Locus 575

Sequence ID X_DroMel_CAF1
Location 1,633,663 – 1,633,863
Length 200
Max. P 0.995429
window912 window913 window914 window915 window916 window917

overview

Window 2

Location 1,633,663 – 1,633,783
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.61
Mean single sequence MFE -29.25
Consensus MFE -26.56
Energy contribution -27.12
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.77
Structure conservation index 0.91
SVM decision value 1.98
SVM RNA-class probability 0.984770
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633663 120 + 22224390
GCAUGGCACAUGUGCCUUCCCUUUAAAAGGGUAUAUAAAUAUCGAGCUCCUCGAGAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACA
....((((....))))..((((.....))))..........(((((...)))))....((((.((((.......)))).)))).....((((.((((((((....)))))))).)))).. ( -33.60)
>DroSim_CAF1 45372 115 + 1
G-----CACAUGUGCCUUCCCUUUAAAAGGGUAUAUAAAUAUCGAGCUCCUCGAGAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACA
.-----...(((((((((.........))))))))).....(((((...)))))....((((.((((.......)))).)))).....((((.((((((((....)))))))).)))).. ( -30.90)
>DroEre_CAF1 29944 115 + 1
C-----CACAUGCGCCUUCCCUUUAAAAGGGUAUAUAAAUAUCGAGCUCUUCGAAAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACUUGUGUUUUUACACAUGUAUGUACA
.-----....(((((...((((.....)))).............((((...((....)).))))....)))))...............((((.((.(((((....))))).)).)))).. ( -25.20)
>DroYak_CAF1 33245 115 + 1
C-----CACAUGUGCCUUCCCUUUAAAAGGGUAUAUAAAUAUCGAGCUCCUCAAAAUCGCUGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACA
.-----....(((((...((((.....))))............(((...)))......((.((.....)))).........)))))..((((.((((((((....)))))))).)))).. ( -27.30)
>consensus
C_____CACAUGUGCCUUCCCUUUAAAAGGGUAUAUAAAUAUCGAGCUCCUCGAAAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACA
..........(((((...((((.....))))..........(((((...)))))....((.((.....)))).........)))))..((((.((((((((....)))))))).)))).. (-26.56 = -27.12 +   0.56)

alignment

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secondary structure

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Window 3

Location 1,633,663 – 1,633,783
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.61
Mean single sequence MFE -35.22
Consensus MFE -34.75
Energy contribution -34.88
Covariance contribution 0.12
Combinations/Pair 1.05
Mean z-score -2.72
Structure conservation index 0.99
SVM decision value 2.58
SVM RNA-class probability 0.995429
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633663 120 - 22224390
UGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUCUCGAGGAGCUCGAUAUUUAUAUACCCUUUUAAAGGGAAGGCACAUGUGCCAUGC
..((((.((((((((....)))))))).))))((((((((((...))))))).)))((((.(........).)))).............((((.....))))..((((....)))).... ( -38.30)
>DroSim_CAF1 45372 115 - 1
UGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUCUCGAGGAGCUCGAUAUUUAUAUACCCUUUUAAAGGGAAGGCACAUGUG-----C
..((((.((((((((....)))))))).)))).(((((((((((..((((((.....)).))))..(((((...)))))))))).....((((.....))))...))))))...-----. ( -36.90)
>DroEre_CAF1 29944 115 - 1
UGUACAUACAUGUGUAAAAACACAAGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUUUCGAAGAGCUCGAUAUUUAUAUACCCUUUUAAAGGGAAGGCGCAUGUG-----G
..((((.((.(((((....))))).)).)))).(((((((((((..((((((.....)).))))..((((.....))))))))).....((((.....))))...))))))...-----. ( -30.80)
>DroYak_CAF1 33245 115 - 1
UGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCAGCGAUUUUGAGGAGCUCGAUAUUUAUAUACCCUUUUAAAGGGAAGGCACAUGUG-----G
..((((.((((((((....)))))))).)))).(((((((((((..((((((.....)).))))..(((((...)))))))))).....((((.....))))...))))))...-----. ( -34.90)
>consensus
UGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUCUCGAGGAGCUCGAUAUUUAUAUACCCUUUUAAAGGGAAGGCACAUGUG_____C
..((((.((((((((....)))))))).)))).(((((((((((..((((((.....)).))))..(((((...)))))))))).....((((.....))))...))))))......... (-34.75 = -34.88 +   0.12)

