Hg18 44way alignment

see also

• Genome size statistics
• Hg18 44way blastz 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%