Locus 9306

Sequence ID 3R_DroMel_CAF1
Location 24,776,961 – 24,777,117
Length 156
Max. P 0.995962
window14875 window14876 window14877 window14878

overview

Window 5

Location 24,776,961 – 24,777,081
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -36.70
Consensus MFE -36.70
Energy contribution -36.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 1.00
SVM decision value 2.64
SVM RNA-class probability 0.995962
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24776961 120 + 27905053
ACAGAAUUCGGUUGCGGCGGUUUUGUGUUUACACUUUACAAUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAG
..........((((((((((((((((((.........)).)))))))))))....(((((((((((........))))))).((((.((((....)))).)))))))))))))....... ( -36.70)
>DroSec_CAF1 8102 120 + 1
ACAGAAUUCGGUUGCGGCGGUUUUGUGUUUACACUUUACAAUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAG
..........((((((((((((((((((.........)).)))))))))))....(((((((((((........))))))).((((.((((....)))).)))))))))))))....... ( -36.70)
>DroSim_CAF1 3484 120 + 1
ACAGAAUUCGGUUGCGGCGGUUUUGUGUUUACACUUUACAAUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAG
..........((((((((((((((((((.........)).)))))))))))....(((((((((((........))))))).((((.((((....)))).)))))))))))))....... ( -36.70)
>DroEre_CAF1 17023 120 + 1
ACAGAAUUCGGUUGCGGCGGUUUUGUGUUUACACUUUACAAUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAG
..........((((((((((((((((((.........)).)))))))))))....(((((((((((........))))))).((((.((((....)))).)))))))))))))....... ( -36.70)
>DroYak_CAF1 8636 120 + 1
ACAGAAUUCGGUUGCGGCGGUUUUGUGUUUACACUUUACAAUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAG
..........((((((((((((((((((.........)).)))))))))))....(((((((((((........))))))).((((.((((....)))).)))))))))))))....... ( -36.70)
>consensus
ACAGAAUUCGGUUGCGGCGGUUUUGUGUUUACACUUUACAAUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAG
..........((((((((((((((((((.........)).)))))))))))....(((((((((((........))))))).((((.((((....)))).)))))))))))))....... (-36.70 = -36.70 +  -0.00)

alignment

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secondary structure

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Window 6

Location 24,776,961 – 24,777,081
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -28.70
Consensus MFE -28.70
Energy contribution -28.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 1.00
SVM decision value 1.30
SVM RNA-class probability 0.939353
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24776961 120 - 27905053
CUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAUUGUAAAGUGUAAACACAAAACCGCCGCAACCGAAUUCUGU
..((((((((((((((((.((((((((......(((...)))......))))))))...))))))....(((....(....)....(((....)))......))))))).)))))).... ( -28.70)
>DroSec_CAF1 8102 120 - 1
CUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAUUGUAAAGUGUAAACACAAAACCGCCGCAACCGAAUUCUGU
..((((((((((((((((.((((((((......(((...)))......))))))))...))))))....(((....(....)....(((....)))......))))))).)))))).... ( -28.70)
>DroSim_CAF1 3484 120 - 1
CUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAUUGUAAAGUGUAAACACAAAACCGCCGCAACCGAAUUCUGU
..((((((((((((((((.((((((((......(((...)))......))))))))...))))))....(((....(....)....(((....)))......))))))).)))))).... ( -28.70)
>DroEre_CAF1 17023 120 - 1
CUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAUUGUAAAGUGUAAACACAAAACCGCCGCAACCGAAUUCUGU
..((((((((((((((((.((((((((......(((...)))......))))))))...))))))....(((....(....)....(((....)))......))))))).)))))).... ( -28.70)
>DroYak_CAF1 8636 120 - 1
CUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAUUGUAAAGUGUAAACACAAAACCGCCGCAACCGAAUUCUGU
..((((((((((((((((.((((((((......(((...)))......))))))))...))))))....(((....(....)....(((....)))......))))))).)))))).... ( -28.70)
>consensus
CUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAUUGUAAAGUGUAAACACAAAACCGCCGCAACCGAAUUCUGU
..((((((((((((((((.((((((((......(((...)))......))))))))...))))))....(((....(....)....(((....)))......))))))).)))))).... (-28.70 = -28.70 +  -0.00)

