Locus 2933

Sequence ID 3L_DroMel_CAF1
Location 8,392,808 – 8,393,078
Length 270
Max. P 0.989746
window4575 window4576 window4577 window4578 window4579 window4580 window4581 window4582

overview

Window 5

Location 8,392,808 – 8,392,918
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 97.58
Mean single sequence MFE -46.30
Consensus MFE -44.63
Energy contribution -44.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.80
Structure conservation index 0.96
SVM decision value 2.11
SVM RNA-class probability 0.988240
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392808 110 + 23771897
GAGCAGACGCAUUCUCAGCUUAAUGGACUCGGAUGCUUCUCUGGCUGGAUGCGAGUCCGAAUCUGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAA
..((....)).(((((.(((((((((.((((((((((((((((..(((((.((....)).)))).)..))))))....))))))).)))...)))))))))...))))). ( -46.90)
>DroSec_CAF1 39 110 + 1
GAGCAGACGCAUUCUCAGCUUAAUGGACUCGGAUGCUUCUCUGGCUGGAUGCGAAUCCGAAUCGGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCACGGAGAAA
..((....)).(((((.(((((((((.((((((((((...(.....)(((((...(((((.......))))).)))))))))))).)))...)))))))))...))))). ( -46.50)
>DroSim_CAF1 30 110 + 1
GAGCAGACGCAUUCUCAGCUUAAUGGACUCGGAUGCUUCUCUGGCUGGAUGCGAAUACGAAUCGGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAA
..((....)).(((((.(((((((((.((((((((((((((((.((((...((....))..))))...))))))....))))))).)))...)))))))))...))))). ( -45.50)
>consensus
GAGCAGACGCAUUCUCAGCUUAAUGGACUCGGAUGCUUCUCUGGCUGGAUGCGAAUCCGAAUCGGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAA
..((....)).(((((.(((((((((.((((((((((...(.....)(((((...(((((.......))))).)))))))))))).)))...)))))))))...))))). (-44.63 = -44.97 +   0.33)

alignment

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secondary structure

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Window 6

Location 8,392,808 – 8,392,918
Length 110
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 97.58
Mean single sequence MFE -40.47
Consensus MFE -39.50
Energy contribution -39.83
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.18
Structure conservation index 0.98
SVM decision value 2.18
SVM RNA-class probability 0.989746
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392808 110 - 23771897
UUUCUCCGCGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUCCGAUUCAGAUUCGGACUCGCAUCCAGCCAGAGAAGCAUCCGAGUCCAUUAAGCUGAGAAUGCGUCUGCUC
.(((((...((((((((((((((((((.((..(((((.(((((.......)))))...))))))).))))))........))).))))))))).))))).((....)).. ( -41.50)
>DroSec_CAF1 39 110 - 1
UUUCUCCGUGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUCCGAUUCCGAUUCGGAUUCGCAUCCAGCCAGAGAAGCAUCCGAGUCCAUUAAGCUGAGAAUGCGUCUGCUC
.(((((...((((((((((((((((((.((..(((((.(((((.......)))))...))))))).))))))........))).))))))))).))))).((....)).. ( -42.20)
>DroSim_CAF1 30 110 - 1
UUUCUCCGCGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUCCGAUUCCGAUUCGUAUUCGCAUCCAGCCAGAGAAGCAUCCGAGUCCAUUAAGCUGAGAAUGCGUCUGCUC
.(((((...((((((((((((..((((((((.(((((...((....))....))))).))))))))...((......)).))).))))))))).))))).((....)).. ( -37.70)
>consensus
UUUCUCCGCGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUCCGAUUCCGAUUCGGAUUCGCAUCCAGCCAGAGAAGCAUCCGAGUCCAUUAAGCUGAGAAUGCGUCUGCUC
.(((((...((((((((((((((((((.((..(((((.(((((.......)))))...))))))).))))))........))).))))))))).))))).((....)).. (-39.50 = -39.83 +   0.33)

