Locus 3658

Sequence ID X_DroMel_CAF1
Location 9,794,143 – 9,794,456
Length 313
Max. P 0.987910
window5987 window5988 window5989 window5990 window5991 window5992 window5993

overview

Window 7

Location 9,794,143 – 9,794,245
Length 102
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 97.39
Mean single sequence MFE -27.00
Consensus MFE -25.17
Energy contribution -25.83
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.93
SVM decision value 0.19
SVM RNA-class probability 0.627047
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9794143 102 - 22224390
AACACAAAGAGCAGGGGAAUUGCUGUAGCCAAUUUAUUGGUUAAUUGCCAUUUCAAUCAUUUUGAUUGUGGAAUUCAGCUAAGCUCUUGGACCACAAGACCA
...........((((((....(((((((((((....)))))))....((((.((((.....))))..))))....))))....))))))............. ( -25.30)
>DroSec_CAF1 8865 102 - 1
AACACAAAGAGCAGGGGAAUUGCUGGAGCCAAUUUAUUGGUUAAUUGCCAUUUCAAUCAUUUUGAUUGUGGAAUUCAGCUAAGCUCUUCGGCCACAAGCCCA
......((((((....(((((((....).)))))).((((((((((.((((.((((.....))))..)))))))).)))))))))))).(((.....))).. ( -25.60)
>DroSim_CAF1 9999 102 - 1
AACACAAAGAGCAGGGGAAUUGCUGGAGCCAAUUUAUUGGUUAAUUGCCAUUUCAAUCAUUUUGAUUGUGGAAUUCAGCUAAGCUCUUGGGCCACAAGCCCA
......((((((....(((((((....).)))))).((((((((((.((((.((((.....))))..)))))))).))))))))))))((((.....)))). ( -30.10)
>consensus
AACACAAAGAGCAGGGGAAUUGCUGGAGCCAAUUUAUUGGUUAAUUGCCAUUUCAAUCAUUUUGAUUGUGGAAUUCAGCUAAGCUCUUGGGCCACAAGCCCA
......((((((....(((((((....).)))))).((((((((((.((((.((((.....))))..)))))))).))))))))))))((((.....)))). (-25.17 = -25.83 +   0.67)

alignment

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secondary structure

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Window 8

Location 9,794,245 – 9,794,340
Length 95
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 98.60
Mean single sequence MFE -26.77
Consensus MFE -26.35
Energy contribution -26.13
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.41
Structure conservation index 0.98
SVM decision value 0.02
SVM RNA-class probability 0.543023
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9794245 95 + 22224390
UGCCAGUUGGGCGGUGAGGAAUGCCCACGAGGCCUUCAUAGAUUCAAAUAUGCAAUCAAAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUA
.....((.(((((........)))))))..((((.....((((((......((.......))(((((((...)))))))...))))))))))... ( -25.80)
>DroSec_CAF1 8967 95 + 1
UGCCAGUUGGGCGGCGAGGAAUGCCCACGAGGCCUUCAUAGACUCAAAUAUGCAAUCAAAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUA
.....((.(((((........)))))))..(((((((.(((.((((((.((((.........))))))))))......))).)))...))))... ( -27.60)
>DroSim_CAF1 10101 95 + 1
UGCCAGUUGGGCGGCGAGGAAUGCCCACGAGGCCUUCAUAGAUUCAAAUAUGCAAUCAAAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUA
.(((.....)))(((...(((.(((.....))).))).(((((((......((.......))(((((((...)))))))...))))))))))... ( -26.90)
>consensus
UGCCAGUUGGGCGGCGAGGAAUGCCCACGAGGCCUUCAUAGAUUCAAAUAUGCAAUCAAAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUA
.....((.(((((........)))))))..(((((((.(((.((((((.((((.........))))))))))......))).)))...))))... (-26.35 = -26.13 +  -0.22)

