Locus 5348

Sequence ID X_DroMel_CAF1
Location 13,933,563 – 13,933,760
Length 197
Max. P 0.769550
window8676 window8677 window8678

overview

Window 6

Location 13,933,563 – 13,933,680
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.72
Mean single sequence MFE -25.98
Consensus MFE -22.16
Energy contribution -22.24
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.30
Structure conservation index 0.85
SVM decision value 0.21
SVM RNA-class probability 0.633120
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13933563 117 + 22224390
CGUGGGUCAAUGACUUGGCCAAAA-GUUUUUUUUUUGGUUAUUGCUUUUGUUAUUACAACAGCCCACACAC--AUGCCCUGUCAUCCGUGGGCCACUUUUUCUUCUGUCAUUCUUAUUUC
.((((.((((((((.(((((((((-(.....))))))))))..(((.((((....)))).)))........--.......)))))...))).))))........................ ( -27.40)
>DroSec_CAF1 13466 116 + 1
CGUGGGUCAAUGACUUGGCCAAAA-GCUUUU-GUUUGGUUAUUGCUUUUGUUAUUACAACAGCCCACACAC--AUGCCCUGUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUC
.((((.((((((((..(((...((-((....-))))((.....(((.((((....)))).)))))......--..)))..)))))...))).))))........................ ( -25.80)
>DroSim_CAF1 18266 116 + 1
CGUGGGUCAAUGACUUGGCCAAAA-GCUUUU-GUUUGGUUAUUGCUUUUGUUAUUACAACAGCCCACACAC--AUGCCCUGUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUC
.((((.((((((((..(((...((-((....-))))((.....(((.((((....)))).)))))......--..)))..)))))...))).))))........................ ( -25.80)
>DroEre_CAF1 14999 117 + 1
CGUGGGUCAACGACUUGGCCAAAA-GCUUUU-GUUUGGUUAUUGCUUUCGGUACUACAACAGCCCACACAU-CCUGCCAUGUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUC
.(((((((((....))))))....-.....(-(((((((.((((....)))))))).))))((((((((((-......)))).....)))))))))........................ ( -23.70)
>DroYak_CAF1 16421 119 + 1
CGUGGGUCAGUGACUUGGCCAGAAUGCUUUU-GUUUGGUUAUUGCUUUUGUUAUUACAACAGCCCACUCACAUGUGCCCUGUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUC
.((((.((((((((..(((....(((....(-(..(((.....(((.((((....)))).))))))..)))))..)))..)))))...))).))))........................ ( -27.20)
>consensus
CGUGGGUCAAUGACUUGGCCAAAA_GCUUUU_GUUUGGUUAUUGCUUUUGUUAUUACAACAGCCCACACAC__AUGCCCUGUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUC
.((((.((((((((.((((((((..........))))))))..(((.(((......))).))).................)))))...))).))))........................ (-22.16 = -22.24 +   0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,933,602 – 13,933,720
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.10
Mean single sequence MFE -29.60
Consensus MFE -25.47
Energy contribution -25.49
Covariance contribution 0.02
Combinations/Pair 1.12
Mean z-score -1.54
Structure conservation index 0.86
SVM decision value 0.53
SVM RNA-class probability 0.769550
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13933602 118 - 22224390
UCUGUCGGCCUUAUCAAGUCGAGGGAAAAAAAGCCGAGCCGAAAUAAGAAUGACAGAAGAAAAAGUGGCCCACGGAUGACAGGGCAU--GUGUGUGGGCUGUUGUAAUAACAAAAGCAAU
(((((((..(((((....(((.((.........))....))).)))))..)))))))......((..(((((((.((..........--)).)))))))..))................. ( -30.90)
>DroSec_CAF1 13504 117 - 1
UCUGUCGGCCUUAUCAAGUCGAGGUA-AAAAAGCCGAGCCGAAAUAAGAAUGGCAGAAGAAAAAGUGGCCCACGGAUGACAGGGCAU--GUGUGUGGGCUGUUGUAAUAACAAAAGCAAU
(((((((..(((((....(((.(((.-.....)))....))).)))))..)))))))......((..(((((((.((..........--)).)))))))..))................. ( -32.90)
>DroSim_CAF1 18304 117 - 1
