Locus 6018

Sequence ID 3L_DroMel_CAF1
Location 16,055,212 – 16,055,529
Length 317
Max. P 0.999902
window9626 window9627 window9628 window9629 window9630

overview

Window 6

Location 16,055,212 – 16,055,332
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.67
Mean single sequence MFE -36.26
Consensus MFE -36.16
Energy contribution -35.28
Covariance contribution -0.88
Combinations/Pair 1.17
Mean z-score -2.28
Structure conservation index 1.00
SVM decision value 4.46
SVM RNA-class probability 0.999902
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16055212 120 + 23771897
CACAUCAAAACCAUAUCCGCUCUGGCCAGCCGGCCAUCCUUGGAGAAACCCAGGCCGGCAAAGCCUCGUGUGUGAACAGUUACUUCAAAGUAAAUGCUAUUUUCGUUGGCGUUUAUCCAC
...........((((..((....(((..(((((((.....(((......))))))))))...))).))..))))...............((((((((((.......)))))))))).... ( -35.60)
>DroSec_CAF1 5237 120 + 1
CACAACAAAACCAUAUCCGCUCUGGCCAGCCGGCCAUCCUUGGAGAAGCCCAGGCCGGCAAAGCCUCGCGUGUGAACAGUUACUUCGAAGUAAAUGCUAUUUUCGUUGGCAUUUAUCCAC
...........((((..(((...(((..(((((((.....(((......))))))))))...)))..)))))))...............((((((((((.......)))))))))).... ( -36.60)
>DroSim_CAF1 3752 120 + 1
CACAACAAAACCAUAUCCGCUCUGGCCAGCCGGCCAUCCUUGGAGAAGCCCAGGCCGGCAAAGCCUCGCGUGUGAACAGUUACUUCGAAGUAAAUGCUAUUUUCGUUGGCAUUUAUCCAC
...........((((..(((...(((..(((((((.....(((......))))))))))...)))..)))))))...............((((((((((.......)))))))))).... ( -36.60)
>DroEre_CAF1 4340 120 + 1
CACAAUAGAACCAUAUCCGCUCUGGCCAGCCGGCCAUCCUUGGAGAAACCUAGGCCGGCAAAGCCUCGCGUAUGAACAGUAACUUCGAAGUAAAUGCUAUUUUCGUUGGCAUUUAUCCAC
...........((((..(((...(((..(((((((......((.....))..)))))))...)))..)))))))...............((((((((((.......)))))))))).... ( -34.80)
>DroYak_CAF1 4260 120 + 1
CACAAUAAAACCACAUCCGCUCUGGCCAGCCGGCCAUCCUUGGAGAAACCCAGGCCGGCAAAGCCUCGCGUAUGAACAGUAACUUCGAAGUAAAUGCUAUUUUCGUUGGCAUUUAUCCAC
.............(((.(((...(((..(((((((.....(((......))))))))))...)))..))).)))...............((((((((((.......)))))))))).... ( -37.70)
>consensus
CACAACAAAACCAUAUCCGCUCUGGCCAGCCGGCCAUCCUUGGAGAAACCCAGGCCGGCAAAGCCUCGCGUGUGAACAGUUACUUCGAAGUAAAUGCUAUUUUCGUUGGCAUUUAUCCAC
.............(((.(((...(((..(((((((.....(((......))))))))))...)))..))).)))...............((((((((((.......)))))))))).... (-36.16 = -35.28 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,055,252 – 16,055,369
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 95.21
Mean single sequence MFE -34.74
Consensus MFE -32.42
Energy contribution -33.06
Covariance contribution 0.64
Combinations/Pair 1.09
Mean z-score -1.31
Structure conservation index 0.93
SVM decision value 0.88
SVM RNA-class probability 0.873246
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16055252 117 - 23771897
