Locus 4557

Sequence ID 3R_DroMel_CAF1
Location 12,062,246 – 12,062,446
Length 200
Max. P 0.963320
window7440 window7441 window7442 window7443

overview

Window 0

Location 12,062,246 – 12,062,366
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.06
Mean single sequence MFE -45.77
Consensus MFE -39.48
Energy contribution -41.57
Covariance contribution 2.09
Combinations/Pair 1.07
Mean z-score -2.96
Structure conservation index 0.86
SVM decision value 1.55
SVM RNA-class probability 0.963320
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12062246 120 - 27905053
AAAAAUAUAUAGCCCGUACAUACAACGUGGGAUUGUAUGUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUGCGCUGUCAGAGGCAAAUGGCUUGAUGGCCGUACACUCGUU
.........(((((((((((((((((....).)))))))))))..)))))...(((((..((((.(((((((((...))))))))))))).....((((((....))))))....))))) ( -44.80)
>DroSec_CAF1 34292 106 - 1
AAAAAUAUAUAGCCUGCGC--------------UAUAUAUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUGCGCUGUCAGAGGCAAAUGGCUUGAUGGCCGUACAGUCGAU
.........(((((.((((--------------.......)))).))))).((((((...((((.(((((((((...)))))))))))))..)..((((((....))))))...))))). ( -44.00)
>DroSim_CAF1 43761 120 - 1
AAAAAUAUAUAGCCCGUACAUACAACGUCGGAUUGUAUGUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUGCGCUGUCAGAGGCAAAUGGCUUGAUGGCCGUACAGUCGAU
.........(((((((((((((((((....).)))))))))))..))))).((((((...((((.(((((((((...)))))))))))))..)..((((((....))))))...))))). ( -48.50)
>consensus
AAAAAUAUAUAGCCCGUACAUACAACGU_GGAUUGUAUGUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUGCGCUGUCAGAGGCAAAUGGCUUGAUGGCCGUACAGUCGAU
.........((((((((((((((((.......)))))))))))..))))).((((((...((((.(((((((((...)))))))))))))..)..((((((....))))))...))))). (-39.48 = -41.57 +   2.09)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,062,286 – 12,062,406
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.61
Mean single sequence MFE -44.80
Consensus MFE -36.48
Energy contribution -37.43
Covariance contribution 0.95
Combinations/Pair 1.11
Mean z-score -2.90
Structure conservation index 0.81
SVM decision value 1.14
SVM RNA-class probability 0.920598
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12062286 120 + 27905053
CACACGAUGCGCCGCACAAAUAUCGCCGAGCAGCCAGCGCACAUACAAUCCCACGUUGUAUGUACGGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCUGUCGGUGGAGCGGUG
.........((((((.......(((((((.(((((..((.(((((((((.....))))))))).))((((((((((...((.....))...)))))))))))))))))))))).)))))) ( -47.90)
>DroSec_CAF1 34332 106 + 1
CACACGAUGCGCCGCACAAAUAUCGCCGAGCAGCCAGCGCAUAUAUA--------------GCGCAGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCGGUCGGUGGAGCGGUG
.........((((((.......(((((((.(.((((((..(((((((--------------.((.((.(((((......))))).)).))))))))).))))))).))))))).)))))) ( -41.60)
>DroSim_CAF1 43801 120 + 1
CACACGAUGCGCCGCACAAAUAUCGCCGAGCAGCCAGCGCACAUACAAUCCGACGUUGUAUGUACGGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCGGUCGGUGGAGCGGUG
.........((((((.......(((((((.(.(((((((((((((...((((((((...)))).))))(((((......)))))..))))))).....))))))).))))))).)))))) ( -44.90)
>consensus
CACACGAUGCGCCGCACAAAUAUCGCCGAGCAGCCAGCGCACAUACAAUCC_ACGUUGUAUGUACGGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCGGUCGGUGGAGCGGUG
