Locus 4440

Sequence ID 3L_DroMel_CAF1
Location 12,946,652 – 12,946,812
Length 160
Max. P 0.984076
window6893 window6894

overview

Window 3

Location 12,946,652 – 12,946,772
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.92
Mean single sequence MFE -27.52
Consensus MFE -20.86
Energy contribution -21.66
Covariance contribution 0.80
Combinations/Pair 1.07
Mean z-score -1.97
Structure conservation index 0.76
SVM decision value 0.56
SVM RNA-class probability 0.782884
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12946652 120 - 23771897
CACCACUAUAUCAGCCUUAUCCAUAGCUUUUUUUAAACCAUUCUUACCCUCGAAUGGGCACACUGAAGCACGGGUGUUGAUAUGAGAUAAGUCUACUCCUACACCGGUUGUAUUCUUAAU
......(((((((((...((((...(((((.......((((((........)))))).......)))))..)))))))))))))...((((..(((.((......))..)))..)))).. ( -29.94)
>DroSec_CAF1 63908 120 - 1
CACCACUAUAUCAGCCUUAUCCAUAGCUUUUUUUAAACCAUUCUUACCCUCAAAUGGGCACACUGAAGCCCGGGUGUUGAUAUGAGAUAAGUCUACUCCCACUCCGGUUGUAUUCUUAAU
......(((((((((...((((...(((((.......(((((..........))))).......)))))..)))))))))))))...((((..(((..((.....))..)))..)))).. ( -26.44)
>DroSim_CAF1 68260 120 - 1
CACCACUAUAUCAGCCUUAUCCAUAGCUUUUUUUAAACCAUUCUUACCCUCGAAUGGGCAUACUGAAGCCCUGGUGUUGAUAUGAGAUAAGUCUACUCCCACUCCGGUUGUAUUCUUAAU
......(((((((((.....(((..(((((.......((((((........)))))).......)))))..))).)))))))))...((((..(((..((.....))..)))..)))).. ( -31.24)
>DroEre_CAF1 69974 120 - 1
CACCACUAUAUCAGCCUUGUCCAUAGCCUUUUUUAAACCAUCCUUACCCUCGAAUGGGCACACCGAAGCACGGGUGUUGAUAUGGGAUAGAUCUACCCCUACUCCGGUUGUGUUCUUUAU
(((.((((((((((((((((.................((((.(........).))))((........))))))).))))))))((..(((........)))..))))).)))........ ( -25.70)
>DroYak_CAF1 67632 120 - 1
CACCACUAUGUCAGCCUUAUCCAUAGCUUUUUUCAAACCAUCCUUACCCUCGAACGGGCACACCGUAGCACGGGUGUUGAUAUGGGAUAGAUCUACGCCCACUCCGGUUGUAUUCUUAAU
.....((((((((((((.......))...................((((....((((.....)))).....))))))))))))))...(((..((((.((.....)).)))).))).... ( -24.30)
>consensus
CACCACUAUAUCAGCCUUAUCCAUAGCUUUUUUUAAACCAUUCUUACCCUCGAAUGGGCACACUGAAGCACGGGUGUUGAUAUGAGAUAAGUCUACUCCCACUCCGGUUGUAUUCUUAAU
.(((..(((((((((.....((...(((((.......((((((........)))))).......)))))...)).)))))))))(((....)))...........)))............ (-20.86 = -21.66 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,946,692 – 12,946,812
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.67
Mean single sequence MFE -41.72
Consensus MFE -36.30
Energy contribution -36.74
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.89
Structure conservation index 0.87
SVM decision value 1.96
SVM RNA-class probability 0.984076
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12946692 120 + 23771897
UCAACACCCGUGCUUCAGUGUGCCCAUUCGAGGGUAAGAAUGGUUUAAAAAAAGCUAUGGAUAAGGCUGAUAUAGUGGUGAUACCGGCGGGUUUGCCACGUAAGCCCGGAAUGAAGCGCG
........(((((((((...(((((......)))))...(((((((.....)))))))......((((......((((..(.(((....))))..))))...)))).....))))))))) ( -40.90)
>DroSec_CAF1 63948 120 + 1
UCAACACCCGGGCUUCAGUGUGCCCAUUUGAGGGUAAGAAUGGUUUAAAAAAAGCUAUGGAUAAGGCUGAUAUAGUGGUGAUACCGGCGGGUUUGCCACGUAAGCCCGGAAUGAAGCGCG
.......((((((((((((.(((((......)))))...(((((((.....))))))).......)))))....((((..(.(((....))))..))))...)))))))........... ( -42.20)
>DroSim_CAF1 68300 120 + 1
UCAACACCAGGGCUUCAGUAUGCCCAUUCGAGGGUAAGAAUGGUUUAAAAAAAGCUAUGGAUAAGGCUGAUAUAGUGGUGAUACCGGCGGGUUUGCCACGUAAGCCCGGAAUGAAGCGCG
(((...((.((((((((((.(((((......)))))...(((((((.....))))))).......)))))....((((..(.(((....))))..))))...)))))))..)))...... ( -38.90)
>DroEre_CAF1 70014 120 + 1
UCAACACCCGUGCUUCGGUGUGCCCAUUCGAGGGUAAGGAUGGUUUAAAAAAGGCUAUGGACAAGGCUGAUAUAGUGGUGGUACCGGCGGGCUUGCCACGUAAGCCCGGAAUGAAGCGCG
........(((((((((((((((((......)))))...(((((((.....)))))))...((..((((...))))..)).))))..(((((((((...)))))))))....)))))))) ( -43.40)
>DroYak_CAF1 67672 120 + 1
UCAACACCCGUGCUACGGUGUGCCCGUUCGAGGGUAAGGAUGGUUUGAAAAAAGCUAUGGAUAAGGCUGACAUAGUGGUGAUACCGGCGGGCUUGCCACGUAAGCCCGGAAUGAAGCGCG
........((((((.((((((((((((((........)))))...........((((((...........))))))))).)))))).(((((((((...)))))))))......)))))) ( -43.20)
>consensus
UCAACACCCGUGCUUCAGUGUGCCCAUUCGAGGGUAAGAAUGGUUUAAAAAAAGCUAUGGAUAAGGCUGAUAUAGUGGUGAUACCGGCGGGUUUGCCACGUAAGCCCGGAAUGAAGCGCG
.........((((((((...(((((......)))))...(((((((.....)))))))......((((......((((..(.(((....))))..))))...)))).....)))))))). (-36.30 = -36.74 +   0.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:51 2006