Locus 3753

Sequence ID X_DroMel_CAF1
Location 9,961,131 – 9,961,251
Length 120
Max. P 0.724981
window6164 window6165

overview

Window 4

Location 9,961,131 – 9,961,251
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -30.33
Consensus MFE -28.82
Energy contribution -28.93
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.63
Structure conservation index 0.95
SVM decision value 0.15
SVM RNA-class probability 0.608403
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9961131 120 + 22224390
GUGUCUGCCCAAAUAGUUAAAGGGCAAAAUAAAUAAACGUCGUCGUCGGUCGACAAAUGUGACGACAACGCCGGCAAAGAAGAAACUCUUGCCUAUAACGAUGUGCCGAUAAUGAAAGAG
.(((((((((...........)))))..........(((((((.((((.((.((....))))))))......(((((.((......)))))))....)))))))...))))......... ( -30.90)
>DroEre_CAF1 23720 120 + 1
GUGUCUGCCCAAAUAGUUAAAGGGCAAAAUAAAUAAACGUCGUUGUCGGUCGACAAAUGUGACGACAACGCCGACGAAGAAGAAACUCUUGCCUAUAACGAUGUGCCGAUAAUGAAAGAG
.((((.((.((....((((..((((............((.((((((((.((.((....)))))))))))).))...((((......)))))))).))))..)).)).))))......... ( -30.50)
>DroYak_CAF1 23647 120 + 1
GUGUCUGCCCAAAUAGUUAAAGGGCAAAAUAAAUAAACGUCGUUGUCGGUCGACAAAUGUGACGACAAUGCCGACGAAGAAGAAACUCUUGCCUAUAACGAUGUGCCGAUAAUGAAAGAG
.((((.((.((....((((..((((............(((((((((((.((.((....))))))))))...)))))((((......)))))))).))))..)).)).))))......... ( -29.60)
>consensus
GUGUCUGCCCAAAUAGUUAAAGGGCAAAAUAAAUAAACGUCGUUGUCGGUCGACAAAUGUGACGACAACGCCGACGAAGAAGAAACUCUUGCCUAUAACGAUGUGCCGAUAAUGAAAGAG
.((((.((.((....((((..((((............((.((((((((.((.((....)))))))))))).))...((((......)))))))).))))..)).)).))))......... (-28.82 = -28.93 +   0.11)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 5

Location 9,961,131 – 9,961,251
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -30.83
Consensus MFE -28.04
Energy contribution -27.93
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.01
Structure conservation index 0.91
SVM decision value 0.41
SVM RNA-class probability 0.724981
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9961131 120 - 22224390
CUCUUUCAUUAUCGGCACAUCGUUAUAGGCAAGAGUUUCUUCUUUGCCGGCGUUGUCGUCACAUUUGUCGACCGACGACGACGUUUAUUUAUUUUGCCCUUUAACUAUUUGGGCAGACAC
............(((((....((.....))(((((....))))))))))(((((((((((.............)))))))))))........(((((((...........)))))))... ( -34.02)
>DroEre_CAF1 23720 120 - 1
CUCUUUCAUUAUCGGCACAUCGUUAUAGGCAAGAGUUUCUUCUUCGUCGGCGUUGUCGUCACAUUUGUCGACCGACAACGACGUUUAUUUAUUUUGCCCUUUAACUAUUUGGGCAGACAC
(((((...((((.(((.....)))))))..)))))..........((((.((((((((((((....)).)).)))))))).)............(((((...........)))))))).. ( -30.20)
>DroYak_CAF1 23647 120 - 1
CUCUUUCAUUAUCGGCACAUCGUUAUAGGCAAGAGUUUCUUCUUCGUCGGCAUUGUCGUCACAUUUGUCGACCGACAACGACGUUUAUUUAUUUUGCCCUUUAACUAUUUGGGCAGACAC
...........((.((.((..((((..(((((((..........(((((...((((((((((....)).)).)))))))))))........)))))))...))))....)).)).))... ( -28.27)
>consensus
CUCUUUCAUUAUCGGCACAUCGUUAUAGGCAAGAGUUUCUUCUUCGUCGGCGUUGUCGUCACAUUUGUCGACCGACAACGACGUUUAUUUAUUUUGCCCUUUAACUAUUUGGGCAGACAC
....................((((...((((((((....))))).)))...(((((((((((....)).)).))))))))))).........(((((((...........)))))))... (-28.04 = -27.93 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:34 2006