Locus 2608

Sequence ID 3L_DroMel_CAF1
Location 7,224,937 – 7,225,106
Length 169
Max. P 0.997885
window4081 window4082 window4083 window4084 window4085

overview

Window 1

Location 7,224,937 – 7,225,047
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 95.09
Mean single sequence MFE -26.17
Consensus MFE -21.17
Energy contribution -22.50
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -4.42
Structure conservation index 0.81
SVM decision value 0.76
SVM RNA-class probability 0.842232
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7224937 110 + 23771897
AUAAGUGGUUUAUAUGUGGCUAUUCAUAUUUCUUCUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAUACAUAUGUACAUAUGCAUAACAAUC
....(((((((...((.(((..................)))))((((....)))).....))))))).((((((((((((((......)))))))))..)))))...... ( -26.17)
>DroSec_CAF1 6630 102 + 1
AUAAGUGGUUUAUAUGUGGCUAUUCAUAUUUCUUCUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAU--------ACAUAUGCAUAACAAUC
......(((((...((.(((..................)))))((((....)))).....)))))((((((((((((....))))--------))))))))......... ( -27.07)
>DroSim_CAF1 6583 106 + 1
AUAAGUGGUUUAUAUGUGGCUAUUCAUAUUUCUUCUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAU----AUGUACAUAUGCAUAACAAUC
......(((((...((.(((..................)))))((((....)))).....)))))(((((((((((((......)----))))))))))))......... ( -25.27)
>consensus
AUAAGUGGUUUAUAUGUGGCUAUUCAUAUUUCUUCUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAU____AUGUACAUAUGCAUAACAAUC
....(((((((...((.(((..................)))))((((....)))).....))))))).(((((((((((((........))))))))..)))))...... (-21.17 = -22.50 +   1.33)