alignment

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secondary structure

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Window 4

Location 1,633,703 – 1,633,823
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.39
Mean single sequence MFE -23.02
Consensus MFE -21.31
Energy contribution -21.62
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.48
Structure conservation index 0.93
SVM decision value 1.52
SVM RNA-class probability 0.960677
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633703 120 + 22224390
AUCGAGCUCCUCGAGAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUAAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACA
.(((((...)))))....((.((.....)))).......(((((....((((.((((((((....)))))))).)))).......((((....)))).......)))))........... ( -24.70)
>DroSim_CAF1 45407 118 + 1
AUCGAGCUCCUCGAGAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUUAAAUUU--UUUUCAUAAUUGCAGUUCCUUCUACA
.(((((...)))))....((.((.....)))).......((((.....((((.((((((((....)))))))).)))).........((((.--.......))))))))........... ( -24.70)
>DroEre_CAF1 29979 120 + 1
AUCGAGCUCUUCGAAAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACUUGUGUUUUUACACAUGUAUGUACAUUUUUAAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACA
...((((((...((((..((((.((((.......)))).)))).....((((.((.(((((....))))).)).)))).................))))......).)))))........ ( -19.10)
>DroYak_CAF1 33280 120 + 1
AUCGAGCUCCUCAAAAUCGCUGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUUAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACA
...(((...)))......(((((.(((.(.(((.......))).))))((((.((((((((....)))))))).))))...........................))))).......... ( -23.60)
>consensus
AUCGAGCUCCUCGAAAUCGCAGCUAGUCGCGCAAAUUAUCUGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUAAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACA
...(((((...(((....((((.((((.......)))).)))).....((((.((((((((....)))))))).)))).........................))).)))))........ (-21.31 = -21.62 +   0.31)

alignment

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secondary structure

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Window 5

Location 1,633,703 – 1,633,823
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.39
Mean single sequence MFE -28.85
Consensus MFE -27.14
Energy contribution -26.95
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -2.64
Structure conservation index 0.94
SVM decision value 1.77
SVM RNA-class probability 0.976669
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633703 120 - 22224390
UGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUUAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUCUCGAGGAGCUCGAU
.((((..((.((((((.((.(((((......))))).)).)))(((.((((((((....)))))))).))).)))(((((((...)))))))..))..))))....(((((...))))). ( -30.60)
>DroSim_CAF1 45407 118 - 1
UGUAGAAGGAACUGCAAUUAUGAAAA--AAAUUUAAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUCUCGAGGAGCUCGAU
(((((......)))))..........--..............((((.((((((((....)))))))).))))((((((((((...))))))).)))((((.(........).)))).... ( -30.40)
>DroEre_CAF1 29979 120 - 1
UGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUUAAAAAUGUACAUACAUGUGUAAAAACACAAGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUUUCGAAGAGCUCGAU
(((((......)))))..........................((((.((.(((((....))))).)).))))((((((((((...))))))).)))((((.((....))...)))).... ( -25.10)
>DroYak_CAF1 33280 120 - 1
UGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUAAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCAGCGAUUUUGAGGAGCUCGAU
...........((((...........................((((.((((((((....)))))))).))))((((((((((...))))))).))).)))).....(((((...))))). ( -29.30)
>consensus
UGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUAAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCAGAUAAUUUGCGCGACUAGCUGCGAUCUCGAGGAGCUCGAU
(((((......)))))..........................((((.((((((((....)))))))).))))((((((((((...))))))).))).....(((.(((...))).))).. (-27.14 = -26.95 +  -0.19)

