Hg38 100-way conservation lastz parameters
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See Also
- Human 100-way Hg38 100-way Genome size statistics
- Human 100-way Hg38 100-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: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
O=400 E=30 |
O=400 E=30 |
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 hg38 matched (chainLink table) |
% of query matched (chainLinkHg38) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Chimp panTro4 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-05-27 | 93.112% | 95.664% |
Gorilla gorGor3 | no | 254 | 3000 | 3000 | hg38.gorGor3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 88.005% | 91.695% |
Orangutan ponAbe2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-09-02 | 89.187% | 89.656% |
Gibbon nomLeu3 | no | 254 | 3000 | 3000 | hg38.nomLeu3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-12 | 86.379% | 90.470% |
Rhesus rheMac3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.66/bin/lastz | 150 | 2000 | 600 | 2 | 2015-04-09 | 80.828% | 88.220% |
Crab-eating macaque macFas5 | no | 254 | 3000 | 3000 | hg38.macFas5.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-14 | 85.675% | 87.749% |
Baboon papAnu2 | no | 254 | 3000 | 3000 | hg38.papAnu2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 84.179% | 84.502% |
Green monkey chlSab2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-07-11 | 84.393% | 88.264% |
Marmoset calJac3 | no | 254 | 3000 | 3000 | hg38.calJac3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 71.709% | 76.757% |
Squirrel monkey saiBol1 | no | 254 | 3000 | 3000 | hg38.saiBol1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 70.565% | 81.466% |
Bushbaby otoGar3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-23 | 53.196% | 64.899% |
Chinese tree shrew tupChi1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 45.256% | 50.350% |
Squirrel speTri2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 48.283% | 61.854% |
Lesser Egyptian jerboa jacJac1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 34.153% | 40.300% |
Prairie vole micOch1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-14 | 31.489% | 43.539% |
Chinese hamster criGri1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-20 | 33.169% | 42.426% |
Golden hamster mesAur1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 30.803% | 43.095% |
Mouse mm10 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-09 | 31.653% | 35.372% |
Rat rn6 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-14 | 31.077% | 34.899% |
Naked mole-rat hetGla2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 46.248% | 58.855% |
Guinea pig cavPor3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 42.371% | 48.000% |
Chinchilla chiLan1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 45.665% | 58.002% |
Brush-tailed rat octDeg1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-24 | 40.238% | 47.651% |
Rabbit oryCun2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 42.911% | 48.360% |
Pika ochPri3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 33.618% | 49.837% |
Pig susScr3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 44.676% | 57.273% |
Alpaca vicPac2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 48.909% | 68.755% |
Bactrian camel camFer1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-24 | 49.095% | 71.268% |
Dolphin turTru2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 49.728% | 61.393% |
Killer whale orcOrc1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 50.709% | 64.364% |
Tibetan antelope panHod1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 45.619% | 52.526% |
Cow bosTau8 | no | 254 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2014-10-16 | 45.975% | 50.440% |
Sheep oviAri3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 2 | 2015-04-27 | 45.352% | 51.787% |
Domestic goat capHir1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 45.257% | 52.668% |
Horse equCab2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-23 | 55.459% | 66.600% |
White rhinoceros cerSim1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-23 | 56.633% | 69.232% |
Cat felCat8 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 51.684% | 58.750% |
Dog canFam3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-10 | 50.395% | 60.861% |
Ferret musFur1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 49.631% | 62.396% |
Panda ailMel1 | no | 50 | 3000 | 3000 | hg38.ailMel1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 48.226% | 61.650% |
Pacific walrus odoRosDiv1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 52.193% | 64.897% |
Weddell seal lepWed1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 51.073% | 65.642% |
Black flying-fox pteAle1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 48.281% | 71.168% |
Megabat pteVam1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 43.924% | 69.545% |
Big brown bat eptFus1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-24 | 39.123% | 62.229% |
David's myotis (bat) myoDav1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 38.713% | 60.286% |
Microbat myoLuc2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-28 | 38.591% | 59.729% |
Hedgehog eriEur2 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 25.488% | 31.297% |
Shrew sorAra2 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-20 | 26.905% | 35.760% |
Star-nosed mole conCri1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 35.911% | 61.017% |
Elephant loxAfr3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 45.214% | 42.303% |
Cape elephant shrew eleEdw1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 26.839% | 24.181% |
Manatee triMan1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 45.346% | 46.939% |
Cape golden mole chrAsi1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-20 | 33.314% | 29.068% |
Tenrec echTel2 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 29.310% | 32.753% |
Aardvark oryAfe1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-23 | 40.563% | 34.102% |
Armadillo dasNov3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-29 | 45.349% | 41.895% |
Opossum monDom5 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.52/bin/lastz | 30 | 2000 | 400 | 1 | 2014-05-29 | 14.370% | 11.996% |
Tasmanian devil sarHar1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-14 | 12.754% | 12.925% |
Wallaby macEug2 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 6.378% | 7.213% |
Platypus ornAna1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 7.769% | 11.784% |
Rock pigeon colLiv1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 4.712% | 10.220% |
Saker falcon falChe1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 4.828% | 9.878% |
Peregrine falcon falPer1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 4.926% | 10.027% |
Collared flycatcher ficAlb2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 4.822% | 10.748% |
White-throated sparrow zonAlb1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 4.494% | 10.570% |
Medium ground finch geoFor1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 4.445% | 10.366% |
Zebra finch taeGut2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 5.893% | 12.356% |
Tibetan ground jay pseHum1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 5.146% | 11.937% |
Budgerigar melUnd1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 4.474% | 9.862% |
Parrot amaVit1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 4.186% | 9.480% |
Scarlet Macaw araMac1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-17 | 3.787% | 9.039% |
Mallard duck anaPla1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 4.268% | 9.679% |
Chicken galGal4 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 4.696% | 10.888% |
Turkey melGal1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-13 | 4.328% | 10.927% |
American alligator allMis1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-14 | 7.561% | 8.665% |
Green seaturtle cheMyd1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 6.296% | 7.960% |
Painted turtle chrPic2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 6.708% | 8.554% |
Chinese softshell turtle pelSin1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-14 | 5.716% | 7.207% |
Spiny softshell turtle apaSpi1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-14 | 4.611% | 6.320% |
Lizard anoCar2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 3.593% | 5.222% |
X. tropicalis xenTro7 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 3.811% | 7.967% |
Coelacanth latCha1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-20 | 2.873% | 3.449% |
Tetraodon tetNig2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 1.743% | 14.323% |
Fugu fr3 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 1.784% | 12.394% |
Yellowbelly pufferfish takFla1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 1.548% | 11.317% |
Nile tilapia oreNil2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 1.868% | 6.241% |
Princess of Burundi neoBri1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 1.767% | 6.840% |
Burton's mouthbreeder hapBur1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 1.783% | 6.861% |
Zebra Mbuna mayZeb1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-07 | 1.805% | 6.780% |
Pundamilia nyererei punNye1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 1.787% | 6.864% |
Medaka oryLat2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 2.002% | 6.853% |
Southern platyfish xipMac1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 1.898% | 7.435% |
Stickleback gasAcu1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 2.080% | 11.956% |
Atlantic cod gadMor1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 1.660% | 6.911% |
Zebrafish danRer10 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-08 | 3.357% | 7.110% |
Mexican tetra (cavefish) astMex1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-18 | 2.225% | 6.365% |
Spotted gar lepOcu1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-19 | 2.511% | 6.634% |
Lamprey petMar2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 1.265% | 3.960% |