Locus 3574

Sequence ID X_DroMel_CAF1
Location 9,594,615 – 9,594,767
Length 152
Max. P 0.999994
window5846 window5847 window5848 window5849

overview

Window 6

Location 9,594,615 – 9,594,727
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.58
Mean single sequence MFE -40.50
Consensus MFE -37.04
Energy contribution -36.28
Covariance contribution -0.76
Combinations/Pair 1.14
Mean z-score -2.46
Structure conservation index 0.91
SVM decision value 4.02
SVM RNA-class probability 0.999759
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9594615 112 + 22224390
UCCACCGACUCCAAAUCGAAUCGGAUCGCAAUAGUUAACAAUUUGUUUGGC--------ACUCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGUUUGAAAA
...........(((((((((..((..((((((((........)))))((((--------.((((((....))))))((((((....)))))).)))))))..))...))))))))).... ( -37.50)
>DroSec_CAF1 53328 112 + 1
UCCACCGACUCCAAAUCGAAUCGGAUCACAAUAGUUAACAAUUUGUUUGGC--------ACUCUGGCACCCCAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAA
....(((((((((((.(((((.(....((....))...).)))))))))).--------.((((((....))))))((((((....))))))))))))((.((((.....)))))).... ( -39.80)
>DroSim_CAF1 39821 112 + 1
UCCACCGACUCCAAAUCGAAUCGGAUCACAAUAGUUAACAAUUUGUUUGGC--------ACUCUGGCACCCCAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAA
....(((((((((((.(((((.(....((....))...).)))))))))).--------.((((((....))))))((((((....))))))))))))((.((((.....)))))).... ( -39.80)
>DroEre_CAF1 58139 112 + 1
UCCACCGAUUCCAAAUCGAAUCGGAUCACAAUAGUUAACCAUUUGUUUGGC--------ACCCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAA
.((.(((((((......)))))))........................(((--------.((((((....))))))((((((....)))))).)))))((.((((.....)))))).... ( -40.60)
>DroYak_CAF1 56547 120 + 1
UCCACCGACUCCACAUCGAAUCGGAUCACAAUAGUUAACAAUUUGUUUGGCACUCUGGCACCCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGUUCGAGAA
...............((((((((((..((((...........))))..((.((.(((((.((((((....))))))((((((....)))))).))))).)).))...))))))))))... ( -44.80)
>consensus
UCCACCGACUCCAAAUCGAAUCGGAUCACAAUAGUUAACAAUUUGUUUGGC________ACUCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAA
....(((((((((((.(((((.(....((....))...).))))))))))..........((((((....))))))((((((....))))))))))))((..((......))..)).... (-37.04 = -36.28 +  -0.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,594,615 – 9,594,727
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -46.90
Consensus MFE -36.64
Energy contribution -36.68
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -3.01
Structure conservation index 0.78
SVM decision value 2.03
SVM RNA-class probability 0.986194
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9594615 112 - 22224390
UUUUCAAACCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGAGU--------GCCAAACAAAUUGUUAACUAUUGCGAUCCGAUUCGAUUUGGAGUCGGUGGA
.......(((......))).(((((((((((((....((((((((....))))))))..))--------))))......((((........))))(((((......)))))))))))).. ( -44.80)
>DroSec_CAF1 53328 112 - 1
UUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUGGGGUGCCAGAGU--------GCCAAACAAAUUGUUAACUAUUGUGAUCCGAUUCGAUUUGGAGUCGGUGGA
((((((...)))))).....(((((((((((((....((((((((....))))))))..))--------)))...(((((((......((((.....)))).))))))).)))))))).. ( -46.20)
>DroSim_CAF1 39821 112 - 1
UUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUGGGGUGCCAGAGU--------GCCAAACAAAUUGUUAACUAUUGUGAUCCGAUUCGAUUUGGAGUCGGUGGA
((((((...)))))).....(((((((((((((....((((((((....))))))))..))--------)))...(((((((......((((.....)))).))))))).)))))))).. ( -46.20)
>DroEre_CAF1 58139 112 - 1
UUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGGGU--------GCCAAACAAAUGGUUAACUAUUGUGAUCCGAUUCGAUUUGGAAUCGGUGGA
((((((...)))))).....((((((.(((((((...((((((((....)))))))).)))--------)))).((((.(((....)))))))..(((((......))))).)))))).. ( -47.20)
>DroYak_CAF1 56547 120 - 1
UUCUCGAACCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGGGUGCCAGAGUGCCAAACAAAUUGUUAACUAUUGUGAUCCGAUUCGAUGUGGAGUCGGUGGA
........(((.....(((((.....((((((((...((((((((....)))))))).)))))))).)))))........................(((((((......)))))))))). ( -50.10)
>consensus
UUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGAGU________GCCAAACAAAUUGUUAACUAUUGUGAUCCGAUUCGAUUUGGAGUCGGUGGA
(((((.....))))).(((((.((....((((((....)))))).....)))))))..............((((((.....)))............(((((((......)))))))))). (-36.64 = -36.68 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,594,655 – 9,594,767
