Mm10 conservation alignment: Difference between revisions

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(updated data with altered species list)
(updated data)
Line 198: Line 198:
   <TD ALIGN=RIGHT>2009-09-02</TD>
   <TD ALIGN=RIGHT>2009-09-02</TD>
   <TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-22</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-22</TD><TD ALIGN=RIGHT>18.019%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/10467 26]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=triMan1 triMan1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AHIN01 Trichechus<BR>manatus<BR>latirostris]</TD><TD>Manatee</TD>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/10467 26]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=triMan1 triMan1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AHIN01 Trichechus<BR>manatus<BR>latirostris]</TD><TD>Manatee</TD>
Line 205: Line 205:
   <TD ALIGN=RIGHT>2012-03-28</TD>
   <TD ALIGN=RIGHT>2012-03-28</TD>
   <TD ALIGN=RIGHT>2012-03-29</TD>
   <TD ALIGN=RIGHT>2012-03-29</TD>
   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-30</TD><TD ALIGN=RIGHT>26.546%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/megabat/Ptevap1.0/ 27]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=pteVam1 pteVam1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABRP00 Pteropus<BR>vampyrus]</TD><TD>Megabat</TD>
   <TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/megabat/Ptevap1.0/ 27]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=pteVam1 pteVam1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABRP00 Pteropus<BR>vampyrus]</TD><TD>Megabat</TD>
Line 317: Line 317:
   <TD ALIGN=RIGHT>2009-08-14</TD>
   <TD ALIGN=RIGHT>2009-08-14</TD>
   <TD ALIGN=RIGHT>2009-08-14</TD>
   <TD ALIGN=RIGHT>2009-08-14</TD>
   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-30</TD><TD ALIGN=RIGHT>9.584%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/3066 43]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=sarHar1 sarHar1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEFK00 Sarcophilus<BR>harrisii]</TD><TD>Tasmanian&nbsp;devil</TD>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/3066 43]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=sarHar1 sarHar1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEFK00 Sarcophilus<BR>harrisii]</TD><TD>Tasmanian&nbsp;devil</TD>
Line 324: Line 324:
   <TD ALIGN=RIGHT>2012-02-02</TD>
   <TD ALIGN=RIGHT>2012-02-02</TD>
   <TD ALIGN=RIGHT>2012-02-08</TD>
   <TD ALIGN=RIGHT>2012-02-08</TD>
   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-30</TD><TD ALIGN=RIGHT>8.479%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/10765 44]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 melUnd1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGAI01 Melopsittacus<BR>undulatus]</TD><TD>Budgerigar</TD>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/10765 44]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 melUnd1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGAI01 Melopsittacus<BR>undulatus]</TD><TD>Budgerigar</TD>
Line 331: Line 331:
   <TD ALIGN=RIGHT>2012-03-27</TD>
   <TD ALIGN=RIGHT>2012-03-27</TD>
   <TD ALIGN=RIGHT>2012-03-28</TD>
   <TD ALIGN=RIGHT>2012-03-28</TD>
   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-30</TD><TD ALIGN=RIGHT>3.589%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/110 45]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna1 ornAna1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAPN00 Ornithorhynchus<BR>anatinus]</TD><TD>Platypus</TD>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/110 45]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna1 ornAna1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAPN00 Ornithorhynchus<BR>anatinus]</TD><TD>Platypus</TD>
Line 338: Line 338:
   <TD ALIGN=RIGHT>2009-08-15</TD>
   <TD ALIGN=RIGHT>2009-08-15</TD>
   <TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=RIGHT>N/A</TD>
   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-30</TD><TD ALIGN=RIGHT>5.348%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/12107 46]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=chrPic1 chrPic1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AHGY01 Chrysemys<BR>picta<BR>bellii]</TD><TD>Painted&nbsp;turtle</TD>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/12107 46]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=chrPic1 chrPic1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AHGY01 Chrysemys<BR>picta<BR>bellii]</TD><TD>Painted&nbsp;turtle</TD>
Line 345: Line 345:
   <TD ALIGN=RIGHT>2012-03-27</TD>
   <TD ALIGN=RIGHT>2012-03-27</TD>
   <TD ALIGN=RIGHT>2012-03-29</TD>
   <TD ALIGN=RIGHT>2012-03-29</TD>
   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2012-03-30</TD><TD ALIGN=RIGHT>4.731%</TD>
</TR><TR>
</TR><TR>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/111 47]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 galGal4]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AADN00 Gallus<BR>gallus]</TD><TD>Chicken</TD>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/111 47]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 galGal4]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AADN00 Gallus<BR>gallus]</TD><TD>Chicken</TD>

Revision as of 17:19, 2 April 2012

see also

do not edit

This table is automatically generated off-line from the UCSC databases. Please do not edit it.

