Locus 1377

Sequence ID 3R_DroMel_CAF1
Location 4,012,824 – 4,012,919
Length 95
Max. P 0.909679
window2270 window2271

overview

Window 0

Location 4,012,824 – 4,012,919
Length 95
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 83.18
Mean single sequence MFE -31.97
Consensus MFE -28.03
Energy contribution -28.37
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.13
Structure conservation index 0.88
SVM decision value 0.08
SVM RNA-class probability 0.572199
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4012824 95 + 27905053
UUGGAGCUAGUGCUCCUG------------------------UUCCUGCUAAAGAAAGCUUGGCUAAGCACCUGUGCAAACUUAUUGUUAGCCUGCGCAUUGUGUUCGAUCGAAGCGGA
..(((((....)))))..------------------------...(((((.......((..((((..(((....))).(((.....))))))).))(.((((....)))))..))))). ( -27.40)
>DroSec_CAF1 18506 95 + 1
UUGGAGCUAGGGCUCCUG------------------------CUCCUGCUAACGAAAGCUUGGCUAAGCACCUGUGCAAACUUAUUGUUAGCCUGCGCAUUGUGUUCGAUCCAAGCGGA
..(((((.(((...))))------------------------))))...........((((((...(((((.((((((..((.......))..))))))..)))))....))))))... ( -31.90)
>DroSim_CAF1 19088 119 + 1
UUGGAGCUAGGGCUCCUGCUCCUGCUAGUGCUACUUCUCCUGCUCCUGCUAACGAAAGCUUGGCUAAGCACCUGUGCAAACUUAUUGUUAGCCUGCGCAUUGUGUUCGAUCCAAGCGGA
..(((((.(((((....)).)))((....))..........)))))...........((((((...(((((.((((((..((.......))..))))))..)))))....))))))... ( -36.60)
>consensus
UUGGAGCUAGGGCUCCUG________________________CUCCUGCUAACGAAAGCUUGGCUAAGCACCUGUGCAAACUUAUUGUUAGCCUGCGCAUUGUGUUCGAUCCAAGCGGA
..(((((....))))).........................................((((((...(((((.((((((..((.......))..))))))..)))))....))))))... (-28.03 = -28.37 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,012,824 – 4,012,919
Length 95
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 83.18
Mean single sequence MFE -32.83
Consensus MFE -28.47
Energy contribution -28.80
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.87
SVM decision value 1.07
SVM RNA-class probability 0.909679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4012824 95 - 27905053
UCCGCUUCGAUCGAACACAAUGCGCAGGCUAACAAUAAGUUUGCACAGGUGCUUAGCCAAGCUUUCUUUAGCAGGAA------------------------CAGGAGCACUAGCUCCAA
((((((((....)).(((..((.(((((((.......))))))).)).)))...)))...(((......))).))).------------------------..(((((....))))).. ( -27.20)
>DroSec_CAF1 18506 95 - 1
UCCGCUUGGAUCGAACACAAUGCGCAGGCUAACAAUAAGUUUGCACAGGUGCUUAGCCAAGCUUUCGUUAGCAGGAG------------------------CAGGAGCCCUAGCUCCAA
...((((((...((.(((..((.(((((((.......))))))).)).))).))..))))))...........((((------------------------((((...))).))))).. ( -32.80)
>DroSim_CAF1 19088 119 - 1
UCCGCUUGGAUCGAACACAAUGCGCAGGCUAACAAUAAGUUUGCACAGGUGCUUAGCCAAGCUUUCGUUAGCAGGAGCAGGAGAAGUAGCACUAGCAGGAGCAGGAGCCCUAGCUCCAA
(((((((((...((.(((..((.(((((((.......))))))).)).))).))..))))))........((....)).)))......((....)).((((((((...))).))))).. ( -38.50)
>consensus
UCCGCUUGGAUCGAACACAAUGCGCAGGCUAACAAUAAGUUUGCACAGGUGCUUAGCCAAGCUUUCGUUAGCAGGAG________________________CAGGAGCCCUAGCUCCAA
(((((((((...((.(((..((.(((((((.......))))))).)).))).))..))))))...(....)..)))...........................(((((....))))).. (-28.47 = -28.80 +   0.33)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:33 2006