Locus 4165

Sequence ID 3R_DroMel_CAF1
Location 11,327,969 – 11,328,165
Length 196
Max. P 0.997328
window6680 window6681 window6682

overview

Window 0

Location 11,327,969 – 11,328,089
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.32
Mean single sequence MFE -25.34
Consensus MFE -20.84
Energy contribution -21.76
Covariance contribution 0.92
Combinations/Pair 1.12
Mean z-score -2.76
Structure conservation index 0.82
SVM decision value 2.84
SVM RNA-class probability 0.997328
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11327969 120 - 27905053
CUACGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCAUAAGGUAAUGGGCAGCGCCCCUUCCCAAUUAUUACAAGAUCAUAACUCAUGUCACA
..............(((((........((((..((((((((..(((((((......)))))))......))))))))))))....................((.......)))))))... ( -25.40)
>DroSec_CAF1 67124 110 - 1
CUAUGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUACUAUA-----CGUA-----UAAUGGGCAGCGCCCCUUCCCAAUUAUUACAAGAUCAUAACUCAUGUCACA
..............(((((........((((..((((((((..((((((...)))-----))).-----))))))))))))....................((.......)))))))... ( -24.40)
>DroSim_CAF1 65294 120 - 1
CUAUGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAUGCGUAUACCAUAAAAUAUGCAUAAGGUAAUGGGCAGCGCCCCUUCCCAAUUAUUACAAGAUCAUAACUCAUGUCACA
..............(((((........((((..((((((((((((((((........))))))))....))))))))))))....................((.......)))))))... ( -27.10)
>DroEre_CAF1 62587 118 - 1
CUAUGACCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCACGAGGUAGUGGGGAGCGCCCCUUCCCAAUUAUUACAAGAUCAUAACUCAUGUC--G
..............(((((........(((((..(((((((..(((((((......)))))))......))))))))))))....................((.......)))))))--. ( -24.90)
>DroYak_CAF1 64427 118 - 1
CUAUGACCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCAUAAGGUAAUGGGGAGCGCCCCUUCCCAAUUAUUACAAGAUCAUAACUCAUGUC--A
..............(((((........(((((..(((((((..(((((((......)))))))......))))))))))))....................((.......)))))))--. ( -24.90)
>consensus
CUAUGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCAUAAGGUAAUGGGCAGCGCCCCUUCCCAAUUAUUACAAGAUCAUAACUCAUGUCACA
..............(((((........((((..((((((((..(((((((......)))))))......))))))))))))....................((.......)))))))... (-20.84 = -21.76 +   0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,328,009 – 11,328,126
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.96
Mean single sequence MFE -23.73
Consensus MFE -15.60
Energy contribution -16.72
Covariance contribution 1.12
Combinations/Pair 1.11
Mean z-score -1.75
Structure conservation index 0.66
SVM decision value 0.04
SVM RNA-class probability 0.554358
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11328009 117 - 27905053
GGAACUCU---CCACACAACGUUAACCUAAUUAGUACAAACUACGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCAUAAGGUAAUGGGCAGC
(((....)---)).......((((......(((((.....(....)...)))))....))))......(((..((((((((..(((((((......)))))))......))))))))))) ( -23.90)
>DroSec_CAF1 67164 110 - 1
GGGACUCUCCUCCACACAACGUUAACCUAAUUAGUCCAAACUAUGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUACUAUA-----CGUA-----UAAUGGGCAGC
.(((......))).......((((......((((((((.....)))...)))))....))))......(((..((((((((..((((((...)))-----))).-----))))))))))) ( -24.50)
>DroSim_CAF1 65334 120 - 1
