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: PRIO_TRIVU
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence TVPRP_5
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 685.09 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.
PRIO_TRIVU 1 MGKIQLGYWILVLFIVTWSDLGLCKKPKPRPGGGWNSGGSNRYPGQPGS
MGKIQLGYWILVLFIVTWSDLGLCKKPKPRPGGGWNSGGSNRYPGQPGS
MGKIQLGYWILVLFIVTWSDLGLCKKPKPRPGGGWNSGGSNRYPGQPGS
TVPRP_5 1 agaactgttatgctagatagcgctaacacacgggtaaggaactcgccga
tgatatgagtttttttcggatgtgaacacgcggggaggggagacgacgg
gaacagacgcgtccttcgttacctgaagaacagggccaaccccacgttc
PRIO_TRIVU 50 PGGNRYPGWGHPQGGGTNWGQPHPGGSNWGQPHPGGSSWGQPHGGSNWG
PGGNRYPGWGHPQGGGTNWGQPHPGGSNWGQPHPGGSSWGQPHGGSNWG
PGGNRYPGWGHPQGGGTNWGQPHPGGSNWGQPHPGGSSWGQPHGGSNWG
TVPRP_5 148 cggactcgtgcccgggaatgccccggtatgccccggtatgcccggtatg
cggagacgggacagggcaggacacggcaggacacggcgggacaggcagg
taccactcggctgatcctgtgctcgtctgtgcttgtctgtgattatcgt
PRIO_TRIVU 99 QGGYNKWKPDKPKTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPVIHFG
QGGYNKWKPDKPKTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPVIHFG
QGGYNKWKPDKPKTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPVIHFG
TVPRP_5 295 cggtaatacgacaaacacgggggggggggggcggtacgagaaacgactg
aggaaagacaacacataatcgccccgcttggtggattggctggcttatg
gccccggaatacaccaatgtactttgatgagttccgggtcgcgccactc
PRIO_TRIVU 148 NEYEDRYYRENQYRYPNQVMYRPIDQYSSQNNFVHDCVNITVKQHTTTT
NEYEDRYYRENQYRYPNQVMYRPIDQYSSQNNFVHDCVNITVKQHTTTT
NEYEDRYYRENQYRYPNQVMYRPIDQYSSQNNFVHDCVNITVKQHTTTT
TVPRP_5 442 agtggcttcgactctcacgatccagctaacaatgcgtgaaagaccaaaa
aaaaagaagaaaagacaattagctaaaggaaattaagtatctaaacccc
tacaccctaacgcccccacgcgcccgcccgcttgtcccccggaaccccc
PRIO_TRIVU 197 TTKGENFTETDIKIMERVVEQMCITQYQAEYEAAAQRAYNMAFFSAPPV
TTKGENFTETDIKIMERVVEQMCITQYQAEYEAAAQRAYNMAFFSAPPV
TTKGENFTETDIKIMERVVEQMCITQYQAEYEAAAQRAYNMAFFSAPPV
TVPRP_5 589 aaaggatagagaaaagcgggcataactcggtggggccgtaagtttgccg
ccagaatcacatattagttaatgtcaaacaaacccagcaatcttcccct
ccaggccaattcgtggtgggggccggcatgcgtctgcgccgacctcgag
PRIO_TRIVU 246 TLLFLSFLIFLIVS
TLLFLSFLIFLIVS
TLLFLSFLIFLIVS
TVPRP_5 736 acctcatcatcaga
cttttgtttttttg
cccccccttcgtgc
//
cmbi.ru.nl), 18-Aug-2005