.........((((((.......(((((((.(.((((((...((((((((.....))))))))((((..(((((......)))))....))))......)))))).)))))))).)))))) (-36.48 = -37.43 +   0.95)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,062,286 – 12,062,406
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.61
Mean single sequence MFE -36.40
Consensus MFE -30.11
Energy contribution -31.53
Covariance contribution 1.42
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.83
SVM decision value 0.29
SVM RNA-class probability 0.668934
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12062286 120 - 27905053
CACCGCUCCACCGACAGCCAGCUAUAUACACAUAACCUACAAAAAUAUAUAGCCCGUACAUACAACGUGGGAUUGUAUGUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUG
..((((.((.((((((((((((((((((.................)))))))).((((((((((((....).))))))))))).)))))).)))).)......).))))(((.....))) ( -40.43)
>DroSec_CAF1 34332 106 - 1
CACCGCUCCACCGACCGCCAGCUAUAUACACAUAACCUACAAAAAUAUAUAGCCUGCGC--------------UAUAUAUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUG
........((((((.((((.((((((((.................))))))))..((((--------------...((((.((((((....))))))))))..))))))))..))).))) ( -32.93)
>DroSim_CAF1 43801 120 - 1
CACCGCUCCACCGACCGCCAGCUAUAUACACAUAACCUACAAAAAUAUAUAGCCCGUACAUACAACGUCGGAUUGUAUGUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUG
..((((.((.(((((.((((((((((((.................)))))))).((((((((((((....).))))))))))).)))).).)))).)......).))))(((.....))) ( -35.83)
>consensus
CACCGCUCCACCGACCGCCAGCUAUAUACACAUAACCUACAAAAAUAUAUAGCCCGUACAUACAACGU_GGAUUGUAUGUGCGCUGGCUGCUCGGCGAUAUUUGUGCGGCGCAUCGUGUG
..((((.((.(((((.((((((((((((.................)))))))).(((((((((((.......))))))))))).)))).).)))).)......).))))(((.....))) (-30.11 = -31.53 +   1.42)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,062,326 – 12,062,446
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.61
Mean single sequence MFE -34.97
Consensus MFE -28.75
Energy contribution -30.70
Covariance contribution 1.95
Combinations/Pair 1.03
Mean z-score -2.03
Structure conservation index 0.82
SVM decision value 0.27
SVM RNA-class probability 0.662508
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12062326 120 + 27905053
ACAUACAAUCCCACGUUGUAUGUACGGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCUGUCGGUGGAGCGGUGGAGCAUUGCGAUUGUGGGAGAGAACGAACGAAACACCGAA
(((((((((.....))))))))).(.((((((((((...((.....))...)))))))))).)...((((((..((((((...))))))(.((((........)))).)....)))))). ( -36.20)
>DroSec_CAF1 34372 106 + 1
AUAUAUA--------------GCGCAGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCGGUCGGUGGAGCGGUGGAGCAUUGCGAUUGUGGGAGAGAACGAACGAAACACCGAA
.......--------------.(((.((((((((((...((.....))...)))))))))).))).((((((..((((((...))))))(.((((........)))).)....)))))). ( -32.50)
>DroSim_CAF1 43841 120 + 1
ACAUACAAUCCGACGUUGUAUGUACGGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCGGUCGGUGGAGCGGUGGAGCAUUGCGAUUGUGGGAGAGAACGAACGAAACACCGAA
(((((((((.....))))))))).(.((((((((((...((.....))...)))))))))).)...((((((..((((((...))))))(.((((........)))).)....)))))). ( -36.20)
>consensus
ACAUACAAUCC_ACGUUGUAUGUACGGGCUAUAUAUUUUUGUAGGUUAUGUGUAUAUAGCUGGCGGUCGGUGGAGCGGUGGAGCAUUGCGAUUGUGGGAGAGAACGAACGAAACACCGAA
(((((((((.....))))))))).(.((((((((((...((.....))...)))))))))).)...((((((..((((((...))))))(.((((........)))).)....)))))). (-28.75 = -30.70 +   1.95)

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 11:32:16 2006