UCUGUCGGCCUUAUCAAGUCGAGGUA-AAAAAGCCGAGCCGAAAUAAGAAUGGCAGAAGAAAAAGUGGCCCACGGAUGACAGGGCAU--GUGUGUGGGCUGUUGUAAUAACAAAAGCAAU
(((((((..(((((....(((.(((.-.....)))....))).)))))..)))))))......((..(((((((.((..........--)).)))))))..))................. ( -32.90)
>DroEre_CAF1 15037 99 - 1
UCUAUCAGCCUUAUCAA--------------------GCCGAAAUAAGAAUGGCAGAAGAAAAAGUGGCCCACGGAUGACAUGGCAGG-AUGUGUGGGCUGUUGUAGUACCGAAAGCAAU
(((..((..(((((...--------------------......)))))..))..)))......((..(((((((.((..(......).-)).)))))))..)).......(....).... ( -22.30)
>DroYak_CAF1 16460 119 - 1
UCUGUCGGCCUUAUCAAGUUGAGGGA-AAAAAGCCGAGCCGAAAUAAGAAUGGCAGAAGAAAAAGUGGCCCACGGAUGACAGGGCACAUGUGAGUGGGCUGUUGUAAUAACAAAAGCAAU
(((((((..(((((...(((..((..-......)).)))....)))))..)))))))......((..((((((...(.(((.......))).)))))))..))................. ( -29.00)
>consensus
UCUGUCGGCCUUAUCAAGUCGAGGGA_AAAAAGCCGAGCCGAAAUAAGAAUGGCAGAAGAAAAAGUGGCCCACGGAUGACAGGGCAU__GUGUGUGGGCUGUUGUAAUAACAAAAGCAAU
(((((((..(((((........((.........))........)))))..)))))))......((..(((((((.((............)).)))))))..))................. (-25.47 = -25.49 +   0.02)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,933,640 – 13,933,760
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.45
Mean single sequence MFE -30.64
Consensus MFE -23.37
Energy contribution -25.05
Covariance contribution 1.68
Combinations/Pair 1.08
Mean z-score -1.71
Structure conservation index 0.76
SVM decision value 0.33
SVM RNA-class probability 0.692866
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13933640 120 + 22224390
GUCAUCCGUGGGCCACUUUUUCUUCUGUCAUUCUUAUUUCGGCUCGGCUUUUUUUCCCUCGACUUGAUAAGGCCGACAGACGCUGCCCAUACCGGCCACCUGACAAACACCUGUCUGGCC
.......((((((..........((((((..(((((((..((.((((...........)))))).)))))))..))))))....))))))...(((((...((((......))))))))) ( -32.44)
>DroSec_CAF1 13542 119 + 1
GUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUCGGCUCGGCUUUUU-UACCUCGACUUGAUAAGGCCGACAGACGCUGCCCAUCCCGGCCACCUGACAAACACCUGUCUGGCC
.......((((((.............(((...........)))((((((((.(-((........))).))))))))........))))))...(((((...((((......))))))))) ( -33.50)
>DroSim_CAF1 18342 119 + 1
GUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUCGGCUCGGCUUUUU-UACCUCGACUUGAUAAGGCCGACAGACGCUGCCCAUCCCGGCCACCUGACAAACACCUGUCUGGCC
.......((((((.............(((...........)))((((((((.(-((........))).))))))))........))))))...(((((...((((......))))))))) ( -33.50)
>DroEre_CAF1 15076 100 + 1
GUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUCGGC--------------------UUGAUAAGGCUGAUAGACGCUGCCCAUCCCGCCCGCCUGACAAACACCUGUCUGGCC
.......((((((.............((...(((....(((((--------------------((....))))))).))).)).)))))).......(((.((((......)))).))). ( -26.44)
>DroYak_CAF1 16500 119 + 1
GUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUCGGCUCGGCUUUUU-UCCCUCAACUUGAUAAGGCCGACAGACGCUGCCCAUCCCGUCCACCUGACAAACACCUGUCUGGCC
.......((((((.............(((...........)))((((((((..-((.........)).))))))))........))))))........((.((((......)))).)).. ( -27.30)
>consensus
GUCAUCCGUGGGCCACUUUUUCUUCUGCCAUUCUUAUUUCGGCUCGGCUUUUU_UACCUCGACUUGAUAAGGCCGACAGACGCUGCCCAUCCCGGCCACCUGACAAACACCUGUCUGGCC
.......((((((.............(((...........)))((((((((.................))))))))........))))))...(((((...((((......))))))))) (-23.37 = -25.05 +   1.68)

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 11:45:47 2006