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Genomic alignments

Pairwise whole genome alignments can be used to determine conservation or differences between pairs of species, or to match up regions between species, so as to study the same genomic region in multiple species.

LastZ and its predecessor BlastZ are used to align the genome sequences at the DNA level.

Genomes are compared to one another, for comparison between species, and to themselves, to identify paralogous regions. In self-alignment analyses, the trivial alignments (i.e. regions against themselves) are removed, such that only the paralogous regions remain.

The actual whole-genome alignments are the results of post-processing the raw LastZ (or BlastZ) results. In the first step, original blocks are chained according to their location in both genomes. The netting process chooses for the reference species the best sub-chain in each region.

These alignments are used to calculate synteny and for scoring orthologue quality.

Alignments available

Toggle All Toggle All or click a species names to expand/collapse its alignment list

Human (Homo sapiens) 64 alignments   17 syntenies
Human (Homo sapiens) [self-alignment]
  LastZ | example stats
Chimpanzee (Pan troglodytes)
  LastZ | example stats
  Synteny | example stats
Gorilla (Gorilla gorilla gorilla)
  LastZ | example stats
  Synteny | example stats
Orangutan (Pongo abelii)
  LastZ | example stats
  Synteny | example stats
Gibbon (Nomascus leucogenys)
  LastZ | example stats
Macaque (Macaca mulatta)
  LastZ | example stats
  Synteny | example stats
Marmoset (Callithrix jacchus)
  LastZ | example stats
  Synteny | example stats
Tarsier (Tarsius syrichta)
  BlastZ | example stats
Bushbaby (Otolemur garnettii)
  LastZ | example stats
Mouse Lemur (Microcebus murinus)
  BlastZ | example stats
Tree Shrew (Tupaia belangeri)
  BlastZ | example stats
Guinea Pig (Cavia porcellus)
  BlastZ | example stats
Kangaroo rat (Dipodomys ordii)
  BlastZ | example stats
Squirrel (Ictidomys tridecemlineatus)
  LastZ | example stats
Mouse (Mus musculus)
  LastZ | example stats
  Synteny | example stats
Rat (Rattus norvegicus)
  LastZ | example stats
  Synteny | example stats
Pika (Ochotona princeps)
  BlastZ | example stats
Rabbit (Oryctolagus cuniculus)
  LastZ | example stats
  Synteny | example stats
Lesser hedgehog tenrec (Echinops telfairi)
  BlastZ | example stats
Elephant (Loxodonta africana)
  BlastZ | example stats
Hyrax (Procavia capensis)
  BlastZ | example stats
Horse (Equus caballus)
  BlastZ | example stats
  Synteny | example stats
Megabat (Pteropus vampyrus)
  BlastZ | example stats
Microbat (Myotis lucifugus)
  LastZ | example stats
Panda (Ailuropoda melanoleuca)
  LastZ | example stats
Ferret (Mustela putorius furo)
  LastZ | example stats
Dog (Canis lupus familiaris)
  LastZ | example stats
  Synteny | example stats
Cat (Felis catus)
  LastZ | example stats
  Synteny | example stats
Hedgehog (Erinaceus europaeus)
  BlastZ | example stats
Shrew (Sorex araneus)
  BlastZ | example stats
Alpaca (Vicugna pacos)
  BlastZ | example stats
Pig (Sus scrofa)
  LastZ | example stats
  Synteny | example stats
Sheep (Ovis aries)
  LastZ | example stats
  Synteny | example stats
Cow (Bos taurus)
  LastZ | example stats
  Synteny | example stats
Dolphin (Tursiops truncatus)
  BlastZ | example stats
Armadillo (Dasypus novemcinctus)
  LastZ | example stats
Sloth (Choloepus hoffmanni)
  BlastZ | example stats
Tasmanian devil (Sarcophilus harrisii)
  LastZ | example stats
Wallaby (Macropus eugenii)
  BlastZ | example stats
Opossum (Monodelphis domestica)
  BlastZ | example stats
  Synteny | example stats
Platypus (Ornithorhynchus anatinus)
  BlastZ | example stats
  Synteny | example stats
Anole lizard (Anolis carolinensis)
  Translated Blat | example stats
Flycatcher (Ficedula albicollis)
  LastZ | example stats
Zebra Finch (Taeniopygia guttata)
  Translated Blat | example stats
Duck (Anas platyrhynchos)
  LastZ | example stats
Turkey (Meleagris gallopavo)
  Translated Blat | example stats
Chicken (Gallus gallus)
  Translated Blat | example stats
  LastZ | example stats
  Synteny | example stats
Chinese softshell turtle (Pelodiscus sinensis)
  LastZ | example stats
Xenopus (Xenopus tropicalis)
  Translated Blat | example stats
Coelacanth (Latimeria chalumnae)
  Translated Blat | example stats
Spotted gar (Lepisosteus oculatus)
