Locus 6561

Sequence ID X_DroMel_CAF1
Location 16,412,076 – 16,412,245
Length 169
Max. P 0.999875
window10713 window10714 window10715 window10716 window10717 window10718

overview

Window 3

Location 16,412,076 – 16,412,177
Length 101
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 87.14
Mean single sequence MFE -20.60
Consensus MFE -17.60
Energy contribution -18.10
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.85
SVM decision value 1.82
SVM RNA-class probability 0.978706
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16412076 101 + 22224390
UUUUCCUCUGCUUUCUUUCUCAGACAU---UUUUUUU---UUUUUUGGUUAGUUGCCCGCUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA
......((((..........))))...---...((((---(.(((((.((((((((.(((.....)))((((......))))..))))))))))))).))))).... ( -19.50)
>DroSec_CAF1 32735 104 + 1
UUUUCCUCUGCUUUAGUUCUCAGACAUCUCUUUUUUU---UUUUUUUGUUAGUUGCCCGUUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA
......((((..........))))..........(((---((.(((((((((((((....((((((((........))))))))))))))))))))).))))).... ( -22.60)
>DroSim_CAF1 28946 107 + 1
UUUUCCUCUGCUUUCUUUAUCAGACAUCUCUUUUUUUUUUUUUUUUUGUUAGUUGCCCGUUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA
......((((.(......).)))).............(((((.(((((((((((((....((((((((........))))))))))))))))))))).))))).... ( -22.90)
>DroYak_CAF1 30794 95 + 1
UUCUCCUCUAUUUUCUUUUGCAGU---------UCUU---UUUUUUUUUUAGUUGCCCGCUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACACA
..........((((.(((((((((---------(...---...........(.....)((((((((((........)))))))))))))).)))))).))))..... ( -17.40)
>consensus
UUUUCCUCUGCUUUCUUUCUCAGACAU___UUUUUUU___UUUUUUUGUUAGUUGCCCGCUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA
...........................................(((((((((((((....((((((((........))))))))))))))))))))).......... (-17.60 = -18.10 +   0.50)

alignment

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secondary structure

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Window 4

Location 16,412,076 – 16,412,177
Length 101
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 87.14
Mean single sequence MFE -18.52
Consensus MFE -13.90
Energy contribution -13.78
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.57
Structure conservation index 0.75
SVM decision value 0.20
SVM RNA-class probability 0.628797
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16412076 101 - 22224390
UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAGCGGGCAACUAACCAAAAAA---AAAAAAA---AUGUCUGAGAAAGAAAGCAGAGGAAAA
.....((((.(((((((..((((((((((......))))......))))))................---.......---...(((.....))).))))))).)))) ( -18.90)
>DroSec_CAF1 32735 104 - 1
UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAACGGGCAACUAACAAAAAAA---AAAAAAAGAGAUGUCUGAGAACUAAAGCAGAGGAAAA
((((((((.(((((((.....))..((((......)))).........((((((.((..........---........)).))))))))))).))))))))...... ( -18.87)
>DroSim_CAF1 28946 107 - 1
UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAACGGGCAACUAACAAAAAAAAAAAAAAAAAGAGAUGUCUGAUAAAGAAAGCAGAGGAAAA
.....((((.(((((((..((....((((......)))).........((((((.((.....................)).))))))....))..))))))).)))) ( -19.20)
>DroYak_CAF1 30794 95 - 1
UGUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAGCGGGCAACUAAAAAAAAAA---AAGA---------ACUGCAAAAGAAAAUAGAGGAGAA
(.(((((((.((((((...((((((((((......))))......))))((....))..........---.)).---------...))))))))))))).)...... ( -17.10)
>consensus
UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAACGGGCAACUAACAAAAAAA___AAAAAAA___AUGUCUGAGAAAGAAAGCAGAGGAAAA
((((((((((((((((.....))..((((......)))).....)))))((....))...................................)))))))))...... (-13.90 = -13.78 +  -0.12)

