Locus 7743

Sequence ID 3R_DroMel_CAF1
Location 20,784,657 – 20,784,932
Length 275
Max. P 0.984664
window12482 window12483 window12484 window12485

overview

Window 2

Location 20,784,657 – 20,784,772
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -24.71
Consensus MFE -24.60
Energy contribution -24.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 1.00
SVM decision value 1.98
SVM RNA-class probability 0.984664
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20784657 115 + 27905053
GCAUUUGAAAAUAUAUAAAAGAUCACAAAUAAUAAACAAAAU-----CAAAUCAAAUGGAAUCCAUGCCCAUGCCCAACGGCGGCACUCGCAUUUUUGCGCCUGUCAAGGCCAAUUGCAU
(((.(((...................................-----........((((...))))(((...(((....)))((((..((((....))))..))))..)))))).))).. ( -24.60)
>DroSec_CAF1 436 120 + 1
GCAUUUGAAAAUAUAUAAAAGAUCACAAAUAAUAUAAAAAAUCAAAUCAAAUCAAAUGGAGUCCAUGCCCAUGCCCAACGGCGGCACUCGCAUUUUUGCGCCUGUCAAGGCCAAUUGCAU
.(((((((...........................................)))))))((((....(((...(((....))))))))))(((...(((.((((....))))))).))).. ( -24.93)
>DroSim_CAF1 438 120 + 1
GCAUUUGAAAAUACAUAAAAGAUCACAAAUAAUAUAAAAAAUCAAAUCAAAUCAAAUGGAAUCCAUGCCCAUGCCCAACGGCGGCACUCGCAUUUUUGCGCCUGUCAAGGCCAAUUGCAU
(((.(((................................................((((...))))(((...(((....)))((((..((((....))))..))))..)))))).))).. ( -24.60)
>consensus
GCAUUUGAAAAUAUAUAAAAGAUCACAAAUAAUAUAAAAAAUCAAAUCAAAUCAAAUGGAAUCCAUGCCCAUGCCCAACGGCGGCACUCGCAUUUUUGCGCCUGUCAAGGCCAAUUGCAU
(((.(((................................................((((...))))(((...(((....)))((((..((((....))))..))))..)))))).))).. (-24.60 = -24.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,784,772 – 20,784,892
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -34.40
Consensus MFE -32.88
Energy contribution -32.66
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.96
SVM decision value 0.56
SVM RNA-class probability 0.782064
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20784772 120 - 27905053
AAGCUCGAGCGUGAGCAAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUUCGGUCAGUUUUGAAUGAAAAAUCGGAGCGCGGCUUCCAGGUAAACUAACGCGAUUAUUAUGAAAUUA
..((((..((....)).......((((((.((((..(((((......)))))..)))).))))))............))))(((.................)))................ ( -31.53)
>DroSec_CAF1 556 119 - 1
AAGCUCGAGCGUGAGCGAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUU-GGCCAGUUUUGAAUGAAAAAUCGGAGCGCGGCUUCCAGGUAAACUAACGCGAUUAUUAUGAAAUUA
..((((..((....)).......((((((.(((((.(((((......))))))-)))).))))))............))))(((.................)))................ ( -35.83)
>DroSim_CAF1 558 119 - 1
AAGCUCGAGCGUGAGCGAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUU-GGCCAGUUUUGAAUGAAAAAUCGGAGCGCGGCUUCCAGGUAAACUAACGCGAUUAUUAUGAAAUUA
..((((..((....)).......((((((.(((((.(((((......))))))-)))).))))))............))))(((.................)))................ ( -35.83)
>consensus
AAGCUCGAGCGUGAGCGAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUU_GGCCAGUUUUGAAUGAAAAAUCGGAGCGCGGCUUCCAGGUAAACUAACGCGAUUAUUAUGAAAUUA
..((((..((....)).......((((((.((((..(((((......)))))..)))).))))))............))))(((.................)))................ (-32.88 = -32.66 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,784,812 – 20,784,932
