Locus 5970

Sequence ID 3R_DroMel_CAF1
Location 15,759,998 – 15,760,337
Length 339
Max. P 0.979069
window9742 window9743 window9744 window9745

overview

Window 2

Location 15,759,998 – 15,760,118
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.69
Mean single sequence MFE -56.50
Consensus MFE -50.66
Energy contribution -51.23
Covariance contribution 0.56
Combinations/Pair 1.02
Mean z-score -1.91
Structure conservation index 0.90
SVM decision value 0.71
SVM RNA-class probability 0.829302
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15759998 120 + 27905053
UGGCUGCCGAAUGCAGAGGAGUGGAUGCCGCUGUUGAGGCGCCACUUCCGCUUCCGGUGGCCGUAUCCGUGUGACUGGGAGUCGGACGGAAGCGUAGGCGCUGCGGCAACGAAGGAGUAC
.(((..(((...((.(.(((((((.((((........))))))))))))))...)))..)))((.(((((.((((.....)))).))))).))(((..(.((.((....)).)))..))) ( -56.20)
>DroSec_CAF1 17194 120 + 1
UUGCUGCCGAAUGCAGAGGAGUGGAUGCCGCUGUUGAGGCUCCACUUCCGCUUCCGGUGGCCGUAUCCGUGUGACUGGGAGUCGGACGGAAGCGCAGGCGCUGCGGCAACGAAGGAGUAC
.((((.(((((.((.(.((((((((.(((........)))))))))))))))))((...(((((.(((((.((((.....)))).)))))((((....)))))))))..))..)))))). ( -55.40)
>DroSim_CAF1 17152 120 + 1
UGGCAGCCGAGUGCAGAGGAGUGGAUGCCGCUGUUGAGGCUCCACUUCCGCUUCCAGUGGCCGUAUCCGUGUGACUGGGUGUCGGACGGAAGCGCAGGCGCUGCGGCAACGAAGGAGUAC
..((.(((((((((...((((((((.(((........)))))))))))(((((((.((..(((((((((......)))))).))))))))))))...))))).))))..(....).)).. ( -54.70)
>DroEre_CAF1 19594 120 + 1
UGGCUGCCGAAUGCAGCGGAGUGGAUGCCGCUGUUGAGGCGCCACUUCCGCUUCCGGUGGCCGCAUCCGUGUGACUGGGAGUCGGACGGAAGCGCAGUCGCUGCGGCAACGAAGGAGUAC
.(((..(((...(.((((((((((.((((........)))))))).)))))).))))..)))((.(((((.((((.....)))).))))).))..(.((.((.((....)).)))).).. ( -59.70)
>consensus
UGGCUGCCGAAUGCAGAGGAGUGGAUGCCGCUGUUGAGGCGCCACUUCCGCUUCCGGUGGCCGUAUCCGUGUGACUGGGAGUCGGACGGAAGCGCAGGCGCUGCGGCAACGAAGGAGUAC
...((((.....)))).((((((((.(((........))))))))))).(((((..((.(((((.(((((.((((.....)))).)))))((((....))))))))).))...))))).. (-50.66 = -51.23 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,759,998 – 15,760,118
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.69
Mean single sequence MFE -46.67
Consensus MFE -43.09
Energy contribution -43.65
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.92
SVM decision value 0.91
SVM RNA-class probability 0.879969
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15759998 120 - 27905053
GUACUCCUUCGUUGCCGCAGCGCCUACGCUUCCGUCCGACUCCCAGUCACACGGAUACGGCCACCGGAAGCGGAAGUGGCGCCUCAACAGCGGCAUCCACUCCUCUGCAUUCGGCAGCCA
..........(((((((..((......(((((((.(((..(((.........)))..)))....)))))))(((.((((.(((.(....).)))..)))))))...))...))))))).. ( -43.80)
>DroSec_CAF1 17194 120 - 1
