Locus 10311

Sequence ID 3R_DroMel_CAF1
Location 27,649,266 – 27,649,361
Length 95
Max. P 0.639130
window16413 window16414

overview

Window 3

Location 27,649,266 – 27,649,361
Length 95
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 83.17
Mean single sequence MFE -31.67
Consensus MFE -19.95
Energy contribution -20.95
Covariance contribution 1.00
Combinations/Pair 1.27
Mean z-score -2.22
Structure conservation index 0.63
SVM decision value 0.08
SVM RNA-class probability 0.574853
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27649266 95 + 27905053
U--GUUAACGCC--GACUGCAAUUAGUCUAGUGCCAAGGCAAA-CGCCGGCGGCAUUAAUUGCCGAUGAAGGCACUUAAAGGGCAAUUUACCGUGGGCCU
.--......(((--.((...((((.((((((((((..(((...-.)))..(((((.....))))).....))))))....))))))))....)).))).. ( -33.20)
>DroPse_CAF1 36761 100 + 1
UUGGGUAACACACCGGUUGCAAUUAGUCUAAGGCCAAGGCAAAAAACUAGCGGCAUUAAUUGCCAAUGAAGGCACUUAAAAGGUAAUUUAGCAUCCGAGG
((((((.....(((.(((((...((((.....((....)).....))))))))).((((.((((......)))).))))..)))........)))))).. ( -23.22)
>DroSec_CAF1 29456 95 + 1
U--GUUAACGCC--GACUGCAAUUAGUCUAGUGCCAAGGCAAA-CGCCGGCGGCAUUAAUUGCCGAUGAAGGCACUUAAAGGGCAAUUUAGCGUGGGCCU
.--......(((--.((.((((((.((((((((((..(((...-.)))..(((((.....))))).....))))))....))))))))..)))).))).. ( -35.30)
>DroSim_CAF1 34281 95 + 1
U--GUUAACGCC--GACUGCAAUUAGUCUAGUGCCAAGGCAAA-CGCCGGCGGCAUUAAUUGCCGAUGAAGGCACUUAAAGGGCAAUUUAGCGUGGGCCU
.--......(((--.((.((((((.((((((((((..(((...-.)))..(((((.....))))).....))))))....))))))))..)))).))).. ( -35.30)
>DroEre_CAF1 29576 95 + 1
U--GUUAACGCC--GACUGCAAUUAGUCUAGUGCCAAGGCAAA-AGCCGGCGGCAUUAAUUGCCAAUGAAGGCACUUAAAGGGCAAUUUAGCGUGGACCU
.--(((((.(((--(((((....))))).((((((..(((...-.)))...((((.....))))......)))))).....)))...)))))........ ( -32.20)
>DroAna_CAF1 28286 90 + 1
U--GUUAACAGC--GGCUGCAAUUAGCCAAGUGCCAAGGAGAG-UGGCGGCGGCAUUAAUUGCUGGUGAGGGCAGUUAGAG-GCAAUUUAGUGC----CG
.--.......((--(((((....)))))...(((((.......-)))))))(((((((((((((..(((......)))..)-)))).)))))))----). ( -30.80)
>consensus
U__GUUAACGCC__GACUGCAAUUAGUCUAGUGCCAAGGCAAA_CGCCGGCGGCAUUAAUUGCCGAUGAAGGCACUUAAAGGGCAAUUUAGCGUGGGCCU
.........(((..(((((....))))).((((((..(((.....)))..(((((.....))))).....)))))).....)))................ (-19.95 = -20.95 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 27,649,266 – 27,649,361
Length 95
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 83.17
Mean single sequence MFE -28.03
Consensus MFE -19.21
Energy contribution -19.72
Covariance contribution 0.51
Combinations/Pair 1.35
Mean z-score -2.06
Structure conservation index 0.69
SVM decision value 0.22
SVM RNA-class probability 0.639130
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27649266 95 - 27905053
AGGCCCACGGUAAAUUGCCCUUUAAGUGCCUUCAUCGGCAAUUAAUGCCGCCGGCG-UUUGCCUUGGCACUAGACUAAUUGCAGUC--GGCGUUAAC--A
..(((...(((.....))).....((((((.....(((((.....)))))..(((.-...)))..)))))).((((......))))--)))......--. ( -30.10)
>DroPse_CAF1 36761 100 - 1
CCUCGGAUGCUAAAUUACCUUUUAAGUGCCUUCAUUGGCAAUUAAUGCCGCUAGUUUUUUGCCUUGGCCUUAGACUAAUUGCAACCGGUGUGUUACCCAA
..((((.(((..(((((...((((((.(((......(((((..(((.......)))..)))))..))))))))).)))))))).))))............ ( -24.20)
>DroSec_CAF1 29456 95 - 1
AGGCCCACGCUAAAUUGCCCUUUAAGUGCCUUCAUCGGCAAUUAAUGCCGCCGGCG-UUUGCCUUGGCACUAGACUAAUUGCAGUC--GGCGUUAAC--A
.(((....))).....(((.....((((((.....(((((.....)))))..(((.-...)))..)))))).((((......))))--)))......--. ( -30.00)
>DroSim_CAF1 34281 95 - 1
AGGCCCACGCUAAAUUGCCCUUUAAGUGCCUUCAUCGGCAAUUAAUGCCGCCGGCG-UUUGCCUUGGCACUAGACUAAUUGCAGUC--GGCGUUAAC--A
.(((....))).....(((.....((((((.....(((((.....)))))..(((.-...)))..)))))).((((......))))--)))......--. ( -30.00)
>DroEre_CAF1 29576 95 - 1
AGGUCCACGCUAAAUUGCCCUUUAAGUGCCUUCAUUGGCAAUUAAUGCCGCCGGCU-UUUGCCUUGGCACUAGACUAAUUGCAGUC--GGCGUUAAC--A
..((..(((((.............((((((......((((.....))))...(((.-...)))..)))))).((((......))))--)))))..))--. ( -31.10)
>DroAna_CAF1 28286 90 - 1
CG----GCACUAAAUUGC-CUCUAACUGCCCUCACCAGCAAUUAAUGCCGCCGCCA-CUCUCCUUGGCACUUGGCUAAUUGCAGCC--GCUGUUAAC--A
.(----(((......)))-)..((((.((........(((((((..((((..((((-.......))))...)))))))))))....--)).))))..--. ( -22.80)
>consensus
AGGCCCACGCUAAAUUGCCCUUUAAGUGCCUUCAUCGGCAAUUAAUGCCGCCGGCG_UUUGCCUUGGCACUAGACUAAUUGCAGUC__GGCGUUAAC__A
......(((((..(((((...((.((((((.....(((((.....)))))..(((.....)))..)))))).))......)))))...)))))....... (-19.21 = -19.72 +   0.51)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:48 2006