URL to
assembly
sequence		 UCSC db name/
genome-preview
browser		 Scientific name/
assembly information		 Common
name		 assembly date source
version		 Repeat
Masker		 Window
Masker		 chain
on mm10		 % of mm10
matched
(chainLink table)
01mm10Mus
musculus		Mouse Dec. 2011 (GRCm38/mm10) Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) 2012-02-06 2012-02-07 N/AN/A
02rn4Rattus
norvegicus		Rat Nov. 2004 (Baylor 3.4/rn4) Baylor HGSC v. 3.4 2009-08-15 N/A 2012-03-0854.645%
03speTri2Spermophilus
tridecemlineatus		Squirrel Nov. 2011 (Broad SpeTri2/speTri2) Broad Institute (GCA_000236235.1) 2012-03-14 2012-03-15 2012-03-1634.217%
04micMur1Microcebus
murinus		Mouse lemur Jun. 2003 (Broad/micMur1) Broad Institute micMur1 (NCBI project 19967, ABDC00000000) 2009-09-02 N/A 2012-03-1326.636%
05dipOrd1Dipodomys
ordii		Kangaroo rat Jul. 2008 (Broad/dipOrd1) Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000) 2009-09-02 N/A 2012-03-1619.460%
06saiBol1Saimiri
boliviensis		Squirrel monkey Oct. 2011 (SaiBol1.0/saiBol1) Broad SaiBol1.0 (GCA_000235385.1) 2012-01-07 2012-01-09 2012-03-0932.339%
07hetGla1Heterocephalus
glaber		Naked mole-rat Jul. 2011 (HetGla_1.0/hetGla1) HetGla_1.0 (NCBI project 68323, accession GCA_000230455.1) 2011-12-03 2011-12-06 2012-03-1632.163%
08hg19Homo
sapiens		Human Feb. 2009 (GRCh37/hg19) GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) 2009-08-15 N/A 2012-03-0838.226%
09gorGor3Gorilla
gorilla
gorilla		Gorilla May 2011 (gorGor3.1/gorGor3) Wellcome Trust Sanger Institute May 2011 (NCBI project 31265, GCA_000151905.1) 2011-11-16 N/A 2012-03-0833.987%
10panTro4Pan
troglodytes		Chimp Feb. 2011 (Pan_troglodytes-2.1.4/panTro4) CSAC Pan_troglodytes-2.1.4 (GCA_000001515.4) 2012-01-09 2012-01-09 2012-03-1034.674%
11nomLeu1Nomascus
leucogenys		Gibbon Jan. 2010 (GGSC Nleu1.0/nomLeu1) GGSC (NCBI project 13975, accession GCA_000146795.1) 2011-11-16 N/A 2012-03-0834.132%
12ponAbe2Pongo
pygmaeus
abelii		Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) WUSTL 3.0 2009-08-15 N/A 2012-03-0934.496%
13tarSyr1Tarsius
syrichta		Tarsier Aug. 2008 (Broad/tarSyr1) Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000) 2009-09-02 N/A 2012-03-1224.560%
14rheMac3Macaca
mulatta		Chinese rhesus Oct. 2010 (BGI CR_1.0/rheMac3) Beijing Genomics Institute, Shenzhen (GCA_000230795.1) 2011-12-30 2012-01-03 2012-03-0933.931%
15papHam1Papio
hamadryas		Baboon Nov. 2008 (Baylor 1.0/papHam1) Baylor BCM HGSC Pham_1.0 2009-09-02 N/A 2012-03-1033.577%
16otoGar3Otolemur
garnettii		Bushbaby Mar. 2011 (Broad OtoGar3/otoGar3) Broad Institute (GCA_000181295.3) 2012-03-13 2012-03-14 2012-03-1329.795%
17calJac3Callithrix
jacchus		Marmoset March 2009 (WUGSC 3.2/calJac3) WUSTL 3.2 (GCA_000004665.1) 2010-02-05 N/A 2012-03-0932.450%
18equCab2Equus
caballus		Horse Sep. 2007 (Broad/equCab2) Broad Institute EquCab2 2009-08-14 N/A 2012-03-1634.415%
19cavPor3Cavia
porcellus		Guinea pig Feb. 2008 (Broad/cavPor3) Broad Institute cavPor3 2009-08-15 2009-08-15 2012-03-1728.447%
20vicPac1Vicugna
pacos		Alpaca Jul. 2008 (Broad/vicPac1) Broad Institute vicPac1 2009-09-02 N/A 2012-03-1722.636%
