Locus 8420

Sequence ID 3L_DroMel_CAF1
Location 22,125,087 – 22,125,221
Length 134
Max. P 0.635194
window13770 window13771

overview

Window 0

Location 22,125,087 – 22,125,197
Length 110
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 78.55
Mean single sequence MFE -25.74
Consensus MFE -16.28
Energy contribution -16.53
Covariance contribution 0.25
Combinations/Pair 1.35
Mean z-score -1.44
Structure conservation index 0.63
SVM decision value 0.21
SVM RNA-class probability 0.635194
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22125087 110 + 23771897
CUCCCCCUCCUCAACCGAUAAACCCAGCCCAACCAGACCUGGCCGCAAUUUUCGUUGCGUUUGCAAAAUAUUUCCAAGUGUCUUGGCCGCUCAAUUUAUGAGCGUUGAAA
..........(((((.(.(((((((((..(.....)..))))..(((((....))))))))))).........(((((...)))))..(((((.....)))))))))).. ( -23.70)
>DroSec_CAF1 110886 94 + 1
CUCUCCCUC----------------AUCCCAACCAGGCCUGGCCGCAAUUUUCGUUGCGUUUGCAAAAUAUUCGCUGGUGUCUCACCAGCUCAAUUUAUGAGCGUUGAAA
.((..((((----------------((..(((.(.(((...)))(((((....)))))).)))..........(((((((...))))))).......))))).)..)).. ( -23.30)
>DroSim_CAF1 118977 94 + 1
CUCUCCCUC----------------AUCCCAACCAGGCCUGGCCGCAAUUUUCGUUGCGUUUGCAAAAUAUUCGCUGGUGUCUCACCAGCUCAAUUUAUGAGCGUUGAAA
.((..((((----------------((..(((.(.(((...)))(((((....)))))).)))..........(((((((...))))))).......))))).)..)).. ( -23.30)
>DroEre_CAF1 109804 105 + 1
CUCCCCC-----AAUCAACAAAGCCAGCCCAACCAGGCCAAGCCGCAAUUUUCAUUGCGUUUGCAAAAUAUUUGCUGGUGUCUUGCCGGCUCAAUUUAUGAGCGUUGAAA
.......-----..(((((...((((((........((.((((.(((((....))))))))))).........)))))).........(((((.....)))))))))).. ( -29.73)
>DroYak_CAF1 153569 104 + 1
CUCCCCC-----AAUCGCCA-ACCCAGCCCAACCAGGCCAGGCCGCAAUUUUCGUUGCGUUUGCAAGAUAUUUGCCGGUGUCUUAGCCGCUCAAUUUAUGAGCGUUGAAA
.......-----......((-((...(((......)))..(((((((((....)))))).....(((((((......))))))).)))(((((.....)))))))))... ( -28.20)
>DroAna_CAF1 128593 105 + 1
CACCGCC-----AAUCAUUUUCCCUCGCAUGCCGCGGCCUGGCCGCAAUUUUCAUUGCGUUUGCAAAAUAUUUUCUGGUGUCUUGGCCCCGCGAUUUAUGAGCGUUGAAA
((.(((.-----..((((......((((..((((((((...)))))........((((....))))..................)))...))))...))))))).))... ( -26.20)
>consensus
CUCCCCC_____AAUC___A_ACCCAGCCCAACCAGGCCUGGCCGCAAUUUUCGUUGCGUUUGCAAAAUAUUUGCUGGUGUCUUACCCGCUCAAUUUAUGAGCGUUGAAA
.............................((((..((((((((((((((....))))))..............))))).)))......(((((.....)))))))))... (-16.28 = -16.53 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,125,127 – 22,125,221
Length 94
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 82.38
Mean single sequence MFE -23.58
Consensus MFE -13.31
Energy contribution -13.92
Covariance contribution 0.61
Combinations/Pair 1.06
Mean z-score -2.17
Structure conservation index 0.56
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22125127 94 - 23771897
CUCGCC----------------UUCGCGUUUUCUAAGCCUUUUCAACGCUCAUAAAUUGAGCGGCCAAGACACUUGGAAAUAUUUUGCAAACGCAACGAAAAUUGCGGCC
...(((----------------...(((.((((((((..((((...((((((.....))))))...))))..)))))))).....)))....((((......))))))). ( -28.40)
>DroSec_CAF1 110910 98 - 1
CUCCCC------------CCUUUUCGCGUUUUCUAAGCCUUUUCAACGCUCAUAAAUUGAGCUGGUGAGACACCAGCGAAUAUUUUGCAAACGCAACGAAAAUUGCGGCC
......------------.....((((((((((...((.........(((((.....)))))(((((...))))))).......((((....)))).))))).))))).. ( -24.10)
>DroSim_CAF1 119001 98 - 1
CUCCCC------------CCUUUUCGCGUUUUCUAAGCCUUUUCAACGCUCAUAAAUUGAGCUGGUGAGACACCAGCGAAUAUUUUGCAAACGCAACGAAAAUUGCGGCC
......------------.....((((((((((...((.........(((((.....)))))(((((...))))))).......((((....)))).))))).))))).. ( -24.10)
>DroEre_CAF1 109839 105 - 1
CUCCCCCCACCGC-----CCUCUUCGCGAUUUCUAAGCCUUUUCAACGCUCAUAAAUUGAGCCGGCAAGACACCAGCAAAUAUUUUGCAAACGCAAUGAAAAUUGCGGCU
...........((-----(......((.........)).........(((((.....))))).))).........((((.....))))...((((((....))))))... ( -24.10)
>DroYak_CAF1 153603 94 - 1
CUCC----------------ACUUCCCGAUUUCUAAGCCUUUUCAACGCUCAUAAAUUGAGCGGCUAAGACACCGGCAAAUAUCUUGCAAACGCAACGAAAAUUGCGGCC
..((----------------......((...(((.((((........(((((.....))))))))).)))...))((((.(.((((((....)))).)).).)))))).. ( -22.60)
>DroAna_CAF1 128628 107 - 1
CUCCCA---CCUCCCAUCCCCCACCACUCGUUCUAAGCCUUUUCAACGCUCAUAAAUCGCGGGGCCAAGACACCAGAAAAUAUUUUGCAAACGCAAUGAAAAUUGCGGCC
......---.................((.(((((..((((......(((.........)))))))..))).)).))...............((((((....))))))... ( -18.20)
>consensus
CUCCCC____________CCUCUUCGCGUUUUCUAAGCCUUUUCAACGCUCAUAAAUUGAGCGGCCAAGACACCAGCAAAUAUUUUGCAAACGCAACGAAAAUUGCGGCC
....................................(((........(((((.....))))).............((((.....((((....))))......))))))). (-13.31 = -13.92 +   0.61)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:55 2006