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: RORB_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AL137018_4
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 1138.95 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.
RORB_HUMAN 1 MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQ
MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQ
MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQ
AL137018_4 1 acgcaggactaatggattgactggaatggtagttaaaccaagttttcac
tgcatattcgatggaaccgtaagttcgaggagttgggaaaaccacgcga
gaaatagaacattctgctgcccaccataccgactggcggcttttccagg
RORB_HUMAN 50 RNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLYAEVQ
RNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLYAEVQ
RNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLYAEVQ
AL137018_4 148 aattagaaaaactcctcccatcgcgatagggatgaataacagactgggc
gagttagcagaggaaggtaagtctgtcgactatggtcaaagagtacata
actatcagcactcaccagggttcaagaattggtgggcggagccgttggg
RORB_HUMAN 99 KHQQRLQEQRQQQSGEAEALARVYSSSISNGLSNLNNETSGTYANGHVI
KHQQRLQEQRQQQSGEAEALARVYSSSISNGLSNLNNETSGTYANGHVI
KHQQRLQEQRQQQSGEAEALARVYSSSISNGLSNLNNETSGTYANGHVI
AL137018_4 295 accccccgcccccagggggcgagtaaaaaagcaacaagaagatgagcga
aaaagtaaagaaaggacactcgtagggtgagtgataaacggcacagatt
gcgggggagggggtggaactcggcccctcccgccgccgcccttccgcct
RORB_HUMAN 148 DLPKSEGYYNVDSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYS
DLPKSEGYYNVDSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYS
DLPKSEGYYNVDSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYS
AL137018_4 442 gccatggttaggtgcctcgctgcgaagaacaacgcatgcatgcattata
atcacagaaatacgacccaacgtatcgtaataaactaatcctcattcag
cgcgtgttccctctggcttgaatcgtacagagaatctccacaccgtctc
RORB_HUMAN 197 SFNNGQLAPGITMTEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYE
SFNNGQLAPGITMTEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYE
SFNNGQLAPGITMTEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYE
AL137018_4 589 ttaagctgcgaaaagagcagcaaaatctgatctaaggccccgtcacatg
ctaagatccgtctcatagtcaattacatacgaactaataatcgacacaa
tcctggaaagacgtaccatagcctgctggataccgaggcgggggcccta
RORB_HUMAN 246 EIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILL
EIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILL
EIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILL
AL137018_4 736 gaagtcaataggctcctgacaacgactgggtgacaagtagctcagcacc
atacaagacgactgaagctatcactaattatcagtcgttatgaaaattt
ataatacgcgaaggaatccgctcccacgggtaggaaccggctattatat
RORB_HUMAN 295 LKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSDDLVNEAF
LKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSDDLVNEAF
LKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSDDLVNEAF
AL137018_4 883 catgttgggtgaatcgtactaaagctggatggacatagtgtggcgaggt
tacggtattttgtggctactaactttagaaggtattactgcaattaact
ggatcgagtagagctcccaaccttgtaaataagagcacatttcagtaat
RORB_HUMAN 344 DFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIEPRKVQKLQEKIYFAL
DFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIEPRKVQKLQEKIYFAL
DFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIEPRKVQKLQEKIYFAL
AL137018_4 1030 gtgaattttccagggagttttggcatcgcgtcagcaagcaccgaattgc
atcaatgctatcaaatcttccctttccagcgttacgataataaatatct
ctagtgtcgggcgggctgcatttgatacacgtaaagacggtgaatttat
RORB_HUMAN 393 QHVIQKNHLDDETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPEIVNTL
QHVIQKNHLDDETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPEIVNTL
QHVIQKNHLDDETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPEIVNTL
AL137018_4 1177 ccgacaaccgggatgatagaacaaaggtatcggaccgtactccgagaac
aattaaaataaactcattcatcctcctgatagaatattaacacattact
atgtggtcgttgcgagaacgaaccgatccgcgggggatgattagagtag
RORB_HUMAN 442 FPPLYKELFNPDCATGCK
FPPLYKELFNPDCATGCK
FPPLYKELFNPDCATGCK
AL137018_4 1324 tccttagctacgtgagta
tcctaaattacagccgga
ttgacggctttctcccca
//
cmbi.kun.nl), 18-Feb-2005