alignment

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secondary structure

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Window 2

Location 7,224,937 – 7,225,047
Length 110
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 95.09
Mean single sequence MFE -28.94
Consensus MFE -24.47
Energy contribution -24.47
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.85
SVM decision value 0.89
SVM RNA-class probability 0.875528
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7224937 110 - 23771897
GAUUGUUAUGCAUAUGUACAUAUGUAUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAGAAGAAAUAUGAAUAGCCACAUAUAAACCACUUAU
.........(((((((((....(((((....))))))))))))))((((((((((((((....))))).(((..................))).))).))))))...... ( -28.67)
>DroSec_CAF1 6630 102 - 1
GAUUGUUAUGCAUAUGU--------AUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAGAAGAAAUAUGAAUAGCCACAUAUAAACCACUUAU
.........((((((((--------((((....))))))))))))((((((((((((((....))))).(((..................))).))).))))))...... ( -31.47)
>DroSim_CAF1 6583 106 - 1
GAUUGUUAUGCAUAUGUACAU----AUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAGAAGAAAUAUGAAUAGCCACAUAUAAACCACUUAU
.........(((((((((..(----((....)))..)))))))))((((((((((((((....))))).(((..................))).))).))))))...... ( -26.67)
>consensus
GAUUGUUAUGCAUAUGUACAU____AUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAGAAGAAAUAUGAAUAGCCACAUAUAAACCACUUAU
.........((((((((........((((....))))))))))))((((((((((((((....))))).(((..................))).))).))))))...... (-24.47 = -24.47 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,224,971 – 7,225,066
Length 95
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 93.59
Mean single sequence MFE -23.17
Consensus MFE -17.37
Energy contribution -18.70
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -3.84
Structure conservation index 0.75
SVM decision value 0.55
SVM RNA-class probability 0.779034
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7224971 95 + 23771897
CUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAUACAUAUGUACAUAUGCAUAACAAUCAGUAUCGCUGGCUCUCGCG
...(((..(((((....))))).........((((((((((((....))))))))))))...............((((.....)))).....))) ( -22.30)
>DroSec_CAF1 6664 87 + 1
CUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAU--------ACAUAUGCAUAACAAUCAGUAUCGCUGGCUCUCGCG
...(((..(((((....))))).........((((((((((((....))))--------)))))))).......((((.....)))).....))) ( -24.70)
>DroSim_CAF1 6617 91 + 1
CUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAU----AUGUACAUAUGCAUAACAAUCCGUAUCGCUGGCUCUCGCG
....(((.(((((....))))).........(((((((((((((......)----))))))))))))..................)))....... ( -22.50)
>consensus
CUCCGCCCAAAGGAUCCCCUUUCAUCAAACCGCAUAUGUAUGUACAUACAU____AUGUACAUAUGCAUAACAAUCAGUAUCGCUGGCUCUCGCG
....(((.(((((....))))).........((((((((((((............))))))))))))..................)))....... (-17.37 = -18.70 +   1.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,224,971 – 7,225,066
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 93.59
Mean single sequence MFE -30.07
Consensus MFE -25.60
Energy contribution -25.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.91
Structure conservation index 0.85
SVM decision value 1.07
SVM RNA-class probability 0.910157
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7224971 95 - 23771897
CGCGAGAGCCAGCGAUACUGAUUGUUAUGCAUAUGUACAUAUGUAUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAG
(((..(((((((((((....))))))..(((((((((....(((((....)))))))))))))))))))..(.(((((....))))).))))... ( -29.80)
>DroSec_CAF1 6664 87 - 1
CGCGAGAGCCAGCGAUACUGAUUGUUAUGCAUAUGU--------AUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAG
(((..(((((((((((....))))))..((((((((--------((((....)))))))))))))))))..(.(((((....))))).))))... ( -32.60)
>DroSim_CAF1 6617 91 - 1
CGCGAGAGCCAGCGAUACGGAUUGUUAUGCAUAUGUACAU----AUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAG
(((..(((((((((((....))))))..(((((((((..(----((....)))..))))))))))))))..(.(((((....))))).))))... ( -27.80)
>consensus
CGCGAGAGCCAGCGAUACUGAUUGUUAUGCAUAUGUACAU____AUGUAUGUACAUACAUAUGCGGUUUGAUGAAAGGGGAUCCUUUGGGCGGAG
(((..(((((((((((....))))))..((((((((........((((....)))))))))))))))))..(.(((((....))))).))))... (-25.60 = -25.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,225,010 – 7,225,106
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 81.56
Mean single sequence MFE -31.65
Consensus MFE -21.67
Energy contribution -22.68
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -3.29
Structure conservation index 0.68
SVM decision value 2.95
SVM RNA-class probability 0.997885
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7225010 96 - 23771897
UCGCUAUUCGGUUAGCAAGCUGAGUGGCAAAUACUCGGAUCGCGAGAGCCAGCGAUACUGAUUGUUAUGCAUAUGUACAUAUGUAUGUAUGUACAU
..(((((((((((....))))))))))).((((.(((((((((........))))).)))).)))).(((((((((((....)))))))))))... ( -37.40)
>DroSec_CAF1 6703 88 - 1
UCGCUAUUCGGUUAGCAAGCUGAGUGGCAAAUACUCGGAUCGCGAGAGCCAGCGAUACUGAUUGUUAUGCAUAUGU--------AUGUAUGUACAU
..(((((((((((....))))))))))).((((.(((((((((........))))).)))).)))).(((((((..--------..)))))))... ( -31.70)
>DroSim_CAF1 6656 92 - 1
UCGCUAUUCGGUUAGCAAGCUGAGUGGCAAAUACUCCGAUCGCGAGAGCCAGCGAUACGGAUUGUUAUGCAUAUGUACAU----AUGUAUGUACAU
..(((((((((((....)))))))))))......(((((((((........))))).)))).((((((((((((....))----))))))).))). ( -36.10)
>DroAna_CAF1 6539 86 - 1
UCGGUAUUCGGUCAGCAAGCUGAGUGGAAAAUAUUCGGAUCGGGAGAGCCAGCGAUACUAAUCCAGAUGCGAAGACCCAU----CUGCAA------
..(((.((((.((((....)))).)))).....((((.(((.(((................))).))).)))).)))...----......------ ( -21.39)
>consensus
UCGCUAUUCGGUUAGCAAGCUGAGUGGCAAAUACUCGGAUCGCGAGAGCCAGCGAUACUGAUUGUUAUGCAUAUGUACAU____AUGUAUGUACAU
..((((((((((......))))))))))......(((((((((........))))).))))....(((((((............)))))))..... (-21.67 = -22.68 +   1.00)

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 10:37:23 2006