Locus 1918

Sequence ID 3R_DroMel_CAF1
Location 5,440,844 – 5,440,998
Length 154
Max. P 0.679140
window3152 window3153

overview

Window 2

Location 5,440,844 – 5,440,958
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.88
Mean single sequence MFE -18.22
Consensus MFE -15.44
Energy contribution -15.40
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -1.35
Structure conservation index 0.85
SVM decision value 0.05
SVM RNA-class probability 0.556882
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5440844 114 - 27905053
CAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCCAU-----CGCUGCGA-AGCAAAAAAUUGAUUAAAUCGAAUUUGUUAUUCUAACAGAAUCCAUUAAAAAGUUAACGAUUACA
.((((.(((((..........((((((..(((.....))).-----.(((....-)))......)))))).(((.((.(((((((...))))))).)).))).....))))))))).... ( -18.00)
>DroSec_CAF1 27326 114 - 1
CAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU-----CGCUGCGA-AGCAAAAAAUCGAUUAAAUCGAAUUUGUUAUUCUAACAGAAUCCAUUAAAAAGUUAACGAUUACA
.((((.(((((..........((((((...(((......))-----)(((....-)))......)))))).(((.((.(((((((...))))))).)).))).....))))))))).... ( -17.60)
>DroSim_CAF1 22494 115 - 1
CAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU-----CGCUGCGAAAGCAAAAAAUCGAUUAAAUCGAAUUUGUUAUUCUAACAGAAUCCAUUAAAAAGUUAACGAUUACA
.((((.(((((..........((((((........(((...-----.)))((....))......)))))).(((.((.(((((((...))))))).)).))).....))))))))).... ( -21.20)
>DroEre_CAF1 27981 114 - 1
CAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU-----CGCUGCGA-AACAAAAAAUUGAUUAAAUCGAAUUUGUUAUUCUAACAGAAUCCAUUAAAAAGUUAACGAUUACA
.((((.(((((..........((((((....((...(((..-----...)))..-.))......)))))).(((.((.(((((((...))))))).)).))).....))))))))).... ( -14.40)
>DroYak_CAF1 28457 119 - 1
CAUCGAUUAAUAAUAAAUACAAGUCGAACAGGUAGAGCCAUCGCAUCGCUGCGA-AGCAAAAAAUUGAUUAAAUCGAAUUUGUUAUUCUAACAGAAUCCAUUAAAAAGUUAACGAUUACA
.((((.(((((..........((((((...((.....)).(((((....)))))-.........)))))).(((.((.(((((((...))))))).)).))).....))))))))).... ( -19.90)
>consensus
CAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU_____CGCUGCGA_AGCAAAAAAUUGAUUAAAUCGAAUUUGUUAUUCUAACAGAAUCCAUUAAAAAGUUAACGAUUACA
.((((.(((((..........((((((........(((.........)))((....))......)))))).(((.((.(((((((...))))))).)).))).....))))))))).... (-15.44 = -15.40 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,440,884 – 5,440,998
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.37
Mean single sequence MFE -23.52
Consensus MFE -18.34
Energy contribution -19.10
Covariance contribution 0.76
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.78
SVM decision value 0.30
SVM RNA-class probability 0.679140
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5440884 114 - 27905053
AUCGAAUACAUUCAAUUCAAUUGAUGAGCGUCGUGUGCAUCAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCCAU-----CGCUGCGA-AGCAAAAAAUUGAUUAAAUCGAAUU
.((((.............((((((((((((.....))).))))))))).............((((((..(((.....))).-----.(((....-)))......))))))...))))... ( -24.00)
>DroSec_CAF1 27366 114 - 1
CUCGAAUACAUUCAAUUCAAUUGAUGAGCGUCGUGUGCGUCAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU-----CGCUGCGA-AGCAAAAAAUCGAUUAAAUCGAAUU
.((((.............((((((((((((.....))).))))))))).............((((((...(((......))-----)(((....-)))......))))))...))))... ( -23.40)
>DroSim_CAF1 22534 115 - 1
CUCGAAUACAUUCAAUUCAAUUGAUGAGCGGCGUGUGCAUCAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU-----CGCUGCGAAAGCAAAAAAUCGAUUAAAUCGAAUU
.((((.............((((((((((((.....))).))))))))).............((((((........(((...-----.)))((....))......))))))...))))... ( -26.90)
>DroEre_CAF1 28021 106 - 1
CUCG-----AAUACUUCCAAUUGAUGAGC---GUGUGCAUCAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU-----CGCUGCGA-AACAAAAAAUUGAUUAAAUCGAAUU
.(((-----(........(((((((((((---....)).))))))))).............((((((....((...(((..-----...)))..-.))......))))))...))))... ( -19.50)
>DroYak_CAF1 28497 116 - 1
CUCGCUUCCAAUACUUCCAAUUGAUGAGC---GUGUGCAUCAUCGAUUAAUAAUAAAUACAAGUCGAACAGGUAGAGCCAUCGCAUCGCUGCGA-AGCAAAAAAUUGAUUAAAUCGAAUU
...(((((((((.......))))...(((---(.((((....((((((.............))))))...((.....))...))))))))..))-)))......(((((...)))))... ( -23.82)
>consensus
CUCGAAUACAUUCAAUUCAAUUGAUGAGCG_CGUGUGCAUCAUCGAUUAAUAAUAAAUACAAGUCGAACUGGUAAAGCAAU_____CGCUGCGA_AGCAAAAAAUUGAUUAAAUCGAAUU
.((((.............((((((((((((.....))).))))))))).............((((((........(((.........)))((....))......))))))...))))... (-18.34 = -19.10 +   0.76)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:48 2006