Locus 4101

Sequence ID X_DroMel_CAF1
Location 10,830,881 – 10,831,019
Length 138
Max. P 0.962244
window6739 window6740 window6741

overview

Window 9

Location 10,830,881 – 10,830,998
Length 117
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 86.89
Mean single sequence MFE -38.67
Consensus MFE -30.88
Energy contribution -31.63
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.80
SVM decision value 0.35
SVM RNA-class probability 0.701771
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10830881 117 + 22224390
UGCGGACUGUUUUCCGGUCCCGCCAAAUAGCAUUUCCUCGAUGCCAGUGCAGCACUGAUUCAACGGCACUGCGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCA
.(.((((((.....)))))))((.((.((((((......(((((((((((((..(((......)))..)))))).(((......)))......))))))))))))).)).))..... ( -39.50)
>DroSim_CAF1 36989 117 + 1
UGCGGACUGUUUUCCGGUCCCGCCAAAGAGCAUUUGCUCGAUGCCAGUGCAGCACUGAUUCAACGGCACUGUGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCA
.((((((((.....)))).))))....((((....))))((((((((..(((..(((......)))..)))..).(((......)))......))))))).((((....)))).... ( -40.20)
>DroEre_CAF1 54050 100 + 1
UGCGGACUGCUUUCCGGUGCCGCCAAG-----------------CAGUGCAGCACUGAUUCCACGGCACUGUGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCA
....((.((((...((((((((.....-----------------(((((...)))))......)))))))).(((((.(((..(........)..)))....)))))..)))).)). ( -36.30)
>consensus
UGCGGACUGUUUUCCGGUCCCGCCAAA_AGCAUUU_CUCGAUGCCAGUGCAGCACUGAUUCAACGGCACUGUGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCA
(((((((((.....)))))).(((.....(((((.....)))))(((((...))))).......))).....(((((.(((..(........)..)))....)))))...))).... (-30.88 = -31.63 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,830,921 – 10,831,019
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 95.92
Mean single sequence MFE -31.17
Consensus MFE -28.49
Energy contribution -28.27
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.91
SVM decision value 0.23
SVM RNA-class probability 0.643412
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10830921 98 + 22224390
AUGCCAGUGCAGCACUGAUUCAACGGCACUGCGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCAUGCCACUUGAUUGUUGUGGUG
((((((((((((..(((......)))..)))))).(((......)))......))))))...((..(..((((((((.......)))))))))..)). ( -32.90)
>DroSim_CAF1 37029 98 + 1
AUGCCAGUGCAGCACUGAUUCAACGGCACUGUGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCAUGCCACUUGAUUGUUGUGGUG
(((((((..(((..(((......)))..)))..).(((......)))......))))))...((..(..((((((((.......)))))))))..)). ( -30.50)
>DroEre_CAF1 54077 94 + 1
----CAGUGCAGCACUGAUUCCACGGCACUGUGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCAUGCCACUUGAUUGUUGUGGUG
----(((((...)))))...(((((((.(((.(((((.(((..(........)..)))....))))).))).(((((.......)))))))))))).. ( -30.10)
>consensus
AUGCCAGUGCAGCACUGAUUCAACGGCACUGUGCAGCUUGUUGUGGCAAUAAAUGGCAUUAUGCUGCUUAGCAAUCAUGCCACUUGAUUGUUGUGGUG
....(((((...))))).........(((..((((((.(((..(........)..)))....)))))..((((((((.......)))))))))..))) (-28.49 = -28.27 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,830,921 – 10,831,019
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 95.92
Mean single sequence MFE -30.30
Consensus MFE -27.43
Energy contribution -27.43
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.05
Structure conservation index 0.91
SVM decision value 1.54
SVM RNA-class probability 0.962244
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10830921 98 - 22224390
CACCACAACAAUCAAGUGGCAUGAUUGCUAAGCAGCAUAAUGCCAUUUAUUGCCACAACAAGCUGCGCAGUGCCGUUGAAUCAGUGCUGCACUGGCAU
........((((.(((((((((...((((....))))..))))))))))))).........((((.((((..(.(......).)..)))).).))).. ( -31.40)
>DroSim_CAF1 37029 98 - 1
CACCACAACAAUCAAGUGGCAUGAUUGCUAAGCAGCAUAAUGCCAUUUAUUGCCACAACAAGCUGCACAGUGCCGUUGAAUCAGUGCUGCACUGGCAU
........((((.(((((((((...((((....))))..)))))))))))))...........(((.((((((.((.........)).))))))))). ( -31.40)
>DroEre_CAF1 54077 94 - 1
CACCACAACAAUCAAGUGGCAUGAUUGCUAAGCAGCAUAAUGCCAUUUAUUGCCACAACAAGCUGCACAGUGCCGUGGAAUCAGUGCUGCACUG----
..((((..((((.(((((((((...((((....))))..))))))))))))).........((........)).))))...(((((...)))))---- ( -28.10)
>consensus
CACCACAACAAUCAAGUGGCAUGAUUGCUAAGCAGCAUAAUGCCAUUUAUUGCCACAACAAGCUGCACAGUGCCGUUGAAUCAGUGCUGCACUGGCAU
........((((.(((((((((...((((....))))..)))))))))))))...............((((((.((.........)).)))))).... (-27.43 = -27.43 +   0.00)

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 11:16:22 2006