Locus 6273

Sequence ID 3R_DroMel_CAF1
Location 16,379,939 – 16,380,154
Length 215
Max. P 0.972549
window10229 window10230 window10231 window10232

overview

Window 9

Location 16,379,939 – 16,380,038
Length 99
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 95.29
Mean single sequence MFE -23.60
Consensus MFE -22.42
Energy contribution -22.53
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.65
Structure conservation index 0.95
SVM decision value 1.69
SVM RNA-class probability 0.972549
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16379939 99 + 27905053
GAAAAUGAAUAGAAAAUCUCAAUAUGCAUUCAUACCCGAAUGCGCGACUAUGGAUAAAUAAACGGAGGGACAUAGGAAACUUUGACACUCCACUACGCU
.........................((((((......))))))(((..(((......)))...((((...((.((....)).))...))))....))). ( -22.20)
>DroSec_CAF1 1298 99 + 1
GAAAAUAAAUGGAAAAUCUCAAUAUGCAUUCAUACCCGAAUGCGCGACUAUGGAUCAAUAAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACU
.........(((...((((.....(((((((......))))))).......))))........((((((.((.((....)).)).)))))).))).... ( -23.30)
>DroSim_CAF1 1294 99 + 1
GAAAAUGAAUAGUAAAUCUCAAUAUGCAUUCAUACCCGAAUGCGCGACUAUGGAUAAACAAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACU
.........((((..((((.....(((((((......))))))).......))))........((((((.((.((....)).)).)))))))))).... ( -25.30)
>consensus
GAAAAUGAAUAGAAAAUCUCAAUAUGCAUUCAUACCCGAAUGCGCGACUAUGGAUAAAUAAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACU
.........(((...((((.....(((((((......))))))).......))))........((((((.((.((....)).)).)))))).))).... (-22.42 = -22.53 +   0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,379,968 – 16,380,078
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 95.76
Mean single sequence MFE -25.83
Consensus MFE -25.63
Energy contribution -25.30
Covariance contribution -0.33
Combinations/Pair 1.06
Mean z-score -1.66
Structure conservation index 0.99
SVM decision value 0.57
SVM RNA-class probability 0.786691
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16379968 110 + 27905053
UCAUACCCGAAUGCGCGACUAUGGAUAAAUAAACGGAGGGACAUAGGAAACUUUGACACUCCACUACGCUCUAUAAUUUAGUUCGGUUUGAAGUCAAAUACUCGACAUUU
(((...((((((....((.((((((.........((((...((.((....)).))...)))).......)))))).))..))))))..))).(((........))).... ( -24.19)
>DroSec_CAF1 1327 110 + 1
UCAUACCCGAAUGCGCGACUAUGGAUCAAUAAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACUCUAUAAUUUAGUUUGGUUUGCAGUCAAAUACUCGACAUUU
.......(((.((...((((..(((((((.....((((((.((.((....)).)).))))))........(((.....))).)))))))..))))...)).)))...... ( -26.40)
>DroSim_CAF1 1323 110 + 1
UCAUACCCGAAUGCGCGACUAUGGAUAAACAAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACUCUAAAAUUUAGUUUGGUUUGCAGUCAAAUACUCGACAUUU
........(((((..(((.(((.(((...(((((((((((.((.((....)).)).))))))....((..(((.....)))..)))))))..)))..))).))).))))) ( -26.90)
>consensus
UCAUACCCGAAUGCGCGACUAUGGAUAAAUAAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACUCUAUAAUUUAGUUUGGUUUGCAGUCAAAUACUCGACAUUU
........(((((..(((.(((.(((...(((((((((((.((.((....)).)).))))))....((..(((.....)))..)))))))..)))..))).))).))))) (-25.63 = -25.30 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,379,998 – 16,380,118