alignment

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secondary structure

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Window 7

Location 8,392,838 – 8,392,958
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -38.47
Consensus MFE -38.10
Energy contribution -38.43
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.99
SVM decision value 0.48
SVM RNA-class probability 0.752202
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392838 120 + 23771897
GGAUGCUUCUCUGGCUGGAUGCGAGUCCGAAUCUGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCC
((((((((((((((((.(((((...(((((.......))))).)))))(((.(((...))))))....))).))))))......))).(((((((...)))))))...........)))) ( -39.60)
>DroSec_CAF1 69 120 + 1
GGAUGCUUCUCUGGCUGGAUGCGAAUCCGAAUCGGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCACGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCC
((((((((((((((((.(((((...(((((.......))))).)))))(((.(((...))))))....))).))))))......))).(((((((...)))))))...........)))) ( -40.70)
>DroSim_CAF1 60 120 + 1
GGAUGCUUCUCUGGCUGGAUGCGAAUACGAAUCGGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCC
((((((((((((((((.(((((.....(((.......)))...)))))(((.(((...))))))....))).))))))......))).(((((((...)))))))...........)))) ( -35.10)
>consensus
GGAUGCUUCUCUGGCUGGAUGCGAAUCCGAAUCGGAAUCGGAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCC
((((((((((((((((.(((((...(((((.......))))).)))))(((.(((...))))))....))).))))))......))).(((((((...)))))))...........)))) (-38.10 = -38.43 +   0.33)

alignment

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secondary structure

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Window 8

Location 8,392,878 – 8,392,998
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -37.58
Consensus MFE -36.42
Energy contribution -36.75
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.97
SVM decision value 1.25
SVM RNA-class probability 0.936208
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392878 120 + 23771897
GAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAAAGCCGAGACCACAGCCAAU
..(((.(((((.(((...)))))).......(((((............(((((((...)))))))............)))))..)).(((((...(((....)))..)))))..)))... ( -38.55)
>DroSec_CAF1 109 120 + 1
GAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCACGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAGAGCCGAGACCACAGCCAAU
........(((.(((((....((......)).((((............(((((((...)))))))............))))))))).(((((...(((....)))..)))))..)))... ( -35.65)
>DroSim_CAF1 100 120 + 1
GAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAAAGCCGAGACCACAGCCAAU
..(((.(((((.(((...)))))).......(((((............(((((((...)))))))............)))))..)).(((((...(((....)))..)))))..)))... ( -38.55)
>consensus
GAGGCAUCGGCAUCCAGAGGAGCCAUUAAGCGCGGAGAAAAUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAAAGCCGAGACCACAGCCAAU
..(((.(((((.(((...)))))).......(((((............(((((((...)))))))............)))))..)).(((((...(((....)))..)))))..)))... (-36.42 = -36.75 +   0.33)

alignment

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secondary structure

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Window 9

Location 8,392,878 – 8,392,998
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -36.31
Consensus MFE -36.16
Energy contribution -35.94
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.37
Structure conservation index 1.00
SVM decision value 1.55
SVM RNA-class probability 0.963325
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392878 120 - 23771897
AUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAUUUUCUCCGCGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUC
((((((.((((((..(((....)))...))))))(((((.((((((((.....((((..............................))))..))))).))).))))).))))))..... ( -36.81)
>DroSec_CAF1 109 120 - 1
AUUGGCUGUGGUCUCGGCUCUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAUUUUCUCCGUGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUC
((((((.((((((..(((....)))...))))))(((((.((((((((..((((...(((((...(....)....)))))......))))...))))).))).))))).))))))..... ( -35.30)
>DroSim_CAF1 100 120 - 1
AUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAUUUUCUCCGCGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUC
((((((.((((((..(((....)))...))))))(((((.((((((((.....((((..............................))))..))))).))).))))).))))))..... ( -36.81)
>consensus
AUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAUUUUCUCCGCGCUUAAUGGCUCCUCUGGAUGCCGAUGCCUC
((((((.((((((..(((....)))...))))))(((((.((((((((.....((((..............................))))..))))).))).))))).))))))..... (-36.16 = -35.94 +  -0.22)

