Locus 6348

Sequence ID 3L_DroMel_CAF1
Location 16,990,278 – 16,990,438
Length 160
Max. P 0.981760
window10170 window10171 window10172 window10173

overview

Window 0

Location 16,990,278 – 16,990,398
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -50.50
Consensus MFE -47.69
Energy contribution -48.47
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -3.02
Structure conservation index 0.94
SVM decision value 1.90
SVM RNA-class probability 0.981760
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16990278 120 + 23771897
UAUCCGCUAUCCGGAGGAGUUGUCCCUGUGCAAACCACUGGAAGCGGAGCACCUGAAGCGUAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUCGCUGAACCAGAUGGCACCAC
..((((((.(((((.((..((((......)))).)).)))))))))))(((((((..(((......))).)))))))(((.......))).((((((....(((...))).))))))... ( -49.40)
>DroSim_CAF1 1840 120 + 1
UAUCCGCUAUCCGGAGGAGUUGUCCCUGUGCAAACCUCUGGAAGCGGAGCACCUGAAGCGUAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUUGCUGAGCCAGAUGGCACCAC
..((((((.((((((((..((((......)))).))))))))))))))(((((((..(((......))).)))))))(((.......))).((((((.(((......))).))))))... ( -55.00)
>DroYak_CAF1 2033 120 + 1
UAUCCGCUACCCGGAGGAGUUGUCCCUGUGCAAACCUCUGGAAGCCGAGCACCUGAAGCGCAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUCGCUGAGCCCGAUGGCACCAC
....((((..(((((((..((((......)))).)))))))..((.(.(((((((..(((......))).))))))))))......)))).((((((.(((.......)))))))))... ( -47.10)
>consensus
UAUCCGCUAUCCGGAGGAGUUGUCCCUGUGCAAACCUCUGGAAGCGGAGCACCUGAAGCGUAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUCGCUGAGCCAGAUGGCACCAC
..((((((.((((((((..((((......)))).))))))))))))))(((((((..(((......))).)))))))(((.......))).((((((.((.........))))))))... (-47.69 = -48.47 +   0.78)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,990,278 – 16,990,398
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -50.87
Consensus MFE -47.57
Energy contribution -47.80
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -1.80
Structure conservation index 0.94
SVM decision value 0.36
SVM RNA-class probability 0.705937
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16990278 120 - 23771897
GUGGUGCCAUCUGGUUCAGCGAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUACGCUUCAGGUGCUCCGCUUCCAGUGGUUUGCACAGGGACAACUCCUCCGGAUAGCGGAUA
..(((((((..((......))..)))))))(((.......)))(((((((((((......))).))))))))(((((((((.(((.....))).((((....))))..))).)))))).. ( -50.20)
>DroSim_CAF1 1840 120 - 1
GUGGUGCCAUCUGGCUCAGCAAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUACGCUUCAGGUGCUCCGCUUCCAGAGGUUUGCACAGGGACAACUCCUCCGGAUAGCGGAUA
..(((((((..((......))..)))))))(((.......)))(((((((((((......))).))))))))(((((((((.((((.(((........)))..)))).))).)))))).. ( -53.00)
>DroYak_CAF1 2033 120 - 1
GUGGUGCCAUCGGGCUCAGCGAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUGCGCUUCAGGUGCUCGGCUUCCAGAGGUUUGCACAGGGACAACUCCUCCGGGUAGCGGAUA
((((((((((((.......))).))))))..(((((((..((((((((((((((......))).)))))))))..))...)))))))...)))..(((....)))((((.....)))).. ( -49.40)
>consensus
GUGGUGCCAUCUGGCUCAGCGAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUACGCUUCAGGUGCUCCGCUUCCAGAGGUUUGCACAGGGACAACUCCUCCGGAUAGCGGAUA
