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aloraine |
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Options +Indexes |
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IndexOptions FancyIndexing HTMLTable SuppressRules |
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IndexOptions IconsAreLinks ScanHTMLTitles NameWidth=* DescriptionWidth=* |
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# Autoindex-Strapdown Directives |
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AddType text/plain .md |
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HeaderName HEADER.md |
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ReadmeName README.md |
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# Customize by setting theme and title |
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IndexHeadInsert "<script>conf = {theme: 'united', title: 'Integrated Genome Browser QuickLoad Site'};</script> \ |
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strapdown: '/styling/strapdown/v/0.2/strapdown.js'};</script> \ |
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<script src='/styling/autoindex_strapdown.js'></script> \ |
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<link rel='stylesheet' href='/styling/autoindex_strapdown.css'>" |
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# Icons using Bootstrap's Glyphicon set |
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DefaultIcon /styling/icons/glyphicon-file.svg |
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AddIcon /styling/icons/blank.svg ^^BLANKICON^^ |
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AddIcon /styling/icons/glyphicon-folder-open.svg ^^DIRECTORY^^ |
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AddIcon /styling/icons/glyphicon-circle-arrow-up.svg .. |
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AddIconByType (TXT,/styling/icons/glyphicon-file.svg) text/* |
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AddIconByType (IMG,/styling/icons/glyphicon-picture.svg) image/* |
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AddIconByType (SND,/styling/icons/glyphicon-music.svg) audio/* |
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AddIconByType (VID,/styling/icons/glyphicon-film.svg) video/* |
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IndexIgnore HEADER* README* FOOTER* /styling *~ *# |
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AddDescription "Tells search engines what to ignore" robots.txt |
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AddDescription "Taxonomic and common names for species, shown in IGB species menu" species.txt |
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AddDescription "Chromosome synonyms" chromosome.txt |
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AddDescription "Lists size of largest transcript, for RNA-Seq normalization" tx_sizes.txt.gz |
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AddDescription "Icon IGB displays for this data source in the Data Access tab" favicon.ico |
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AddDescription "Sequence data in blat 2bit format" *.2bit |
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AddDescription "Sequence data in fastq format" *.fastq.gz |
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AddDescription "BedGraph (wiggle) format file" *.wig.gz |
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AddDescription "BedGraph (wiggle) format file" *.bedgraph.gz |
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AddDescription "Cytobands file" cytoBand.cyt |
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AddDescription "Tabix index file" *.gz.tbi |
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AddDescription "PSL (alignments) blat output file" *.psl.gz |
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AddDescription "Loraine Lab FindJunctions file" *.FJ.bed.gz |
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AddDescription "Data from UCSC refGene table" *_refGene.bed.gz |
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AddDescription "Annotation or junction file" *.bed.gz |
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AddDescription "Annotation or junction file" *.bed |
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AddDescription "EST alignments" EST |
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AddDescription "mRNA alignments" mRNA |
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aloraine |
93 |
AddDescription "Anguilla rostrata" (Oct 2016) American eel (LTYT01/Dryad)" A_rostrata_Oct_2016 |
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AddDescription "Anopheles gambiae (Oct 2006) mosquito (AgamP3/anoGam3)" A_gambiae_Oct_2006 |
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aloraine |
66 |
AddDescription "Anopheles gambiae (Feb 2003) mosquito (anoGam1/IAGP v.MOZ2)" A_gambiae_Feb_2003 |
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AddDescription "Ailuropoda melanoleuca (Dec 2009) giant panda (ailMel1/BGI-Shenzhen AilMel 1.0)" A_melanoleuca_Dec_2009 |