21turTru1Tursiops
truncatus		Dolphin Feb. 2008 (Broad/turTru1) Broad Institute turTru1 (NCBI project 20367, ABRN01000000) 2009-09-02 N/A 2012-03-1728.761%
22tupBel1Tupaia
belangeri		Tree shrew Dec. 2006 (Broad/tupBel1) Broad Institute tupBel1 (NCBI project 13971, AAPY01000000) 2009-09-02 N/A 2012-03-1719.766%
23susScr2Sus
scrofa		Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) SGSC Sscrofa9.2 (NCBI project 10718, GCA_000003025.2) 2010-03-25 N/A 2012-03-1723.248%
24oryCun2Oryctolagus
cuniculus		Rabbit Apr. 2009 (Broad/oryCun2) Broad Institute oryCun2 (NCBI project 12819, AAGW00000000) 2009-09-02 N/A 2012-03-1725.248%
25choHof1Choloepus
hoffmanni		Sloth Jul. 2008 (Broad/choHof1) Broad Institute choHof1 2009-09-02 N/A 2012-03-2218.019%
26triMan1Trichechus
manatus
latirostris		Manatee Oct. 2011 (BROAD v1.0/triMan1) Broad Institute of MIT and Harvard TriManLat1.0 (GCA_000243295.1) 2012-03-28 2012-03-29 2012-03-3026.546%
27pteVam1Pteropus
vampyrus		Megabat Jul. 2008 (Broad/pteVam1) Broad Institute pteVam1 (NCBI project 20325, ABRP01000000) 2009-09-02 N/A 2012-03-2027.345%
28felCat4Felis
catus		Cat Dec. 2008 (NHGRI/GTB V17e/felCat4) NHGRI/Genome Technology Branch (NCBI project 10703, accession ACBE0100000) 2010-05-26 N/A 2012-03-2024.033%
29ailMel1Ailuropoda
melanoleuca		Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) BGI-Shenzhen AilMel 1.0 Dec. 2009 2010-02-03 N/A 2012-03-2030.979%
30canFam3Canis
lupus
familiaris		Dog Sep. 2011 (Broad CanFam3.1/canFam3) Broad CanFam3.1 (GCA_000002285.2) 2012-01-05 2012-01-06 2012-03-2029.144%
31loxAfr3Loxodonta
africana		Elephant Jul. 2009 (Broad/loxAfr3) Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000) 2009-09-02 N/A 2012-03-2025.823%
32dasNov2Dasypus
novemcinctus		Armadillo Jul. 2008 (Broad/dasNov2) Broad Institute dasNov2 (NCBI project 12594, AAGV020000000) 2009-09-02 N/A 2012-03-2317.004%
33myoLuc2Myotis
lucifugus		Microbat Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) Broad Institute (NCBI Project ID: 16951, Accession: GCA_000147115.1) 2010-11-03 N/A 2012-03-2224.363%
34bosTau7Bos
taurus		Cow Oct. 2011 (Btau_4.6.1/bosTau7) Btau_4.6.1 (NCBI project 12555, accession GCA_000003205.4) 2012-01-04 2012-01-06 2012-03-2226.255%
35oviAri1Ovis
aries		Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) ISGC (NCBI project 10709, accession GCA_000005525.1) 2010-04-14 N/A 2012-03-2215.341%
36ochPri2Ochotona
princeps		Pika Jul. 2008 (Broad/ochPri2) Broad Institute ochPri2 2009-09-02 N/A 2012-03-2414.542%
37proCap1Procavia
capensis		Rock hyrax Jul. 2008 (Broad/proCap1) Broad Institute proCap1 (NCBI project 13972, ABRQ01000000) 2009-09-02 N/A 2012-03-2315.147%
38eriEur1Erinaceus
europaeus		Hedgehog June 2006 (Broad/eriEur1) Broad Institute eriEur1 (Draft_v1, NCBI project 12575) 2009-09-02 2009-09-02 2012-03-249.856%
39echTel1Echinops
telfairi		Tenrec July 2005 (Broad/echTel1) Broad July 2005 2009-09-02 N/A 2012-03-2410.947%
40sorAra1Sorex
araneus		Shrew June 2006 (Broad/sorAra1) Broad Institute sorAra1 (Draft_v2) 2009-09-02 2009-09-02 2012-03-249.382%
