Locus 3365

Sequence ID X_DroMel_CAF1
Location 8,980,864 – 8,981,096
Length 232
Max. P 0.897328
window5512 window5513

overview

Window 2

Location 8,980,864 – 8,980,980
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.83
Mean single sequence MFE -36.91
Consensus MFE -28.81
Energy contribution -28.38
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.78
SVM decision value 1.00
SVM RNA-class probability 0.897328
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8980864 116 + 22224390
GGAGCUGGCUCCCGGGUUAGCUCUUUGAUGAUUCUGGGGUGGCAGAGCAUAAAGCCAAAACCAAAGGUUCUGCUC--UCUCCACUCCACUACACUCCACUUCAUC--GUCCGCCACUGCG
((((((((((....))))))))))..(((((...((((((((.((((((...((((.........)))).)))))--)..))))))))............)))))--...(((....))) ( -41.36)
>DroSec_CAF1 9400 106 + 1
GGAGCUAGCUCCCGGGUUAGCUCUUUGAUGAUUCUGGGGUGGCAGAGCAUAAAGCCAAAACCAAAGGUUCUCCUC--UCUCCACUCC----------ACUUCAAC--GCACGCCACUGCG
((((((((((....))))))))))....(((...((((((((.((((.....((((.........)))).....)--))))))))))----------)..))).(--(((......)))) ( -39.70)
>DroEre_CAF1 2997 96 + 1
GGAGCUAGCUCCCGGGUUAGCUCUUUGAUGAUACUGGGGUGGCAGAGCAUAAAGCCAAAACCAAAGGUUCUCCUC--UCUCC--------------------AUC--ACCCGCCACUGCG
((((((((((....))))))))))...........(((((((.((((.....((((.........)))).....)--)))))--------------------)))--.))(((....))) ( -31.00)
>DroYak_CAF1 1967 100 + 1
GGGGCUGGCUCCCGGGUUAGCUCUUUGAUGAUUCUGGGGUGGCAGAGCAUAAAGCCAAAACCAAAGGUUCUGCUCUCUCUCC--------------------AUCUGGCCCGCCACUGCG
((((((((((....))))))))))...........(.((((((((((((...((((.........)))).))))))....((--------------------....))...)))))).). ( -35.60)
>consensus
GGAGCUAGCUCCCGGGUUAGCUCUUUGAUGAUUCUGGGGUGGCAGAGCAUAAAGCCAAAACCAAAGGUUCUCCUC__UCUCC____________________AUC__GCCCGCCACUGCG
((((((((((....))))))))))...........(.((((((.(.((.....)))..((((...))))..........................................)))))).). (-28.81 = -28.38 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,980,980 – 8,981,096
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.28
Mean single sequence MFE -27.10
Consensus MFE -25.84
Energy contribution -25.88
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.24
Structure conservation index 0.95
SVM decision value 0.50
SVM RNA-class probability 0.760720
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8980980 116 + 22224390
GACAUGCAGAUGAAUCAAAGCGGCCGCUGAUUAUAGCAACAAUAUGAAAUGCCGCUACCCUUAACCCCCUAUUGACC---ACCUUAUAGGGGCAUUGUUUAUUUAUACCCACC-CUGGAG
.......(((((((.(((((((((.((((....))))..(.....)....)))))).........(((((((.....---.....)))))))..))))))))))....((...-..)).. ( -26.20)
>DroSec_CAF1 9506 117 + 1
GACAUGCAGAUGAAUCAAAGCGGCCGCUGAUUAUAGCAACAAUAUGAAAUGCCGCUACCCUUAACCCCCUAUUGACC---ACCUUAUAGGGGCAUUGUUUAUUUAUACCCACCCCUGUAG
....(((((.........((((((.((((....))))..(.....)....)))))).........(((((((.....---.....)))))))......................))))). ( -26.30)
>DroSim_CAF1 5249 116 + 1
GACAUGCAGAUGAAUCAAAGCGGCCGCUGAUUAUAGCAACAAUAUGAAAUGCCGCUACCCUUAACCCCCUAUUGACC---ACCUUAUAGGGGCAUUGUUUAUUUAUACCCACC-CUGUAG
....(((((.........((((((.((((....))))..(.....)....)))))).........(((((((.....---.....))))))).....................-))))). ( -26.30)
>DroEre_CAF1 3093 119 + 1
GACAUGCAGAUGAAUCAAAGCGGCCGCUGAUUAUAGCAACAAUAUGAAAUGCCGCUGCCCUUAACCCCCUAUUGACCACCACCUUAUAGGGGCAUUGUUUAUUUAUACCCACC-CUGCAG
....(((((..........(((((.((...(((((.......)))))...)).))))).......(((((((.............))))))).....................-))))). ( -28.42)
>DroYak_CAF1 2067 116 + 1
GACAUGCAGAUGAAUCAAAGCGGCCGCUGAUUAUAGCAACAAUAUGAAAUGCCGCUACCCUUAACCCCCUAUUGACC---ACCUUAUAGGGGCAUUGUUUAUUUAUACACACC-CUGCAG
....(((((.........((((((.((((....))))..(.....)....)))))).........(((((((.....---.....))))))).....................-))))). ( -28.30)
>consensus
GACAUGCAGAUGAAUCAAAGCGGCCGCUGAUUAUAGCAACAAUAUGAAAUGCCGCUACCCUUAACCCCCUAUUGACC___ACCUUAUAGGGGCAUUGUUUAUUUAUACCCACC_CUGCAG
....(((((.........((((((.((((....))))..(.....)....)))))).........(((((((.............)))))))......................))))). (-25.84 = -25.88 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:36 2006