GalGal6 77-way conservation lastz parameters

See Also

• Chicken 77-way GalGal6 77-way Genome size statistics
• Chicken 77-way GalGal6 77-way conservation alignment
• all other UCSC Multiple Alignments

The default scoring matrix is:		The HoxD55 scoring matrix is:		The human-chimp.v2 scoring matrix is:
A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 O=400 E=30		A C G T A 91 -90 -25 -100 C -90 100 -100 -25 G -25 -100 100 -90 T -100 -25 -90 91 O=400 E=30		A C G T A 90 -330 -236 -356 C -330 100 -318 -236 G -236 -318 100 -330 T -356 -236 -330 90 O=600 E=150

do not edit, automatically generated table

query	abridged repeats(no)	M(0)	K(3000)	L(3000)	Q	Y(9400)	program run	E(30)	H(0)	O(400)	T(1)	chain table date	% of galGal6 matched (chainLink table)	% of query matched (chainLinkGalGal6)
Turkey melGal5	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	94.495%	92.491%
Japanese quail cotJap2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-26	90.071%	96.366%
Golden eagle aquChr2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	87.687%	78.786%
Bald eagle halLeu1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	86.923%	78.856%
Crested ibis nipNip1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	86.903%	78.539%
Emperor penguin aptFor1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	86.834%	77.790%
Peregrine falcon falPer1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	86.500%	79.824%
Saker falcon falChe1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	86.342%	79.770%
Killdeer chaVoc2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	86.267%	78.316%
Adelie penguin pygAde1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	85.892%	77.561%
Little egret egrGar1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	85.589%	77.936%
Mallard duck anaPla1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	85.509%	83.814%
Dalmatian pelican pelCri1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	85.344%	77.377%
Northern fulmar fulGla1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	85.332%	78.234%
Red-legged seriema carCri1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	85.094%	78.856%
Cuckoo roller lepDis1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	85.021%	78.924%
White-tailed eagle halAlb1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	84.997%	78.352%
American flamingo phoRub1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	84.793%	78.057%
Red-throated loon gavSte1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	84.717%	78.429%
Crowned crain balPav1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	84.687%	78.619%
Hoatzin opiHoa1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	84.579%	78.069%
White-tailed tropicbird phaLep1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	84.519%	78.068%
Red crested turaco tauEry1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	84.485%	77.102%
Great cormorant phaCar1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	84.182%	78.405%
Barn owl tytAlb1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	84.122%	79.540%
Chuck-will's-widow capCar1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	83.573%	77.901%
Common cuckoo cucCan1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	83.150%	78.921%
Rock pigeon colLiv1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	83.073%	79.480%
Houbara bustard chlUnd1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	83.041%	78.986%
Brown roatelo mesUni1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	82.649%	79.029%
Yellow-throated sandgrouse pteGut1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	82.523%	79.317%
Sunbittern eurHel1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	82.426%	78.684%
Ostrich strCam1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	82.389%	74.035%
Budgerigar melUnd1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	81.694%	78.351%
Northern carmine bee-eater merNub1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	81.018%	79.394%
Bar tailed trogon apaVit1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	81.010%	79.322%
Speckled mousebird colStr1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	80.987%	78.528%
American crow corBra1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	80.978%	80.022%
Rhinoceros hornbill bucRhi1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	80.812%	78.727%
Tibetan ground jay pseHum1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	80.622%	80.898%
Parrot amaVit1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	80.577%	77.539%
Hooded crow corCor1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	80.574%	80.730%
Canary serCan1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	79.903%	74.870%
Anna's hummingbird calAnn1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	79.733%	79.955%
Rifleman acaChl1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	79.489%	79.366%
Collared flycatcher ficAlb2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	79.354%	75.638%
Medium ground finch geoFor1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-19	79.299%	79.439%
White-throated sparrow zonAlb1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-16	78.645%	79.381%
Scarlet macaw araMac1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	76.180%	77.878%
Downy woodpecker picPub1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	74.258%	69.321%
Zebra finch taeGut2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	73.989%	73.358%
White throated tinamou tinGut2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	73.577%	75.473%
Painted turtle chrPic2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	51.724%	33.105%
Green seaturtle cheMyd1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-18	51.019%	33.557%
Chinese alligator allSin1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	46.056%	23.607%
American alligator allMis1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	44.801%	24.041%
Chinese softshell turtle pelSin1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	41.985%	25.358%
Spiny softshell turtle apaSpi1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	38.375%	25.398%
Burmese python pytBiv1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	15.806%	11.426%
Lizard anoCar2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	14.527%	8.505%
Garter snake thaSir1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	11.754%	9.922%
X. tropicalis xenTro9	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	8.102%	6.961%
African clawed frog xenLae2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	7.927%	5.220%
Tibetan frog nanPar1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	7.564%	4.273%
Human hg38	no	50	2200	6000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-12	11.459%	4.977%
Mouse mm10	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-12	8.388%	3.813%
Zebrafish danRer11	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	6.352%	5.913%
Japanese eel angJap1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	5.408%	7.077%
Nile tilapia oreNil3	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	4.925%	6.828%
Stickleback gasAcu1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	4.623%	12.925%
Medaka oryLat2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	4.565%	7.741%
Zebra mbuna mayZeb1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	4.539%	7.874%
Tetraodon tetNig2	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-21	4.148%	15.780%
Fugu fr3	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	4.007%	13.581%
Lamprey petMar3	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-17	3.658%	4.837%
Arctic lamprey letCam1	no	254	2200	4000	HoxD55.q	3400	lastz-distrib-1.04.00/bin/lastz	30	2000	400	1	2018-10-20	3.335%	4.611%