41macEug2Macropus
eugenii		Wallaby Sep. 2009 (TWGS Meug_1.1/macEug2) TWGS (NCBI Project ID: 12586, Accession: GCA_000004035.1) 2010-11-05 2011-12-02 2012-03-244.353%
42monDom5Monodelphis
domestica		Opossum Oct. 2006 (Broad/monDom5) Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000) 2009-08-14 2009-08-14 2012-03-309.584%
43sarHar1Sarcophilus
harrisii		Tasmanian devil Feb. 2011 (WTSI Devil_ref v7.0/sarHar1) Wellcome Trust Sanger Institute Devil_ref v7.0 (GCA_000189315.1) 2012-02-02 2012-02-08 2012-03-308.479%
44melUnd1Melopsittacus
undulatus		Budgerigar Sep. 2011 (WUSTL v6.3/melUnd1) WUSTL Melopsittacus undulatus Budgerigar Version 6.3 (GCA_000238935.1) 2012-03-27 2012-03-28 2012-03-303.589%
45ornAna1Ornithorhynchus
anatinus		Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) WUSTL version 5.0.1 2009-08-15 N/A 2012-03-305.348%
46chrPic1Chrysemys
picta
bellii		Painted turtle Dec. 2011 (v3.0.1/chrPic1) International Painted Turtle Genome Sequencing Consortium (GCA_000241765.1) 2012-03-27 2012-03-29 2012-03-304.731%
47galGal4Gallus
gallus		Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) ICGSC Gallus_gallus-4.0 (GCA_000002315.2) 2012-01-04 2012-01-04 N/AN/A
48taeGut1Taeniopygia
guttata		Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) Washington University taeGut1 2009-08-14 2009-08-14 N/AN/A
49anoCar2Anolis
carolinensis		Lizard May 2010 (Broad AnoCar2.0/anoCar2) Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1) 2011-04-12 2011-04-13 N/AN/A
50melGal1Meleagris
gallopavo		Turkey Dec. 2009 (TGC Turkey_2.01/melGal1) TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1) 2010-11-04 N/A N/AN/A
51xenTro3Xenopus
tropicalis		X. tropicalis Nov. 2009 (JGI 4.2/xenTro3) US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1) 2011-09-08 2011-09-08 N/AN/A
52latCha1Latimeria
chalumnae		Coelacanth Aug. 2011 (LatCha1/latCha1) Broad LatCha1 (GCA_000225785.1) 2012-01-11 2012-01-12 N/AN/A
53gadMor1Gadus
morhua		Atlantic cod May. 2010 (Genofisk GadMor_May2010/gadMor1) Genofisk GadMor_May2010 (GCA_000231765.1) 2011-12-29 2012-01-04 N/AN/A
54oreNil1Oreochromis
niloticus		Nile tilapia Jan. 2011 (Nile tilapia/oreNil1) Broad Institute of MIT and Harvard Orenil1.0 (GCA_000188235.1) 2011-11-30 2011-11-30 N/AN/A
55gasAcu1Gasterosteus
aculeatus		Stickleback Feb. 2006 (Broad/gasAcu1) Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000) 2009-08-15 2009-08-15 N/AN/A
56fr3Takifugu
rubripes		Fugu Oct. 2011 (FUGU5/fr3) Fugu Genome Sequencing Consortium - FUGU5 (NCBI project 1434, GCA_000180615.2) 2011-11-16 2011-11-17 N/AN/A
57tetNig2Tetraodon
nigroviridis		Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000) 2010-06-07 2009-09-02 N/AN/A
58danRer7Danio
rerio		Zebrafish Jul. 2010 (Zv9/danRer7) Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2) 2010-12-03 N/A N/AN/A
59oryLat2Oryzias
latipes		Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000) 2009-08-15 2009-08-15 N/AN/A
60petMar1Petromyzon
marinus		Lamprey Mar. 2007 (WUGSC 3.0/petMar1) WUSTL v.3.0 (March 2007) N/A 2009-08-14 N/AN/A
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