Locus 1212

Sequence ID 3R_DroMel_CAF1
Location 3,653,699 – 3,653,797
Length 98
Max. P 0.558921
window1979 window1980

overview

Window 9

Location 3,653,699 – 3,653,797
Length 98
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 97.45
Mean single sequence MFE -25.75
Consensus MFE -23.41
Energy contribution -23.23
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.66
Structure conservation index 0.91
SVM decision value 0.01
SVM RNA-class probability 0.537225
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3653699 98 + 27905053
GCGUACUAAAUGUACUACAAAACGUGGCAACAACCAACCACCGAGACAGCGACACCAACGAAGCUAUGACGUCGGUGCUGAAGUGUUGCCAACACUUU
..((((.....)))).........((((((((......((((((...(((..(......)..)))......))))))......))))))))....... ( -26.80)
>DroSec_CAF1 12418 98 + 1
GCGUACUAAAUGUACUACAAAACGUGGCAACAACCAACCACAGAGACAGCGACACCAACGAAGCUAUGACGUCGGUGCUGAAGUGUUGCCAACACUCU
..((((.....)))).........((((((((......(((...((((((..(......)..))).....))).)))......))))))))....... ( -23.60)
>DroSim_CAF1 14636 98 + 1
GCGUACUAAAUGUACUACAAAACGUGGCAACAACCAACCACAGAGACAGCGACACCAACGAAGCUAUGACGUCGGUGCUGAAGUGUUGCCAACACUCU
..((((.....)))).........((((((((......(((...((((((..(......)..))).....))).)))......))))))))....... ( -23.60)
>DroEre_CAF1 11885 98 + 1
GCGUACUAAAUGUACUACAAAACGUGGCAACAACCAACCGCAGAGACAGCGACACCAGCGAAGCUAUGACGUCGGUGCUGAGGUGUUGCCAACACUCU
..((((.....)))).........((((((((.((...(((.......))).((((.(((.........))).))))....))))))))))....... ( -29.00)
>consensus
GCGUACUAAAUGUACUACAAAACGUGGCAACAACCAACCACAGAGACAGCGACACCAACGAAGCUAUGACGUCGGUGCUGAAGUGUUGCCAACACUCU
..((((.....)))).........((((((((......(((...((((((..(......)..))).....))).)))......))))))))....... (-23.41 = -23.23 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 3,653,699 – 3,653,797
Length 98
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 97.45
Mean single sequence MFE -31.65
Consensus MFE -31.02
Energy contribution -30.90
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.52
Structure conservation index 0.98
SVM decision value 0.05
SVM RNA-class probability 0.558921
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3653699 98 - 27905053
AAAGUGUUGGCAACACUUCAGCACCGACGUCAUAGCUUCGUUGGUGUCGCUGUCUCGGUGGUUGGUUGUUGCCACGUUUUGUAGUACAUUUAGUACGC
(((((((.(((((((..((((((((((((.........)))))))..(((((...)))))))))).))))))))))))))...((((.....)))).. ( -33.20)
>DroSec_CAF1 12418 98 - 1
AGAGUGUUGGCAACACUUCAGCACCGACGUCAUAGCUUCGUUGGUGUCGCUGUCUCUGUGGUUGGUUGUUGCCACGUUUUGUAGUACAUUUAGUACGC
(((((((.(((((((..((((((((((((.........)))))))..(((.......)))))))).))))))))))))))...((((.....)))).. ( -31.60)
>DroSim_CAF1 14636 98 - 1
AGAGUGUUGGCAACACUUCAGCACCGACGUCAUAGCUUCGUUGGUGUCGCUGUCUCUGUGGUUGGUUGUUGCCACGUUUUGUAGUACAUUUAGUACGC
(((((((.(((((((..((((((((((((.........)))))))..(((.......)))))))).))))))))))))))...((((.....)))).. ( -31.60)
>DroEre_CAF1 11885 98 - 1
AGAGUGUUGGCAACACCUCAGCACCGACGUCAUAGCUUCGCUGGUGUCGCUGUCUCUGCGGUUGGUUGUUGCCACGUUUUGUAGUACAUUUAGUACGC
(((((((.(((((((((...((((((.((.........)).))))))(((.......)))...)).))))))))))))))...((((.....)))).. ( -30.20)
>consensus
AGAGUGUUGGCAACACUUCAGCACCGACGUCAUAGCUUCGUUGGUGUCGCUGUCUCUGUGGUUGGUUGUUGCCACGUUUUGUAGUACAUUUAGUACGC
(((((((.(((((((..((((((((((((.........)))))))..(((.......)))))))).))))))))))))))...((((.....)))).. (-31.02 = -30.90 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:43 2006