Locus 3109

Sequence ID 2R_DroMel_CAF1
Location 10,631,021 – 10,631,154
Length 133
Max. P 0.998589
window5130 window5131 window5132

overview

Window 0

Location 10,631,021 – 10,631,120
Length 99
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 69.15
Mean single sequence MFE -26.38
Consensus MFE -13.51
Energy contribution -14.23
Covariance contribution 0.72
Combinations/Pair 1.33
Mean z-score -3.04
Structure conservation index 0.51
SVM decision value 3.15
SVM RNA-class probability 0.998589
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10631021 99 + 20766785
AUCCCCCCGCACCCACCUAUCGUAACCCCCUUA-GUUUCUCGCUCCUGGGUGGGUGGUUGUUUUUCACAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUA
.(((......(((((((((.((.(((.......-)))...))....)))))))))((((((.....)))))))))(((((..........)))))..... ( -27.70)
>DroPse_CAF1 99218 86 + 1
ACUACCAGACACCCACAUUCCGCCACCUUU-------------UUGGGGGUGGGUGGUUGUUUUUC-CAACAGAGCCACAUCAUAAAUUUCGUGUCUAUA
......((((((.......(((((.(((..-------------..))))))))(((((((((....-.))))..)))))............))))))... ( -27.70)
>DroSec_CAF1 73210 98 + 1
A-CCCCCCGCACCCACCUAUCGUAACCCCCUUG-GUUUCUCGCUCCUUGGUGGGUGGUUGUUUUUCACAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUA
.-....(((((((((((...((.((((.....)-)))...))......))))))))(((((.....)))))))).(((((..........)))))..... ( -28.10)
>DroEre_CAF1 73727 76 + 1
C----UCCCCAUCGUUUCCUUA--------------------CUUCUGGGUGGGUGGUUGUUUUUCACAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUA
.----..((((((.........--------------------......)))))).((((((.....))))))(((.((((..........)))))))... ( -18.46)
>DroYak_CAF1 80825 96 + 1
C----ACCUCACCCUUCCCUUACCACCCCCUGGCUUUUCCUGCUUCUGGGUGGGUGGUUGUUUUUCACAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUA
.----..........(((....((((((...(((.......)))...))))))..((((((.....)))))))))(((((..........)))))..... ( -28.60)
>DroPer_CAF1 100493 86 + 1
ACUACCAGACACCCACAUUCCGCCACCUUU-------------UUGGGGGUGGGUGGUUGUUUUUC-CAACAGAGCCACAUCAUAAAUUUCGUGUCUAUA
......((((((.......(((((.(((..-------------..))))))))(((((((((....-.))))..)))))............))))))... ( -27.70)
>consensus
A___CCCCACACCCACCUAUCGCCACCCCC____________CUUCUGGGUGGGUGGUUGUUUUUCACAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUA
.........((((((((((...........................))))))))))((((.......)))).(((.((((..........)))))))... (-13.51 = -14.23 +   0.72)