GUACUCCUUCGUUGCCGCAGCGCCUGCGCUUCCGUCCGACUCCCAGUCACACGGAUACGGCCACCGGAAGCGGAAGUGGAGCCUCAACAGCGGCAUCCACUCCUCUGCAUUCGGCAGCAA
..........((((((((((((....))))(((((..(((.....)))..)))))....))....(((.((((((((((((((.(....).))).))))))..))))).))))))))).. ( -48.60)
>DroSim_CAF1 17152 120 - 1
GUACUCCUUCGUUGCCGCAGCGCCUGCGCUUCCGUCCGACACCCAGUCACACGGAUACGGCCACUGGAAGCGGAAGUGGAGCCUCAACAGCGGCAUCCACUCCUCUGCACUCGGCUGCCA
....(((...((.((((.((((....))))(((((..(((.....)))..)))))..)))).)).))).((((((((((((((.(....).))).))))))..)))))............ ( -44.30)
>DroEre_CAF1 19594 120 - 1
GUACUCCUUCGUUGCCGCAGCGACUGCGCUUCCGUCCGACUCCCAGUCACACGGAUGCGGCCACCGGAAGCGGAAGUGGCGCCUCAACAGCGGCAUCCACUCCGCUGCAUUCGGCAGCCA
..........(((((....)))))...((.(((((..(((.....)))..))))).))(((..(((((((((((.((((.(((.(....).)))..))))))))))...)))))..))). ( -50.00)
>consensus
GUACUCCUUCGUUGCCGCAGCGCCUGCGCUUCCGUCCGACUCCCAGUCACACGGAUACGGCCACCGGAAGCGGAAGUGGAGCCUCAACAGCGGCAUCCACUCCUCUGCAUUCGGCAGCCA
..........(((((((..((......(((((((...(((.....)))....((......))..)))))))(((.((((((((.(....).))).))))))))...))...))))))).. (-43.09 = -43.65 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,760,118 – 15,760,238
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -39.72
Consensus MFE -34.46
Energy contribution -34.74
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -1.19
Structure conservation index 0.87
SVM decision value -0.02
SVM RNA-class probability 0.521812
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15760118 120 - 27905053
GCAAGGAGCAGAUCGAGAAGUUCUUCAAGGACGCCGUGCGUUUCGCGUCCAGCUCGAAGGAGGCCAAGGAAUUUGCCAUUCCCAAGGAGGACAAAAAGUCAAAGGGAUUACGUCUGUUCC
....((((((((.((....(((((((..((((((.(......).))))))..(((....))).....(((((.....)))))...)))))))....((((.....)))).)))))))))) ( -40.70)
>DroSec_CAF1 17314 120 - 1
GCAAGGAGCAGAUCGAGAAGUUCUUCAAGGACGCCGUGCGUUUCGCGUCCAGCUCGAAGGAGGCCAAGGAAUUCGCCAUUCCCAAGGAGGACAAAAAGUCAAAGGGAUUACGCCUGUUCC
....(((((((.....(((.(((((...((((((.(......).))))))..(((....)))...))))).)))((...((((......(((.....)))...))))....))))))))) ( -37.80)
>DroSim_CAF1 17272 120 - 1
GCAAGGAGCAGAUCGAGAAGUUCUUCAAGGACGCCGUGCGUUUCGCGUCCAGCUCGAAGGAGGCCAAGGAAUUCGCCAUUCCCAAGGAGGACAAAAAGUCAAAGGGAUUACGCCUGUUCC
....(((((((.....(((.(((((...((((((.(......).))))))..(((....)))...))))).)))((...((((......(((.....)))...))))....))))))))) ( -37.80)
>DroEre_CAF1 19714 120 - 1
GCAAGGAGCAGAUCGAAAAGUUCUUCAAGGACGCCGUGCGUUUCGCGUCCAGCUCGAAGGACGCCAAGGAAUUCGCCAUUCCCAAGGAGGACAAGAAGUCCAAGGGAUUACGCCUGUUCC
....(((((((..((....(((((((..((((((...)))))).((((((........))))))...(((((.....)))))...)))))))....(((((...))))).)).))))))) ( -39.50)
>DroPer_CAF1 17448 120 - 1