AAAUGAUGGACAGCUUGGGCUUGUACUGGCUCAAAUGGUGGAUAAACGCCAACGAAAAUAGCAUUUACUUUGAAGUAACUGUUCACACACGAGGCUUUGCCGGCCUGGGUUUCUCCA
......((((.((((..((((.(((..(.(((...(((((......)))))........((((.(((((....))))).)))).......))).)..))).))))..))))..)))) ( -38.60)
>DroSec_CAF1 5277 117 - 1
AAAUGAUGGACAGCUUGGGCUUGUACUGGCUCAAAUGGUGGAUAAAUGCCAACGAAAAUAGCAUUUACUUCGAAGUAACUGUUCACACGCGAGGCUUUGCCGGCCUGGGCUUCUCCA
......((((.((((..((((.(((..(.(((.....((((((((((((...........)))))((((....))))..)))))))....))).)..))).))))..))))..)))) ( -38.30)
>DroSim_CAF1 3792 117 - 1
AAAUGAUGGACAGCUUGGGCUUGUACUGGCUCAAAUGGUGGAUAAAUGCCAACGAAAAUAGCAUUUACUUCGAAGUAACUGUUCACACGCGAGGCUUUGCCGGCCUGGGCUUCUCCA
......((((.((((..((((.(((..(.(((.....((((((((((((...........)))))((((....))))..)))))))....))).)..))).))))..))))..)))) ( -38.30)
>DroEre_CAF1 4380 117 - 1
AAAUGAUGGAUAGCUUGGGAAUGUACUGGCUCAAAUGGUGGAUAAAUGCCAACGAAAAUAGCAUUUACUUCGAAGUUACUGUUCAUACGCGAGGCUUUGCCGGCCUAGGUUUCUCCA
......((((.((((((((...(((..(.(((.(((..(((((((((((...........))))))).))))..)))...((....))..))).)..)))...))))))))..)))) ( -29.30)
>DroYak_CAF1 4300 117 - 1
AAAUGAUGGAUAGCUUGGGAAUGUACUGGCUCAAGUGGUGGAUAAAUGCCAACGAAAAUAGCAUUUACUUCGAAGUUACUGUUCAUACGCGAGGCUUUGCCGGCCUGGGUUUCUCCA
......((((.((((..((...(((..((((...((((((((((...((...((((............))))..))...))))))).)))..)))).)))...))..))))..)))) ( -29.20)
>consensus
AAAUGAUGGACAGCUUGGGCUUGUACUGGCUCAAAUGGUGGAUAAAUGCCAACGAAAAUAGCAUUUACUUCGAAGUAACUGUUCACACGCGAGGCUUUGCCGGCCUGGGUUUCUCCA
......((((.((((((((((.(((..(.(((...(((((......)))))........((((.(((((....))))).)))).......))).)..))).))))))))))..)))) (-32.42 = -33.06 +   0.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,055,369 – 16,055,489
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.17
Mean single sequence MFE -28.46
Consensus MFE -23.42
Energy contribution -24.06
Covariance contribution 0.64
Combinations/Pair 1.09
Mean z-score -1.86
Structure conservation index 0.82
SVM decision value 0.86
SVM RNA-class probability 0.869010
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16055369 120 + 23771897
CGUUACGCACCCAGUUUUUGUGGUGUACAGAACCAUUUUUAUCGACAUCAUAGUCCUGCGUCCUUUGAUUGUUUUCAAAAUACGCAAGACCAAAACUCAACUGCACCGUGAGUACGAUCC
(((.((.(((.(((((..((((((((...((..........)).))))))))(((.(((((..(((((......)))))..))))).)))........)))))....))).))))).... ( -30.60)
>DroSec_CAF1 5394 120 + 1
CGUUACGCACCCAGUUUUUGUGGUGUACAGAACCAUUUUUAUCGACAUCAUAGUCCUGCGUCCUUUGGUUGUUUUCAAAAUACGCAAGACCAAAACUCAACUGCACCGUGAGUACGAUCC
(((.((.(((.(((((..((((((((...((..........)).))))))))(((.(((((..(((((......)))))..))))).)))........)))))....))).))))).... ( -29.70)
>DroSim_CAF1 3909 120 + 1