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AddDescription "Apis mellifera (honeybee) Jan 2005 (apiMel2/Baylor College of Medicine HGSC v.Amel_2.0 )" A_mellifera_Jan_2005 |
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AddDescription "Arabidopsis thaliana TAIR9, TAIR10 genome assembly" A_thaliana_Jun_2009 |
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AddDescription "Arabidopsis thaliana TAIR8 genome assembly" A_thaliana_Apr_2008 |
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AddDescription "Arabidopsis thaliana TIGR5 genome assembly" A_thaliana_Jan_2004 |
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AddDescription "Slime mold" D_discoideum |
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AddDescription "Medicago truncatula" M_truncatula_Mar_2009 |
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AddDescription "Castor bean" R_communis |
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AddDescription "Arabidopsis lyrata JGI v1.0 assembly" A_lyrata_Apr_2011 |
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AddDescription "Escherichia coli K12-MG1655" E_coli_K12-MG1655_Jan_2012 |
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AddDescription "Fragaria vesca (woodland strawberry) v1.1" F_vesca_Sep_2011 |
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pkulzer |
200 |
AddDescription "Capitella teleta Jan 2013 (Capca1)" C_teleta_Jan_2013 |
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aloraine |
66 |
AddDescription "Cavia porcellus (Feb 2008) guinea pig (cavPor3)" C_porcellus_Feb_2008 |
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aloraine |
88 |
AddDescription "C. elegans Feb 2013 (WBcel235/ce11)" C_elegans_Feb_2013 |
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aloraine |
66 |
AddDescription "C. elegans Oct 2010 (WS220/ce10)" C_elegans_Oct_2010 |
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aloraine |
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AddDescription "Chlorocebus sabaeus (Mar 2014) African green monkey (Chlorocebus_sabaeus 1.1/chlSab2)" C_sabaeus_Mar_2014 |
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aloraine |
87 |
AddDescription "Danio rerio (May 2017) zebrafish (GRCz11/danRer11)" D_rerio_May_2017 |
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aloraine |
66 |
AddDescription "Danio rerio (Jul 2010) zebrafish (danRer7/Zv9)" D_rerio_Jul_2010 |
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aloraine |
104 |
AddDescription "Daphnia magna Xinb3 v2.4 (Apr 2010) water flea" D_magna_Apr_2010 |
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AddDescription "Daphnia magna SK v1.0 (Jan 2019) water flea" D_magna_Jan_2019 |
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AddDescription "Daphnia pulex TCO v1.0 (Feb 2011) water flea" D_pulex_Feb_2011 |
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AddDescription "Daphnia pulex PA42 v3.0 (Sep 2016) water flea" D_pulex_Sep_2016 |
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aloraine |
66 |
AddDescription "Drosophila melanogaster (Apr 2006) fruit fly (dm3/BDGP R5)" D_melanogaster_Apr_2006 |
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nfreese |
161 |
AddDescription "Drosophila melanogaster (Aug 2014) fruit fly (BDGP Release 6 + ISO1 MT/dm6)" D_melanogaster_Aug_2014 |
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aloraine |
66 |
AddDescription "Drosophila melanogaster (July 2014) fruit fly (dmel_r6.03_FB2014_06)" D_melanogaster_Jul_2014 |
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AddDescription "Equus caballus (Sep 2007) horse (equCab2)" E_caballus_Sep_2007 |
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AddDescription "Felis catus (Dec 2008) cat (NHGRI/GTB V17e/felCat4)" F_catus_Dec_2008 |
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nfreese |
152 |
AddDescription "Ficedula albicollis (Jun 2013) collared flycatcher (FicAlb1.5)" F_albicollis_Jun_2013 |
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aloraine |
66 |
AddDescription "Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0)" G_gallus_Nov_2011 |
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AddDescription "Loxodonta africana (Jul 2009) elephant (loxAfr3)" L_africana_Jul_2009 |
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AddDescription "Papaya" C_papaya_Aug_2010 |
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aloraine |
181 |
AddDescription "Brachypodium distachyon (a model grass) JGI v1.0 8x assembly" B_distachyon_Aug_201 |
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pkulzer |
200 |
AddDescription "Hydra vulgaris (Apr 2024) Swiftwater hydra (HydraT2T_AEP)" H_vulgaris_Apr_2024 |
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aloraine |
181 |
AddDescription "Hypsibius exemplaris strain Z151 (Apr 2017) water bear (nHd_3.1 assembly)" H_exemplaris_Z151_Apr_2017 |
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pkulzer |
200 |
AddDescription "Homo sapiens T2T hs1 (T2T Consortium T2T-CHM13 v2.0)" H_sapiens_T2T_Jan_2022 |
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aloraine |