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.97
Mean single sequence MFE -48.14
Consensus MFE -47.28
Energy contribution -47.04
Covariance contribution -0.24
Combinations/Pair 1.09
Mean z-score -3.40
Structure conservation index 0.98
SVM decision value 5.80
SVM RNA-class probability 0.999994
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9594655 112 + 22224390
AUUUGUUUGGC--------ACUCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGUUUGAAAACCCAUCGAUCCCAGCGGCAAAUUAGCCACUGCAACGCCCC
........(((--------.((((((....))))))((((((....)))))).)))(((((.........((.((((.......)))).))(((.(((......))).)))..))))).. ( -41.70)
>DroSec_CAF1 53368 112 + 1
AUUUGUUUGGC--------ACUCUGGCACCCCAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAACCCAUCGAUCCCAGCGGCAAAUUAGCCACUGCAACGCCCC
........(((--------.((((((....))))))((((((....)))))).)))(((((.........(((((((.......)))))))(((.(((......))).)))..))))).. ( -50.00)
>DroSim_CAF1 39861 112 + 1
AUUUGUUUGGC--------ACUCUGGCACCCCAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAACCCAUCGAUCCCAGCGGCAAAUUAGCCACUGCAACGCCCC
........(((--------.((((((....))))))((((((....)))))).)))(((((.........(((((((.......)))))))(((.(((......))).)))..))))).. ( -50.00)
>DroEre_CAF1 58179 112 + 1
AUUUGUUUGGC--------ACCCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAACCCAUCGAUCCCAGCGGCAAAUUAGCCACUGCAACGCCCC
........(((--------.((((((....))))))((((((....)))))).)))(((((.........(((((((.......)))))))(((.(((......))).)))..))))).. ( -50.70)
>DroYak_CAF1 56587 120 + 1
AUUUGUUUGGCACUCUGGCACCCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGUUCGAGAACCCAUCGAUCCCAGCGGCAAAUUAGCCACUGCAACGCCCC
........(((((.(((((.((((((....))))))((((((....)))))).))))).)).........((.((((.......)))).))(((.(((......))).)))....))).. ( -48.30)
>consensus
AUUUGUUUGGC________ACUCUGGCACCCUAGGGGGCGCCACUUGGCGCCAGUCGGCGUACCUUCUUCGGGUCGAAAACCCAUCGAUCCCAGCGGCAAAUUAGCCACUGCAACGCCCC
........(((.........((((((....))))))((((((....)))))).)))(((((.........(((((((.......)))))))(((.(((......))).)))..))))).. (-47.28 = -47.04 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,594,655 – 9,594,767
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.97
Mean single sequence MFE -55.24
Consensus MFE -48.32
Energy contribution -48.52
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.49
Structure conservation index 0.87
SVM decision value 4.14
SVM RNA-class probability 0.999814
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9594655 112 - 22224390
GGGGCGUUGCAGUGGCUAAUUUGCCGCUGGGAUCGAUGGGUUUUCAAACCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGAGU--------GCCAAACAAAU
..((((((.(((((((......))))))).))((..(.((((....)))).).)).....))))...((((((....((((((((....))))))))..))--------))))....... ( -48.70)
>DroSec_CAF1 53368 112 - 1
GGGGCGUUGCAGUGGCUAAUUUGCCGCUGGGAUCGAUGGGUUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUGGGGUGCCAGAGU--------GCCAAACAAAU
..(((((.((((((((......))))))(((.((((.......))))))).......)))))))...((((((....((((((((....))))))))..))--------))))....... ( -54.70)
>DroSim_CAF1 39861 112 - 1
GGGGCGUUGCAGUGGCUAAUUUGCCGCUGGGAUCGAUGGGUUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUGGGGUGCCAGAGU--------GCCAAACAAAU
..(((((.((((((((......))))))(((.((((.......))))))).......)))))))...((((((....((((((((....))))))))..))--------))))....... ( -54.70)
>DroEre_CAF1 58179 112 - 1
GGGGCGUUGCAGUGGCUAAUUUGCCGCUGGGAUCGAUGGGUUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGGGU--------GCCAAACAAAU
..(((((.((((((((......))))))(((.((((.......))))))).......)))))))...(((((((...((((((((....)))))))).)))--------))))....... ( -57.50)
>DroYak_CAF1 56587 120 - 1
GGGGCGUUGCAGUGGCUAAUUUGCCGCUGGGAUCGAUGGGUUCUCGAACCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGGGUGCCAGAGUGCCAAACAAAU
(((((((..(((((((......)))))))((.((((.......)))).)).........)))))..((((((((...((((((((....)))))))).))))))))....))........ ( -60.60)
>consensus
GGGGCGUUGCAGUGGCUAAUUUGCCGCUGGGAUCGAUGGGUUUUCGACCCGAAGAAGGUACGCCGACUGGCGCCAAGUGGCGCCCCCUAGGGUGCCAGAGU________GCCAAACAAAU
(((((((..(((((((......)))))))((.((((.......)))).)).........)))))..((((((((....)))((((....)))))))))............))........ (-48.32 = -48.52 +   0.20)

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 11:02:46 2006