alignment

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secondary structure

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Window 6

Location 1,633,743 – 1,633,863
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.19
Mean single sequence MFE -27.93
Consensus MFE -27.95
Energy contribution -28.20
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -3.28
Structure conservation index 1.00
SVM decision value 1.82
SVM RNA-class probability 0.978772
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633743 120 + 22224390
UGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUAAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACAAAAUUAGCUGCAGUUGGCUUUUGUCGUUGUCAGAUAAAUG
.((.....((((.((((((((....)))))))).))))......................(((((((((((..((......))..))))))))))))).((((((.......)))))).. ( -29.00)
>DroSim_CAF1 45447 118 + 1
UGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUUAAAUUU--UUUUCAUAAUUGCAGUUCCUUCUACAAAAUUAGCUGCAGUUGGCUUUUGUCGUUGUCAGAUAAAUG
.((.....((((.((((((((....)))))))).))))..............--......(((((((((((..((......))..))))))))))))).((((((.......)))))).. ( -29.00)
>DroEre_CAF1 30019 120 + 1
UGCACACUUACAAACUUGUGUUUUUACACAUGUAUGUACAUUUUUAAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACAAAAUUAGCUGCAGUUGGCUUUUGUCGUUGUCAGAUAAAUG
.((.....((((.((.(((((....))))).)).))))......................(((((((((((..((......))..))))))))))))).((((((.......)))))).. ( -24.70)
>DroYak_CAF1 33320 120 + 1
UGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUUAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACAAAAUUAGCUGCAGUUGGCUUUUGUCGUUGUCAGAUAAAUG
.((.....((((.((((((((....)))))))).))))......................(((((((((((..((......))..))))))))))))).((((((.......)))))).. ( -29.00)
>consensus
UGCACACUUACAAACAUGUGUUUUUACACAUGUAUGUACAUUUUUAAAAUUUUUUUUUCAUAAUUGCAGUUCCUUCUACAAAAUUAGCUGCAGUUGGCUUUUGUCGUUGUCAGAUAAAUG
.((.....((((.((((((((....)))))))).))))......................(((((((((((..((......))..))))))))))))).((((((.......)))))).. (-27.95 = -28.20 +   0.25)

alignment

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secondary structure

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Window 7

Location 1,633,743 – 1,633,863
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.19
Mean single sequence MFE -22.00
Consensus MFE -21.55
Energy contribution -21.80
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.98
SVM decision value 0.47
SVM RNA-class probability 0.750152
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633743 120 - 22224390
CAUUUAUCUGACAACGACAAAAGCCAACUGCAGCUAAUUUUGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUUAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCA
.......................((..((((((......))))))..))....(((....(((((......)))))......((((.((((((((....)))))))).))))....))). ( -23.40)
>DroSim_CAF1 45447 118 - 1
CAUUUAUCUGACAACGACAAAAGCCAACUGCAGCUAAUUUUGUAGAAGGAACUGCAAUUAUGAAAA--AAAUUUAAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCA
.............................((((((....((((((......)))))).........--..............((((.((((((((....)))))))).))))))).))). ( -22.60)
>DroEre_CAF1 30019 120 - 1
CAUUUAUCUGACAACGACAAAAGCCAACUGCAGCUAAUUUUGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUUAAAAAUGUACAUACAUGUGUAAAAACACAAGUUUGUAAGUGUGCA
(((((((..(((...........((..((((((......))))))..))...((((.((.(((((......))))).)).))))......(((((....))))).))).))))))).... ( -19.40)
>DroYak_CAF1 33320 120 - 1
CAUUUAUCUGACAACGACAAAAGCCAACUGCAGCUAAUUUUGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUAAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCA
.............................((((((....((((((......)))))).........................((((.((((((((....)))))))).))))))).))). ( -22.60)
>consensus
CAUUUAUCUGACAACGACAAAAGCCAACUGCAGCUAAUUUUGUAGAAGGAACUGCAAUUAUGAAAAAAAAAUUUAAAAAAUGUACAUACAUGUGUAAAAACACAUGUUUGUAAGUGUGCA
.............................((((((....((((((......)))))).........................((((.((((((((....)))))))).))))))).))). (-21.55 = -21.80 +   0.25)

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 09:48:19 2006