2005, NucleaRDB.
The pairwise alignment has been generated with the "genewise" program of the Wise2 package. The output shows the protein sequence on the first line, followed by a line indicating the similarity level of the match, followed by 4 lines representing the DNA sequence; The DNA sequence descending in triplets, each triplet being a codon. The translation of each codon is shown above it.
Between the two protein sequences a line indicating the similarity of the match is printed. "+" indicates a conservative mismatch while "- "indicates a dramatic one. Mismatches are indicated by "***" in the left column in addition to "!" at the relevant position(s).
genewise $Name: wise2-2-0 $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright
Query protein: Q9QWM0_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AB012961_2
Strand: forward
Start/End (protein) default
Gene Paras: human.gf
Codon Table: codon.table
Subs error: 1e-05
Indel error: 1e-05
Model splice? model
Model codon bias? flat
Model intron bias? tied
Null model syn
Algorithm 623
genewise output
Score 1337.48 bits over entire alignment
Scores as bits over a synchronous coding model
Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info.
Q9QWM0_RAT 1 MSASSITGDFQDFLKHGLPAIGAGLPDRHRRPIPARSRLVMLPKVETEA
MSASSITGDFQDFLKHGLPAIGAGLPDRHRRPIPARSRLVMLPKVETEA
MSASSITGDFQDFLKHGLPAIGAGLPDRHRRPIPARSRLVMLPKVETEA
AB012961_2 1 atgataaggtcgtcacgccgagggccgcccccacgcaccgaccaggagg
tccgctcgataattaagtcctgcgtcagaggctccgggttttcatacac
gtttgttgttacttgtatattttgtgcacagctccccctcggcagggac
Q9QWM0_RAT 50 SGLVRSHGEQGQMPENMQVSQFKMVNYSYDEDLEELCPVCGDKVSGYHY
SGLVRSHGEQGQMPENMQVSQFKMVNYSYDEDLEELCPVCGDKVSGYHY
SGLVRSHGEQGQMPENMQVSQFKMVNYSYDEDLEELCPVCGDKVSGYHY
AB012961_2 148 tgcgctcggcgcacgaacgtctaagatttgggcggctcgtggagtgtct
cgttgcagaagatcaatatcatattaacaaaataatgctggaatcgaaa
aagcagtgagggggacgagtataggtccttatgaggttgtctaatgttc
Q9QWM0_RAT 99 GLLTCESCKGFFKRTVQNQKRYTCIENQNCQIDKTQRKRCPYCRFKKCI
GLLTCESCKGFFKRTVQNQKRYTCIENQNCQIDKTQRKRCPYCRFKKCI
GLLTCESCKGFFKRTVQNQKRYTCIENQNCQIDKTQRKRCPYCRFKKCI
AB012961_2 295 gccatgatagttacagcacaatatagacatcagaacaactcttctaata
gttcgaggagttagctaaaagacgtaaaagataacagaggcaggtaagt
tccctaccgtctgaacacgagcgcagcgccatcgagaaattctgcaatc
Q9QWM0_RAT 148 DVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQKKALIRANGLKLEAM
DVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQKKALIRANGLKLEAM
DVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQKKALIRANGLKLEAM
AB012961_2 442 gggaacgggaggcacggaaatgcataagagtaccaagcacgagcacgga
atgtatactgcagtggggaatgctaagagctaaaaacttgcagtatact
ctaggggcgatccgaacatgcgagcgacgcgagggacctactatggacg
Q9QWM0_RAT 197 SQVIQAMPSDLTSAIQNIHSASKGLPLSHVALPPTDYDRSPFVTSPISM
SQVIQAMPSDLTSAIQNIHSASKGLPLSHVALPPTDYDRSPFVTSPISM
SQVIQAMPSDLTSAIQNIHSASKGLPLSHVALPPTDYDRSPFVTSPISM
AB012961_2 589 tcgacgactgcatgacaactgtagcccacggtccagtgaactgatcaaa
cattactccatccctaatacccagtctgatctcccaaaggcttccctgt
tggcaggcacgctatgctttccacatgctacgtgactcatctcttctcg
Q9QWM0_RAT 246 TMPPHGSLHGYQPYGHFPNRAIKSEYPDPYSSSPESMMGYSYMDGYQTS
TMPPHGSLHGYQPYGHFPNRAIKSEYPDPYSSSPESMMGYSYMDGYQTS
TMPPHGSLHGYQPYGHFPNRAIKSEYPDPYSSSPESMMGYSYMDGYQTS
AB012961_2 736 aacccgaccgtcctgctcacgaatgtcgcttatcgtaagtttaggtcaa
ctccaggtagaacagatcagctacaacacacgccacttgacatagaacg
agattctgttcaattctttgccgtgcacccccgagaggccccgttcgac
Q9QWM0_RAT 295 SPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQNNRNRQEKLSAFGLL
SPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQNNRNRQEKLSAFGLL
SPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQNNRNRQEKLSAFGLL
AB012961_2 883 tcgaacccatgctatgcggccgcgaaagtcccgcaacaacgacagtgct
cccgtcatttattagacaacatacattcataaaaaagagaaatgctgtt
cgaccttgagatggtactgtatagacgtcagaggtcgcggaggcgtgcg
Q9QWM0_RAT 344 CKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQ
CKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQ
CKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQ
AB012961_2 1030 taaggcacttaggtgaaaattagcagggcaacccattagctacgcatcc
gatcaacttcttagcgggtttgatataaatattaagggattttaataga
caggcgcgccttggcgttcccgaggttcagggtgccgtgcgcgtctcga
Q9QWM0_RAT 393 VAHGKEGTIFLVTGEHVDYSSIISNTEVAFNNLLSLAQELVVRLRSLQF
VAHGKEGTIFLVTGEHVDYSSIISNTEVAFNNLLSLAQELVVRLRSLQF
VAHGKEGTIFLVTGEHVDYSSIISNTEVAFNNLLSLAQELVVRLRSLQF
AB012961_2 1177 ggcgaggaatcgaggcggttaaataagggtaaccacgcgcggacctcct
tcagaagcttttcgaataacgttcacatctaattgtcaatttgtgctat
aatggagaccgtcaacgccccccacaacaccccgcccggcggactctgt
Q9QWM0_RAT 442 DQREFVCLKFLVLFSSDVKNLENFQLVEGVQEQVNAALLDYTLCNYPQQ
DQREFVCLKFLVLFSSDVKNLENFQLVEGVQEQVNAALLDYTLCNYPQQ
DQREFVCLKFLVLFSSDVKNLENFQLVEGVQEQVNAALLDYTLCNYPQQ
AB012961_2 1324 gccgtgtcatcgctatggaacgatccggggcgcgaggccgtactatccc
aagattgtatttttgcataataatattagtaaataccttaactgaacaa
tgggtgtggcgggccatcgttgccgggaccaggcttcggccatcccaaa
Q9QWM0_RAT 491 TEKFGQLLLRLPEIRAISKQAEDYLYYKHVNGDVPYNNLLIEMLHAKRA
TEKFGQLLLRLPEIRAISKQAEDYLYYKHVNGDVPYNNLLIEMLHAKRA
TEKFGQLLLRLPEIRAISKQAEDYLYYKHVNGDVPYNNLLIEMLHAKRA
AB012961_2 1471 agatgcccccccgacgaaacgggtcttacgagggctaaccagaccgaag
caatgatttgtcatgctgaacaaataaaatagatcaaatttattacagc
tgataagttaaaacgaccagaaccgccgcgtgtgcctctctaggccaac
//
cmbi.kun.nl), 18-Feb-2005