Locus 3966

Sequence ID 2R_DroMel_CAF1
Location 13,098,723 – 13,098,908
Length 185
Max. P 0.846000
window6404 window6405 window6406

overview

Window 4

Location 13,098,723 – 13,098,829
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.82
Mean single sequence MFE -36.33
Consensus MFE -32.39
Energy contribution -32.73
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -1.61
Structure conservation index 0.89
SVM decision value 0.77
SVM RNA-class probability 0.846000
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13098723 106 + 20766785
CCAAUGGAGGCGCCCAUGCAGAGGGCACCAAAGCUGGCCGACAAGCCAGCAAUAUAUUGUGGCAACACCGAUCCCUUGGACAUGGCGAGGGGUUUUUUUUUUAAAU--------------
........((.((((.......)))).))...((((((......))))))........(((....))).(((((((((.......)))))))))............-------------- ( -38.40)
>DroSim_CAF1 9899 120 + 1
CCGAUGGAGGCGCCCAUGCAGAGGGCACCAAAACUGGCCGACAAGCCAGCAAUAUAUUGUGGCAACACCGAUCCCUUGGACAUGGCGAGGGAUUUUUUUUUUGAAUUUGAAUUUUUUGAU
........((.((((.......)))).))....(((((......)))))(((...((((((....))).(((((((((.......)))))))))...............)))...))).. ( -34.90)
>DroYak_CAF1 10219 103 + 1
CCGAUGGAGGCCCCCAUGCAGAGGGCACCAAAGCUGGCCGACAAGCCGGCAAUAUAUUGUGGCAAUACCGAUCCCUUGGACAUGGCGAGGGAUGUAU---UAGAAA--------------
(((.(((..((((.(.....).)))).)))..((((((......)))))).........))).(((((..((((((((.......))))))))))))---).....-------------- ( -35.70)
>consensus
CCGAUGGAGGCGCCCAUGCAGAGGGCACCAAAGCUGGCCGACAAGCCAGCAAUAUAUUGUGGCAACACCGAUCCCUUGGACAUGGCGAGGGAUUUUUUUUUUGAAU______________
........((.((((.......)))).))...((((((......))))))........(((....))).(((((((((.......))))))))).......................... (-32.39 = -32.73 +   0.34)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,098,723 – 13,098,829
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.82
Mean single sequence MFE -34.00
Consensus MFE -29.84
Energy contribution -30.73
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -1.41
Structure conservation index 0.88
SVM decision value 0.36
SVM RNA-class probability 0.704218
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13098723 106 - 20766785
--------------AUUUAAAAAAAAAACCCCUCGCCAUGUCCAAGGGAUCGGUGUUGCCACAAUAUAUUGCUGGCUUGUCGGCCAGCUUUGGUGCCCUCUGCAUGGGCGCCUCCAUUGG
--------------...................((((..((((...)))).))))......((((.....(((((((....)))))))...(((((((.......)))))))...)))). ( -34.70)
>DroSim_CAF1 9899 120 - 1
AUCAAAAAAUUCAAAUUCAAAAAAAAAAUCCCUCGCCAUGUCCAAGGGAUCGGUGUUGCCACAAUAUAUUGCUGGCUUGUCGGCCAGUUUUGGUGCCCUCUGCAUGGGCGCCUCCAUCGG
...........................((((((.(.......).))))))(((((...............(((((((....)))))))...(((((((.......)))))))..))))). ( -35.20)
>DroYak_CAF1 10219 103 - 1
--------------UUUCUA---AUACAUCCCUCGCCAUGUCCAAGGGAUCGGUAUUGCCACAAUAUAUUGCCGGCUUGUCGGCCAGCUUUGGUGCCCUCUGCAUGGGGGCCUCCAUCGG
--------------....((---((((((((((.(.......).))))))..))))))((..........((.((((....)))).))..(((.((((((.....))))))..)))..)) ( -32.10)
>consensus
______________AUUCAAAAAAAAAAUCCCUCGCCAUGUCCAAGGGAUCGGUGUUGCCACAAUAUAUUGCUGGCUUGUCGGCCAGCUUUGGUGCCCUCUGCAUGGGCGCCUCCAUCGG
...........................((((((.(.......).))))))(((((...............(((((((....)))))))...(((((((.......)))))))..))))). (-29.84 = -30.73 +   0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,098,803 – 13,098,908
Length 105
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.19
Mean single sequence MFE -22.18
Consensus MFE -20.53
Energy contribution -20.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.76
Structure conservation index 0.93
SVM decision value 0.28
SVM RNA-class probability 0.667101
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13098803 105 - 20766785
AUUUUUCCAGCGUAAUAACGGUCGCGUGGCGAAUUCAGUUCGUUUCCGGCGAUCGACAAGGAAACACCUAUAAAAACCA---------------AUUUAAAAAAAAAACCCCUCGCCAUG
.........(((......(((((((..(((((((...)))))))....)))))))....(....)..............---------------...................))).... ( -20.60)
>DroSim_CAF1 9979 120 - 1
AUUUUUCCAGCGUAAUAACGGUCGCGUGGCGAAUUCAGUUCGUUUCCGGCGAUCGAGAGGGAAACACCUAUAAAAACCAUAUCAAAAAAUUCAAAUUCAAAAAAAAAAUCCCUCGCCAUG
.........((.......(((((((..(((((((...)))))))....))))))).((((((..............................................)))))))).... ( -25.35)
>DroYak_CAF1 10299 102 - 1
AUUUUUCCAGCGUAAUAACGGUCGCGUGGCGAAUUCAGUUCGUUUCCGGCGAUCGAGAAGGAAACACCUAUACAAAAUA---------------UUUCUA---AUACAUCCCUCGCCAUG
.........(((......(((((((..(((((((...)))))))....)))))))....(....)..............---------------......---..........))).... ( -20.60)
>consensus
AUUUUUCCAGCGUAAUAACGGUCGCGUGGCGAAUUCAGUUCGUUUCCGGCGAUCGAGAAGGAAACACCUAUAAAAACCA_______________AUUCAAAAAAAAAAUCCCUCGCCAUG
.........(((......(((((((..(((((((...)))))))....)))))))....(....)................................................))).... (-20.53 = -20.53 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:33 2006