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -29.37
Consensus MFE -26.17
Energy contribution -26.73
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.81
Structure conservation index 0.89
SVM decision value 1.21
SVM RNA-class probability 0.931661
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16379998 120 + 27905053
AAACGGAGGGACAUAGGAAACUUUGACACUCCACUACGCUCUAUAAUUUAGUUCGGUUUGAAGUCAAAUACUCGACAUUUUACUGUCGACAAACACAAAAAUUCAAGAGUUUUCAUUGUG
....((((...((.((....)).))...))))....((..(((.....)))..))(((((....)))))..((((((......))))))....((((((((((....)))))...))))) ( -26.10)
>DroSec_CAF1 1357 120 + 1
AAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACUCUAUAAUUUAGUUUGGUUUGCAGUCAAAUACUCGACAUUUUACUGCCGACAAACACAAAAAUUCAAGAGUUUUCAUUGUG
....((((((.((.((....)).)).)))))).....(((((..(((((.(((((.((.(((((.((((.......)))).))))).)))))))....)))))..))))).......... ( -30.60)
>DroSim_CAF1 1353 120 + 1
AAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACUCUAAAAUUUAGUUUGGUUUGCAGUCAAAUACUCGACAUUUUACUGCCGACAAACACAAAAAUUCAAGAGUUUUCAUUGUA
....((((((.((.((....)).)).)))))).....(((((..(((((.(((((.((.(((((.((((.......)))).))))).)))))))....)))))..))))).......... ( -31.40)
>consensus
AAACGGAGGGACAUAGGAAACUUUGACUCUCCACUACACUCUAUAAUUUAGUUUGGUUUGCAGUCAAAUACUCGACAUUUUACUGCCGACAAACACAAAAAUUCAAGAGUUUUCAUUGUG
....((((((.((.((....)).)).)))))).....(((((..(((((.(((((.((.(((((.((((.......)))).))))).)))))))....)))))..))))).......... (-26.17 = -26.73 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,380,038 – 16,380,154
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 95.40
Mean single sequence MFE -26.37
Consensus MFE -24.31
Energy contribution -23.87
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.47
Structure conservation index 0.92
SVM decision value 1.21
SVM RNA-class probability 0.931553
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16380038 116 - 27905053
AACAAAAAUUAGGGAAACGCUAAAUUACAUUGGCGACACAAUGAAAACUCUUGAAUUUUUGUGUUUGUCGACAGUAAAAUGUCGAGUAUUUGACUUCAAACCGAACUAAAUUAUAG
.(((((((((..(((..((((((......)))))).(.....).....)))..)))))))))(((((((((((......))))))...((((....)))).))))).......... ( -25.80)
>DroSec_CAF1 1397 116 - 1
AACAAAAAUUAGGGGAACGCUAAAUUAUAUUGGCGACACAAUGAAAACUCUUGAAUUUUUGUGUUUGUCGGCAGUAAAAUGUCGAGUAUUUGACUGCAAACCAAACUAAAUUAUAG
.((((((((((((((..((((((......)))))).(.....)....)))))).))))))))(((((...(((((.(((((.....))))).)))))....))))).......... ( -27.90)
>DroSim_CAF1 1393 116 - 1
AACAAAAAUUAGGAAAACGCUAAAUUAUAUUGGCGAUACAAUGAAAACUCUUGAAUUUUUGUGUUUGUCGGCAGUAAAAUGUCGAGUAUUUGACUGCAAACCAAACUAAAUUUUAG
.(((((((((.......((((((......))))))...(((.((....))))))))))))))(((((...(((((.(((((.....))))).)))))....))))).......... ( -25.40)
>consensus
AACAAAAAUUAGGGAAACGCUAAAUUAUAUUGGCGACACAAUGAAAACUCUUGAAUUUUUGUGUUUGUCGGCAGUAAAAUGUCGAGUAUUUGACUGCAAACCAAACUAAAUUAUAG
.(((((((((.......((((((......))))))...(((.((....))))))))))))))(((((((((((......))))))...((((....)))).))))).......... (-24.31 = -23.87 +  -0.44)

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 12:17:22 2006