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: Q17982_CAEEL
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence CEC14C11_19
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 511.05 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.
Warning: mismatch(es) found
Q17982_CAEEL 220 QCASSCMPSCQPSC----VQQACAPACQPMCSSQCVEQQQAQIVVVQQP
QC-S+C+-SCQ-SC-----QQ-------PMC---C------Q++VVQQP
QCVSACQNSCQQSCGNQQQQQVIVVQSSPMCGQAC------QVIVVQQP
CEC14C11_19 229 ctgtgtcaatccttgacccccgaggctacatgcgt cgaggccc
agtccgaaggaacggaaaaaattttacgctggacg attttaac
acctacactcaggtataggaagtttgtcggtagtt gttctgga
*** ! ! !! ! !!!!! !!!!!!! !!! !!!!!! !
Q17982_CAEEL 265 QQQCTSSCMPACQSSCVQQACAPACQPKCSSQCVEQQQAQIVVVQPPTS
QQ----+C+-ACQ--C--QACAPACQPKCSSQCVEQQQAQIVVVQPPTS
QQ---NNCVQACQPQC--QACAPACQPKCSSQCVEQQQAQIVVVQPPTS
CEC14C11_19 358 cc aatgcgtccct cgtgcgtccatttctggcccgcagggcccat
aa aagtacgacag acgcccgacagccagtaaaacattttacccc
ga ctctatcaagc gcctattaagctcaccaaagtgccttaacga
*** !!!!! !! !! !!
Q17982_CAEEL 314 SSNNCASSCMPQCTPQCVQQQTICAAACQPSCQSSCSSNAQCVQACLPS
SSNNCASSCMPQCTPQCVQQQTICAAACQPSCQSSCSSNAQCVQACLPS
SSNNCASSCMPQCTPQCVQQQTICAAACQPSCQSSCSSNAQCVQACLPS
CEC14C11_19 490 ttaatgtttacctacctgcccaatgggtccttctttatagctgcgtcca
ccaagcccgtcagccagtaaactgcccgaccgaccggcacagtacgtcg
accctttatgagttaatcaaacccttccgaccgtactctcattattcac
Q17982_CAEEL 363 CESSCVQQQQPSVVVVQDSQSSCPSACQPSCSQQCIQAQNLCQSACQPS
CESSCVQQQQPSVVVVQDSQSSCPSACQPSCSQQCIQAQNLCQSACQPS
CESSCVQQQQPSVVVVQDSQSSCPSACQPSCSQQCIQAQNLCQSACQPS
CEC14C11_19 637 tgtttgccccctggggcgtctttctgtcctttcctacgcactctgtcct
gaccgtaaaaccttttaacaccgcccgaccgcaagtacaatgaccgacc
tacgttagaaaacattattaaccacccaagctagctgtgttcgtctaac
Q17982_CAEEL 412 CQSSCGSNTQCVQACIPSCQQTCGQQAQP--------------------
CQSSCGSNTQCVQACIPSCQQTCGQQAQP
CQSSCGSNTQCVQACIPSCQQTCGQQAQPACAPACQPMCSSQCVEQQQA
CEC14C11_19 784 tctttgaaactgcgtacatccatgccgccgtgcgtccatttctggcccg
gaccgggacagtacgtcggaacggaacaccgcccgactgccagtaaaac
catattctgattgcttaccaatcaaataatttatcgagcttgctggaat
***
Q17982_CAEEL 441 -VIVVQQPQQNNCVQACQPQCQQTCGSNVQCVSACQNSCQQSCGNQQQQ
-++VVQQPQQ--C--+C-P-CQ-+C-----C--ACQ--C--SC--QQQQ
QIVVVQQPQQQ-CTSSCMPACQSSCVQQ-SCAPACQPMCSSSCVQQQQQ
CEC14C11_19 931 cagggcccccc tatttacgtctatgcc ttgcgtccatttttgccccc
attttaacaaa gcccgtccgacggtaa cgcccgactgcccgtaaaaa
gctacagagaa tctgcgatcgacttag tttattgagcgaattagggg
*** !! !! !! ! ! !! !!!!! !! !! !! !!
Q17982_CAEEL 489 QVIVVQSSPMCGQACQAPPVLQCVPQCQPSCQPSCMQQYQFIQAPAITM
Q+IVVQ------------P--QC---C-PSCQPSC+QQ---+Q-P---+
QIIVVQQ-----------PQQQCASSCMPSCQPSCVQQIIVVQQPQQQQ
CEC14C11_19 1072 caaggcc cccctgtttacttccttgccaaggccccccc
attttaa caaagcccgtccgaccgtaattttaacaaaa
gcctcaa agaattaccgaacgatttagcctggaagggg
*** ! !!!!!!!!!!!! !! !!! ! ! !!!! ! !!!!
Q17982_CAEEL 538 C
C
C
CEC14C11_19 1186 t
g
c
//
cmbi.ru.nl), 18-Aug-2005