CGUUACGCACCCAGUUUUUGUGGUGUACAGAACCAUUUUUAUCGACAUCAUAGUCCUGCGUCCUUUGGUUGUUUUCAAAAUACGCAAGACCAAAACUCAACUGCACCGUGAGUACGAUCC
(((.((.(((.(((((..((((((((...((..........)).))))))))(((.(((((..(((((......)))))..))))).)))........)))))....))).))))).... ( -29.70)
>DroEre_CAF1 4497 120 + 1
CGUCACGCACCCAGUUUUUGUGGUGUACAGAACCAUUUUUAUCGACAUCAUAGUCCUGCGUCCUUUGGUUAUUUUCAAAAUAACCAAGACCAAAACUCAACUGCACCGUGAGUACAAUCC
..(((((....(((((..((((((((...((..........)).))))))))((..((.(((..(((((((((.....))))))))))))))..))..)))))...)))))......... ( -28.40)
>DroYak_CAF1 4417 120 + 1
CGUCACGCACCCAGUUUUUGUGGUGUACAGAACCAUUUUUAUCGACAUCGUAGUCCUGCGUCCUUUGGUUAUUUUCAAAAUAACAAACACCAAAACUCAACUGCACCGUGAGUACAAUCC
..(((((....(((((....((((((................(((...((((....))))....)))((((((.....))))))..))))))......)))))...)))))......... ( -23.90)
>consensus
CGUUACGCACCCAGUUUUUGUGGUGUACAGAACCAUUUUUAUCGACAUCAUAGUCCUGCGUCCUUUGGUUGUUUUCAAAAUACGCAAGACCAAAACUCAACUGCACCGUGAGUACGAUCC
..(((((....(((((..((((((((...((..........)).))))))))(((.(((((..(((((......)))))..))))).)))........)))))...)))))......... (-23.42 = -24.06 +   0.64)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,055,369 – 16,055,489
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.17
Mean single sequence MFE -36.65
Consensus MFE -32.54
Energy contribution -33.26
Covariance contribution 0.72
Combinations/Pair 1.05
Mean z-score -2.25
Structure conservation index 0.89
SVM decision value 2.84
SVM RNA-class probability 0.997322
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16055369 120 - 23771897
GGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAAUCAAAGGACGCAGGACUAUGAUGUCGAUAAAAAUGGUUCUGUACACCACAAAAACUGGGUGCGUAACG
(((((((((.....)))).((((((((.(((((((((((.((((((......)))))).))))))))))).))).)))))......))))).((((.(((.......)))))))...... ( -39.90)
>DroSec_CAF1 5394 120 - 1
GGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAACCAAAGGACGCAGGACUAUGAUGUCGAUAAAAAUGGUUCUGUACACCACAAAAACUGGGUGCGUAACG
(((((((((.....)))).((((((((.(((((((((((.(((((........))))).))))))))))).))).)))))......))))).((((.(((.......)))))))...... ( -38.50)
>DroSim_CAF1 3909 120 - 1
GGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAACCAAAGGACGCAGGACUAUGAUGUCGAUAAAAAUGGUUCUGUACACCACAAAAACUGGGUGCGUAACG
(((((((((.....)))).((((((((.(((((((((((.(((((........))))).))))))))))).))).)))))......))))).((((.(((.......)))))))...... ( -38.50)
>DroEre_CAF1 4497 120 - 1
GGAUUGUACUCACGGUGCAGUUGAGUUUUGGUCUUGGUUAUUUUGAAAAUAACCAAAGGACGCAGGACUAUGAUGUCGAUAAAAAUGGUUCUGUACACCACAAAAACUGGGUGCGUGACG
.((((((((.....))))))))..(((.((((((((((((((.....))))))))..))))((((((((((.............)))))))))).((((.((.....)))))))).))). ( -36.62)
>DroYak_CAF1 4417 120 - 1