  LastZ | example stats
Cod (Gadus morhua)
  Translated Blat | example stats
Tetraodon (Tetraodon nigroviridis)
  Translated Blat | example stats
Fugu (Takifugu rubripes)
  Translated Blat | example stats
Tilapia (Oreochromis niloticus)
  Translated Blat | example stats
Medaka (Oryzias latipes)
  Translated Blat | example stats
Platyfish (Xiphophorus maculatus)
  Translated Blat | example stats
Stickleback (Gasterosteus aculeatus)
  Translated Blat | example stats
Cave fish (Astyanax mexicanus)
  LastZ | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Lamprey (Petromyzon marinus)
  Translated Blat | example stats
C.intestinalis (Ciona intestinalis)
  Translated Blat | example stats
C.savignyi (Ciona savignyi)
  Translated Blat | example stats
Chimpanzee (Pan troglodytes) 1 alignment   1 synteny
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Gorilla (Gorilla gorilla gorilla) 1 alignment   1 synteny
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Orangutan (Pongo abelii) 1 alignment   1 synteny
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Gibbon (Nomascus leucogenys) 1 alignment    
Human (Homo sapiens)
  LastZ | example stats
Macaque (Macaca mulatta) 1 alignment   1 synteny
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Marmoset (Callithrix jacchus) 1 alignment   1 synteny
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Tarsier (Tarsius syrichta) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Bushbaby (Otolemur garnettii) 1 alignment    
Human (Homo sapiens)
  LastZ | example stats
Mouse Lemur (Microcebus murinus) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Tree Shrew (Tupaia belangeri) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Guinea Pig (Cavia porcellus) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Kangaroo rat (Dipodomys ordii) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Squirrel (Ictidomys tridecemlineatus) 1 alignment    
Human (Homo sapiens)
  LastZ | example stats
Mouse (Mus musculus) 11 alignments   7 syntenies
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Rat (Rattus norvegicus)
  LastZ | example stats
  Synteny | example stats
Ferret (Mustela putorius furo)
  LastZ | example stats
Dog (Canis lupus familiaris)
  LastZ | example stats
  Synteny | example stats
Pig (Sus scrofa)
  LastZ | example stats
  Synteny | example stats
Cow (Bos taurus)
  LastZ | example stats
  Synteny | example stats
Platypus (Ornithorhynchus anatinus)
  LastZ | example stats
  Synteny | example stats
Chicken (Gallus gallus)
  LastZ | example stats
  Synteny | example stats
Xenopus (Xenopus tropicalis)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
C.intestinalis (Ciona intestinalis)
  Translated Blat | example stats
Rat (Rattus norvegicus) 5 alignments   2 syntenies
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Mouse (Mus musculus)
  LastZ | example stats
  Synteny | example stats
Xenopus (Xenopus tropicalis)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
C.intestinalis (Ciona intestinalis)
  Translated Blat | example stats
Pika (Ochotona princeps) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Rabbit (Oryctolagus cuniculus) 1 alignment   1 synteny
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Lesser hedgehog tenrec (Echinops telfairi) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Elephant (Loxodonta africana) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Hyrax (Procavia capensis) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Horse (Equus caballus) 2 alignments   2 syntenies
Human (Homo sapiens)
  BlastZ | example stats
  Synteny | example stats
Dog (Canis lupus familiaris)
  LastZ | example stats
  Synteny | example stats
Megabat (Pteropus vampyrus) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Microbat (Myotis lucifugus) 1 alignment    
Human (Homo sapiens)
  LastZ | example stats
Panda (Ailuropoda melanoleuca) 2 alignments    
Human (Homo sapiens)
  LastZ | example stats
Dog (Canis lupus familiaris)
  LastZ | example stats
Ferret (Mustela putorius furo) 2 alignments    
Human (Homo sapiens)
  LastZ | example stats
Mouse (Mus musculus)
  LastZ | example stats
Dog (Canis lupus familiaris) 4 alignments   3 syntenies
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Mouse (Mus musculus)
  LastZ | example stats
  Synteny | example stats
Horse (Equus caballus)
  LastZ | example stats
  Synteny | example stats