alignment

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secondary structure

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Window 1

Location 10,631,060 – 10,631,154
Length 94
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 82.22
Mean single sequence MFE -30.59
Consensus MFE -17.57
Energy contribution -18.57
Covariance contribution 1.00
Combinations/Pair 1.14
Mean z-score -4.56
Structure conservation index 0.57
SVM decision value 1.68
SVM RNA-class probability 0.971796
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10631060 94 + 20766785
CGC---UCCUGGGUGGGUGGUUGUUUUUCA------CAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUAACAAUUUUUGUUAUAUUCA-ACCACC--CCACCCACC-
...---...((((((((.((((((.....)------)))))((.(((((..........))))).(((((((.....)))))))....-.))..)--)))))))..- ( -32.40)
>DroSim_CAF1 74560 94 + 1
CGC---UCCUUGGUGGGUGGUUGUUUUUCA------CAGCCGGAGUUUAUCAUAAAUUUUGUGUCUAUAACAAUUUUUGUUAUAUUCA-ACCACC--CCACCCACC-
...---.....((((((((((((.......------..(((((((((((...))))))))).)).(((((((.....)))))))..))-)))).)--)))))....- ( -27.90)
>DroEre_CAF1 73745 94 + 1
--C---UUCUGGGUGGGUGGUUGUUUUUCA------CAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUAACAAUUUUUGUUAUAUUCAAACCACC--CCACCCACCA
--.---...((((((((.((((((.....)------)))))((.(((((..........))))).(((((((.....)))))))......))..)--)))))))... ( -32.40)
>DroYak_CAF1 80861 90 + 1
UGC---UUCUGGGUGGGUGGUUGUUUUUCA------CAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUAACAAUUUUUGUUAUAUUCA------C--CCACCCAACA
...---...(((((((((((((((.....)------)))))((((((((..........))))).(((((((.....)))))))))))------)--)))))))... ( -33.00)
>DroMoj_CAF1 137973 98 + 1
CGC---AUUGGGUUGGGUGGUUGUUUUUCCUACCACCAGGCGGCGCAUAUCAUAAAUUUUGUGUCUAUAACAAUUUUUGGUUCUCCCA-----CCGCCCACACACC-
...---....(((((((((((.(......).)))))).(((((.(.......((((..((((.......))))..)))).......).-----)))))..)).)))- ( -25.44)
>DroAna_CAF1 108186 96 + 1
CCCUUUUUGGGGGUGGGUGGUUGUUUUUCACA----CAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUAACAAUUUUUGUUAUAUUC----CCCC--UCACCCACA-
((((....))))((((((((((((.......)----)))))((((((((..........))))).(((((((.....))))))).))----)...--..)))))).- ( -32.40)
>consensus
CGC___UUCUGGGUGGGUGGUUGUUUUUCA______CAGCCGGAGCACAUCAUAAAUUUUGUGUCUAUAACAAUUUUUGUUAUAUUCA___CACC__CCACCCACC_
...........(((((((((........................(((((..........))))).(((((((.....))))))).............))))))))). (-17.57 = -18.57 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,631,060 – 10,631,154
Length 94
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 82.22
Mean single sequence MFE -29.90
Consensus MFE -15.26
Energy contribution -16.20
Covariance contribution 0.94
Combinations/Pair 1.05
Mean z-score -3.58
Structure conservation index 0.51
SVM decision value 0.96
SVM RNA-class probability 0.890623
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10631060 94 - 20766785
-GGUGGGUGG--GGUGGU-UGAAUAUAACAAAAAUUGUUAUAGACACAAAAUUUAUGAUGUGCUCCGGCUG------UGAAAAACAACCACCCACCCAGGA---GCG
-..(((((((--(.((((-((..(((((((.....)))))))((((((..........)))).))......------.......))))))))))))))...---... ( -32.30)
>DroSim_CAF1 74560 94 - 1
-GGUGGGUGG--GGUGGU-UGAAUAUAACAAAAAUUGUUAUAGACACAAAAUUUAUGAUAAACUCCGGCUG------UGAAAAACAACCACCCACCAAGGA---GCG
-(((((((((--(((.((-((....)))).....((((((((((.......)))))))))))))))((.((------(.....))).))))))))).....---... ( -29.70)
>DroEre_CAF1 73745 94 - 1
UGGUGGGUGG--GGUGGUUUGAAUAUAACAAAAAUUGUUAUAGACACAAAAUUUAUGAUGUGCUCCGGCUG------UGAAAAACAACCACCCACCCAGAA---G--
.(((((((((--(.(((......(((((((.....)))))))(.((((..........))))).))).)((------(.....))).))))))))).....---.-- ( -28.70)
>DroYak_CAF1 80861 90 - 1
UGUUGGGUGG--G------UGAAUAUAACAAAAAUUGUUAUAGACACAAAAUUUAUGAUGUGCUCCGGCUG------UGAAAAACAACCACCCACCCAGAA---GCA
..((((((((--(------(...(((((((.....)))))))((((((..........)))).)).((.((------(.....))).))))))))))))..---... ( -28.90)
>DroMoj_CAF1 137973 98 - 1
-GGUGUGUGGGCGG-----UGGGAGAACCAAAAAUUGUUAUAGACACAAAAUUUAUGAUAUGCGCCGCCUGGUGGUAGGAAAAACAACCACCCAACCCAAU---GCG
-((..((.((((((-----((((....))......(((((((((.......)))))))))..))))))))((((((.(......).))))))))..))...---... ( -32.20)
>DroAna_CAF1 108186 96 - 1
-UGUGGGUGA--GGGG----GAAUAUAACAAAAAUUGUUAUAGACACAAAAUUUAUGAUGUGCUCCGGCUG----UGUGAAAAACAACCACCCACCCCCAAAAAGGG
-.((((((..--((((----...(((((((.....)))))))..((((..........))))))))((.((----(.......))).)))))))).(((.....))) ( -27.60)
>consensus
_GGUGGGUGG__GGUG___UGAAUAUAACAAAAAUUGUUAUAGACACAAAAUUUAUGAUGUGCUCCGGCUG______UGAAAAACAACCACCCACCCAGAA___GCG
.(((((((((.........................(((((((((.......))))))))).((....))..................)))))))))........... (-15.26 = -16.20 +   0.94)

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 10:47:46 2006