Hg18 44way alignment
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see also
- Genome size statistics
- Hg18 44way blastz parameters
- Hg19 Genome size statistics
- Hg19 conservation alignment
- Hg19 conservation lastz parameters
sanity
The table below needs to be examined for sanity. The "chain on hg18" date should be after the masking date. Some of these existing pair-wise alignments need to be re-done since the genomes have been properly repeat masked. When all the chain tables exist, that is a good sign that the multiple alignment can be done.
do not edit
This table is automatically generated off-line from the UCSC databases. Please do not edit it.
| UCSC db name |
Scientific name |
Common name |
assembly date |
source version |
Repeat Masker |
Window Masker |
chain on hg18 |
% of hg18 matched (chainLink table) |
|
|---|---|---|---|---|---|---|---|---|---|
| 01 | hg18 | Homo sapiens | Human | Mar. 2006 | NCBI Build 36.1 | 2005-12-09 | 2006-12-05 | N/A | N/A |
| 02 | panTro2 | Pan troglodytes | Chimp | Mar. 2006 | Washington University Build 2 Version 1 | 2006-03-24 | N/A | 2006-07-15 | 94.888% |
| 03 | gorGor1 | Gorilla gorilla gorilla | Gorilla | Oct. 2008 | Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000) | 2008-11-03 | N/A | 2008-11-05 | 61.731% |
| 04 | ponAbe2 | Pongo pygmaeus abelii | Orangutan | July 2007 | WUSTL 3.0 | 2007-09-15 | N/A | 2007-10-03 | 92.892% |
| 05 | rheMac2 | Macaca mulatta | Rhesus | Jan. 2006 | Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4 | 2006-01-30 | N/A | 2006-03-17 | 85.552% |
| 06 | calJac1 | Callithrix jacchus | Marmoset | June 2007 | WUSTL 2.0.2 | 2007-08-23 | N/A | 2007-11-13 | 78.351% |
| 07 | tarSyr1 | Tarsier syrichta | Tarsier | Aug. 2008 | Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000) | 2008-10-15 | N/A | 2008-10-27 | 47.999% |
| 08 | otoGar1 | Otolemur garnettii | Bushbaby | Dec. 2006 | Broad version 1 (NCBI project 16955, AAQR00000000) | 2006-12-20 | N/A | 2007-02-27 | 44.638% |
| 09 | micMur1 | Microcebus murinus | Mouse lemur | Jun. 2003 | Broad Institute micMur1 (NCBI project 19967, ABDC00000000) | 2008-08-03 | N/A | 2008-08-04 | 46.445% |
| 10 | tupBel1 | Tupaia belangeri | TreeShrew | Dec. 2006 | Broad Institute tupBel1 (NCBI project 13971, AAPY01000000) | 2008-10-15 | N/A | 2006-12-20 | 37.348% |
| 11 | mm9 | Mus musculus | Mouse | July 2007 | NCBI Build 37 | 2007-07-20 | N/A | 2007-08-14 | 35.201% |
| 12 | rn4 | Rattus norvegicus | Rat | Nov. 2004 | Baylor HGSC v. 3.4 | 2006-03-16 | N/A | 2006-02-17 | 32.893% |
| 13 | dipOrd1 | Dipodomys ordii | Kangaroo rat | Jul. 2008 | Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000) | 2008-10-15 | N/A | 2008-10-22 | 27.282% |
| 14 | cavPor3 | Cavia porcellus | Guinea Pig | Feb. 2008 | Broad Institute cavPor3 | 2008-04-05 | 2008-04-08 | 2008-04-11 | 43.971% |
| 15 | speTri1 | Spermophilus tridecemlineatus | Squirrel | Feb. 2008 | Broad Institute speTri1 | 2008-08-03 | N/A | 2008-08-05 | 35.828% |
| 16 | oryCun1 | Oryctolagus cuniculus | Rabbit | May 2005 | Broad May 2005 | 2005-05-22 | N/A | 2007-04-17 | 34.015% |
| 17 | ochPri2 | Ochotona princeps | Pika | Jul. 2008 | Broad Institute ochPri2 | 2008-07-28 | N/A | 2008-07-30 | 27.974% |
| 18 | sorAra1 | Sorex araneus | Shrew | June 2006 | Broad Institute sorAra1 (Draft_v2) | 2008-10-20 | 2008-10-21 | 2007-03-10 | 20.056% |
| 19 | eriEur1 | Erinaceus europaeus | hedgehog | June 2006 | Broad Institute eriEur1 (Draft_v1) | 2008-10-21 | 2008-10-21 | 2007-03-11 | 19.622% |
