Locus 3188

Sequence ID 3R_DroMel_CAF1
Location 8,460,263 – 8,460,423
Length 160
Max. P 0.986990
window5165 window5166 window5167

overview

Window 5

Location 8,460,263 – 8,460,383
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.77
Mean single sequence MFE -32.40
Consensus MFE -31.97
Energy contribution -32.30
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.99
SVM decision value 2.06
SVM RNA-class probability 0.986990
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8460263 120 + 27905053
CACCACAUGGACUUCGUGCACUCUAUGACCGUCGCUAAUGUGAUUAACAAGCCGGUCAUUGAAAUUUUUAAAAGGUUUGAGCAACCUAUCGACUGUAAAGGAAGUCUAUAAUAAAUAAUA
......(((((((((.((((.((.(((((((..(((..(((.....))))))))))))).............(((((.....)))))...)).))))...)))))))))........... ( -31.40)
>DroSec_CAF1 6166 119 + 1
CACCACAUGGACUUCGUGCACUCCAUGACCGUCGCUAAUGUGAUCAACAAGCCGGUCAUUGAAAUUUUUAAAAGGUUUGAGCAACCUAUCGACUGUG-AGGAAGUCUAUAAUAAAUAAUA
......(((((((((.(.(((((.(((((((..(((..(((.....))))))))))))).))..........(((((.....))))).......)))-).)))))))))........... ( -32.90)
>DroSim_CAF1 6224 119 + 1
CACCACAUGGACUUCGUGCACUCCAUGACCGUCGCUAAUGUGAUCAACAAGCCGGUCAUUGAAAUUUUUAAAAGGUUUGAGCAACCUAUCGACUGUG-AGGAAGUCUAUAAUAAAUAAUA
......(((((((((.(.(((((.(((((((..(((..(((.....))))))))))))).))..........(((((.....))))).......)))-).)))))))))........... ( -32.90)
>consensus
CACCACAUGGACUUCGUGCACUCCAUGACCGUCGCUAAUGUGAUCAACAAGCCGGUCAUUGAAAUUUUUAAAAGGUUUGAGCAACCUAUCGACUGUG_AGGAAGUCUAUAAUAAAUAAUA
......(((((((((.(.(((((.(((((((..(((..(((.....))))))))))))).))..........(((((.....))))).......))).).)))))))))........... (-31.97 = -32.30 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,460,263 – 8,460,383
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -31.07
Consensus MFE -31.71
Energy contribution -31.27
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.73
Structure conservation index 1.02
SVM decision value 0.82
SVM RNA-class probability 0.858101
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8460263 120 - 27905053
UAUUAUUUAUUAUAGACUUCCUUUACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUAAUCACAUUAGCGACGGUCAUAGAGUGCACGAAGUCCAUGUGGUG
.......(((((((((((((...(((....((.(((((.....))))).)).......((.(((((((..((((((((...))))))))))))))).)))))...))))))..))))))) ( -30.00)
>DroSec_CAF1 6166 119 - 1
UAUUAUUUAUUAUAGACUUCCU-CACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUGAUCACAUUAGCGACGGUCAUGGAGUGCACGAAGUCCAUGUGGUG
.......(((((((((((((..-(((....((.(((((.....))))).)).......((.(((((((..((((((((...))))))))))))))).)))))...))))))..))))))) ( -31.60)
>DroSim_CAF1 6224 119 - 1
UAUUAUUUAUUAUAGACUUCCU-CACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUGAUCACAUUAGCGACGGUCAUGGAGUGCACGAAGUCCAUGUGGUG
.......(((((((((((((..-(((....((.(((((.....))))).)).......((.(((((((..((((((((...))))))))))))))).)))))...))))))..))))))) ( -31.60)
>consensus
UAUUAUUUAUUAUAGACUUCCU_CACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUGAUCACAUUAGCGACGGUCAUGGAGUGCACGAAGUCCAUGUGGUG
.......(((((((((((((...(((....((.(((((.....))))).)).......((.(((((((..((((((((...))))))))))))))).)))))...))))))..))))))) (-31.71 = -31.27 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,460,303 – 8,460,423
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.10
Mean single sequence MFE -29.73
Consensus MFE -28.80
Energy contribution -29.13
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.97
SVM decision value 0.26
SVM RNA-class probability 0.655397
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8460303 120 - 27905053
AAAGACCGGACGUAGUCGAUAAUGGCGGGCUGGUACUCGAUAUUAUUUAUUAUAGACUUCCUUUACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUAAUCA
...(((........)))(((..((((((((((((....((.(((..........((((........))))((.(((((.....))))).))...))).))....))))))))))))))). ( -28.60)
>DroSec_CAF1 6206 119 - 1
AAAGACCAGACGUUGUCGAUCAUGGCGGGCUGGUACUCCAUAUUAUUUAUUAUAGACUUCCU-CACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUGAUCA
...(((........)))(((((..((((((((((....................((((....-...))))((.(((((.....))))).)).............))))))))))))))). ( -30.20)
>DroSim_CAF1 6264 119 - 1
AAAGACCAGACGUAGUCGAUCAUGGCGGGCUGGUACUCCAUAUUAUUUAUUAUAGACUUCCU-CACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUGAUCA
...(((........)))(((((..((((((((((....................((((....-...))))((.(((((.....))))).)).............))))))))))))))). ( -30.40)
>consensus
AAAGACCAGACGUAGUCGAUCAUGGCGGGCUGGUACUCCAUAUUAUUUAUUAUAGACUUCCU_CACAGUCGAUAGGUUGCUCAAACCUUUUAAAAAUUUCAAUGACCGGCUUGUUGAUCA
...(((........)))(((((..((((((((((....................((((........))))((.(((((.....))))).)).............))))))))))))))). (-28.80 = -29.13 +   0.33)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:16 2006