Locus 6665

Sequence ID X_DroMel_CAF1
Location 16,634,483 – 16,634,637
Length 154
Max. P 0.998425
window10885 window10886

overview

Window 5

Location 16,634,483 – 16,634,601
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 94.92
Mean single sequence MFE -27.64
Consensus MFE -25.40
Energy contribution -26.04
Covariance contribution 0.64
Combinations/Pair 1.09
Mean z-score -1.93
Structure conservation index 0.92
SVM decision value 2.77
SVM RNA-class probability 0.996926
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16634483 118 - 22224390
CACUUGGAAAGAUUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGAUCGUGAAGCCGGAGGUGUUUAUCUACAAAAUACCACCCCG
.....((.....(((((((((...............)))))))))(((((.....(((.(.((((....))))..).))).)))))))((.(((((((.......))))))).))... ( -28.86)
>DroSec_CAF1 1954 118 - 1
CACUUGGCAAGAUUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGAUCGUGAAGCCGGAGGUGUUUAUCUACAAAAUACCGCCCCG
.....((((((.(((((((((...............)))))))))))).......(((.(.((((....))))..).))).....)))((.(((((((.......))))))).))... ( -31.06)
>DroSim_CAF1 1960 118 - 1
CACUUGGCAAGACUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGAUCGUGAAGCCGGAGGUGUUUAUCUACAAAAUACCGCCCCG
.....(((.....((((((((...............))))))))..((((.....(((.(.((((....))))..).))).)))))))((.(((((((.......))))))).))... ( -29.96)
>DroEre_CAF1 2163 118 - 1
CACUUGGCAAAAUUCAGAUAAUAAACAAAGUCAAAAAUAGUUGAAUUUCAAAUAAGAUGGAAUACGAAAGUGUGCUGAUCGUGAAGCCGGAGGUGUUUAUCUACAAAAUACCGCCCCG
.....(((......................((((......))))..((((.....(((.(.((((....))))..).))).)))))))((.(((((((.......))))))).))... ( -24.70)
>DroYak_CAF1 1982 118 - 1
CACUUGGCAAAAUUCAGAUAAUAAACAAAAUCAAAAAUAGUUGAAUUUCGAAUAAGAUGGAGUACGAAAGUGUGCUGAUCGUGAAGCCGGAGGUGUUUAUCUACAAAAUACCGCCCCG
.....(((......................((((......))))..((((.....(((((..(((....)))..)).))).)))))))((.(((((((.......))))))).))... ( -23.60)
>consensus
CACUUGGCAAGAUUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGAUCGUGAAGCCGGAGGUGUUUAUCUACAAAAUACCGCCCCG
.....(((....(((((((((...............))))))))).((((.....(((.(.((((....))))..).))).)))))))((.(((((((.......))))))).))... (-25.40 = -26.04 +   0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,634,523 – 16,634,637
Length 114
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 93.28
Mean single sequence MFE -23.92
Consensus MFE -22.06
Energy contribution -22.18
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -2.01
Structure conservation index 0.92
SVM decision value 3.10
SVM RNA-class probability 0.998425
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16634523 114 - 22224390
UCGCCCGCCGGUCACACUGGCUAAAGCUUAAA----AAAACACUUGGAAAGAUUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGA
......(((((.....)))))...(((.....----....((((((..(((.(((((((((...............))))))))))))....)))).))..((((....))))))).. ( -27.06)
>DroSec_CAF1 1994 114 - 1
UCGCCCGCCGGUCACACUGGCUAAAGCUUAAA----AAAACACUUGGCAAGAUUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGA
......(((((.....)))))...(((.....----....((((((..(((.(((((((((...............))))))))))))....)))).))..((((....))))))).. ( -27.06)
>DroSim_CAF1 2000 115 - 1
UCGCCCGCCGGUCACACUGGCUAAAGCUUAAAA---AAAACACUUGGCAAGACUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGA
......(((((.....)))))...(((......---....((((((....((.((((((((...............))))))))...))...)))).))..((((....))))))).. ( -25.16)
>DroEre_CAF1 2203 118 - 1
UCGCCCGCCGGUCACACUGGCUAAAGCUUAAAAAAAAAAACACUUGGCAAAAUUCAGAUAAUAAACAAAGUCAAAAAUAGUUGAAUUUCAAAUAAGAUGGAAUACGAAAGUGUGCUGA
......(((((.....)))))...(((.............((((((...((((((((.......................))))))))....)))).))..((((....))))))).. ( -20.40)
>DroYak_CAF1 2022 115 - 1
UCGCUCGCCGGUCACACUGGCUAAAGCUUAAAA---AAAACACUUGGCAAAAUUCAGAUAAUAAACAAAAUCAAAAAUAGUUGAAUUUCGAAUAAGAUGGAGUACGAAAGUGUGCUGA
..(((((((((.....)))))............---....((((((...((((((((.......................))))))))....)))).))))))((....))....... ( -19.90)
>consensus
UCGCCCGCCGGUCACACUGGCUAAAGCUUAAAA___AAAACACUUGGCAAGAUUCAGAUAAUAAACAAAAUCAAAUUUAUCUGAACUUCGAAUAAGAUGGAAUACGAAAGUGUGCUGA
......(((((.....)))))...(((.............((((((..(((.(((((((((...............))))))))))))....)))).))..((((....))))))).. (-22.06 = -22.18 +   0.12)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:33 2006