Panda (Ailuropoda melanoleuca)
  LastZ | example stats
Cat (Felis catus) 1 alignment   1 synteny
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Hedgehog (Erinaceus europaeus) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Shrew (Sorex araneus) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Alpaca (Vicugna pacos) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Pig (Sus scrofa) 4 alignments   4 syntenies
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Mouse (Mus musculus)
  LastZ | example stats
  Synteny | example stats
Sheep (Ovis aries)
  LastZ | example stats
  Synteny | example stats
Cow (Bos taurus)
  LastZ | example stats
  Synteny | example stats
Sheep (Ovis aries) 3 alignments   3 syntenies
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Pig (Sus scrofa)
  LastZ | example stats
  Synteny | example stats
Cow (Bos taurus)
  LastZ | example stats
  Synteny | example stats
Cow (Bos taurus) 4 alignments   4 syntenies
Human (Homo sapiens)
  LastZ | example stats
  Synteny | example stats
Mouse (Mus musculus)
  LastZ | example stats
  Synteny | example stats
Pig (Sus scrofa)
  LastZ | example stats
  Synteny | example stats
Sheep (Ovis aries)
  LastZ | example stats
  Synteny | example stats
Dolphin (Tursiops truncatus) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Armadillo (Dasypus novemcinctus) 1 alignment    
Human (Homo sapiens)
  LastZ | example stats
Sloth (Choloepus hoffmanni) 1 alignment    
Human (Homo sapiens)
  BlastZ | example stats
Tasmanian devil (Sarcophilus harrisii) 2 alignments    
Human (Homo sapiens)
  LastZ | example stats
Opossum (Monodelphis domestica)
  LastZ | example stats
Wallaby (Macropus eugenii) 2 alignments    
Human (Homo sapiens)
  BlastZ | example stats
Opossum (Monodelphis domestica)
  BlastZ | example stats
Opossum (Monodelphis domestica) 3 alignments   1 synteny
Human (Homo sapiens)
  BlastZ | example stats
  Synteny | example stats
Tasmanian devil (Sarcophilus harrisii)
  LastZ | example stats
Wallaby (Macropus eugenii)
  BlastZ | example stats
Platypus (Ornithorhynchus anatinus) 2 alignments   2 syntenies
Human (Homo sapiens)
  BlastZ | example stats
  Synteny | example stats
Mouse (Mus musculus)
  LastZ | example stats
  Synteny | example stats
Anole lizard (Anolis carolinensis) 3 alignments   1 synteny
Human (Homo sapiens)
  Translated Blat | example stats
Chicken (Gallus gallus)
  LastZ | example stats
  Synteny | example stats
Chinese softshell turtle (Pelodiscus sinensis)
  LastZ | example stats
Flycatcher (Ficedula albicollis) 2 alignments    
Human (Homo sapiens)
  LastZ | example stats
Chicken (Gallus gallus)
  LastZ | example stats
Zebra Finch (Taeniopygia guttata) 2 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Chicken (Gallus gallus)
  LastZ | example stats
Duck (Anas platyrhynchos) 2 alignments    
Human (Homo sapiens)
  LastZ | example stats
Chicken (Gallus gallus)
  LastZ | example stats
Turkey (Meleagris gallopavo) 2 alignments   1 synteny
Human (Homo sapiens)
  Translated Blat | example stats
Chicken (Gallus gallus)
  LastZ | example stats
  Synteny | example stats
Chicken (Gallus gallus) 12 alignments   4 syntenies
Human (Homo sapiens)
  Translated Blat | example stats
  LastZ | example stats
  Synteny | example stats
Mouse (Mus musculus)
  LastZ | example stats
  Synteny | example stats
Anole lizard (Anolis carolinensis)
  LastZ | example stats
  Synteny | example stats
Flycatcher (Ficedula albicollis)
  LastZ | example stats
Zebra Finch (Taeniopygia guttata)
  LastZ | example stats
Duck (Anas platyrhynchos)
  LastZ | example stats
Turkey (Meleagris gallopavo)
  LastZ | example stats
  Synteny | example stats
Chinese softshell turtle (Pelodiscus sinensis)
  LastZ | example stats
Xenopus (Xenopus tropicalis)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
C.savignyi (Ciona savignyi)
  Translated Blat | example stats
Chinese softshell turtle (Pelodiscus sinensis) 3 alignments    
Human (Homo sapiens)
  LastZ | example stats
Anole lizard (Anolis carolinensis)
  LastZ | example stats
Chicken (Gallus gallus)
  LastZ | example stats
Xenopus (Xenopus tropicalis) 7 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Mouse (Mus musculus)
  Translated Blat | example stats
Rat (Rattus norvegicus)
  Translated Blat | example stats
Chicken (Gallus gallus)
  Translated Blat | example stats
Coelacanth (Latimeria chalumnae)
  Translated Blat | example stats
