Locus 4057

Sequence ID 3R_DroMel_CAF1
Location 11,047,332 – 11,047,612
Length 280
Max. P 0.965467
window6500 window6501 window6502 window6503 window6504 window6505

overview

Window 0

Location 11,047,332 – 11,047,452
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -42.90
Consensus MFE -40.63
Energy contribution -40.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.34
Structure conservation index 0.95
SVM decision value 1.11
SVM RNA-class probability 0.916062
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11047332 120 - 27905053
CAGCACCUCCAACCAGAGGUGAAGAACCUGUUCGUUGAGGCCCAAACAGAUCAGCGAGCGUAACUUAACAUCCAUUUGUGCGUGCGCAUCAUCGUGCGUCUGAUUGAUGGCCUGAACGCA
...((((((......))))))..(((....)))(((.((((((((.(((((..(((((((((.....(((......)))...)))))....))))..))))).)))..))))).)))... ( -42.10)
>DroSec_CAF1 10102 120 - 1
CAGCACCUCCAACCACAGGUGAAGAACCUGUUCGUUGAGGCCCAAACAGAUCAGCGAGCGUAACUUAACAUCCAUUUGUGCGUGCGCAUCGUCGUGCGUCUGAUUGAUGGCCUGAACGCA
..((..........((((((.....))))))..(((.((((((((.((((((((((((((((.....(((......)))...))))).))))..)).))))).)))..))))).))))). ( -43.40)
>DroSim_CAF1 10120 120 - 1
CAGCACCUCCAACCAGAGGUGAAGAACCUGUUCGUUGAGGCCCAAACAGAUCAGCGAGCGUAACUUAACAUCCAUUUGUGCGUGCGCAUCGUCGUGCGUCUGAUUGAUGGCCUGAACGCA
...((((((......))))))..(((....)))(((.((((((((.((((((((((((((((.....(((......)))...))))).))))..)).))))).)))..))))).)))... ( -43.20)
>consensus
CAGCACCUCCAACCAGAGGUGAAGAACCUGUUCGUUGAGGCCCAAACAGAUCAGCGAGCGUAACUUAACAUCCAUUUGUGCGUGCGCAUCGUCGUGCGUCUGAUUGAUGGCCUGAACGCA
...((((((......))))))..(((....)))(((.((((((((.(((((..(((((((((.....(((......)))...)))))....))))..))))).)))..))))).)))... (-40.63 = -40.97 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,047,412 – 11,047,532
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -41.33
Consensus MFE -39.57
Energy contribution -40.23
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.96
SVM decision value 0.60
SVM RNA-class probability 0.795824
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11047412 120 - 27905053
CACUUGAUCUGCACCCAACCGGGUGAGUCAAUAAAGCUCCAGGAAUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCACAGCACCUCCAACCAGAGGUGAAGAACCUGUUCGUUGAGG
...(((((...(((((....))))).)))))........(((((.((....)).))))).....(((((..(((((..(....((((((......))))))..)..)))))..)..)))) ( -36.80)
>DroSec_CAF1 10182 120 - 1
CACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCCAGGAGUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCACAGCACCUCCAACCACAGGUGAAGAACCUGUUCGUUGAGG
....((...(((.((..((((((.((((.......))))((((((((....))))))))........)))))).)).)))...))((((.(((.((((((.....))))))..))))))) ( -44.40)
>DroSim_CAF1 10200 120 - 1
CACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCCAGGAGUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCACAGCACCUCCAACCAGAGGUGAAGAACCUGUUCGUUGAGG
...(((((...(((((....))))).)))))........((((((((....)))))))).....(((((..(((((..(....((((((......))))))..)..)))))..)..)))) ( -42.80)
>consensus
CACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCCAGGAGUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCACAGCACCUCCAACCAGAGGUGAAGAACCUGUUCGUUGAGG
...(((((...(((((....))))).)))))........((((((((....)))))))).....(((((..(((((..(....((((((......))))))..)..)))))..)..)))) (-39.57 = -40.23 +   0.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,047,452 – 11,047,572
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -43.53
Consensus MFE -41.21
Energy contribution -40.77
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.62
Structure conservation index 0.95
SVM decision value 0.11
SVM RNA-class probability 0.588160
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11047452 120 + 27905053
UGCGCCUGCCAGGAGGUCGUACAGAAGUGGUAUCAUUCCUGGAGCUUUAUUGACUCACCCGGUUGGGUGCAGAUCAAGUGCGAGCUGCGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAAC
...((...(((((((...((((.......))))..))))))).))..........(((((....)))))(((((.(((.((((((((((........)))))))))))))..)))))... ( -45.80)
>DroSec_CAF1 10222 120 + 1
UGCGCCUGCCAGGAGGUCGUACAGAAGUGGUAUCACUCCUGGAGCUUUAUUGACUCACCCGGCUGGGUGCAGAUCAAGUGCGAGCUACGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAAC
.(((((((((.((........(((.((((....)))).)))((((......).))).)).))).))))))((((.(((.(((((((.((........)).))))))))))..)))).... ( -42.40)
>DroSim_CAF1 10240 120 + 1
UGCGCCUGCCAGGAGGUCGUACAGAAGUGGUAUCACUCCUGGAGCUUUAUUGACUCACCCGGCUGGGUGCAGAUCAAGUGCGAGCUACGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAAC
.(((((((((.((........(((.((((....)))).)))((((......).))).)).))).))))))((((.(((.(((((((.((........)).))))))))))..)))).... ( -42.40)
>consensus
UGCGCCUGCCAGGAGGUCGUACAGAAGUGGUAUCACUCCUGGAGCUUUAUUGACUCACCCGGCUGGGUGCAGAUCAAGUGCGAGCUACGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAAC
.(((((((((.((........(((.((((....)))).)))((((......).))).)).))).))))))((((.(((.(((((((.((........)).))))))))))..)))).... (-41.21 = -40.77 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,047,452 – 11,047,572
