Locus 5190

Sequence ID	3R_DroMel_CAF1
Location	13,606,228 – 13,606,338
Length	110
Max. P	0.780705

overview

Window 2

Location	13,606,228 – 13,606,338
Length	110
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.11
Mean single sequence MFE	-56.23
Consensus MFE	-41.19
Energy contribution	-42.13
Covariance contribution	0.95
Combinations/Pair	1.24
Mean z-score	-1.39
Structure conservation index	0.73
SVM decision value	0.56
SVM RNA-class probability	0.780705
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13606228 110 + 27905053
UGCGGGGUGGUGGCACCGGUGGCGGCGGAGGUGGUGGCGGAGUGGGCGUGGACGAGGCGCGGGAACUACUGCCACCGCCGCCUCC------UCCCCGCAAAAGUUCCGUUAGCUCG
(((((((.((.(((.(((.......))).((((((((((((((...((((.......))))...))).)))))))))))))).))------.)))))))................. ( -58.90)
>DroSim_CAF1 48899 110 + 1
UGCGGGGUGGUGGCACCGGUGGCGGCGGAGGCGGUGGCGGAGUGGGCGUGGACGAGGCGCGGGAACUACUGCCACCGCCGCCUCC------UCCCCGCAAAAGUUCCGUUAGCUCG
(((((((.((.(((.(((.......))).((((((((((((((...((((.......))))...))).)))))))))))))).))------.)))))))................. ( -60.80)
>DroEre_CAF1 46327 110 + 1
UUCGGGGUGGUGGCACCGGUGGCGGCGGAGGCGGUGGCGGAGUGGGCGUGGAGGAGGCGCGGGAACUACUGCCACCGCCGCCUCC------UCCCCGCAAUAGUUCCGUUAGCUCG
..((((.(..(((.((..((((.((.(((((((((((.(((((((.((((.......))))....))))).)).)))))))))))------.))))))....)).)))..).)))) ( -58.90)
>DroYak_CAF1 47589 110 + 1
UGCGGGGUGGUGGCACUGGUGGCGGCGGAGGCGGUGGCGGAGUGGGCGUGGACGAGGCUCGAGAACUGCUGCCACCGCCGCCUCC------UCCCCGCAAAAGUUCCGUUAGCUCG
..((((.(..(((.(((.((((.((.(((((((((((.((((..(.((.(.......).))....)..)).)).)))))))))))------.))))))...))).)))..).)))) ( -58.40)
>DroMoj_CAF1 17285 86 + 1
UGCGUGGCGGCGGCACUGGCGG---------------CGGAGUGGGCGUCGAGGAGGCACGGGAGCUGUUGCCACCA---------------CCACGCAAAAGCUCCGUCAGUUCU
.((.((((.((.((....)).)---------------)(((((..((((.(.((.(((((((...))).)))).)).---------------).))))....)))))))))))... ( -35.00)
>DroAna_CAF1 46047 116 + 1
UUCGUGGUGGCGGGACCGGCGGCGGAGGCGGCGGGGGCGGAGUUGGCGUGGAGGAGGCACGGGAGCUGCCGCCGCCACCUCCCCCGCUGCUACCACGCAAUAGUUCUGUCAGCUCA
...(.(.(((((((((..(((..((.(((((((((((.((...((((((((....(((......))).))).))))))).))))))))))).)).)))....))))))))).).). ( -65.40)
>consensus
UGCGGGGUGGUGGCACCGGUGGCGGCGGAGGCGGUGGCGGAGUGGGCGUGGACGAGGCGCGGGAACUACUGCCACCGCCGCCUCC______UCCCCGCAAAAGUUCCGUUAGCUCG
(((((((..((.((....)).))((.((.((((((((((((((...((((.......))))...))).))))))))))).)).)).......)))))))................. (-41.19 = -42.13 +   0.95)

alignment

secondary structure

dotplot

Window 3

Location	13,606,228 – 13,606,338
Length	110
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.11
Mean single sequence MFE	-46.80
Consensus MFE	-30.31
Energy contribution	-31.38
Covariance contribution	1.07
Combinations/Pair	1.22
Mean z-score	-1.26
Structure conservation index	0.65
SVM decision value	-0.04
SVM RNA-class probability	0.512618
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13606228 110 - 27905053
CGAGCUAACGGAACUUUUGCGGGGA------GGAGGCGGCGGUGGCAGUAGUUCCCGCGCCUCGUCCACGCCCACUCCGCCACCACCUCCGCCGCCACCGGUGCCACCACCCCGCA
.................(((((((.------((.(((((.((((((.(.(((....(((.........)))..)))).)))))).))...((((....))))))).)).))))))) ( -46.40)
>DroSim_CAF1 48899 110 - 1
CGAGCUAACGGAACUUUUGCGGGGA------GGAGGCGGCGGUGGCAGUAGUUCCCGCGCCUCGUCCACGCCCACUCCGCCACCGCCUCCGCCGCCACCGGUGCCACCACCCCGCA
.................(((((((.------((.((((((((((((.(.(((....(((.........)))..)))).)))))))))...((((....))))))).)).))))))) ( -51.80)
>DroEre_CAF1 46327 110 - 1
CGAGCUAACGGAACUAUUGCGGGGA------GGAGGCGGCGGUGGCAGUAGUUCCCGCGCCUCCUCCACGCCCACUCCGCCACCGCCUCCGCCGCCACCGGUGCCACCACCCCGAA
...................(((((.------((.((((((((((((.(.(((....(((.........)))..)))).)))))))))...((((....))))))).)).))))).. ( -47.90)
>DroYak_CAF1 47589 110 - 1
CGAGCUAACGGAACUUUUGCGGGGA------GGAGGCGGCGGUGGCAGCAGUUCUCGAGCCUCGUCCACGCCCACUCCGCCACCGCCUCCGCCGCCACCAGUGCCACCACCCCGCA
.................(((((((.------((((((((.(((((..((.((...((.....))...)))).....))))).))))))))(.(((.....))).)....))))))) ( -45.80)
>DroMoj_CAF1 17285 86 - 1
AGAACUGACGGAGCUUUUGCGUGG---------------UGGUGGCAACAGCUCCCGUGCCUCCUCGACGCCCACUCCG---------------CCGCCAGUGCCGCCGCCACGCA
.................(((((((---------------((((((((...((...((........))..((.......)---------------).))...))))))))))))))) ( -33.00)
>DroAna_CAF1 46047 116 - 1
UGAGCUGACAGAACUAUUGCGUGGUAGCAGCGGGGGAGGUGGCGGCGGCAGCUCCCGUGCCUCCUCCACGCCAACUCCGCCCCCGCCGCCUCCGCCGCCGGUCCCGCCACCACGAA
...................((((((.((.((((.(((((((((((.(((((....((((.......))))....))..))).))))))))))).)))).(....))).)))))).. ( -55.90)
>consensus
CGAGCUAACGGAACUUUUGCGGGGA______GGAGGCGGCGGUGGCAGCAGUUCCCGCGCCUCCUCCACGCCCACUCCGCCACCGCCUCCGCCGCCACCGGUGCCACCACCCCGCA
.................(((((((.......((.(((((.(((((..((.(.....(((.........))).....).))..))))).))))).))...((.....)).))))))) (-30.31 = -31.38 +   1.07)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:41 2006