66 |
AddDescription "Homo sapiens hg38 (Genome Reference Consortium GRCh38)" H_sapiens_Dec_2013 |
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AddDescription "Homo sapiens hg19 (Genome Reference Consortium GRCh37)" H_sapiens_Feb_2009 |
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AddDescription "Homo sapiens hg18 (Genome Reference Consortium GRCh36)" H_sapiens_Mar_2006 |
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AddDescription "Homo sapiens hg17 (Genome Reference Consortium GRCh35)" H_sapiens_May_2004 |
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AddDescription "Nematostella vectensis, starlet sea anemone" N_vectensis_Jun_2007 |
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AddDescription "Chlamy (an algal genome)" C_reinhardtii_Nov_2010 |
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AddDescription "Camelina, false flax, an oilseed crop" C_sativa_DH55_Apr_2014 |
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aloraine |
122 |
AddDescription "Cannabis sativa CBDRx Dec 2018" C_sativa_CBDRx_Dec_2018 |
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aloraine |
66 |
AddDescription "Rice, japonic variety" O_sativa_japonica_Jun_2009 |
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AddDescription "Rice, japonic variety Os-Nipponbare-Reference-IRGSP-1.0 assembly" O_sativa_japonica_Oct_2011 |
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AddDescription "Soybean Glyma1" G_max_Aug_2010 |
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AddDescription "Soybean Glyma2" G_max_Jan_2014 |
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aloraine |
84 |
AddDescription "S. cerevisiae strain S288C (Apr 2011) budding yeast (sacCer3)" S_cerevisiae_Apr_2011 |
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AddDescription "S. cerevisiae strain S288C (Jun 2008) budding yeast (sacCer2)" S_cerevisiae_Jun_2008 |
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aloraine |
66 |
AddDescription "Fission yeast" S_pombe_Aug_2007 |
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AddDescription "Volvox" V_carteri_Jul_2010 |
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AddDescription "Wine grape 12x assembly" V_vinifera_Mar_2010 |
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AddDescription "Physcomitrella patens (moss)" P_patens_Jan_2008 |
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aloraine |
141 |
AddDescription "Physcomitrella patens (moss) v3.3" P_patens_Jan_2018 |
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aloraine |
66 |
AddDescription "Black cottonwood (poplar)" P_trichocarpa_Aug_2012 |
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AddDescription "Black cottonwood (poplar)" P_trichocarpa_Jan_2010 |
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AddDescription "Sorghum bicolor" S_bicolor_Jan_2009 |
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AddDescription "Sorghum bicolor" S_bicolor_Jun_2013 |
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aloraine |
93 |
AddDescription "Candida albicans WO-1 (Dec 2013)" C_albicans_WO-1_Dec_2013 |
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aloraine |
66 |
AddDescription "Candida albicans" C_albicans |
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AddDescription "Zea mays B73 RefGen_v2 assembly" Z_mays_B73_Mar_2010 |
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aloraine |
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AddDescription "Bos taurus (Jun 2014) cow (UMD_3.1.1/bosTau8)" B_taurus_Jun_2014 |
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aloraine |
66 |
AddDescription "Bos taurus (cow) bosTau7 Oct 2011 assembly" B_taurus_Oct_2011 |
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AddDescription "C. elegans May 2008 WS190/ce6" C_elegans_May_2008 |
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AddDescription "Annotation and data file list" annots.[txt|xml] |
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AddDescription "Chromosome lengths and assembly information" mod_chromInfo.txt |
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AddDescription "Chromosome lengths and assembly information" genome.txt |
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AddDescription "IGB synonym file" synonyms.txt |
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AddDescription "Available genome assemblies and their titles" contents.txt |
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AddDescription "Mitochondrial Genome (Fasta format)" [Cc]hrM.fa* |
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AddDescription "Chloroplast Genome (Fasta format)" [Cc]hrC.fa* |
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AddDescription "Peach v1 genome assembly" P_persica_Apr_2010 |
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AddDescription "Thermococcus kodakaraensis" T_kodakaraensis_KOD1_May_2004 |
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AddDescription "Xenopus tropicalis JGI 4.2/xenTro3" X_tropicalis_Nov_2009 |
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aloraine |