GGAUUGUACUCACGGUGCAGUUGAGUUUUGGUGUUUGUUAUUUUGAAAAUAACCAAAGGACGCAGGACUACGAUGUCGAUAAAAAUGGUUCUGUACACCACAAAAACUGGGUGCGUGACG
.........(((((((.(((((...((.((((((..(((.(((((........))))))))(((((((((((....)).......))))))))))))))).)).))))).)).))))).. ( -29.71)
>consensus
GGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAACCAAAGGACGCAGGACUAUGAUGUCGAUAAAAAUGGUUCUGUACACCACAAAAACUGGGUGCGUAACG
(.(((((....))))).).((((((((.(((((((((((.(((((........))))).))))))))))).))).))))).......(((.(((((.(((.......)))))))).))). (-32.54 = -33.26 +   0.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,055,409 – 16,055,529
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.83
Mean single sequence MFE -37.14
Consensus MFE -30.00
Energy contribution -31.60
Covariance contribution 1.60
Combinations/Pair 1.05
Mean z-score -2.19
Structure conservation index 0.81
SVM decision value 1.65
SVM RNA-class probability 0.970150
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16055409 120 - 23771897
AAGUACAAGGCUAACGCCAUGUCCGUUCAAGACGUACUAUGGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAAUCAAAGGACGCAGGACUAUGAUGUCGAU
.(((((..(((....)))..(((.......)))))))).((.(((((....))))).))((((((((.(((((((((((.((((((......)))))).))))))))))).))).))))) ( -44.10)
>DroSec_CAF1 5434 120 - 1
AAGUACAAGGCUACCGACAUGUCCGUUCAAGACGUACUAUGGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAACCAAAGGACGCAGGACUAUGAUGUCGAU
.(((.....)))..((((((.......((((((......((.(((((....))))).)).....))))))(((((((((.(((((........))))).)))))))))....)))))).. ( -37.20)
>DroSim_CAF1 3949 120 - 1
AAGUACAAGGCUACCGACAUGUCCGUUCAAGACGUACUAUGGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAACCAAAGGACGCAGGACUAUGAUGUCGAU
.(((.....)))..((((((.......((((((......((.(((((....))))).)).....))))))(((((((((.(((((........))))).)))))))))....)))))).. ( -37.20)
>DroEre_CAF1 4537 120 - 1
AAGUGCAAGGAUUCCGCCAUGUCCUAUCAAAACGUACUAUGGAUUGUACUCACGGUGCAGUUGAGUUUUGGUCUUGGUUAUUUUGAAAAUAACCAAAGGACGCAGGACUAUGAUGUCGAU
...(((..((......))..(((((((((((((......(.((((((((.....)))))))).))))))))).(((((((((.....))))))))))))))))).(((......)))... ( -35.30)
>DroYak_CAF1 4457 120 - 1
AAGUACAAGGCAUCCGCCAUGUCCUUGCAAGACGUACUAUGGAUUGUACUCACGGUGCAGUUGAGUUUUGGUGUUUGUUAUUUUGAAAAUAACCAAAGGACGCAGGACUACGAUGUCGAU
(((.(((.(((....))).))).)))....(((((......((((((((.....)))))))).(((((((((.(((((((((.....))))))..))).)).)))))))...)))))... ( -31.90)
>consensus
AAGUACAAGGCUACCGCCAUGUCCGUUCAAGACGUACUAUGGAUCGUACUCACGGUGCAGUUGAGUUUUGGUCUUGCGUAUUUUGAAAACAACCAAAGGACGCAGGACUAUGAUGUCGAU
.(((((..(((....)))..(((.......)))))))).((.(((((....))))).))((((((((.(((((((((((.(((((........))))).))))))))))).))).))))) (-30.00 = -31.60 +   1.60)

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 12:06:59 2006