alignment

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secondary structure

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Window 5

Location 16,412,110 – 16,412,205
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 97.19
Mean single sequence MFE -21.81
Consensus MFE -20.22
Energy contribution -19.96
Covariance contribution -0.25
Combinations/Pair 1.05
Mean z-score -2.38
Structure conservation index 0.93
SVM decision value 1.22
SVM RNA-class probability 0.932247
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16412110 95 + 22224390
UUUUUUGGUUAGUUGCCCGCUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAAGCCAGCGAACAAAACCAAAGCAACCGCC
..((((((((..((((..(((((((.((((((......)))...((.....))...)))...)))))))..))))....))))))))........ ( -25.70)
>DroSec_CAF1 32772 95 + 1
UUUUUUUGUUAGUUGCCCGUUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAAGCCAGCCAACAAAACCAAAGCAACCGCC
...(((((((((((((....((((((((........))))))))))))))))))))).............................((....)). ( -20.30)
>DroSim_CAF1 28986 95 + 1
UUUUUUUGUUAGUUGCCCGUUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAAGCCAGCCAACAAAACCAAAGCAACCGCC
...(((((((((((((....((((((((........))))))))))))))))))))).............................((....)). ( -20.30)
>DroYak_CAF1 30822 95 + 1
UUUUUUUUUUAGUUGCCCGCUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACACAGCCAGCCAACAAAACCAAAGCAACCGCC
...........(((((..((((((((((........)))))))))).(((.((..............)).))).............))))).... ( -20.94)
>consensus
UUUUUUUGUUAGUUGCCCGCUUUGUGUGUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAAGCCAGCCAACAAAACCAAAGCAACCGCC
...........(((((..((((((((((........)))))))))).(((.((..............)).))).............))))).... (-20.22 = -19.96 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,412,110 – 16,412,205
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 97.19
Mean single sequence MFE -28.79
Consensus MFE -27.39
Energy contribution -27.39
Covariance contribution 0.00
Combinations/Pair 1.04
Mean z-score -2.60
Structure conservation index 0.95
SVM decision value 1.60
SVM RNA-class probability 0.966955
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16412110 95 - 22224390
GGCGGUUGCUUUGGUUUUGUUCGCUGGCUUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAGCGGGCAACUAACCAAAAAA
((.((((((((..(((((((..((((((..............)))))).....((((......))))...)))))))))))))))..))...... ( -28.54)
>DroSec_CAF1 32772 95 - 1
GGCGGUUGCUUUGGUUUUGUUGGCUGGCUUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAACGGGCAACUAACAAAAAAA
(..((((((((..(((((((.(((((((..............)))))))....((((......))))...)))))))))))))))..)....... ( -29.24)
>DroSim_CAF1 28986 95 - 1
GGCGGUUGCUUUGGUUUUGUUGGCUGGCUUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAACGGGCAACUAACAAAAAAA
(..((((((((..(((((((.(((((((..............)))))))....((((......))))...)))))))))))))))..)....... ( -29.24)
>DroYak_CAF1 30822 95 - 1
GGCGGUUGCUUUGGUUUUGUUGGCUGGCUGUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAGCGGGCAACUAAAAAAAAAA
...((((((((..(((((((.(((((((..............)))))))....((((......))))...))))))))))))))).......... ( -28.14)
>consensus
GGCGGUUGCUUUGGUUUUGUUGGCUGGCUUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCACACACAAAACGGGCAACUAACAAAAAAA
...((((((((..(((((((.(((((((..............)))))))....((((......))))...))))))))))))))).......... (-27.39 = -27.39 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,412,137 – 16,412,245
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.64
Mean single sequence MFE -32.04
Consensus MFE -28.03
Energy contribution -28.07
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -3.25
Structure conservation index 0.87
SVM decision value 4.34
SVM RNA-class probability 0.999875
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16412137 108 + 22224390
GUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA-----GCCAGCGAACAAAACCAAAGCAACC-------GCCUUUGUUGUUGGCUAACGGCAUUGUUUGCAUGCUGAGUGCA
