Locus 3653

Sequence ID X_DroMel_CAF1
Location 9,791,255 – 9,791,507
Length 252
Max. P 0.842408
window5971 window5972 window5973 window5974

overview

Window 1

Location 9,791,255 – 9,791,375
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.96
Mean single sequence MFE -44.47
Consensus MFE -38.22
Energy contribution -39.33
Covariance contribution 1.11
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.86
SVM decision value 0.25
SVM RNA-class probability 0.654598
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9791255 120 + 22224390
UUAAGUUUCUCGGCUCUUUUUUCCGGGCCGAGAACAAUGUCGGCAUAGUUGGUCGAUGGGCGGAGCGAGCAGAAAUUGCCCGGGGGCAAGAAGGCCAACUAAUGGCAAGGACUUGAGUCC
....(((.((((((((........)))))))))))..(((((...(((((((((.....((.......)).....(((((....)))))...))))))))).))))).((((....)))) ( -48.10)
>DroSec_CAF1 5987 117 + 1
UUCAGUUUCUAGGUUCUUUUUUCCGGGCCGAGAACAAUGUCGGC--AGUUGGUCGAUGGGCGGAGCCAGUAGAAAUUGGCCGG-GGCAAGAAGGCCAACUAAUGGCAAGGACUUGAGUCC
....(((.((.(((((........))))).)))))..(((((..--((((((((.....((...((((((....))))))...-.)).....))))))))..))))).((((....)))) ( -39.70)
>DroSim_CAF1 7132 117 + 1
UUAAGUUUCUCGGUUCUUUUUUCCGGGCCGAGAACAAUGUCGGC--AGUUGGUCGAUGGGCGGAGCCAGUAGAAAUUGGCCGG-GGCAAGAAGGCCAACUAAUGGCAAGGACUUGAGUCC
....(((.((((((((........)))))))))))..(((((..--((((((((.....((...((((((....))))))...-.)).....))))))))..))))).((((....)))) ( -45.60)
>consensus
UUAAGUUUCUCGGUUCUUUUUUCCGGGCCGAGAACAAUGUCGGC__AGUUGGUCGAUGGGCGGAGCCAGUAGAAAUUGGCCGG_GGCAAGAAGGCCAACUAAUGGCAAGGACUUGAGUCC
....(((.((((((((........)))))))))))..(((((....((((((((.....((...((((((....)))))).....)).....))))))))..))))).((((....)))) (-38.22 = -39.33 +   1.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,791,375 – 9,791,493
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -18.97
Consensus MFE -18.90
Energy contribution -18.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 1.00
SVM decision value 0.23
SVM RNA-class probability 0.644130
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9791375 118 + 22224390
GCAAAUUCCAGCUAAAUCUAUACCUACAAUACUGCAUUAUCUCGCAUUUGAGCCAAAAACGCAACCCGACAUCGAAUUGGCAAUCGAUUCCAGCUGC--ACUUGCCUUCAAUCCACCAAG
((((....(((((.((((........(((...(((........))).))).(((((...((...........))..)))))....))))..))))).--..))))............... ( -19.10)
>DroSec_CAF1 6104 120 + 1
GCAAAUUCCAGCUAAAUCUAUACCUACAAUACUGCAUUAUCUCGCAUUUGAGCCAAAAACGCAACCCGACAUCGAAUUGGCAAUCGAUUCCAGCUGCACACUUGCCUUCAAUCCACCAAU
((((....(((((.((((........(((...(((........))).))).(((((...((...........))..)))))....))))..))))).....))))............... ( -18.90)
>DroSim_CAF1 7249 120 + 1
GCAAAUUCCAGCUAAAUCUAUACCUACAAUACUGCAUUAUCUCGCAUUUGAGCCAAAAACGCAACCCGACAUCGAAUUGGCAAUCGAUUCCAGCUGCACACUUGCCUUCAACCGACCAAU
((((....(((((.((((........(((...(((........))).))).(((((...((...........))..)))))....))))..))))).....))))............... ( -18.90)
>consensus
GCAAAUUCCAGCUAAAUCUAUACCUACAAUACUGCAUUAUCUCGCAUUUGAGCCAAAAACGCAACCCGACAUCGAAUUGGCAAUCGAUUCCAGCUGCACACUUGCCUUCAAUCCACCAAU
((((....(((((.((((........(((...(((........))).))).(((((...((...........))..)))))....))))..))))).....))))............... (-18.90 = -18.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,791,375 – 9,791,493
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -34.93
Consensus MFE -34.37
Energy contribution -34.37
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.98
SVM decision value 0.76
SVM RNA-class probability 0.842408
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9791375 118 - 22224390
CUUGGUGGAUUGAAGGCAAGU--GCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAGAUAAUGCAGUAUUGUAGGUAUAGAUUUAGCUGGAAUUUGC
(((.(.....).)))((((((--.((((((.((((...((((((((((....))))))((((((((.((......)).))).))))).........))))..))))))))))..)))))) ( -35.00)
>DroSec_CAF1 6104 120 - 1
AUUGGUGGAUUGAAGGCAAGUGUGCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAGAUAAUGCAGUAUUGUAGGUAUAGAUUUAGCUGGAAUUUGC
((((.((.(((..((.((((..(((((((.(((((((........))))).)).)))))))..)))).))..))).))...))))((((.(((.(((.((......)).))).))))))) ( -34.60)
>DroSim_CAF1 7249 120 - 1
AUUGGUCGGUUGAAGGCAAGUGUGCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAGAUAAUGCAGUAUUGUAGGUAUAGAUUUAGCUGGAAUUUGC
((((.(((.((((.(.((((..(((((((.(((((((........))))).)).)))))))..)))).)))))...)))..))))((((.(((.(((.((......)).))).))))))) ( -35.20)
>consensus
AUUGGUGGAUUGAAGGCAAGUGUGCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAGAUAAUGCAGUAUUGUAGGUAUAGAUUUAGCUGGAAUUUGC
...............((((((...((((((.((((...((((((((((....))))))((((((((.((......)).))).))))).........))))..))))))))))..)))))) (-34.37 = -34.37 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,791,415 – 9,791,507
Length 92
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 95.74
Mean single sequence MFE -26.13
Consensus MFE -24.00
Energy contribution -24.33
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.92
SVM decision value 0.09
SVM RNA-class probability 0.576177
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9791415 92 - 22224390
AUAUAAUAUUACAUCUUGGUGGAUUGAAGGCAAGU--GCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAG
...........(((....)))..((((.(.(((((--((((((.(((((((........))))).)).)))))))..)))).)))))....... ( -24.00)
>DroSec_CAF1 6144 94 - 1
AUAUAAUAUUAUAUAUUGGUGGAUUGAAGGCAAGUGUGCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAG
...................((.(((..((.((((..(((((((.(((((((........))))).)).)))))))..)))).))..))).)).. ( -26.70)
>DroSim_CAF1 7289 94 - 1
AUAUAAUAUUAUAUAUUGGUCGGUUGAAGGCAAGUGUGCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAG
...................(((.((((.(.((((..(((((((.(((((((........))))).)).)))))))..)))).)))))...))). ( -27.70)
>consensus
AUAUAAUAUUAUAUAUUGGUGGAUUGAAGGCAAGUGUGCAGCUGGAAUCGAUUGCCAAUUCGAUGUCGGGUUGCGUUUUUGGCUCAAAUGCGAG
..................((...((((.(.((((..(((((((.(((((((........))))).)).)))))))..)))).)))))..))... (-24.00 = -24.33 +   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 11:04:40 2006