Locus 5973

Sequence ID 2R_DroMel_CAF1
Location 18,806,394 – 18,806,528
Length 134
Max. P 0.991332
window9578 window9579 window9580

overview

Window 8

Location 18,806,394 – 18,806,492
Length 98
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 82.60
Mean single sequence MFE -33.84
Consensus MFE -20.96
Energy contribution -21.12
Covariance contribution 0.16
Combinations/Pair 1.06
Mean z-score -2.80
Structure conservation index 0.62
SVM decision value 1.58
SVM RNA-class probability 0.965479
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18806394 98 - 20766785
CGAGGUCCUGG------UUCGGGUCCGGGUCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACGGACCCUUCUGGCCUCUCGCACAAAAUCUACAUUACCAUGA
.((((((..((------...(((((((((.......))....((((((......))))))..))))))).)).))))))......................... ( -36.20)
>DroSec_CAF1 25687 103 - 1
CGAGGUCCGGGCUCGGGUUCGAGUCCGGUUCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACGGACCCUUCUGGCCUCUCGCACAA-AUCUACAUUACCAUGA
.((((((((((((((....)))))))))......((((....((((((......))))))...)))).......)))))........-................ ( -40.60)
>DroSim_CAF1 26159 91 - 1
CGGGGUC------------CGGGUCCGGGUCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACGGACCCUUCUGGCCUCUCGCACAA-AUCUACAUUACCAUGA
.((((((------------.(((((((((.......))....((((((......))))))..)))))))....))))))........-................ ( -34.50)
>DroEre_CAF1 25858 79 - 1
CGGGGU------------------------CCGGGUAAUGAUUCCGGCAUAACAGCCGGAUACGGACCCUUCUGGCCUCUCGCACAA-AUCUACAUUACCAUGA
.(((((------------------------(.((((......((((((......)))))).....))))....))))))........-................ ( -26.10)
>DroYak_CAF1 26196 80 - 1
CGGGGU------------------------CCGGGUCCUGAUUCCGGCAUAACAGCCGGAUACGGACCCUUCUGGCCUCUCGCACAAAAUCUACAUUACCAUGA
.(((((------------------------(.((((((....((((((......))))))...))))))....))))))......................... ( -31.80)
>consensus
CGGGGUC____________CG_GUCCGG_UCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACGGACCCUUCUGGCCUCUCGCACAA_AUCUACAUUACCAUGA
.((((.............................((((....((((((......))))))...))))((....))))))......................... (-20.96 = -21.12 +   0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,806,434 – 18,806,528
Length 94
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 73.34
Mean single sequence MFE -25.69
Consensus MFE -12.00
Energy contribution -12.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.47
SVM decision value 0.06
SVM RNA-class probability 0.564959
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18806434 94 + 20766785
CGUAUCCGGCUGUUAUGCCGGAAUCAGGACGUGGACCCGGACCCGAA------CCAGGACCUCGUACCUCGUACCCCGGACUCAAUUACCUCUUGUCUUU
....((((((......))))))((.((((((.((.((.((.......------)).)).)).))).))).)).....((((.............)))).. ( -26.82)
>DroSec_CAF1 25726 100 + 1
CGUAUCCGGCUGUUAUGCCGGAAUCAGGACGUGGAACCGGACUCGAACCCGAGCCCGGACCUCGUACCAUGAACCCCUGACUCAAUUACCUCUUGUCUUU
....((((((......)))))).((((((((.((..((((.((((....)))).)))).)).))).)).)))......(((.............)))... ( -35.52)
>DroSim_CAF1 26198 74 + 1
CGUAUCCGGCUGUUAUGCCGGAAUCAGGACGUGGACCCGGACCCG------------GACCCCG--------------UACUCAAUUACCUCUUGUCUUU
.(((((((((......))))))...((.(((.((..(((....))------------)..))))--------------).))....)))........... ( -22.70)
>DroEre_CAF1 25897 76 + 1
CGUAUCCGGCUGUUAUGCCGGAAUCAUUACCCGG------------------------ACCCCGAACCCCGGAGCCCGGACUCAAUUACCUCUUGUCUUU
.(((((((((......))))))........((((------------------------.(.(((.....))).).)))).......)))........... ( -23.60)
>DroYak_CAF1 26236 76 + 1
CGUAUCCGGCUGUUAUGCCGGAAUCAGGACCCGG------------------------ACCCCGAACCCCGGACCCCGCACUCAAUUACCUCUUGUCUUU
.((.((((((......))))))....((..((((------------------------..........))))..)).))..................... ( -19.80)
>consensus
CGUAUCCGGCUGUUAUGCCGGAAUCAGGACGUGGA_CCGGAC_CG____________GACCCCGAACCCCGGACCCCGGACUCAAUUACCUCUUGUCUUU
....((((((......)))))).............................................................................. (-12.00 = -12.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,806,434 – 18,806,528
Length 94
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 73.34
Mean single sequence MFE -33.00
Consensus MFE -11.20
Energy contribution -11.20
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.34
SVM decision value 2.26
SVM RNA-class probability 0.991332
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18806434 94 - 20766785
AAAGACAAGAGGUAAUUGAGUCCGGGGUACGAGGUACGAGGUCCUGG------UUCGGGUCCGGGUCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACG
.................(.(((((((((...(((.(((.((.(((((------.......))))).)).)))))).)))))(((......))))))).). ( -33.50)
>DroSec_CAF1 25726 100 - 1
AAAGACAAGAGGUAAUUGAGUCAGGGGUUCAUGGUACGAGGUCCGGGCUCGGGUUCGAGUCCGGUUCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACG
...(((..((.....))..)))......(((.((.(((.((.(((((((((....)))))))))..)).)))))))).((((((......)))))).... ( -40.30)
>DroSim_CAF1 26198 74 - 1
AAAGACAAGAGGUAAUUGAGUA--------------CGGGGUC------------CGGGUCCGGGUCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACG
...........(((..(.((.(--------------((((..(------------((....)))..)).))).)).).((((((......))))))))). ( -28.60)
>DroEre_CAF1 25897 76 - 1
AAAGACAAGAGGUAAUUGAGUCCGGGCUCCGGGGUUCGGGGU------------------------CCGGGUAAUGAUUCCGGCAUAACAGCCGGAUACG
...........(((......(((((((((((.....))))))------------------------))))).......((((((......))))))))). ( -32.10)
>DroYak_CAF1 26236 76 - 1
AAAGACAAGAGGUAAUUGAGUGCGGGGUCCGGGGUUCGGGGU------------------------CCGGGUCCUGAUUCCGGCAUAACAGCCGGAUACG
...........(((........((((..(((((.(....).)------------------------))))..))))..((((((......))))))))). ( -30.50)
>consensus
AAAGACAAGAGGUAAUUGAGUCCGGGGUCCGGGGUACGGGGUC____________CG_GUCCGG_UCCACGUCCUGAUUCCGGCAUAACAGCCGGAUACG
..............................................................................((((((......)))))).... (-11.20 = -11.20 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:22 2006