Tetraodon (Tetraodon nigroviridis)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Coelacanth (Latimeria chalumnae) 4 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Xenopus (Xenopus tropicalis)
  Translated Blat | example stats
Stickleback (Gasterosteus aculeatus)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Spotted gar (Lepisosteus oculatus) 3 alignments    
Human (Homo sapiens)
  LastZ | example stats
Medaka (Oryzias latipes)
  LastZ | example stats
Zebrafish (Danio rerio)
  LastZ | example stats
Cod (Gadus morhua) 4 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Medaka (Oryzias latipes)
  LastZ | example stats
Stickleback (Gasterosteus aculeatus)
  LastZ | example stats
Zebrafish (Danio rerio)
  LastZ | example stats
Tetraodon (Tetraodon nigroviridis) 3 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Xenopus (Xenopus tropicalis)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Fugu (Takifugu rubripes) 2 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Tilapia (Oreochromis niloticus) 3 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Medaka (Oryzias latipes)
  LastZ | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Medaka (Oryzias latipes) 9 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Spotted gar (Lepisosteus oculatus)
  LastZ | example stats
Cod (Gadus morhua)
  LastZ | example stats
Tilapia (Oreochromis niloticus)
  LastZ | example stats
Platyfish (Xiphophorus maculatus)
  Translated Blat | example stats
  LastZ | example stats
Stickleback (Gasterosteus aculeatus)
  BlastZ | example stats
Cave fish (Astyanax mexicanus)
  LastZ | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Platyfish (Xiphophorus maculatus) 4 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Medaka (Oryzias latipes)
  Translated Blat | example stats
  LastZ | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Stickleback (Gasterosteus aculeatus) 6 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Coelacanth (Latimeria chalumnae)
  Translated Blat | example stats
Cod (Gadus morhua)
  LastZ | example stats
Medaka (Oryzias latipes)
  BlastZ | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Lamprey (Petromyzon marinus)
  Translated Blat | example stats
Cave fish (Astyanax mexicanus) 3 alignments    
Human (Homo sapiens)
  LastZ | example stats
Medaka (Oryzias latipes)
  LastZ | example stats
Zebrafish (Danio rerio)
  LastZ | example stats
Zebrafish (Danio rerio) 18 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Mouse (Mus musculus)
  Translated Blat | example stats
Rat (Rattus norvegicus)
  Translated Blat | example stats
Chicken (Gallus gallus)
  Translated Blat | example stats
Xenopus (Xenopus tropicalis)
  Translated Blat | example stats
Coelacanth (Latimeria chalumnae)
  Translated Blat | example stats
Spotted gar (Lepisosteus oculatus)
  LastZ | example stats
Cod (Gadus morhua)
  LastZ | example stats
Tetraodon (Tetraodon nigroviridis)
  Translated Blat | example stats
Fugu (Takifugu rubripes)
  Translated Blat | example stats
Tilapia (Oreochromis niloticus)
  Translated Blat | example stats
Medaka (Oryzias latipes)
  Translated Blat | example stats
Platyfish (Xiphophorus maculatus)
  Translated Blat | example stats
Stickleback (Gasterosteus aculeatus)
  Translated Blat | example stats
Cave fish (Astyanax mexicanus)
  LastZ | example stats
Lamprey (Petromyzon marinus)
  Translated Blat | example stats
C.intestinalis (Ciona intestinalis)
  Translated Blat | example stats
C.savignyi (Ciona savignyi)
  Translated Blat | example stats
Lamprey (Petromyzon marinus) 4 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Stickleback (Gasterosteus aculeatus)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
C.intestinalis (Ciona intestinalis)
  Translated Blat | example stats
C.intestinalis (Ciona intestinalis) 6 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Mouse (Mus musculus)
  Translated Blat | example stats
Rat (Rattus norvegicus)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
Lamprey (Petromyzon marinus)
  Translated Blat | example stats
C.savignyi (Ciona savignyi)
  LastZ | example stats
C.savignyi (Ciona savignyi) 4 alignments    
Human (Homo sapiens)
  Translated Blat | example stats
Chicken (Gallus gallus)
  Translated Blat | example stats
Zebrafish (Danio rerio)
  Translated Blat | example stats
C.intestinalis (Ciona intestinalis)
  LastZ | example stats