Locus 8050

Sequence ID X_DroMel_CAF1
Location 20,065,005 – 20,065,134
Length 129
Max. P 0.980606
window13209 window13210 window13211 window13212

overview

Window 9

Location 20,065,005 – 20,065,101
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 88.91
Mean single sequence MFE -26.92
Consensus MFE -22.62
Energy contribution -22.62
Covariance contribution -0.00
Combinations/Pair 1.06
Mean z-score -1.89
Structure conservation index 0.84
SVM decision value 0.89
SVM RNA-class probability 0.876413
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20065005 96 + 22224390
CGCAUCGUUUUUAUGUGCAUUCGCGCCCGCACACCCAAUUUAUAUAUAAUAUAUAUGUAUGUAUCUGUGUACACUUAAGGGGGCUUGGGUGUGCGC
..............((((....)))).(((((((((((..((((((((...))))))))(((((....)))))...........))))))))))). ( -28.60)
>DroSim_CAF1 1177 93 + 1
CGCAUCGUUUUUAUGUGCAUUCGCGCCCGCACACCCAAUUUAUAUAU---AUAUAUACAUGUAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGC
.(((.(((....))))))...(((((((((.(.(((........(((---(((.(((....))).))))))........)))).)))))))))... ( -29.29)
>DroEre_CAF1 2596 83 + 1
CGCAUCGUUUUUAUGUGCAUUCGCGCUCGCACACCCAAUUUAUAUAUA-------------UAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGC
.(((.(((....))))))...(((((.(.(((.(((..((..((((((-------------....)))))).....))..))).))).).))))). ( -24.90)
>DroYak_CAF1 2665 83 + 1
CGCAUCGUUUUUAUGUGCAUUCGCGCUCGCACACCCAAUUUAUAUAUA-------------UAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGC
.(((.(((....))))))...(((((.(.(((.(((..((..((((((-------------....)))))).....))..))).))).).))))). ( -24.90)
>consensus
CGCAUCGUUUUUAUGUGCAUUCGCGCCCGCACACCCAAUUUAUAUAUA_____________UAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGC
..............(..((((((((((((((((................................)))))...(.....))))))))))))..).. (-22.62 = -22.62 +  -0.00)

alignment

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secondary structure

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Window 0

Location 20,065,005 – 20,065,101
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 88.91
Mean single sequence MFE -23.71
Consensus MFE -18.73
Energy contribution -19.23
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.79
SVM decision value 0.61
SVM RNA-class probability 0.798886
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20065005 96 - 22224390
GCGCACACCCAAGCCCCCUUAAGUGUACACAGAUACAUACAUAUAUAUUAUAUAUAAAUUGGGUGUGCGGGCGCGAAUGCACAUAAAAACGAUGCG
.(((((((((((..........(((((......)))))...((((((...))))))..))))))))))).(((((..............)).))). ( -26.04)
>DroSim_CAF1 1177 93 - 1
GCGCACACCCACGCCCCCUUAAGUGUACACAGAUACAUGUAUAUAU---AUAUAUAAAUUGGGUGUGCGGGCGCGAAUGCACAUAAAAACGAUGCG
((((...(((((((((......((((......)))).((((((...---.))))))....))))))).))))))....((((........).))). ( -26.10)
>DroEre_CAF1 2596 83 - 1
GCGCACACCCACGCCCCCUUAAGUGUACACAGAUA-------------UAUAUAUAAAUUGGGUGUGCGAGCGCGAAUGCACAUAAAAACGAUGCG
.(((((((((((((........)))).......((-------------(....)))....))))))))).(((((..............)).))). ( -21.34)
>DroYak_CAF1 2665 83 - 1
GCGCACACCCACGCCCCCUUAAGUGUACACAGAUA-------------UAUAUAUAAAUUGGGUGUGCGAGCGCGAAUGCACAUAAAAACGAUGCG
.(((((((((((((........)))).......((-------------(....)))....))))))))).(((((..............)).))). ( -21.34)
>consensus
GCGCACACCCACGCCCCCUUAAGUGUACACAGAUA_____________UAUAUAUAAAUUGGGUGUGCGAGCGCGAAUGCACAUAAAAACGAUGCG
((((...(.(((((((..(((.(((((.....................))))).)))...))))))).).))))....((((........).))). (-18.73 = -19.23 +   0.50)