.((((......))))..(((..(((((......((((((.-----((((((.(((((...((((((....-------).)))))))))).)))...))).))))))...)))))..))). ( -32.20)
>DroSec_CAF1 32799 108 + 1
GUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA-----GCCAGCCAACAAAACCAAAGCAACC-------GCCUUUGUUGCUGGCUAACGGCAUUGUUUGCAUGCUGAGUGCA
...........((((...((((..(((((.(((...(..(-----((((((.((((((......((....-------)).)))))))))))))...)...))))))))..))))..)))) ( -32.50)
>DroSim_CAF1 29013 108 + 1
GUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA-----GCCAGCCAACAAAACCAAAGCAACC-------GCCUUUGUUGCUGGCUAACGGCAUUGUUUGCAUGCUGAGUGCA
...........((((...((((..(((((.(((...(..(-----((((((.((((((......((....-------)).)))))))))))))...)...))))))))..))))..)))) ( -32.50)
>DroYak_CAF1 30849 108 + 1
GUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACACA-----GCCAGCCAACAAAACCAAAGCAACC-------GCCUUUGUUGCUGGCUAACGGCAUUGUUUGCAUGCUGAGUGCA
...........((((...((((..(((((.(((...(..(-----((((((.((((((......((....-------)).)))))))))))))...)...))))))))..))))..)))) ( -32.50)
>DroAna_CAF1 34637 120 + 1
GUGCAAAUUUAUGCAAAGCAGCUAGCCAAACAGAAACAAAGCGAAGCCAGCAAACAAAACCAAAGCAACCGAAAGCAGCUUUUGUUGCUCGCUAACGGCAUUGUUUGCAUGCCGAGUGCA
.((((......))))..(((.((................(((((.((.((((((.........(((...(....)..))))))))))))))))..((((((.(....)))))))))))). ( -30.50)
>consensus
GUGCAAAUUUAUGCAAAGCAGCUAGCAAAACAAAAACAAA_____GCCAGCCAACAAAACCAAAGCAACC_______GCCUUUGUUGCUGGCUAACGGCAUUGUUUGCAUGCUGAGUGCA
((((((((..((((...((.....))...................((((((.((((((......................)))))))))))).....)))).))))))))((.....)). (-28.03 = -28.07 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,412,137 – 16,412,245
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.64
Mean single sequence MFE -37.76
Consensus MFE -32.30
Energy contribution -32.18
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -3.33
Structure conservation index 0.86
SVM decision value 4.01
SVM RNA-class probability 0.999753
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16412137 108 - 22224390
UGCACUCAGCAUGCAAACAAUGCCGUUAGCCAACAACAAAGGC-------GGUUGCUUUGGUUUUGUUCGCUGGC-----UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCAC
((((......(((((((....((.(((((((((.(((((((.(-------(((.((.........))..)))).)-----)))))).)))....)))))).))))))))).....)))). ( -32.20)
>DroSec_CAF1 32799 108 - 1
UGCACUCAGCAUGCAAACAAUGCCGUUAGCCAGCAACAAAGGC-------GGUUGCUUUGGUUUUGUUGGCUGGC-----UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCAC
.(((((.((((.((((((((.(((...(((((((((..(((((-------....)))))....))))))))))))-----.))))..))))..)))))).)))..((((......)))). ( -38.10)
>DroSim_CAF1 29013 108 - 1
UGCACUCAGCAUGCAAACAAUGCCGUUAGCCAGCAACAAAGGC-------GGUUGCUUUGGUUUUGUUGGCUGGC-----UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCAC
.(((((.((((.((((((((.(((...(((((((((..(((((-------....)))))....))))))))))))-----.))))..))))..)))))).)))..((((......)))). ( -38.10)
>DroYak_CAF1 30849 108 - 1
UGCACUCAGCAUGCAAACAAUGCCGUUAGCCAGCAACAAAGGC-------GGUUGCUUUGGUUUUGUUGGCUGGC-----UGUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCAC
.(((((.((((.(((((.(((((.((((((((((((..(((((-------....)))))....))))))))))))-----.))))))))))..)))))).)))..((((......)))). ( -40.90)
>DroAna_CAF1 34637 120 - 1
UGCACUCGGCAUGCAAACAAUGCCGUUAGCGAGCAACAAAAGCUGCUUUCGGUUGCUUUGGUUUUGUUUGCUGGCUUCGCUUUGUUUCUGUUUGGCUAGCUGCUUUGCAUAAAUUUGCAC
.......(((((.......)))))((((((((((((..(((((.((.....)).)))))....))))))))))))...((...((((.(((..(((.....)))..))).))))..)).. ( -39.50)
>consensus
UGCACUCAGCAUGCAAACAAUGCCGUUAGCCAGCAACAAAGGC_______GGUUGCUUUGGUUUUGUUGGCUGGC_____UUUGUUUUUGUUUUGCUAGCUGCUUUGCAUAAAUUUGCAC
.(((((.((((.((((((((....((((((((((((..(((((...........)))))....))))))))))))......)))))..)))..)))))).)))..((((......)))). (-32.30 = -32.18 +  -0.12)

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 12:16:57 2006