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -45.83
Consensus MFE -44.85
Energy contribution -45.30
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.48
Structure conservation index 0.98
SVM decision value 1.58
SVM RNA-class probability 0.965467
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11047452 120 - 27905053
GUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGCAGCUCGCACUUGAUCUGCACCCAACCGGGUGAGUCAAUAAAGCUCCAGGAAUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCA
...(((((..(..((((.(((((........))))).))))..)..)))))(((((....)))))..........(((((((((.((.(((.......)))))...))))))..)))... ( -42.50)
>DroSec_CAF1 10222 120 - 1
GUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGUAGCUCGCACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCCAGGAGUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCA
....((((..(..((((.(((((........))))).))))..)..))))((.((..((((((.((((.......))))((((((((....))))))))........)))))).)).)). ( -47.50)
>DroSim_CAF1 10240 120 - 1
GUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGUAGCUCGCACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCCAGGAGUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCA
....((((..(..((((.(((((........))))).))))..)..))))((.((..((((((.((((.......))))((((((((....))))))))........)))))).)).)). ( -47.50)
>consensus
GUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGUAGCUCGCACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCCAGGAGUGAUACCACUUCUGUACGACCUCCUGGCAGGCGCA
((.(((((..(..((((.(((((........))))).))))..)..))))).))((.((((((.((((.......))))((((((((....))))))))........)))))).)).... (-44.85 = -45.30 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,047,492 – 11,047,612
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.94
Mean single sequence MFE -52.37
Consensus MFE -46.24
Energy contribution -45.80
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -3.09
Structure conservation index 0.88
SVM decision value 1.25
SVM RNA-class probability 0.936449
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11047492 120 + 27905053
GGAGCUUUAUUGACUCACCCGGUUGGGUGCAGAUCAAGUGCGAGCUGCGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAACCCCGACUGGGAACUGCCGCCGAAGCGCGGCAAGGAGUCGC
...........(((((.((((((((((..(((((.(((.((((((((((........)))))))))))))..)))))...))))))))))...((((((......))))))..))))).. ( -63.10)
>DroSec_CAF1 10262 120 + 1
GGAGCUUUAUUGACUCACCCGGCUGGGUGCAGAUCAAGUGCGAGCUACGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAACCCCGACUGGGAACUGCCUCCGAAACGCGGCAAGGAGUCGC
...........(((((.((((((.((((.(((((.(((.(((((((.((........)).))))))))))..))))).)))).).)))))...((((.(......).))))..))))).. ( -47.30)
>DroSim_CAF1 10280 120 + 1
GGAGCUUUAUUGACUCACCCGGCUGGGUGCAGAUCAAGUGCGAGCUACGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAACCCCGACUGGGAACUGCCCCCGAAACGCGGUAAGGAGUCGC
...........(((((.((((((.((((.(((((.(((.(((((((.((........)).))))))))))..))))).)))).).))))).(((((.........)))))...))))).. ( -46.70)
>consensus
GGAGCUUUAUUGACUCACCCGGCUGGGUGCAGAUCAAGUGCGAGCUACGCAUUCUCUCGCAGUUCGCCUUCAAUCUGAACCCCGACUGGGAACUGCCCCCGAAACGCGGCAAGGAGUCGC
...........(((((.((((((.((((.(((((.(((.(((((((.((........)).))))))))))..))))).)))).).)))))...((((.(......).))))..))))).. (-46.24 = -45.80 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,047,492 – 11,047,612
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.94
Mean single sequence MFE -50.47
Consensus MFE -47.61
Energy contribution -47.50
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -2.20
Structure conservation index 0.94
SVM decision value 0.99
SVM RNA-class probability 0.895383
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11047492 120 - 27905053
GCGACUCCUUGCCGCGCUUCGGCGGCAGUUCCCAGUCGGGGUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGCAGCUCGCACUUGAUCUGCACCCAACCGGGUGAGUCAAUAAAGCUCC
..(((((.(((((((......)))))))..(((.((..((((.(((((..(..((((.(((((........))))).))))..)..))))).)))).)).))).)))))........... ( -55.80)
>DroSec_CAF1 10262 120 - 1
GCGACUCCUUGCCGCGUUUCGGAGGCAGUUCCCAGUCGGGGUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGUAGCUCGCACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCC
..(((((.(((((.(......).)))))..(((.((..((((.(((((..(..((((.(((((........))))).))))..)..))))).)))).)).))).)))))........... ( -48.40)
>DroSim_CAF1 10280 120 - 1
GCGACUCCUUACCGCGUUUCGGGGGCAGUUCCCAGUCGGGGUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGUAGCUCGCACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCC
..(((((....(((.(((..((((.....)))).....((((.(((((..(..((((.(((((........))))).))))..)..))))).))))))))))..)))))........... ( -47.20)
>consensus
GCGACUCCUUGCCGCGUUUCGGAGGCAGUUCCCAGUCGGGGUUCAGAUUGAAGGCGAACUGCGAGAGAAUGCGUAGCUCGCACUUGAUCUGCACCCAGCCGGGUGAGUCAAUAAAGCUCC
..(((((.(((((.(......).)))))..(((.((..((((.(((((..(..((((.(((((........))))).))))..)..))))).)))).)).))).)))))........... (-47.61 = -47.50 +  -0.11)

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 11:17:06 2006