alignment

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secondary structure

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Window 9

Location 9,794,245 – 9,794,340
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 98.60
Mean single sequence MFE -24.63
Consensus MFE -24.00
Energy contribution -24.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.97
SVM decision value 0.36
SVM RNA-class probability 0.702431
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9794245 95 - 22224390
UAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUUUGAUUGCAUAUUUGAAUCUAUGAAGGCCUCGUGGGCAUUCCUCACCGCCCAACUGGCA
(((((.(((((.....((((((.....))))))((.......))..)))))...)))))...(((...(((((..........)))))...))). ( -24.00)
>DroSec_CAF1 8967 95 - 1
UAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUUUGAUUGCAUAUUUGAGUCUAUGAAGGCCUCGUGGGCAUUCCUCGCCGCCCAACUGGCA
...((((((((.....((((((.....))))))((.......))..))))).((((((((.....)))))))).......)))(((.....))). ( -25.90)
>DroSim_CAF1 10101 95 - 1
UAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUUUGAUUGCAUAUUUGAAUCUAUGAAGGCCUCGUGGGCAUUCCUCGCCGCCCAACUGGCA
(((((.(((((.....((((((.....))))))((.......))..)))))...)))))...(((...(((((..........)))))...))). ( -24.00)
>consensus
UAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUUUGAUUGCAUAUUUGAAUCUAUGAAGGCCUCGUGGGCAUUCCUCGCCGCCCAACUGGCA
(((((.(((((.....((((((.....))))))((.......))..)))))...)))))...(((...(((((..........)))))...))). (-24.00 = -24.00 +   0.00)

alignment

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secondary structure

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Window 0

Location 9,794,303 – 9,794,418
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 98.26
Mean single sequence MFE -43.87
Consensus MFE -43.89
Energy contribution -44.00
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.73
Structure conservation index 1.00
SVM decision value 2.04
SVM RNA-class probability 0.986258
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9794303 115 + 22224390
AAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUAAUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCUGCUACUUCAGUUCCUCCUGACCGCUUUUCGGCGGC
....(((((((...))))))).........((((.........))))..(((((.((((..((((.((((.....)))).)))).....)))).))))).(((((....))))). ( -39.60)
>DroSec_CAF1 9025 115 + 1
AAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUAAUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCGGCUACAUCAGUUCCUCCUGACCGCCUUUCGGCGGC
....(((((((...))))))).........((((.........))))..(((((.((((..(((((((((.....))))))))).....)))).))))).(((((....))))). ( -46.00)
>DroSim_CAF1 10159 115 + 1
AAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUAAUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCGGCUACAUCAGUUCCUCCUGACCGCCUUUCGGCGGC
....(((((((...))))))).........((((.........))))..(((((.((((..(((((((((.....))))))))).....)))).))))).(((((....))))). ( -46.00)
>consensus
AAGCGCAUUUUGAGGAAAUGCUAAGAAUUUGGCCAUAAUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCGGCUACAUCAGUUCCUCCUGACCGCCUUUCGGCGGC
....(((((((...))))))).........((((.........))))..(((((.((((..(((((((((.....))))))))).....)))).))))).(((((....))))). (-43.89 = -44.00 +   0.11)

alignment

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secondary structure

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Window 1

Location 9,794,303 – 9,794,418
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 98.26
Mean single sequence MFE -45.23
Consensus MFE -44.50
Energy contribution -44.83
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.00
Structure conservation index 0.98
SVM decision value 2.10
SVM RNA-class probability 0.987910
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9794303 115 - 22224390
GCCGCCGAAAAGCGGUCAGGAGGAACUGAAGUAGCAGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAUUAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUU
(((((......)))))(((((.((.((...(((((.((((.....)))).))))))).)).)))))..((((.........)))).........((((((.....)))))).... ( -39.90)
>DroSec_CAF1 9025 115 - 1
GCCGCCGAAAGGCGGUCAGGAGGAACUGAUGUAGCCGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAUUAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUU
((((((....))))))(((((.((.((...(((((.((((.....)))).))))))).)).)))))..((((.........)))).........((((((.....)))))).... ( -47.90)
>DroSim_CAF1 10159 115 - 1
GCCGCCGAAAGGCGGUCAGGAGGAACUGAUGUAGCCGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAUUAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUU
((((((....))))))(((((.((.((...(((((.((((.....)))).))))))).)).)))))..((((.........)))).........((((((.....)))))).... ( -47.90)
>consensus
GCCGCCGAAAGGCGGUCAGGAGGAACUGAUGUAGCCGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAUUAUGGCCAAAUUCUUAGCAUUUCCUCAAAAUGCGCUU
((((((....))))))(((((.((.((...(((((.((((.....)))).))))))).)).)))))..((((.........)))).........((((((.....)))))).... (-44.50 = -44.83 +   0.33)