alignment

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secondary structure

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Window 7

Location 24,777,001 – 24,777,117
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.77
Mean single sequence MFE -31.88
Consensus MFE -30.70
Energy contribution -30.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.10
Structure conservation index 0.96
SVM decision value 0.14
SVM RNA-class probability 0.600569
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24777001 116 + 27905053
AUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAGUUUUCGCUGUCCCCAAAAUG----UGUCCUCUGUAACGGA
...((((.((.((((((.((((((((........))))))))((((.((((....)))).))))...(....).....)))))).)).))))........----..(((........))) ( -30.70)
>DroSec_CAF1 8142 116 + 1
AUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAGUUUUCGCUGUCCCCGAAAUG----UGUCCUCUGUAACGGA
...((((.((.((((((.((((((((........))))))))((((.((((....)))).))))...(....).....)))))).)).))))........----..(((........))) ( -30.70)
>DroSim_CAF1 3524 116 + 1
AUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAGUUUUCGCUGUCCCCAAAAUG----UGUCCUCUGUAACGGA
...((((.((.((((((.((((((((........))))))))((((.((((....)))).))))...(....).....)))))).)).))))........----..(((........))) ( -30.70)
>DroEre_CAF1 17063 116 + 1
AUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAGUUUUCGCUGUCCCCAAAAUG----GCUCCACUGUAACGGA
...((((.((.((((((.((((((((........))))))))((((.((((....)))).))))...(....).....)))))).)).))))((.....)----).(((........))) ( -30.90)
>DroYak_CAF1 8676 120 + 1
AUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAGUUUUCGCUGUCCCCAAAAUGGGUAGCUCCACUGUAACGGA
...((((((((.......((((((((........))))))))((((.((((....)))).))))...))))).............((((.(((......))))))))))........... ( -36.40)
>consensus
AUAGGAUUGCCGAGGCUUUGGCGGAAUUUCACAUUUUUGCCAGGGGCUUUCUAAUGAAAUCUCCAAAGGCAACAAAUUAGUUUUCGCUGUCCCCAAAAUG____UGUCCUCUGUAACGGA
...((((.((.((((((.((((((((........))))))))((((.((((....)))).))))...(....).....)))))).)).))))..............(((........))) (-30.70 = -30.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,777,001 – 24,777,117
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.77
Mean single sequence MFE -31.04
Consensus MFE -28.94
Energy contribution -28.78
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.29
Structure conservation index 0.93
SVM decision value 0.62
SVM RNA-class probability 0.803162
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24777001 116 - 27905053
UCCGUUACAGAGGACA----CAUUUUGGGGACAGCGAAAACUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAU
..........((((..----...(((((((.(((((((......)))))))))...((((.((((((......(((...)))......)))))))))).)))))((....))..)))).. ( -30.70)
>DroSec_CAF1 8142 116 - 1
UCCGUUACAGAGGACA----CAUUUCGGGGACAGCGAAAACUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAU
..........((((..----....((((((.(((((((......))))))).((((((.((((((((......(((...)))......))))))))...))))))))))))...)))).. ( -31.30)
>DroSim_CAF1 3524 116 - 1
UCCGUUACAGAGGACA----CAUUUUGGGGACAGCGAAAACUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAU
..........((((..----...(((((((.(((((((......)))))))))...((((.((((((......(((...)))......)))))))))).)))))((....))..)))).. ( -30.70)
>DroEre_CAF1 17063 116 - 1
UCCGUUACAGUGGAGC----CAUUUUGGGGACAGCGAAAACUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAU
((((......))))((----(.....((((.(((((((......))))))).((((((.((((((((......(((...)))......))))))))...)))))))))))))........ ( -31.30)
>DroYak_CAF1 8676 120 - 1
UCCGUUACAGUGGAGCUACCCAUUUUGGGGACAGCGAAAACUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAU
...........((((((.(((.....)))...)))..........((((((.((((((.((((((((......(((...)))......))))))))...))))))...)))))))))... ( -31.20)
>consensus
UCCGUUACAGAGGACA____CAUUUUGGGGACAGCGAAAACUAAUUUGUUGCCUUUGGAGAUUUCAUUAGAAAGCCCCUGGCAAAAAUGUGAAAUUCCGCCAAAGCCUCGGCAAUCCUAU
(((........)))..........((((((.(((((((......))))))).((((((.((((((((......(((...)))......))))))))...))))))))))))......... (-28.94 = -28.78 +  -0.16)

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 13:31:11 2006