ]+|((RP|CT|GS|CH|TAM|MSMG)[[:alnum:]]+)?(-[[:alnum:]_]+)+)
 searchPriority 8
 
 searchTable bacEndPairsBad
 searchMethod exact
 searchType bed
 termRegex ([[:alnum:]_ ]+|((RP|CT|GS|CH|TAM|MSMG)[[:alnum:]]+)?(-[[:alnum:]_]+)+)
 searchPriority 8
 
 searchTable fosEndPairs
 searchMethod exact
 searchType bed
 termRegex ([[:alnum:]]+|(RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+|-[[:alnum:]]+-[[:alnum:]]+)
 searchPriority 9
 
 searchTable fosEndPairsBad
 searchMethod exact
 searchType bed
 termRegex ([[:alnum:]]+|(RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+|-[[:alnum:]]+-[[:alnum:]]+)
 searchPriority 10
 
 searchName stsMapAliasComprehensive
 searchTable stsMap
 searchType bed
 xrefTable stsAlias
 xrefQuery select trueName,alias from %s where alias like '%s'
 searchBoth on
 termRegex [^[:space:]]+
 searchDescription Alias of STS Marker
 searchPriority 11
 padding 100000
 
 searchName mrnaKeyword
 searchTable all_mrna
 searchType mrnaKeyword
 searchPriority 15
 grepIndex genbankGrep
 
 searchName snpMapLong
 searchTable snpMap
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex ([0-9]+|rs[0-9][0-9]?[0-9]?)
 dontCheck (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)
 searchPriority 16.999
 padding 250
 
 searchName snpLong
 searchTable snp
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex ([0-9]+|rs[0-9][0-9]?[0-9]?)
 dontCheck (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)
 searchPriority 16.998
 padding 250
 
 searchTable genieAlt
 searchType genePred
 termRegex A\.chr.*-.*\.[0-9]+
 searchPriority 50
 
 searchTable softberryGene
 searchType genePred
 termRegex C[A-Z0-9][A-Z0-9][0-9]+
 searchPriority 50
 
 searchTable acembly
 searchType genePred
 termRegex [^[:space:]]+
 searchPriority 50
 
 searchTable genscan
 searchType genePred
 termRegex [[:alnum:]_?]+\.?[0-9]+
 searchPriority 50
 
 searchTable twinscan
 searchType genePred
 termRegex (chr)?.*\.[0-9]+\.[0-9]+\.[a-z]
 searchPriority 50
 
 searchTable sgpGene
 searchType genePred
 termRegex chr[^_]+_((gl[0-9]+_)?(random_)?|([a-z0-9]+)_hap[0-9]_)?[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchTable geneid
 searchType genePred
 searchMethod prefix
 termRegex chr[^_]+_((gl[0-9]+_)?(random_)?|([a-z0-9]+)_hap[0-9]_)?[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchTable ECgene
 searchType genePred
 termRegex [[:alnum:]_]+\.[0-9]+
 searchPriority 50
 
 searchTable sangerGene
 searchType genePred
 searchPriority 50
 
 searchTable vegaGene
 searchType genePred
 searchPriority 50
 
 searchTable vegaPseudoGene
 searchType genePred
 searchPriority 50
 
 searchTable vegaGene
 searchName vegaGene2
 searchMethod prefix
 query select chrom, txStart,txEnd, name from %s where name2 like '%s%%'
 searchPriority 50.1
 
 searchTable vegaPseudoGene
 searchName vegaPseudoGene2
 searchMethod prefix
 query select chrom, txStart,txEnd, name from %s where name2 like '%s%%'
 searchPriority 50.1
 
 searchTable slamRat
 searchType genePred
 termRegex [[:alnum:]_]+\.[0-9]+\.[0-9]+
 searchPriority 50
 
 searchTable slamMouse
 searchType genePred
 termRegex [[:alnum:]_]+\.[0-9]+\.[0-9]+
 searchPriority 50
 
 searchTable slamHuman
 searchType genePred
 termRegex [[:alnum:]_]+\.[0-9]+\.[0-9]+
 searchPriority 50
 
 searchTable rgdQtl
 searchType bed
 searchMethod fuzzy
 searchPriority 50
 
 searchTable rgdRatQtl
 searchType bed
 searchMethod fuzzy
 searchPriority 50
 
 searchTable rgdSslp
 searchType bed
 searchPriority 50
 
 searchTable rgdEst
 searchType psl
 searchPriority 50
 
 searchTable rgdGene
 searchType genePred
 searchPriority 50
 
 searchTable NIAGene
 searchMethod prefix
 searchType psl
 searchPriority 50
 
 searchTable rnaCluster
 searchMethod exact
 searchType bed
 termRegex chr[0-9a-z_]+[.][0-9]+
 searchPriority 50
 