alignment

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secondary structure

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Window 2

Location 9,794,340 – 9,794,456
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 97.70
Mean single sequence MFE -46.13
Consensus MFE -45.39
Energy contribution -45.50
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.98
Structure conservation index 0.98
SVM decision value 0.96
SVM RNA-class probability 0.890896
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9794340 116 + 22224390
AUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCUGCUACUUCAGUUCCUCCUGACCGCUUUUCGGCGGCUUGCGGUUGCCCAAAAUCGAAGGCAAAGCGAUGGGGAA
.(((((.((((.(((((.((((..((((.((((.....)))).)))).....)))).)))))..((.((((.((((((.....)))))).)))).)).))))....)))))..... ( -42.80)
>DroSec_CAF1 9062 116 + 1
AUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCGGCUACAUCAGUUCCUCCUGACCGCCUUUCGGCGGCUUGCGGUUGCCCAAAAUCGAAGGCAAAGCGAUGGGAAA
.(((((((((..(((((.((((..(((((((((.....))))))))).....)))).)))))...(((....))))))))((..(((((..........))))).))))))..... ( -47.50)
>DroSim_CAF1 10196 116 + 1
AUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCGGCUACAUCAGUUCCUCCUGACCGCCUUUCGGCGGCUUGCGGUUGCCCAAAAUCGAAGGCAAAGCGAUGGGGAA
........(((((((((.((((..(((((((((.....))))))))).....)))).))))).(((((....))))).((((..(((((..........))))).)))).)))).. ( -48.10)
>consensus
AUAUCGGGCCUCCAGGACGAGCCAUAGCUGGACUUCUGGUCCGGCUACAUCAGUUCCUCCUGACCGCCUUUCGGCGGCUUGCGGUUGCCCAAAAUCGAAGGCAAAGCGAUGGGGAA
.(((((((((..(((((.((((..(((((((((.....))))))))).....)))).)))))...(((....))))))))((..(((((..........))))).))))))..... (-45.39 = -45.50 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,794,340 – 9,794,456
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 97.70
Mean single sequence MFE -47.03
Consensus MFE -46.30
Energy contribution -46.63
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.98
SVM decision value 1.34
SVM RNA-class probability 0.943544
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9794340 116 - 22224390
UUCCCCAUCGCUUUGCCUUCGAUUUUGGGCAACCGCAAGCCGCCGAAAAGCGGUCAGGAGGAACUGAAGUAGCAGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAU
......((((....((((((......((....))....(((((......))))).((((.((.((...(((((.((((.....)))).))))))).)).)))))))))).)))).. ( -41.70)
>DroSec_CAF1 9062 116 - 1
UUUCCCAUCGCUUUGCCUUCGAUUUUGGGCAACCGCAAGCCGCCGAAAGGCGGUCAGGAGGAACUGAUGUAGCCGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAU
......((((....((((((......((....))....((((((....)))))).((((.((.((...(((((.((((.....)))).))))))).)).)))))))))).)))).. ( -49.70)
>DroSim_CAF1 10196 116 - 1
UUCCCCAUCGCUUUGCCUUCGAUUUUGGGCAACCGCAAGCCGCCGAAAGGCGGUCAGGAGGAACUGAUGUAGCCGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAU
......((((....((((((......((....))....((((((....)))))).((((.((.((...(((((.((((.....)))).))))))).)).)))))))))).)))).. ( -49.70)
>consensus
UUCCCCAUCGCUUUGCCUUCGAUUUUGGGCAACCGCAAGCCGCCGAAAGGCGGUCAGGAGGAACUGAUGUAGCCGGACCAGAAGUCCAGCUAUGGCUCGUCCUGGAGGCCCGAUAU
......((((....((((((......((....))....((((((....)))))).((((.((.((...(((((.((((.....)))).))))))).)).)))))))))).)))).. (-46.30 = -46.63 +   0.33)

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 11:04:57 2006