Locus 1265

Sequence ID 3L_DroMel_CAF1
Location 3,662,512 – 3,662,612
Length 100
Max. P 0.950774
window1977 window1978

overview

Window 7

Location 3,662,512 – 3,662,602
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.16
Mean single sequence MFE -23.43
Consensus MFE -21.47
Energy contribution -21.42
Covariance contribution -0.05
Combinations/Pair 1.03
Mean z-score -2.05
Structure conservation index 0.92
SVM decision value 1.40
SVM RNA-class probability 0.950774
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3662512 90 + 23771897
------------------------------CCCUCUGAAUGGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUU
------------------------------.....(((((...(((((.((((((......(((((((((....))))))))).)))))))))))....((((.....)))))))))... ( -22.00)
>DroVir_CAF1 61930 90 + 1
------------------------------CUGGCUGAAUGGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGCUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUU
------------------------------...(((....)))(((((.(((((....)).(((((((((....)))))))))....)))))))).....(((((.......)))))... ( -21.20)
>DroPse_CAF1 76571 99 + 1
--------------------CUCUGAAU-GGUCUCUGAAUGGCGUCCGAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUU
--------------------...(((((-.(((.......)))((((.(((((((......(((((((((....))))))))).)))))))))))....((((.....)))))))))... ( -23.40)
>DroWil_CAF1 71584 120 + 1
CACUGUCUUUGUAGCUGUCUCUGUGAGUCGCUCUCUGAAUGGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUU
.............(((((.((...(((.....))).)))))))(((((.((((((......(((((((((....))))))))).))))))))))).....(((((.......)))))... ( -27.70)
>DroMoj_CAF1 61243 90 + 1
------------------------------CUGGCUGAAUGGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUU
------------------------------...(((....)))(((((.((((((......(((((((((....))))))))).))))))))))).....(((((.......)))))... ( -22.90)
>DroPer_CAF1 115817 99 + 1
--------------------CUCUGAAU-GGUCUCUGAAUGGCGUCCGAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUU
--------------------...(((((-.(((.......)))((((.(((((((......(((((((((....))))))))).)))))))))))....((((.....)))))))))... ( -23.40)
>consensus
______________________________CUCUCUGAAUGGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUU
...................................(((((...(((((.((((((......(((((((((....))))))))).)))))))))))....((((.....)))))))))... (-21.47 = -21.42 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,662,522 – 3,662,612
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.04
Mean single sequence MFE -24.92
Consensus MFE -20.07
Energy contribution -20.02
Covariance contribution -0.06
Combinations/Pair 1.04
Mean z-score -2.45
Structure conservation index 0.81
SVM decision value 0.98
SVM RNA-class probability 0.895070
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3662522 90 + 23771897
GGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUUUCUG----AACAGA--------------------------
...(((((.((((((......(((((((((....))))))))).)))))))))))................((((((.....))----))))..-------------------------- ( -23.50)
>DroVir_CAF1 61940 88 + 1
GGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGCUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUUU--G----AACAGA--------------------------
...(((((.(((((....)).(((((((((....)))))))))....))))))))................(((((.....--)----))))..-------------------------- ( -21.00)
>DroPse_CAF1 76590 113 + 1
GGCGUCCGAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUUUUUUCGACUACAGAGCACAGAG-------CACUCGUACUC
...((((.(((((((......(((((((((....))))))))).))))))))))).....(((((.......)))))........((.(((((.((.....)-------).)).))).)) ( -24.40)
>DroYak_CAF1 37949 90 + 1
GGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUUUCUG----AGCAGA--------------------------
...(((((.((((((......(((((((((....))))))))).)))))))))))................((((((.....))----))))..-------------------------- ( -23.50)
>DroAna_CAF1 54528 90 + 1
GGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUUUUUG----AACAGA--------------------------
...(((((.((((((......(((((((((....))))))))).)))))))))))................((((((.....))----))))..-------------------------- ( -23.30)
>DroPer_CAF1 115836 120 + 1
GGCGUCCGAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUUUUUUCGAGUACAGAGCACAGAGCACUGAGCACUCGUACUC
...((((.(((((((......(((((((((....))))))))).))))))))))).....(((((.......)))))........((((((((.((.(((....))).)).)).)))))) ( -33.80)
>consensus
GGCGUCCAAUUCGAUUAUUCUAACAUGAAUUAUAGUUCGUGUUCGUUGAAUGGACAAUUAUGAAUUUAUCAUGUUCAAUUUUUG____AACAGA__________________________
...(((((.((((((......(((((((((....))))))))).))))))))))).....(((((.......)))))........................................... (-20.07 = -20.02 +  -0.06)

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 10:03:23 2006