GGGACUCUCCUCCACACGACGUUAACCUAAUUAGUCCAAACUAUGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAUGCGUAUACCAUAAAAUAUGCAUAAGGUAAUGGGCAGC
.(((......)))....((.((((......((((((((.....)))...)))))....))))))....(((..((((((((((((((((........))))))))....))))))))))) ( -28.40)
>DroEre_CAF1 62625 106 - 1
--------------CCCAACGUUAACCUAAUUAGUCCAAACUAUGACCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCACGAGGUAGUGGGGAGC
--------------......((((......(((((..............)))))....))))......((((..(((((((..(((((((......)))))))......))))))))))) ( -19.74)
>DroYak_CAF1 64465 117 - 1
GAGCCGCU---UCACCUAACGCUAACCUAAUUAGUCCGAACUAUGACCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCAUAAGGUAAUGGGGAGC
((((....---.........(((((.....)))))..((..((((...........))))..))....))))..(((((((..(((((((......)))))))......))))))).... ( -22.10)
>consensus
GGGACUCU___CCACACAACGUUAACCUAAUUAGUCCAAACUAUGGCCAACUAAGACAUAACUCAUCCGCUCAGCCCAUUAAAGCGUAUUCCAUAAAAUAUGCAUAAGGUAAUGGGCAGC
....................((((......(((((..............)))))....))))......(((..((((((((..(((((((......)))))))......))))))))))) (-15.60 = -16.72 +   1.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,328,049 – 11,328,165
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.44
Mean single sequence MFE -38.58
Consensus MFE -21.45
Energy contribution -22.37
Covariance contribution 0.92
Combinations/Pair 1.16
Mean z-score -3.04
Structure conservation index 0.56
SVM decision value 1.63
SVM RNA-class probability 0.968888
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11328049 116 + 27905053
AAUGGGCUGAGCGGAUGAGUUAUGUCUUAGUUGGCCGUAGUUUGUACUAAUUAGGUUAACGUUGUGUGG---AGAGUUCCC-UUCAAGCCUACUUGCAACUUAAAAGUUGUAGGAAAGUU
..(((((((((.(((....(((..(....(((((((.((((....))))....)))))))...)..)))---.....))).-))).))))))(((((((((....)))))))))...... ( -36.10)
>DroSec_CAF1 67194 120 + 1
AAUGGGCUGAGCGGAUGAGUUAUGUCUUAGUUGGCCAUAGUUUGGACUAAUUAGGUUAACGUUGUGUGGAGGAGAGUCCCGUUUCAAGCCUACUUGCAACUUAAAAGUUGUAGGGAAGUU
..(((((((((((.....((((...((((((((((((.....))).))))))))).)))).......(((......))))))))..))))))(((((((((....)))))))))...... ( -38.30)
>DroSim_CAF1 65374 120 + 1
AAUGGGCUGAGCGGAUGAGUUAUGUCUUAGUUGGCCAUAGUUUGGACUAAUUAGGUUAACGUCGUGUGGAGGAGAGUCCCGUUUUAAGCCUACUUGCAACUUAAAAGUUGUAGGGAAGUU
..(((((((((((.((((((((...((((((((((((.....))).))))))))).)))).))))..(((......))))))))..))))))(((((((((....)))))))))...... ( -40.50)
>DroEre_CAF1 62665 102 + 1
AAUGGGCUGAGCGGAUGAGUUAUGUCUUAGUUGGUCAUAGUUUGGACUAAUUAGGUUAACGUUGGG------------------CCAGCCUACUUCCUCCAGAUAAUUCGUAGGGAAGCU
..(((((((.((......((((...(((((((((((........))))))))))).)))).....)------------------))))))))((((((...((....))...)))))).. ( -36.00)
>DroYak_CAF1 64505 117 + 1
AAUGGGCUGAGCGGAUGAGUUAUGUCUUAGUUGGUCAUAGUUCGGACUAAUUAGGUUAGCGUUAGGUGA---AGCGGCUCAUUUCCAGCCUACUUCCUCCGGAAAAUACGUAGGGAGGUU
..(((((((.(.((((((((.....(((((((((((........)))))))))))....((((......---))))))))))))))))))))((((((.((.......)).))))))... ( -42.00)
>consensus
AAUGGGCUGAGCGGAUGAGUUAUGUCUUAGUUGGCCAUAGUUUGGACUAAUUAGGUUAACGUUGUGUGG___AGAGUCCCGUUUCAAGCCUACUUGCAACUUAAAAGUUGUAGGGAAGUU
..((((((..........((((...((((((((((((.....))).))))))))).))))....((..................))))))))((((((((......))))))))...... (-21.45 = -22.37 +   0.92)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:00 2006