Locus 9601

Sequence ID 3R_DroMel_CAF1
Location 25,358,759 – 25,358,873
Length 114
Max. P 0.963313
window15348 window15349

overview

Window 8

Location 25,358,759 – 25,358,873
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.48
Mean single sequence MFE -26.14
Consensus MFE -21.77
Energy contribution -22.77
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.83
SVM decision value 1.43
SVM RNA-class probability 0.953250
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25358759 114 + 27905053
UGUCACGAUUGGUGGUCUUUUUUGCCACUUU------UCAGCAAUCAUUCAGACAAAUAUCAGAAUAAAAAUGGGCGUAAAAGCUCCUGAUCUUUAUUCAAUUGUAAGACAAGUCAUGAC
.((((.((..((((((.......))))))..------))............(((........(((((((...((((......)).)).....)))))))..(((.....)))))).)))) ( -25.10)
>DroSec_CAF1 43487 113 + 1
UGUCACGAUUGGUGGUCUUU-UAGACACUUU------UCAACAAUCAUUCCGACAAAUAUCAGAAUAAAAAUGGGCGUAAAAGCUCCUGAUUUUUAUUCAAUUGUAAGACAAGUCAUGAC
.((((.((..((((.((...-..))))))..------))............(((........((((((((((((((......))))...))))))))))..(((.....)))))).)))) ( -25.50)
>DroSim_CAF1 43753 119 + 1
UGUCACGAUUGGUGGUCUUU-UAGCCACUUUAGCCACUCAACAAUCAUUCCGACAAAUAUCAGAAUAAAAAUGGGCGUAAAAGCUCCUGAUUUUUAUUCAAUUGUAAGACAAGUCAUGAC
.((((.((((((((((....-..)))))....(.....)..))))).....(((........((((((((((((((......))))...))))))))))..(((.....)))))).)))) ( -27.20)
>DroEre_CAF1 44255 112 + 1
UGUCACGAUUGGUGGUCUCU-UAGCCACUUU------UCAACAAUCAUUCGGACAAAUAAC-GAAUAAAAAUGGGCGUAACAGCUCCUGAUUUUUAUUCAAUUGUAAGACAAGUCAUGAC
.((((.((..((((((....-..))))))..------))............(((.......-((((((((((((((......))))...))))))))))..(((.....)))))).)))) ( -29.00)
>DroYak_CAF1 46815 112 + 1
UGUCACGAUUGGUGGUCUCU-UAGCCACUUU------UCAACAAUCAUGCCGACAAAUAUC-GCAUAUAAAUGGGCGUAAAAGCUCCUGAUUUUUAUUCAAUUGUAAGAAAAGUCAUGAC
.((((.((..((((((....-..))))))..------))............(((.......-..........((((......))))....(((((((......)))))))..))).)))) ( -23.90)
>consensus
UGUCACGAUUGGUGGUCUUU_UAGCCACUUU______UCAACAAUCAUUCCGACAAAUAUCAGAAUAAAAAUGGGCGUAAAAGCUCCUGAUUUUUAUUCAAUUGUAAGACAAGUCAUGAC
.((((.((((((((((.......))))).............))))).....(((........((((((((((((((......))))...))))))))))..(((.....)))))).)))) (-21.77 = -22.77 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 25,358,759 – 25,358,873
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.48
Mean single sequence MFE -29.70
Consensus MFE -23.20
Energy contribution -24.04
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -2.43
Structure conservation index 0.78
SVM decision value 1.55
SVM RNA-class probability 0.963313
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25358759 114 - 27905053
GUCAUGACUUGUCUUACAAUUGAAUAAAGAUCAGGAGCUUUUACGCCCAUUUUUAUUCUGAUAUUUGUCUGAAUGAUUGCUGA------AAAGUGGCAAAAAAGACCACCAAUCGUGACA
(((((((.(((..........((((((((((..((.((......))))))))))))))........((((...((.(..((..------..))..)))....))))...)))))))))). ( -29.40)
>DroSec_CAF1 43487 113 - 1
GUCAUGACUUGUCUUACAAUUGAAUAAAAAUCAGGAGCUUUUACGCCCAUUUUUAUUCUGAUAUUUGUCGGAAUGAUUGUUGA------AAAGUGUCUA-AAAGACCACCAAUCGUGACA
(((((((...(((((......((((((((((..((.((......)))))))))))))).(((((((.((((........))))------.)))))))..-.)))))......))))))). ( -29.20)
>DroSim_CAF1 43753 119 - 1
GUCAUGACUUGUCUUACAAUUGAAUAAAAAUCAGGAGCUUUUACGCCCAUUUUUAUUCUGAUAUUUGUCGGAAUGAUUGUUGAGUGGCUAAAGUGGCUA-AAAGACCACCAAUCGUGACA
(((((((...(((((...(((.(((((......((.((......))))....((((((((((....))))))))))))))).)))((((.....)))).-.)))))......))))))). ( -31.80)
>DroEre_CAF1 44255 112 - 1
GUCAUGACUUGUCUUACAAUUGAAUAAAAAUCAGGAGCUGUUACGCCCAUUUUUAUUC-GUUAUUUGUCCGAAUGAUUGUUGA------AAAGUGGCUA-AGAGACCACCAAUCGUGACA
(((((((.(((.....((((.((((((((((..((.((......))))))))))))))-(((((((....))))))).)))).------...(((((..-...).)))))))))))))). ( -29.20)
>DroYak_CAF1 46815 112 - 1
GUCAUGACUUUUCUUACAAUUGAAUAAAAAUCAGGAGCUUUUACGCCCAUUUAUAUGC-GAUAUUUGUCGGCAUGAUUGUUGA------AAAGUGGCUA-AGAGACCACCAAUCGUGACA
(((((((.(((((..((((((............((.((......))))......((((-(((....))).)))))))))).))------)))(((((..-...).))))...))))))). ( -28.90)
>consensus
GUCAUGACUUGUCUUACAAUUGAAUAAAAAUCAGGAGCUUUUACGCCCAUUUUUAUUCUGAUAUUUGUCGGAAUGAUUGUUGA______AAAGUGGCUA_AAAGACCACCAAUCGUGACA
((((((((...((..((((..((((((((((..((.((......))))))))))))))......))))..))..).................((((((....)).))))...))))))). (-23.20 = -24.04 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:02 2006