GCAAGGAGCAGAUCGAAAAGUUCUUCAAGGAUGCGGUGCGCUUUGCCUCCAGCUCGAAGGAGGCCAAGGAGUUUGCCAUUCCCAAGGAGGACAAAAAGUCCAAGGGUCUGCGUCUGUUCA
...((..(((((((......(((((...(((...((((.(((((((((((........))))))...))))).))))..))).)))))((((.....))))...)))))))..))..... ( -42.80)
>consensus
GCAAGGAGCAGAUCGAGAAGUUCUUCAAGGACGCCGUGCGUUUCGCGUCCAGCUCGAAGGAGGCCAAGGAAUUCGCCAUUCCCAAGGAGGACAAAAAGUCAAAGGGAUUACGCCUGUUCC
....(((((((........(((((((..((((((.(......).)))))).((((....)).))...(((((.....)))))...)))))))....((((.....))))....))))))) (-34.46 = -34.74 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,760,238 – 15,760,337
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.40
Mean single sequence MFE -56.62
Consensus MFE -39.28
Energy contribution -40.32
Covariance contribution 1.04
Combinations/Pair 1.16
Mean z-score -2.28
Structure conservation index 0.69
SVM decision value 1.83
SVM RNA-class probability 0.979069
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15760238 99 + 27905053
GUUCCGGUUGAACGGUUGGCGGA---------------------GCAGCGGCUGCCGAAGACGCGGUGGGCGUGGCACUGCCCGCCGAUCCCGCCGAGCUGUUGGACGCAGCUGGCGAAC
((((.((..((.((((.(((((.---------------------((.(((.(..(((......)))..).))).)).))))).)))).))))(((.((((((.....))))))))))))) ( -51.70)
>DroSec_CAF1 17434 99 + 1
GUUCCGGUUGAACGGUGGGCGGA---------------------GCAGCGGCUGCCGAAGCCGCGGUGGGCGUGGCACUGCCCGCCGAUCCCGCCGAGCUGUUGGACGCAGCUGGCGAAC
((((.((..((.((((((((((.---------------------((.(((.(..(((......)))..).))).)).)))))))))).))))(((.((((((.....))))))))))))) ( -57.50)
>DroSim_CAF1 17392 99 + 1
GUUCCGGUUGAACGGUGGGCGGA---------------------GCAGCGGCUGCCGAAGCCGCGGUGGGCGUGGCACUGCCCGCCGAUCCCGCCGAGCUGUUGGACGCAGCUGGCGAAC
((((.((..((.((((((((((.---------------------((.(((.(..(((......)))..).))).)).)))))))))).))))(((.((((((.....))))))))))))) ( -57.50)
>DroEre_CAF1 19834 84 + 1
GCUCCGGCUGAACGGUGGGCGGA---------------------GCAGC---------------GGUGGGCGUGGCACUGCCCGCCGAUCCCGCCGAGCUGUUGGACGCAGCUGGCGAAC
((((((.((.......)).))))---------------------))..(---------------((((((((......)))))))))....((((.((((((.....))))))))))... ( -47.00)
>DroPer_CAF1 17568 120 + 1
GCUCCGGCUGCACGGGUGCCGGAUUGGCCGCCACAGUGGCGGCUGCGGCGGCCGCAGCAGCUGUUGUGGGCGUGGCACUGCCCGUGGAACCGGCAGAGCUGUUGGAGGCAGCUGGCGAGG
.(.((((((((((((((........(((((((.....)))))))((.(((.(((((((....))))))).))).))...))))))....((((((....))))))..)))))))).)... ( -69.40)
>consensus
GUUCCGGUUGAACGGUGGGCGGA_____________________GCAGCGGCUGCCGAAGCCGCGGUGGGCGUGGCACUGCCCGCCGAUCCCGCCGAGCUGUUGGACGCAGCUGGCGAAC
...(((((((((((((.(((((.........................((((((.....))))))((((((((......))))))))....)))))..)))))).....)))))))..... (-39.28 = -40.32 +   1.04)

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 12:09:21 2006