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: KCNN1_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence HSU69883_3
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 1390.11 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.
KCNN1_HUMAN 1 MPGPRAACSEPNPCTQVVMNSHSYNGSVGRPLGSGPGALGRDPPDPEAG
MPGPRAACSEPNPCTQVVMNSHSYNGSVGRPLGSGPGALGRDPPDPEAG
MPGPRAACSEPNPCTQVVMNSHSYNGSVGRPLGSGPGALGRDPPDPEAG
HSU69883_3 1 acgccggtagcactacggaaacatagaggcccgagcggcgcgccgcggg
tcgcgccggacacgcatttagagaaggtggctgggcgctggaccacacg
ggtcggcccgcccccgacgccccctccgggggccggccgaactgctgcc
KCNN1_HUMAN 50 HPPQPPHSPGLQVVVAKSEPARPSPGSPRGQPQDQDDDEDDEEDEAGRQ
HPPQPPHSPGLQVVVAKSEPARPSPGSPRGQPQDQDDDEDDEEDEAGRQ
HPPQPPHSPGLQVVVAKSEPARPSPGSPRGQPQDQDDDEDDEEDEAGRQ
HSU69883_3 148 cccccccacgccggggaagcgcctcgaccgcccgcggggggggggggac
accaccagcgtatttcagaccgcccggcggacaaaaaaaaaaaaacgga
ccaacgccgccggagcgtgacgcaccccgggcgcgctcgttgatgccgg
KCNN1_HUMAN 99 RASGKPSNVGHRLGHRRALFEKRKRLSDYALIFGMFGIVVMVTETELSW
RASGKPSNVGHRLGHRRALFEKRKRLSDYALIFGMFGIVVMVTETELSW
RASGKPSNVGHRLGHRRALFEKRKRLSDYALIFGMFGIVVMVTETELSW
HSU69883_3 295 agtgactaggcccgcccgctgacaccagtgcatgatgaggagagagctt
gccgaccatgagtgaggcttaagagtgaactttgttgtttttcacatcg
acggacatgcccgccgggccggggcccctcctccgtccccggggcggcg
KCNN1_HUMAN 148 GVYTKESLYSFALKCLISLSTAILLGLVVLYHAREIQLFMVDNGADDWR
GVYTKESLYSFALKCLISLSTAILLGLVVLYHAREIQLFMVDNGADDWR
GVYTKESLYSFALKCLISLSTAILLGLVVLYHAREIQLFMVDNGADDWR
HSU69883_3 442 ggtaagtctttgcatcaactagaccgcggctcgcgacctaggaggggtc
gtacaactactctagttgtccctttgttttaacgatattttaagcaagg
ggccggtgcacacaccccccgccggtctccctcggcggcggccgttcgc
KCNN1_HUMAN 197 IAMTCERVFLISLELAVCAIHPVPGHYRFTWTARLAFTYAPSVAEADVD
IAMTCERVFLISLELAVCAIHPVPGHYRFTWTARLAFTYAPSVAEADVD
IAMTCERVFLISLELAVCAIHPVPGHYRFTWTARLAFTYAPSVAEADVD
HSU69883_3 589 agaatgcgtcatcgcggtgaccgcgctctatagccgtatgctggggggg
tctcgagttttctatctgctactcgaagtcgccgtctcaccctcacata
ccgccgcgcccgaggagcctcggccccccggggggccgcgcggcgccgc
KCNN1_HUMAN 246 VLLSIPMFLRLYLLGRVMLLHSKIFTDASSRSIGALNKITFNTRFVMKT
VLLSIPMFLRLYLLGRVMLLHSKIFTDASSRSIGALNKITFNTRFVMKT
VLLSIPMFLRLYLLGRVMLLHSKIFTDASSRSIGALNKITFNTRFVMKT