| 20 | felCat3 | Felis catus | Cat | Mar. 2006 | Broad Release 3 | 2006-10-16 | N/A | 2006-11-10 | 35.888% |
| 21 | canFam2 | Canis lupus familiaris | Dog | May 2005 | Broad Institute v. 2.0 | 2005-07-10 | N/A | 2005-12-29 | 52.915% |
| 22 | equCab2 | Equus caballus | Horse | Sep. 2007 | Broad Institute EquCab2 | 2008-04-03 | N/A | 2008-04-11 | 57.162% |
| 23 | pteVam1 | Pteropus vampyrus | Megabat | Jul. 2008 | Broad Institute pteVam1 (NCBI project 20325, ABRP01000000) | 2008-10-15 | N/A | 2008-10-22 | 45.502% |
| 24 | myoLuc1 | Myotis lucifugus | Microbat | Mar. 2006 | Broad Institute myoLuc1 | 2008-07-29 | N/A | 2008-08-02 | 33.044% |
| 25 | turTru1 | Tursiops truncatus | Dolphin | Feb. 2008 | Broad Institute turTru1 (NCBI project 20367, ABRN01000000) | 2008-10-15 | N/A | 2008-10-22 | 48.537% |
| 26 | bosTau4 | Bos taurus | Cow | Oct. 2007 | Baylor Release 4.0 | 2008-03-10 | N/A | 2008-03-11 | 46.689% |
| 27 | vicPac1 | Vicugna pacos | Alpaca | Jul. 2008 | Broad Institute vicPac1 | 2008-10-17 | N/A | 2008-10-28 | 39.531% |
| 28 | dasNov2 | Dasypus novemcinctus | Armadillo | Jul. 2008 | Broad Institute dasNov2 (NCBI project 12594, AAGV020000000) | 2008-10-07 | N/A | 2008-10-27 | 33.663% |
| 29 | choHof1 | Choloepus hoffmanni | Sloth | Jul. 2008 | Broad Institute choHof1 | 2008-10-16 | N/A | 2008-10-24 | 34.463% |
| 30 | echTel1 | Echinops telfairi | Tenrec | July 2005 | Broad July 2005 | 2005-08-04 | N/A | 2007-04-17 | 23.645% |
| 31 | loxAfr2 | Loxodonta africana | Elephant | Jul. 2008 | Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000) | 2008-10-07 | N/A | 2008-10-27 | 35.204% |
| 32 | proCap1 | Procavia capensis | Rock hyrax | Jul. 2008 | Broad Institute proCap1 (NCBI project 13972, ABRQ01000000) | 2008-10-16 | N/A | 2008-10-24 | 30.935% |
| 33 | monDom4 | Monodelphis domestica | Opossum | Jan. 2006 | Broad Inst. monDom4 Jan06 | 2006-02-10 | N/A | 2006-02-13 | 12.385% |
| 34 | ornAna1 | Ornithorhynchus anatinus | Platypus | Mar. 2007 | WUSTL version 5.0.1 | 2007-07-20 | N/A | 2007-04-04 | 7.870% |
| 35 | galGal3 | Gallus gallus | Chicken | May 2006 | Chicken Genome Sequencing Consortium May 2006 release | 2006-05-18 | 2007-01-02 | 2006-05-23 | 3.589% |
| 36 | taeGut1 | Taeniopygia guttata | Zebra finch | Jul. 2008 | Washington University taeGut1 | N/A | 2008-08-05 | 2008-09-09 | 3.503% |
| 37 | anoCar1 | Anolis carolinensis | Lizard | Feb. 2007 | Broad Institute AnoCar (1.0) | 2007-03-07 | 2007-02-16 | 2007-02-18 | 4.774% |
| 38 | xenTro2 | Xenopus tropicalis | X. tropicalis | Aug. 2005 | JGI v4.1 | 2006-04-17 | 2007-02-20 | 2006-04-20 | 2.623% |
| 39 | danRer5 | Danio rerio | Zebrafish | July 2007 | Wellcome Trust Sanger Institute, Zv7 assembly | 2007-09-05 | N/A | 2007-10-17 | 2.565% |
| 40 | tetNig1 | Tetraodon nigroviridis | Tetraodon | Feb. 2004 | Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000) | 2004-08-17 | 2006-12-05 | 2006-01-07 | 2.001% |
| 41 | fr2 | Takifugu rubripes | Fugu | Oct. 2004 | JGI V4.0 | 2007-03-07 | 2007-01-22 | 2007-01-24 | 1.766% |
| 42 | gasAcu1 | Gasterosteus aculeatus | Stickleback | Feb. 2006 | Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000) | 2006-10-17 | 2006-12-05 | 2007-02-08 | 1.923% |
| 43 | oryLat2 | Oryzias latipes | Medaka | Oct. 2005 | NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000) | 2008-08-12 | 2008-08-14 | 2008-08-19 | 1.829% |
| 44 | petMar1 | Petromyzon marinus | Lamprey | Mar. 2007 | WUSTL v.3.0 (March 2007) | N/A | 2008-01-28 | 2008-01-29 | 1.251% |