 searchName oreg
 searchTable oreganno
 searchMethod exact
 query select chrom, chromStart, chromEnd, id from %s where id = '%s'
 padding 500
 searchPriority 55
 
 searchTable blastDm2FB
 searchMethod prefix
 searchType psl
 searchPriority 25
 
 searchTable blastDm1FB
 searchMethod prefix
 searchType psl
 searchPriority 25
 
 searchTable blastSacCer1SG
 searchMethod prefix
 searchType psl
 searchPriority 25
 
 searchTable blastHg16KG
 searchMethod prefix
 searchType psl
 searchPriority 25
 
 searchName blastSacCer1SGSprot
 searchTable blastSacCer1SG
 searchMethod prefix
 searchType psl
 xrefTable sacCer1.blastSGRef00
 xrefQuery select acc,extra1 from %s where extra1 like '%s%%'
 searchPriority 25
 
 searchName blastSacCer1SGGene
 searchTable blastSacCer1SG
 searchMethod prefix
 searchType psl
 xrefTable sacCer1.blastSGRef00
 xrefQuery select acc,geneId from %s where geneId like '%s%%'
 
 searchName blastHg16KGSprot
 searchTable blastHg16KG
 searchMethod prefix
 searchType psl
 xrefTable hg16.blastKGRef00
 xrefQuery select acc,extra1 from %s where extra1 like '%s%%'
 searchPriority 25
 
 searchName blastHg16KGGene
 searchTable blastHg16KG
 searchMethod prefix
 searchType psl
 xrefTable hg16.blastKGRef00
 xrefQuery select acc,geneId from %s where geneId like '%s%%'
 
 searchName blastHg17KGSprot
 searchTable blastHg17KG
 searchMethod prefix
 searchType psl
 xrefTable hg17.blastKGRef01
 xrefQuery select acc,extra1 from %s where extra1 like '%s%%'
 searchPriority 25
 
 searchName blastHg17KGGene
 searchTable blastHg17KG
 searchMethod prefix
 searchType psl
 xrefTable hg17.blastKGRef01
 xrefQuery select acc,geneId from %s where geneId like '%s%%'
 searchPriority 25
 
 searchTable blastHg17KG
 searchMethod prefix
 searchType psl
 
 searchName blastHg18KGSprot
 searchTable blastHg18KG
 searchMethod prefix
 searchType psl
 xrefTable hg18.blastKGRef04
 xrefQuery select acc,extra1 from %s where extra1 like '%s%%'
 searchPriority 25
 
 searchName blastHg18KGGene
 searchTable blastHg18KG
 searchMethod prefix
 searchType psl
 xrefTable hg18.blastKGRef04
 xrefQuery select acc,geneId from %s where geneId like '%s%%'
 searchPriority 25
 
 searchTable blastHg18KG
 searchMethod prefix
 searchType psl
 semiShortCircuit 1
 
 searchName blastDm2FBGene
 searchTable blastDm2FB
 searchMethod prefix
 searchType psl
 xrefTable dm2.blastFBRef01
 xrefQuery select acc,geneId from %s where geneId like '%s%%'
 searchPriority 25
 
 searchName blastDm1FBGene
 searchTable blastDm1FB
 searchMethod prefix
 searchType psl
 xrefTable dm1.blastFBRef00
 xrefQuery select acc,geneId from %s where geneId like '%s%%'
 searchPriority 25
 
 searchTable ECgene
 searchType genePred
 searchPriority 50
 
 searchTable phastConsTopPaper
 searchType bed
 searchPriority 50
 termRegex pc[a-z][a-z].[[:alnum:]]+
 
 searchTable allenBrainAli
 searchMethod exact
 searchType psl
 searchPriority 5
 shortCircuit 1
 termRegex RP_.+
 
 track encodeRegions2
 shortLabel ENCODE Region Consensus (Freeze 2)
 longLabel Consensus Orthology of ENCODE Regions from liftOver and Mercator (Freeze 2)
 group encode
 priority 170.5
 color 200,0,0
 visibility pack
 type bed 4 .
 
 searchName assemblyAcc
 searchTable gold
 searchMethod prefix
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s'
 xrefTable contigAcc
 xrefQuery select contig,acc from %s where acc like '%s%%'
 searchPriority 5
 shortCircuit 1
 termRegex [A-Z]{4}[0-9]{8,10}(\.[0-9]+)?
 
 searchTable eponine
 searchType bed
 searchMethod exact
 termRegex chr[0-9]+[.][0-9]+
 searchPriority 50
 
 searchTable ccdsGene
 searchType genePred
 searchPriority 1.1

