Locus 3211

Sequence ID 2L_DroMel_CAF1
Location 9,183,829 – 9,183,937
Length 108
Max. P 0.891752
window5101 window5102

overview

Window 1

Location 9,183,829 – 9,183,937
Length 108
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 90.43
Mean single sequence MFE -23.06
Consensus MFE -17.18
Energy contribution -18.43
Covariance contribution 1.25
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.75
SVM decision value 0.22
SVM RNA-class probability 0.639137
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9183829 108 + 22407834
GCCUCAAAGUAUGCAAUUAAUGAUGCGUAUUUUAUUCUAUUUCGCGUCAUUUCAUUUCGAUAUAAUCGAAAUACAGGACGUUGUAUACGCCCUACUAAUCCGCUUUGA
...(((((((........(((((((((...............)))))))))..((((((((...))))))))..(((.(((.....))).)))........))))))) ( -26.26)
>DroSec_CAF1 19761 108 + 1
GCCUCAAAGUAUGCAAUUAAUGGUGCGUAUUUUAUUCUAUUUCGCGUCAUUUCAUUUCGAUAUAAUCGGAAUACAGGACGUUGUAUACGCCCUACUAAUCCGCUUUGA
...(((((((.....((((.(((.((((((.............(((((.....((((((((...))))))))....)))))...)))))).))).))))..))))))) ( -24.79)
>DroSim_CAF1 20620 108 + 1
GCCUCAAAGUAUGCAAUUAAUGGUGCGUAUUUUAUUCUAUUUCGCGUCAUUUCAUUUCGAUAAAAUCGCAAUGCAGGACGUUGUAUACGCCCUACUAAUCCGCUUUGA
...(((((((.....((((.(((.((((((.............(((((....((((.((((...)))).))))...)))))...)))))).))).))))..))))))) ( -23.89)
>DroYak_CAF1 21698 96 + 1
GCCUCAAAGUAUGCAAUUAAUGGUGCGCAUUUUAUUCUAUUUCGUGUCAUUUCAUUUCGAUAUAAUCGAAAUA------------CACGCCCUAAUAAUCCGCUUUGA
...(((((((..(((........)))................(((((......((((((((...)))))))))------------))))............))))))) ( -17.30)
>consensus
GCCUCAAAGUAUGCAAUUAAUGGUGCGUAUUUUAUUCUAUUUCGCGUCAUUUCAUUUCGAUAUAAUCGAAAUACAGGACGUUGUAUACGCCCUACUAAUCCGCUUUGA
...(((((((........(((((((((...............)))))))))..((((((((...))))))))..(((.(((.....))).)))........))))))) (-17.18 = -18.43 +   1.25)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 2

Location 9,183,829 – 9,183,937
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 90.43
Mean single sequence MFE -25.21
Consensus MFE -21.10
Energy contribution -22.35
Covariance contribution 1.25
Combinations/Pair 1.11
Mean z-score -1.97
Structure conservation index 0.84
SVM decision value 0.97
SVM RNA-class probability 0.891752
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9183829 108 - 22407834
UCAAAGCGGAUUAGUAGGGCGUAUACAACGUCCUGUAUUUCGAUUAUAUCGAAAUGAAAUGACGCGAAAUAGAAUAAAAUACGCAUCAUUAAUUGCAUACUUUGAGGC
((((((........((((((((.....))))))))(((((((((...))))))))).(((((.(((...............))).))))).........))))))... ( -27.16)
>DroSec_CAF1 19761 108 - 1
UCAAAGCGGAUUAGUAGGGCGUAUACAACGUCCUGUAUUCCGAUUAUAUCGAAAUGAAAUGACGCGAAAUAGAAUAAAAUACGCACCAUUAAUUGCAUACUUUGAGGC
((((((((((.((.((((((((.....)))))))))).))))...............((((..(((...............)))..)))).........))))))... ( -25.46)
>DroSim_CAF1 20620 108 - 1
UCAAAGCGGAUUAGUAGGGCGUAUACAACGUCCUGCAUUGCGAUUUUAUCGAAAUGAAAUGACGCGAAAUAGAAUAAAAUACGCACCAUUAAUUGCAUACUUUGAGGC
((((((.......(((((((((.....))))))))).((((((((((((....)))))))..)))))...............(((........)))...))))))... ( -27.70)
>DroYak_CAF1 21698 96 - 1
UCAAAGCGGAUUAUUAGGGCGUG------------UAUUUCGAUUAUAUCGAAAUGAAAUGACACGAAAUAGAAUAAAAUGCGCACCAUUAAUUGCAUACUUUGAGGC
((((((((..(((((..(.((((------------(((((((((...))))))))......)))))...)..)))))..)))(((........)))....)))))... ( -20.50)
>consensus
UCAAAGCGGAUUAGUAGGGCGUAUACAACGUCCUGUAUUUCGAUUAUAUCGAAAUGAAAUGACGCGAAAUAGAAUAAAAUACGCACCAUUAAUUGCAUACUUUGAGGC
((((((..(((((((.((((((((....((((...(((((((((...)))))))))....))))(......)......)))))).))))))))).....))))))... (-21.10 = -22.35 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:03 2006