..(((((((....((...))...)))))))(((.......)))(((((((((((......))).))))))))(((((((((.((((.(((........)))..)))).))).)))))).. (-47.57 = -47.80 +   0.23)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,990,318 – 16,990,438
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -43.60
Consensus MFE -40.79
Energy contribution -41.57
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -1.59
Structure conservation index 0.94
SVM decision value 0.03
SVM RNA-class probability 0.551112
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16990318 120 + 23771897
GAAGCGGAGCACCUGAAGCGUAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUCGCUGAACCAGAUGGCACCACUUACCUGCAGCCUGCUGCGGACACCAACUCAUUUGUGCCC
((.(((..(((((((..(((......))).)))))))))).))..(((.(.((((((....(((...))).))))))).)))..((((((....)))))).................... ( -42.30)
>DroSim_CAF1 1880 120 + 1
GAAGCGGAGCACCUGAAGCGUAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUUGCUGAGCCAGAUGGCACCACUUACCUGCAGCCUGCUGCGGACACUAACUCGUUUGUGCCC
...(((..(((((((..(((......))).))))))))))..((.((((((((((((.(((......))).)))).........((((((....))))))......)))))))).))... ( -47.80)
>DroYak_CAF1 2073 120 + 1
GAAGCCGAGCACCUGAAGCGCAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUCGCUGAGCCCGAUGGCACCACUUACCUACAGCCUGCUGCGGACACCAACUCGUUUGUGCCC
...(((((((....((((.....)))).....(((((((((.((((((.(.((((((.(((.......)))))))))).))).........))).))))).)))).....))))).)).. ( -40.70)
>consensus
GAAGCGGAGCACCUGAAGCGUAACUUCGCCCAGGUGCCGCAUCAGAAGCGAGUGCCAAUCGCUGAGCCAGAUGGCACCACUUACCUGCAGCCUGCUGCGGACACCAACUCGUUUGUGCCC
...(((..(((((((..(((......))).))))))))))..((.((((((((((((.((.........)))))).........((((((....))))))......)))))))).))... (-40.79 = -41.57 +   0.78)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,990,318 – 16,990,438
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -52.37
Consensus MFE -50.41
Energy contribution -49.97
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.88
Structure conservation index 0.96
SVM decision value 0.74
SVM RNA-class probability 0.836794
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16990318 120 - 23771897
GGGCACAAAUGAGUUGGUGUCCGCAGCAGGCUGCAGGUAAGUGGUGCCAUCUGGUUCAGCGAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUACGCUUCAGGUGCUCCGCUUC
((((((..........))))))((((....)))).((.(((((((((((..((......))..)))))).)))))))((.((((((((((((((......))).))))))))..))).)) ( -52.00)
>DroSim_CAF1 1880 120 - 1
GGGCACAAACGAGUUAGUGUCCGCAGCAGGCUGCAGGUAAGUGGUGCCAUCUGGCUCAGCAAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUACGCUUCAGGUGCUCCGCUUC
((((((.((....)).))))))((((....)))).((.(((((((((((..((......))..)))))).)))))))((.((((((((((((((......))).))))))))..))).)) ( -53.50)
>DroYak_CAF1 2073 120 - 1
GGGCACAAACGAGUUGGUGUCCGCAGCAGGCUGUAGGUAAGUGGUGCCAUCGGGCUCAGCGAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUGCGCUUCAGGUGCUCGGCUUC
((((((.((....)).)))))).....((((((..((.((((((((((((((.......))).)))))).))))))).....((((((((((((......))).))))))))))))))). ( -51.60)
>consensus
GGGCACAAACGAGUUGGUGUCCGCAGCAGGCUGCAGGUAAGUGGUGCCAUCUGGCUCAGCGAUUGGCACUCGCUUCUGAUGCGGCACCUGGGCGAAGUUACGCUUCAGGUGCUCCGCUUC
((((((.((....)).))))))((((....)))).((.(((((((((((....((...))...)))))).)))))))((.((((((((((((((......))).)))))))))..)).)) (-50.41 = -49.97 +  -0.44)

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 12:16:12 2006