alignment

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secondary structure

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Window 1

Location 20,065,028 – 20,065,134
Length 106
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 84.84
Mean single sequence MFE -31.00
Consensus MFE -26.03
Energy contribution -25.79
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -1.78
Structure conservation index 0.84
SVM decision value 0.69
SVM RNA-class probability 0.822556
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20065028 106 + 22224390
CGCCCGCACACCCAAUUUAUAUAUAAUAUAUAUGUAUGUAUCUGUGUACACUUAAGGGGGCUUGGGUGUGCGCGCGUAUAUAUCUCCAUGCUUGUAUGUAAGGAC-------G
(((.(((((((((((..((((((((...))))))))(((((....)))))...........))))))))))).)))........(((.(((......))).))).-------. ( -34.60)
>DroSim_CAF1 1200 103 + 1
CGCCCGCACACCCAAUUUAUAUAU---AUAUAUACAUGUAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGCGCGUGUAUAUCUCCAUGCUUGUAUGUAAGGAC-------G
(((.((((((((((...((((((.---(((((....))))).))))))(.(((....))).))))))))))).)))........(((.(((......))).))).-------. ( -32.90)
>DroEre_CAF1 2619 93 + 1
CGCUCGCACACCCAAUUUAUAUAUA-------------UAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGCGCGUGUAUAUCUCCAUGUUUCUAUGUAAGGAC-------G
(((.((((((((((...((((((..-------------....))))))(.(((....))).))))))))))).)))........(((.((........)).))).-------. ( -26.20)
>DroYak_CAF1 2688 100 + 1
CGCUCGCACACCCAAUUUAUAUAUA-------------UAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGCGCGUGUAUAUCUCCAUGUUUCUAUGUAAGGAUCGUGUAAG
(((.((((((((((...((((((..-------------....))))))(.(((....))).))))))))))).)))..........((((.((((.....)))).)))).... ( -30.30)
>consensus
CGCCCGCACACCCAAUUUAUAUAUA_____________UAUCUGUGUACACUUAAGGGGGCGUGGGUGUGCGCGCGUGUAUAUCUCCAUGCUUCUAUGUAAGGAC_______G
(((.((((((((((...((((((...................))))))..((....))....)))))))))).)))........(((.(((......))).)))......... (-26.03 = -25.79 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,065,028 – 20,065,134
Length 106
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 84.84
Mean single sequence MFE -28.82
Consensus MFE -23.74
Energy contribution -23.74
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.82
SVM decision value 1.87
SVM RNA-class probability 0.980606
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20065028 106 - 22224390
C-------GUCCUUACAUACAAGCAUGGAGAUAUAUACGCGCGCACACCCAAGCCCCCUUAAGUGUACACAGAUACAUACAUAUAUAUUAUAUAUAAAUUGGGUGUGCGGGCG
.-------.(((..............)))........(((.(((((((((((..........(((((......)))))...((((((...))))))..))))))))))).))) ( -32.04)
>DroSim_CAF1 1200 103 - 1
C-------GUCCUUACAUACAAGCAUGGAGAUAUACACGCGCGCACACCCACGCCCCCUUAAGUGUACACAGAUACAUGUAUAUAU---AUAUAUAAAUUGGGUGUGCGGGCG
.-------.(((..............)))........(((.((((((((((........((.(((((((........))))))).)---).........)))))))))).))) ( -31.67)
>DroEre_CAF1 2619 93 - 1
C-------GUCCUUACAUAGAAACAUGGAGAUAUACACGCGCGCACACCCACGCCCCCUUAAGUGUACACAGAUA-------------UAUAUAUAAAUUGGGUGUGCGAGCG
.-------.(((..............)))........(((.(((((((((((((........)))).......((-------------(....)))....))))))))).))) ( -25.74)
>DroYak_CAF1 2688 100 - 1
CUUACACGAUCCUUACAUAGAAACAUGGAGAUAUACACGCGCGCACACCCACGCCCCCUUAAGUGUACACAGAUA-------------UAUAUAUAAAUUGGGUGUGCGAGCG
.........(((..............)))........(((.(((((((((((((........)))).......((-------------(....)))....))))))))).))) ( -25.84)
>consensus
C_______GUCCUUACAUACAAACAUGGAGAUAUACACGCGCGCACACCCACGCCCCCUUAAGUGUACACAGAUA_____________UAUAUAUAAAUUGGGUGUGCGAGCG
.........(((..............)))........(((.((((((((((.((........))(....).............................)))))))))).))) (-23.74 = -23.74 +   0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:13 2006