alignment

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secondary structure

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Window 0

Location 8,392,918 – 8,393,038
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -35.73
Consensus MFE -34.20
Energy contribution -35.70
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.96
SVM decision value 0.73
SVM RNA-class probability 0.835685
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392918 120 + 23771897
AUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAAAGCCGAGACCACAGCCAAUCUCAUUCAGCAUUGCAGCAAUGCGACCUCAACCGCCCCAC
.....(.(((((((((....(((((..(((.....(((..((((...(((((...(((....)))..)))))))))..))).)))...)))))(((....)))..))).)).)))).).. ( -35.70)
>DroSec_CAF1 149 120 + 1
AUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAGAGCCGAGACCACAGCCAAUCUCAUUCAGCAUUGCAGCAAUGCGACCUCAACCGCCCCAC
.....(.(((((((((....(((((..(((.....(((..((((...(((((...(((....)))..)))))))))..))).)))...)))))(((....)))..))).)).)))).).. ( -35.70)
>DroSim_CAF1 140 120 + 1
AUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAAAGCCGAGACCACAGCCAAUCUCAUCCAGCAUUGCAGCAAUGCGACCUCAACCGCCCCAC
.....((((.(((.(((.....(((....)))...(((..((((...(((((...(((....)))..)))))))))..)))...)))))).(((((....)))))......))))..... ( -35.80)
>consensus
AUUAAGCGGCGUUAGGAAUUAAUGCACAUGUAAACGAUCCGCUGGAAUGGUCAGAGGCAAAAGCCGAGACCACAGCCAAUCUCAUUCAGCAUUGCAGCAAUGCGACCUCAACCGCCCCAC
.....(.(((((((((....(((((..(((.....(((..((((...(((((...(((....)))..)))))))))..))).)))...)))))(((....)))..))).)).)))).).. (-34.20 = -35.70 +   1.50)

alignment

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secondary structure

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Window 1

Location 8,392,918 – 8,393,038
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -44.27
Consensus MFE -44.49
Energy contribution -44.27
Covariance contribution -0.22
Combinations/Pair 1.02
Mean z-score -2.18
Structure conservation index 1.00
SVM decision value 1.38
SVM RNA-class probability 0.947904
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392918 120 - 23771897
GUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGAAUGAGAUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAU
...(((((((..(((....((((.(((((((.(((((..((((.(((((((((..(((....)))...)))))...)))).)))))))))))).)))).)))).)))...)))))))... ( -44.40)
>DroSec_CAF1 149 120 - 1
GUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGAAUGAGAUUGGCUGUGGUCUCGGCUCUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAU
...(((((((..(((....((((.(((((((.(((((..((((.(((((((((..(((....)))...)))))...)))).)))))))))))).)))).)))).)))...)))))))... ( -44.40)
>DroSim_CAF1 140 120 - 1
GUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGGAUGAGAUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAU
...(((((((..(((....((((.(((((((.(((((..((((.(((((((((..(((....)))...)))))...)))).)))))))))))).)))).)))).)))...)))))))... ( -44.00)
>consensus
GUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGAAUGAGAUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGCGGAUCGUUUACAUGUGCAUUAAUUCCUAACGCCGCUUAAU
...(((((((..(((....((((.(((((((.(((((..((((.(((((((((..(((....)))...)))))...)))).)))))))))))).)))).)))).)))...)))))))... (-44.49 = -44.27 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,392,958 – 8,393,078
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -46.10
Consensus MFE -46.10
Energy contribution -46.10
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 1.00
SVM decision value 0.15
SVM RNA-class probability 0.606259
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8392958 120 - 23771897
GUACCACACUUUUCUGCCAGUGCAGGAUUGGUGAGAGUGGGUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGAAUGAGAUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGC
......((((.((((((....))))))..)))).((((((..((((((((((((..((((..((..((((.((.....))))))))))))..)))))))...)))))...)))))).... ( -46.10)
>DroSec_CAF1 189 120 - 1
GUACCACACUUUUCUGCCAGUGCAGGAUUGGUGAGAGUGGGUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGAAUGAGAUUGGCUGUGGUCUCGGCUCUUGCCUCUGACCAUUCCAGC
......((((.((((((....))))))..)))).((((((..((((((((((((..((((..((..((((.((.....))))))))))))..)))))))...)))))...)))))).... ( -46.10)
>DroSim_CAF1 180 120 - 1
GUACCACACUUUUCUGCCAGUGCAGGAUUGGUGAGAGUGGGUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGGAUGAGAUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGC
......((((.((((((....))))))..)))).((((((..((((((((((((..((((..((..((((.((.....))))))))))))..)))))))...)))))...)))))).... ( -46.10)
>consensus
GUACCACACUUUUCUGCCAGUGCAGGAUUGGUGAGAGUGGGUGGGGCGGUUGAGGUCGCAUUGCUGCAAUGCUGAAUGAGAUUGGCUGUGGUCUCGGCUUUUGCCUCUGACCAUUCCAGC
......((((.((((((....))))))..)))).((((((..((((((((((((..((((..((..((((.((.....))))))))))))..)))))))...)))))...)))))).... (-46.10 = -46.10 +   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 10:45:26 2006