HSU69883_3 736 gcctacatccctccgcgacccaaataggtacaaggcaaaataactgaaa
tttctctttgtattggttttagattcaccgggtgctaatctacgtttac
gggcccgcgcccggcgggagccaccgccgccccgcccgccccgcccgga
KCNN1_HUMAN 295 LMTICPGTVLLVFSISSWIIAAWTVRVCERYHDKQEVTSNFLGAMWLIS
LMTICPGTVLLVFSISSWIIAAWTVRVCERYHDKQEVTSNFLGAMWLIS
LMTICPGTVLLVFSISSWIIAAWTVRVCERYHDKQEVTSNFLGAMWLIS
HSU69883_3 883 caaatcgagccgtaatttaaggtagcgtgatcgacggaaatcggatcat
ttctgcgctttttgtccgttccgctgtgagaaaaaatcgattgctgttc
cgccccccgggccccccgccacgcgcccggcccggagccccggcgggtc
KCNN1_HUMAN 344 ITFLSIGYGDMVPHTYCGKGVCLLTGIMGAGCTALVVAVVARKLELTKA
ITFLSIGYGDMVPHTYCGKGVCLLTGIMGAGCTALVVAVVARKLELTKA
ITFLSIGYGDMVPHTYCGKGVCLLTGIMGAGCTALVVAVVARKLELTKA
HSU69883_3 1030 aatctagtggagccattgaggtccagaagggtagcggggggcacgcaag
tcttctgagattcacaggagtgttcgttgcggcctttcttcgatatcac
ccccctccccggcccccggtgcgctccgatctcgcggtggtggggccgt
KCNN1_HUMAN 393 EKHVHNFMMDTQLTKRVKNAAANVLRETWLIYKHTRLVKKPDQARVRKH
EKHVHNFMMDTQLTKRVKNAAANVLRETWLIYKHTRLVKKPDQARVRKH
EKHVHNFMMDTQLTKRVKNAAANVLRETWLIYKHTRLVKKPDQARVRKH
HSU69883_3 1177 gacgcataagaccaacgaagggagcagatcatacaacgaacgcgcgcac
aaataatttacatcagtaacccattgacgttaaacgttaacaacgtgaa
ggcgcccggctgccggaaccttctcggggcccatcgggggacacgtgac
KCNN1_HUMAN 442 QRKFLQAIHQAQKLRSVKIEQGKLNDQANTLTDLAKTQTVMYDLVSELH
QRKFLQAIHQAQKLRSVKIEQGKLNDQANTLTDLAKTQTVMYDLVSELH
QRKFLQAIHQAQKLRSVKIEQGKLNDQANTLTDLAKTQTVMYDLVSELH
HSU69883_3 1324 ccatccgaccgcaccagaagcgacagcgaacagcgaacagatgcgtgcc
agattactaacaatggtataagataaacactcatcacacttaattcata
gtgccacctgtggcgtggcgagggccgtcgtccacgcgccgcctagggc
KCNN1_HUMAN 491 AQHEELEARLATLESRLDALGASLQALPGLIAQAIRPPPPPLPPRPGPG
AQHEELEARLATLESRLDALGASLQALPGLIAQAIRPPPPPLPPRPGPG
AQHEELEARLATLESRLDALGASLQALPGLIAQAIRPPPPPLPPRPGPG
HSU69883_3 1471 gccggcggccgacgactggcggtccgccgcagcgacccccccccacgcg
caaaatacgtcctaggtactgcctactcgttcactgccccctccgcgcg
tgcggggccgccgaccgtggtctagcgtccccacacacgtcgtcgcccc
KCNN1_HUMAN 540 PQDQAARSSPCRWTPVAPSDCG
PQDQAARSSPCRWTPVAPSDCG
PQDQAARSSPCRWTPVAPSDCG
HSU69883_3 1618 ccgcggcatctctacggctgtg
caaaccggccgggcctcccagg
cacgacgccccgggcgccgccg
//
cmbi.kun.nl), 28-Jun-2005