Locus 5170

Sequence ID 3R_DroMel_CAF1
Location 13,568,340 – 13,568,430
Length 90
Max. P 0.974315
window8448 window8449

overview

Window 8

Location 13,568,340 – 13,568,430
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 95.66
Mean single sequence MFE -29.82
Consensus MFE -25.38
Energy contribution -25.98
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.85
SVM decision value 1.73
SVM RNA-class probability 0.974315
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13568340 90 + 27905053
CAAAGCCAGCAUGUCCUUAAUGCCAUUGGCCAUGGCUUAGUUUUGGCCCCCUUUGGCUGAAAGCGAAGAGCAUGGCUUAAAGGGCACAUU
....(((.((((.......))))....(((((((.(((.(((((((((......)))).))))).)))..))))))).....)))..... ( -30.10)
>DroSec_CAF1 10300 90 + 1
CAAAGCCAGCAUGUCCUUAAUGCCAUUGGCCAUGGCUUAGUUUUGGCCCCCUUUGGCAGAAAGCGAAGAGCAUGGCUUAAAGGGCACAUU
..((((((((...(((((..(((((..(((((..((...))..))))).....)))))..))).))...)).))))))............ ( -31.20)
>DroSim_CAF1 9441 90 + 1
CAAAGCCAGCAUGUCCUUAAUGCCAUUGGCCAUGGCUUAGUUUUGGCCCCCUUUGGCCGAAAGCGAAGAGCAUGGCUUAAAGGGCACAUU
....(((.((((.......))))....(((((((.(((.(((((((((......)))).))))).)))..))))))).....)))..... ( -32.40)
>DroEre_CAF1 9010 89 + 1
CAAAGCCAGCAUGUCCUUAAUGCCAUUGGCCAUGGCUUAGUU-CGGCCCCCUUUGGCAGAAACCGAAGAGCAUGGCUUAAAGGGCACAUU
....(((.((((.......))))....(((((((.(((..((-(.(((......))).)))....)))..))))))).....)))..... ( -27.70)
>DroYak_CAF1 8883 88 + 1
CAAAGCCAGCAUGUCCUUAAUGCCAUUGGCCAUGGCUUAGUU-UGGCCCCCUUU-GCAGGAGCCGAAGAGCACGGCUUAAAGGGCACAUU
....(((.((((.......))))....((((...((((..((-((((((.....-...)).))))))))))..)))).....)))..... ( -27.70)
>consensus
CAAAGCCAGCAUGUCCUUAAUGCCAUUGGCCAUGGCUUAGUUUUGGCCCCCUUUGGCAGAAAGCGAAGAGCAUGGCUUAAAGGGCACAUU
...........(((((((...(((((.(((((.(((...))).)))))..(((((........)))))...)))))...))))))).... (-25.38 = -25.98 +   0.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,568,340 – 13,568,430
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 95.66
Mean single sequence MFE -28.42
Consensus MFE -23.16
Energy contribution -23.04
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.49
Structure conservation index 0.81
SVM decision value 0.02
SVM RNA-class probability 0.544776
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13568340 90 - 27905053
AAUGUGCCCUUUAAGCCAUGCUCUUCGCUUUCAGCCAAAGGGGGCCAAAACUAAGCCAUGGCCAAUGGCAUUAAGGACAUGCUGGCUUUG
...(((.((((...(((((.(((((.((.....))..)))))(((((...........))))).)))))...)))).))).......... ( -25.70)
>DroSec_CAF1 10300 90 - 1
AAUGUGCCCUUUAAGCCAUGCUCUUCGCUUUCUGCCAAAGGGGGCCAAAACUAAGCCAUGGCCAAUGGCAUUAAGGACAUGCUGGCUUUG
............((((((.((...((.(((..(((((.....(((((...........)))))..)))))..)))))...)))))))).. ( -28.00)
>DroSim_CAF1 9441 90 - 1
AAUGUGCCCUUUAAGCCAUGCUCUUCGCUUUCGGCCAAAGGGGGCCAAAACUAAGCCAUGGCCAAUGGCAUUAAGGACAUGCUGGCUUUG
............((((((.((...((.(((..((((......))))........(((((.....)))))...)))))...)))))))).. ( -27.00)
>DroEre_CAF1 9010 89 - 1
AAUGUGCCCUUUAAGCCAUGCUCUUCGGUUUCUGCCAAAGGGGGCCG-AACUAAGCCAUGGCCAAUGGCAUUAAGGACAUGCUGGCUUUG
.....(((......((((((((.((((((..((......))..))))-))...)).))))))....(((((.......)))))))).... ( -30.50)
>DroYak_CAF1 8883 88 - 1
AAUGUGCCCUUUAAGCCGUGCUCUUCGGCUCCUGC-AAAGGGGGCCA-AACUAAGCCAUGGCCAAUGGCAUUAAGGACAUGCUGGCUUUG
............((((((.((..((((((((((..-...))))))).-......(((((.....))))).....)))...)))))))).. ( -30.90)
>consensus
AAUGUGCCCUUUAAGCCAUGCUCUUCGCUUUCUGCCAAAGGGGGCCAAAACUAAGCCAUGGCCAAUGGCAUUAAGGACAUGCUGGCUUUG
...(((.((((...(((((.(((((.(........).)))))(((((...........))))).)))))...)))).))).......... (-23.16 = -23.04 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:17 2006