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AddDescription "Xenopus tropicalis JGI 9.1/xenTro9" X_tropicalis_Jul_2016 |
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nfreese |
171 |
AddDescription "Mus musculus (Jun 2020) mouse (GRCm39/mm39)" M_musculus_Jun_2020 |
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aloraine |
66 |
AddDescription "Mus musculus (Dec 2011) mouse (GRCm38/mm10)" M_musculus_Dec_2011 |
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AddDescription "Mus musculus (Jul 2007) mouse (NCBI37/mm9)" M_musculus_Jul_2007 |
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AddDescription "Mus musculus (Feb 2006) mouse (NCBI36/mm8)" M_musculus_Feb_2006 |
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aloraine |
77 |
AddDescription "Mus musculus (Aug 2005) mouse (NCBI35/mm7)" M_musculus_Aug_2005 |
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aloraine |
66 |
AddDescription "Malus domestica (Jun 2017) apple" M_domestica_Borkh_Jun_2017 |
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AddDescription "Musa acuminata DH Pahang (Jan 2016) banana (v2)" M_acuminata_DH_Pahang_Jan_2016 |
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AddDescription "Pan troglodytes (Oct 2010) chimpanzee (CGSC 2.1.3/panTro3)" P_troglodytes_Oct_2010 |
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pkulzer |
200 |
AddDescription "Oryzias latipes (Jul 2017) Japanese rice fish (Medaka) (ASM223467v1)" O_latipes_Jul_2017 |
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aloraine |
66 |
AddDescription "Ovis aries (Feb 2010) sheep (ISGC Ovis_aries_1/oviAri1)" O_aries_Feb_2010 |
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nfreese |
196 |
AddDescription "Ramazzottius varieornatus strain YOKOZUNA-1 (Nov 2016) water bear (Rvar_4.0 assembly)" R_varieornatus_YOKOZUNA-1_Nov_2016 |
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nfreese |
174 |
AddDescription "Rattus norvegicus (Nov 2020) rat (mRatBN7.2/rn7)" R_norvegicus_Nov_2020 |
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aloraine |
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AddDescription "Rattus norvegicus (Jul 2014) rat (RGSC 6.0/rn6)" R_norvegicus_Jul_2014 |
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aloraine |
119 |
AddDescription "Rattus norvegicus (Mar 2012) rat (RGSC 5.0/rn5)" R_norvegicus_Mar_2012 |
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AddDescription "Solanum lycopersicum (Sep 2019) tomato (SL4.0)" S_lycopersicum_Sep_2019 |
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aloraine |
66 |
AddDescription "Solanum lycopersicum (Feb 2017) tomato (SL3.0)" S_lycopersicum_Feb_2017 |
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AddDescription "Solanum lycopersicum (Feb 2014) tomato (SL2.50)" S_lycopersicum_Feb_2014 |
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AddDescription "Solanum lycopersicum (May 2012) tomato (SL2.40)" S_lycopersicum_May_2012 |
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aloraine |
166 |
AddDescription "Solanum lycopersicum (Jun 2022) tomato (SL5.0)" S_lycopersicum_Jun_2022 |
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aloraine |
66 |
AddDescription "S. pombe (May 2012) fission yeast" S_pombe_May_2012 |
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AddDescription "Takifugu rubripes (Oct 2011) Fugu (FUGU5/fr3)" T_rubripes_Oct_2011 |
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AddDescription "Thellungiella parvula (salt cress) v2, May 2012" T_parvula_May_2012 |
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AddDescription "Felis catus (Sep 2011) cat (ICGSC Felis_catus 6.2/felCat5)" F_catus_Sep_2011 |
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aloraine |
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AddDescription "Solanum tuberosum Group Phureja clone DM1-3 (potato) v4.03" S_tuberosum_DM_Jul_2011 |
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aloraine |
66 |
AddDescription "Tribolium castaneum (March 2008) red flour beetle" T_castaneum_Mar_2008 |
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AddDescription "Lotmaria passim, strain SF, Crithidia mellificae strain SF, whole genome shotgun sequencing project" L_passim_Apr_2014 |
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pkulzer |
200 |
AddDescription "Vanessa cardui (Feb 2021) painted lady (ilVanCard2.1)" V_cardui_Feb_2021 |
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aloraine |
66 |
AddDescription "Yarrowia lipolytica CLIB122 (Jul 2004) Assembly GCA_000002525.2" Y_lipolytica_CLIB122_Jul_2004 |
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AddDescription "Yarrowia lipolytica PO1f (May 2014) Assembly GCA_000590845.2" Y_lipolytica_PO1f_May_2014 |
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AddDescription "Yarrowia lipolytica WSH-Z06 (Mar 2014) Assembly GCA_000613155.1" Y_lipolytica_WSH-Z06_Mar_2014 |
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pkulzer |
200 |
AddDescription "Triticum aestivum (IWGSC v1)" T_aestivum_Aug_2018 |
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