Locus 888

Sequence ID 3L_DroMel_CAF1
Location 2,690,418 – 2,690,511
Length 93
Max. P 0.979011
window1364 window1365

overview

Window 4

Location 2,690,418 – 2,690,511
Length 93
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 93.09
Mean single sequence MFE -21.86
Consensus MFE -18.70
Energy contribution -18.46
Covariance contribution -0.24
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.86
SVM decision value 1.41
SVM RNA-class probability 0.951050
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2690418 93 + 23771897
GCCAAACAAUGCGGCAAAUUUUGUUUGCCUACCGUGCACAAUGAGAAAGAGGUCCUUUCAUUCAUUACAGGGACC-A-AAAUGCAAUAUAUUCGC
.........((((((((((...)))))))..((.((...((((((((((.....)))))..))))).)).))...-.-....))).......... ( -20.50)
>DroSec_CAF1 51459 93 + 1
GCCAAACAAUGCGGCAAAUUUUGUUUGCCUACCGUGCACAAUGAGAAAGAGGUCCUUUCAUUCAUUACAAGGACC-A-AAAUGCAAUAUAUUCGC
.........((((((((((...))))))).....................(((((((...........)))))))-.-....))).......... ( -20.10)
>DroSim_CAF1 50323 93 + 1
GCCAAACAAUGCGGCAAAUUUUCUUUGCCUACCGUGCACAAUGAGAAAGAGGUCCUUUCAUUUAUUACAAGGACC-A-AAAUGCAAUAUAUUCGC
.........(((((((((.....)))))).....................(((((((...........)))))))-.-....))).......... ( -19.60)
>DroEre_CAF1 56300 94 + 1
GCCAAAUAAUGCGGCAAAUUUUGUUUGCCUACCGUGCACAAGGAAAAAGAGGUCCUUUCAUUCAUCACAGGGACCCA-AAAUGCACUGUAUUGGC
((((((((.((((((((((...)))))))..((........)).....(.(((((((...........)))))))).-....))).))).))))) ( -27.30)
>DroYak_CAF1 52084 95 + 1
GCCAAAUAAUGCGGCAAAUUUUGUUUGCCUACCGUGCACAAGGAAAAAGAGGUCCUUUCACUCAUCACAAGGACCAAAAAAUGCAAUAUAUUCGC
.....(((.((((((((((...)))))))..((........)).......(((((((...........))))))).......))).)))...... ( -21.80)
>consensus
GCCAAACAAUGCGGCAAAUUUUGUUUGCCUACCGUGCACAAUGAGAAAGAGGUCCUUUCAUUCAUUACAAGGACC_A_AAAUGCAAUAUAUUCGC
.........(((((((((.....)))))).....................(((((((...........))))))).......))).......... (-18.70 = -18.46 +  -0.24)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 2,690,418 – 2,690,511
Length 93
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 93.09
Mean single sequence MFE -25.88
Consensus MFE -22.72
Energy contribution -23.08
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -1.77
Structure conservation index 0.88
SVM decision value 1.83
SVM RNA-class probability 0.979011
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2690418 93 - 23771897
GCGAAUAUAUUGCAUUU-U-GGUCCCUGUAAUGAAUGAAAGGACCUCUUUCUCAUUGUGCACGGUAGGCAAACAAAAUUUGCCGCAUUGUUUGGC
.((((((...(((....-.-...((.((((...(((((((((....)))).))))).)))).))..((((((.....))))))))).)))))).. ( -23.90)
>DroSec_CAF1 51459 93 - 1
GCGAAUAUAUUGCAUUU-U-GGUCCUUGUAAUGAAUGAAAGGACCUCUUUCUCAUUGUGCACGGUAGGCAAACAAAAUUUGCCGCAUUGUUUGGC
.((((((...(((....-.-(((((((...........))))))).....................((((((.....))))))))).)))))).. ( -24.90)
>DroSim_CAF1 50323 93 - 1
GCGAAUAUAUUGCAUUU-U-GGUCCUUGUAAUAAAUGAAAGGACCUCUUUCUCAUUGUGCACGGUAGGCAAAGAAAAUUUGCCGCAUUGUUUGGC
.((((((...(((....-.-...((.((((...(((((((((....)))).))))).)))).))..((((((.....))))))))).)))))).. ( -26.00)
>DroEre_CAF1 56300 94 - 1
GCCAAUACAGUGCAUUU-UGGGUCCCUGUGAUGAAUGAAAGGACCUCUUUUUCCUUGUGCACGGUAGGCAAACAAAAUUUGCCGCAUUAUUUGGC
(((((...(((((....-.......((((((..(..((((((....))))))..)..).)))))..((((((.....)))))))))))..))))) ( -28.40)
>DroYak_CAF1 52084 95 - 1
GCGAAUAUAUUGCAUUUUUUGGUCCUUGUGAUGAGUGAAAGGACCUCUUUUUCCUUGUGCACGGUAGGCAAACAAAAUUUGCCGCAUUAUUUGGC
.((((((...(((............((((((..((..(((((....)))))..))..).)))))..((((((.....))))))))).)))))).. ( -26.20)
>consensus
GCGAAUAUAUUGCAUUU_U_GGUCCUUGUAAUGAAUGAAAGGACCUCUUUCUCAUUGUGCACGGUAGGCAAACAAAAUUUGCCGCAUUGUUUGGC
.((((((...(((.......(((((((...........))))))).....................((((((.....))))))))).)))))).. (-22.72 = -23.08 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:38 2006