Locus 6425

Sequence ID X_DroMel_CAF1
Location 16,113,259 – 16,113,397
Length 138
Max. P 0.822117
window10490 window10491 window10492

overview

Window 0

Location 16,113,259 – 16,113,357
Length 98
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.62
Mean single sequence MFE -27.51
Consensus MFE -17.30
Energy contribution -18.97
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.63
SVM decision value 0.68
SVM RNA-class probability 0.822117
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16113259 98 + 22224390
AUAAUGUACACUU----------------GAUUUGCGUGGAGUAUGUACAUA------CACAUGUAUGUACAUUCACGUAUUCACAAGAUUAGCAUUUUACGCCCUAUUUAUUUGUGCGC
.....((((((((----------------(...((((((((...((((((((------(....)))))))))))))))))....))))....((.......))..........))))).. ( -28.60)
>DroSim_CAF1 1085 114 + 1
AUAAUGUACACUUGCAUUGCUCAACACAUGAUUUGCGUGGAGUAUGUACAUA------CACAUGUAUGUACAUUCCCGUAUUCACAAGAUUAGCAUUUUACGCCCUAUUUAUUUGUGCGC
..((((((....))))))(((.......(((..((((.(((..(((((((((------(....))))))))))))))))).))).......)))......(((.(.........).))). ( -28.24)
>DroYak_CAF1 1192 120 + 1
AUAAUGUACACUUGCAUUGCUCAACACAUGAUUUGCGUGGAGUAGGUACACAUGUAUGUACAUAUAUGUACAUUCACAUAUUCACAAGAUUAGCAUUUUACGCCCUAAUUAUUUGUGCGC
..((((((....))))))((.((.((.((((((.((((((((((.((((....)))).)))..((((((......))))))...............)))))))...)))))).)))).)) ( -25.70)
>consensus
AUAAUGUACACUUGCAUUGCUCAACACAUGAUUUGCGUGGAGUAUGUACAUA______CACAUGUAUGUACAUUCACGUAUUCACAAGAUUAGCAUUUUACGCCCUAUUUAUUUGUGCGC
.....(((((...................((..((((((((((((((((((..........)))))))))).)))))))).)).........((.......))..........))))).. (-17.30 = -18.97 +   1.67)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,113,259 – 16,113,357
Length 98
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.62
Mean single sequence MFE -28.07
Consensus MFE -16.09
Energy contribution -16.20
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.51
Structure conservation index 0.57
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16113259 98 - 22224390
GCGCACAAAUAAAUAGGGCGUAAAAUGCUAAUCUUGUGAAUACGUGAAUGUACAUACAUGUG------UAUGUACAUACUCCACGCAAAUC----------------AAGUGUACAUUAU
(..(((..........(((((...))))).......(((...((((.((((((((((....)------)))))))))....))))....))----------------).)))..)..... ( -24.00)
>DroSim_CAF1 1085 114 - 1
GCGCACAAAUAAAUAGGGCGUAAAAUGCUAAUCUUGUGAAUACGGGAAUGUACAUACAUGUG------UAUGUACAUACUCCACGCAAAUCAUGUGUUGAGCAAUGCAAGUGUACAUUAU
(..(((..........(((((...)))))..((((((....))))))((((((((((....)------))))))))).(((.(((((.....))))).)))........)))..)..... ( -30.40)
>DroYak_CAF1 1192 120 - 1
GCGCACAAAUAAUUAGGGCGUAAAAUGCUAAUCUUGUGAAUAUGUGAAUGUACAUAUAUGUACAUACAUGUGUACCUACUCCACGCAAAUCAUGUGUUGAGCAAUGCAAGUGUACAUUAU
(..(((.......((((((((...))))...........(((((((.(((((((....))))))).))))))).))))(((.(((((.....))))).)))........)))..)..... ( -29.80)
>consensus
GCGCACAAAUAAAUAGGGCGUAAAAUGCUAAUCUUGUGAAUACGUGAAUGUACAUACAUGUG______UAUGUACAUACUCCACGCAAAUCAUGUGUUGAGCAAUGCAAGUGUACAUUAU
(..(((..........(((((...)))))....(((((.....(.(.(((((((((............))))))))).).)..))))).....................)))..)..... (-16.09 = -16.20 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,113,283 – 16,113,397
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.40
Mean single sequence MFE -37.05
Consensus MFE -27.81
Energy contribution -29.70
Covariance contribution 1.89
Combinations/Pair 1.03
Mean z-score -2.24
Structure conservation index 0.75
SVM decision value 0.02
SVM RNA-class probability 0.541574
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16113283 114 + 22224390
AGUAUGUACAUA------CACAUGUAUGUACAUUCACGUAUUCACAAGAUUAGCAUUUUACGCCCUAUUUAUUUGUGCGCGAGUGUGGGUGCAUUCCCUGGCUCCAGGAGCGGAGUCGGC
.(.(((((((((------(....)))))))))).)..(((((((((......((((..................)))).....))))))))).....((((((((......)))))))). ( -38.97)
>DroSim_CAF1 1125 114 + 1
AGUAUGUACAUA------CACAUGUAUGUACAUUCCCGUAUUCACAAGAUUAGCAUUUUACGCCCUAUUUAUUUGUGCGCGAGUGUGGGUGCAUUCCCUGGCUCCAGGAGCGGAGUCAGC
.(.(((((((((------(....)))))))))).)..(((((((((......((((..................)))).....))))))))).....((((((((......)))))))). ( -38.77)
>DroYak_CAF1 1232 120 + 1
AGUAGGUACACAUGUAUGUACAUAUAUGUACAUUCACAUAUUCACAAGAUUAGCAUUUUACGCCCUAAUUAUUUGUGCGCGAGUGUGGGUGCAUUCCCCUGCUCCAGGAGCGGAGUCAGG
.(((.((((....)))).)))....((((((...(((((...(((((((((((...........))))))..))))).....))))).))))))...((((((((......)))).)))) ( -33.40)
>consensus
AGUAUGUACAUA______CACAUGUAUGUACAUUCACGUAUUCACAAGAUUAGCAUUUUACGCCCUAUUUAUUUGUGCGCGAGUGUGGGUGCAUUCCCUGGCUCCAGGAGCGGAGUCAGC
.((((((((((..........))))))))))......(((((((((......((((..................)))).....))))))))).....((((((((......)))))))). (-27.81 = -29.70 +   1.89)

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 12:13:27 2006