Locus 5647

Sequence ID 3L_DroMel_CAF1
Location 15,499,639 – 15,499,835
Length 196
Max. P 0.910790
window8929 window8930 window8931 window8932

overview

Window 9

Location 15,499,639 – 15,499,755
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.40
Mean single sequence MFE -40.50
Consensus MFE -38.61
Energy contribution -38.17
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.11
Structure conservation index 0.95
SVM decision value 1.07
SVM RNA-class probability 0.910790
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15499639 116 + 23771897
GCGAGUGUUACCAAGCGGCAGCAGCCAAAGUCGGGUCUGGUUGCAGAGCGGGGUACACCCCCCG---U-CCUAUUCCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACA
(((((((((.......(((....))).......((((((..((((((((((((......)))))---)-.........)).))))..))))))......)))))))))............ ( -43.30)
>DroSec_CAF1 40780 117 + 1
GUGAGUGUUACCAAGCGGCAGCAGCCAAAGUCGGGUCUGGUUGCAGAGCGGGGAAGACCCCCCA---UACCUACACCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACA
(((((((((.......(((....))).......((((((..(((.....((((......)))).---.....((......)))))..))))))......)))))))))............ ( -37.80)
>DroSim_CAF1 41032 120 + 1
GCGAGUGUUACCAAGCGGCAGCAGCCAAAGUCGGGUCUGGUUGCAGAGCGGGGAACACCCCCCACCCUACCUACACCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACA
(((((((((.......(((....))).......((((((..(((((.(.((((......)))).).))....((......)))))..))))))......)))))))))............ ( -40.40)
>consensus
GCGAGUGUUACCAAGCGGCAGCAGCCAAAGUCGGGUCUGGUUGCAGAGCGGGGAACACCCCCCA___UACCUACACCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACA
(((((((((.......(((....))).......((((((..(((.....((((......)))).........((......)))))..))))))......)))))))))............ (-38.61 = -38.17 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,499,679 – 15,499,795
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.96
Mean single sequence MFE -24.77
Consensus MFE -22.53
Energy contribution -22.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.91
SVM decision value 0.57
SVM RNA-class probability 0.785099
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15499679 116 + 23771897
UUGCAGAGCGGGGUACACCCCCCG---U-CCUAUUCCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACAAAAUCUAUAAUAAAAAACAGGUUAACAAAUGUUGCCGCAA
..((((..(((((......)))))---.-.))......(((......)))))..............((.((((((......(((((............)))))......)))))).)).. ( -25.50)
>DroSec_CAF1 40820 117 + 1
UUGCAGAGCGGGGAAGACCCCCCA---UACCUACACCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACAAAAUCUAUAAUAAAAAACAGGUUAACAAAUGUUGCCGCAA
.....(((.((((......)))).---..(((.(((....))).....)))............)))((.((((((......(((((............)))))......)))))).)).. ( -23.00)
>DroSim_CAF1 41072 120 + 1
UUGCAGAGCGGGGAACACCCCCCACCCUACCUACACCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACAAAAUCUAUAAUAAAAAACAGGUUAACAAAUGUUGCCGCAA
.....(((.((((......)))).(((......(((....))).....)))............)))((.((((((......(((((............)))))......)))))).)).. ( -25.80)
>consensus
UUGCAGAGCGGGGAACACCCCCCA___UACCUACACCAUCGUGCAUUCGGGCCAAAUCAAAUACUCGCAGCAACAACACAAAAUCUAUAAUAAAAAACAGGUUAACAAAUGUUGCCGCAA
.....(((.((((......)))).................(.((......)))..........)))((.((((((......(((((............)))))......)))))).)).. (-22.53 = -22.53 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,499,679 – 15,499,795
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.96
Mean single sequence MFE -39.50
Consensus MFE -33.92
Energy contribution -34.37
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.74
Structure conservation index 0.86
SVM decision value 0.92
SVM RNA-class probability 0.881569
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15499679 116 - 23771897
UUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCACGAUGGAAUAGG-A---CGGGGGGUGUACCCCGCUCUGCAA
(((((((((((......((.((((........)))).))......)))))))))))(((((((........))))))).........(((.-.---(((((......)))))..)))... ( -37.60)
>DroSec_CAF1 40820 117 - 1
UUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCACGAUGGUGUAGGUA---UGGGGGGUCUUCCCCGCUCUGCAA
(((((((((((......((.((((........)))).))......)))))))))))(((((((........))))))).......((((((..---.(.((((....)))).))))))). ( -36.90)
>DroSim_CAF1 41072 120 - 1
UUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCACGAUGGUGUAGGUAGGGUGGGGGGUGUUCCCCGCUCUGCAA
(((((((((((......((.((((........)))).))......)))))))))))(((((((........)))))))............((((((((((((....)))))))))))).. ( -44.00)
>consensus
UUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCACGAUGGUGUAGGUA___UGGGGGGUGUUCCCCGCUCUGCAA
(((((((((((......((.((((........)))).))......)))))))))))(((((((........))))))).......((((((.....(((((......))))).)))))). (-33.92 = -34.37 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,499,715 – 15,499,835
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -34.70
Consensus MFE -34.70
Energy contribution -34.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 1.00
SVM decision value 0.11
SVM RNA-class probability 0.587174
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15499715 120 - 23771897
CAAGUUUCUUCCGACGCUAUGGGCUGCGUCGACGUCAGCGUUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCAC
...(((......)))((..(((((((.(((((((....))))(((((((((......((.((((........)))).))......)))))))))........))).)))))))...)).. ( -34.70)
>DroSec_CAF1 40857 120 - 1
CAAGUUUCUUCCGACGCUAUGGGCUGCGUCGACGUCAGCGUUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCAC
...(((......)))((..(((((((.(((((((....))))(((((((((......((.((((........)))).))......)))))))))........))).)))))))...)).. ( -34.70)
>DroSim_CAF1 41112 120 - 1
CAAGUUUCUUCCGACGCUAUGGGCUGCGUCGACGUCAGCGUUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCAC
...(((......)))((..(((((((.(((((((....))))(((((((((......((.((((........)))).))......)))))))))........))).)))))))...)).. ( -34.70)
>consensus
CAAGUUUCUUCCGACGCUAUGGGCUGCGUCGACGUCAGCGUUGCGGCAACAUUUGUUAACCUGUUUUUUAUUAUAGAUUUUGUGUUGUUGCUGCGAGUAUUUGAUUUGGCCCGAAUGCAC
...(((......)))((..(((((((.(((((((....))))(((((((((......((.((((........)))).))......)))))))))........))).)))))))...)).. (-34.70 = -34.70 +  -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 11:55:38 2006