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.21
Mean single sequence MFE -34.10
Consensus MFE -29.27
Energy contribution -29.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.86
SVM decision value 0.76
SVM RNA-class probability 0.844425
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20784812 120 + 27905053
CUCCGAUUUUUCAUUCAAAACUGACCGAAAUGCCCAAAUGCAUUGUGGCCCGUUUUGUCAAUUUGCUCACGCUCGAGCUUUAGAAUCGACAGUCCGAAAAUAGUUUCGAUUUUGAGCCAC
.........((((.((.((((((.(((.(((((......))))).)))..((..(((((.((((((((......))))....)))).)))))..))....)))))).))...)))).... ( -27.20)
>DroSec_CAF1 596 119 + 1
CUCCGAUUUUUCAUUCAAAACUGGCC-AAAUGCCCAAAUGCAUUGUGGCCCGUUUUGUCAAUUCGCUCACGCUCGAGCUUUAGAAUCGACGGUUCGAAAAUAGUUUCGAUUUUGAGCCAC
...(((((((.....((((((.((((-((((((......))))).))))).)))))).......((((......))))...)))))))..(((((((((..........))))))))).. ( -39.30)
>DroSim_CAF1 598 119 + 1
CUCCGAUUUUUCAUUCAAAACUGGCC-AAAUGCCCAAAUGCAUUGUGGCCCGUUUUGUCAAUUCGCUCACGCUCGAGCUUUAGAAUCGACGGUCCGAAAAUAGUUUCGAUUUUGAGCCAC
...(((((((.....((((((.((((-((((((......))))).))))).)))))).......((((......))))...)))))))..((..(((((..........)))))..)).. ( -35.80)
>consensus
CUCCGAUUUUUCAUUCAAAACUGGCC_AAAUGCCCAAAUGCAUUGUGGCCCGUUUUGUCAAUUCGCUCACGCUCGAGCUUUAGAAUCGACGGUCCGAAAAUAGUUUCGAUUUUGAGCCAC
((((((((((.....((((((.((((..(((((......)))))..)))).)))))).......((((......))))...)))))))......(((((....))))).....))).... (-29.27 = -29.60 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,784,812 – 20,784,932
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.21
Mean single sequence MFE -37.17
Consensus MFE -36.57
Energy contribution -36.47
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -2.41
Structure conservation index 0.98
SVM decision value 1.62
SVM RNA-class probability 0.968055
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20784812 120 - 27905053
GUGGCUCAAAAUCGAAACUAUUUUCGGACUGUCGAUUCUAAAGCUCGAGCGUGAGCAAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUUCGGUCAGUUUUGAAUGAAAAAUCGGAG
(((((((....((((((....))))))..((((((((.....(((((....))))).))))))))....))))))).((((......))))((((((...((((....)))).)))))). ( -34.40)
>DroSec_CAF1 596 119 - 1
GUGGCUCAAAAUCGAAACUAUUUUCGAACCGUCGAUUCUAAAGCUCGAGCGUGAGCGAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUU-GGCCAGUUUUGAAUGAAAAAUCGGAG
(((((((....((((((....))))))...((((((((....(((((....))))))))))))).....)))))))(((((......))))).-..((.(((((......))))).)).. ( -39.00)
>DroSim_CAF1 598 119 - 1
GUGGCUCAAAAUCGAAACUAUUUUCGGACCGUCGAUUCUAAAGCUCGAGCGUGAGCGAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUU-GGCCAGUUUUGAAUGAAAAAUCGGAG
(((((((....((((((....))))))...((((((((....(((((....))))))))))))).....)))))))(((((......))))).-..((.(((((......))))).)).. ( -38.10)
>consensus
GUGGCUCAAAAUCGAAACUAUUUUCGGACCGUCGAUUCUAAAGCUCGAGCGUGAGCGAAUUGACAAAACGGGCCACAAUGCAUUUGGGCAUUU_GGCCAGUUUUGAAUGAAAAAUCGGAG
(((((((....((((((....))))))...((((((((....(((((....))))))))))))).....)))))))(((((......)))))....((.(((((......))))).)).. (-36.57 = -36.47 +  -0.11)

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 12:53:32 2006