Locus 10939

Sequence ID dm3.chr3R
Location 17,640,240 – 17,640,399
Length 159
Max. P 0.962862
window15034 window15035 window15036 window15037 window15038 window15039

overview

Window 4

Location 17,640,240 – 17,640,351
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 92.15
Shannon entropy 0.10755
G+C content 0.29804
Mean single sequence MFE -22.01
Consensus MFE -15.83
Energy contribution -16.05
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -2.75
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.858197
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17640240 111 + 27905053
UCCUAUACUUUUUCAUUUAAAAUAUUGUAUAUAUAUUACAAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUGAAAGCACUUUGAUCCCAACGAUAUAUGGUUACAAA
..(((((.................((((((((.........))))))))........((((((((((...(....)....)))))))))).........)))))....... ( -17.80, z-score =  -1.42, R)
>droSec1.super_0 18012524 109 + 21120651
GCACAUACUUCUUCAUUUAAAAUA--GUGUAUAUAUUACAAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUCGAACCACUUUGAUCCCGACGAUAUAUGGUUACAAA
...((((..((.((.......(((--((((((((.......)))))).)))))....((((((((((.............))))))))))..)).))..))))........ ( -24.42, z-score =  -3.55, R)
>droSim1.chr3R 17445812 109 + 27517382
GCAUAUACUUCUUCAUUUAAAAUA--UUGUAUAUAUUACAAAUAUGCAACUUUAAAAGGUCAAAGUGAAGCCUUUCGAAGCACUUUGAUCCCGACGAUAUAUGGUUACAAA
.((((((..((.((.((((((...--((((((((.......)))))))).)))))).((((((((((...(.....)...))))))))))..)).))))))))........ ( -23.80, z-score =  -3.26, R)
>consensus
GCAUAUACUUCUUCAUUUAAAAUA__GUGUAUAUAUUACAAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUCGAAGCACUUUGAUCCCGACGAUAUAUGGUUACAAA
...((((..((.((.............(((((((.......))))))).........((((((((((.............))))))))))..)).))..))))........ (-15.83 = -16.05 +   0.23)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,640,240 – 17,640,351
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 92.15
Shannon entropy 0.10755
G+C content 0.29804
Mean single sequence MFE -23.50
Consensus MFE -20.72
Energy contribution -20.17
Covariance contribution -0.55
Combinations/Pair 1.11
Mean z-score -1.84
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.815761
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17640240 111 - 27905053
UUUGUAACCAUAUAUCGUUGGGAUCAAAGUGCUUUCAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUUGUAAUAUAUAUACAAUAUUUUAAAUGAAAAAGUAUAGGA
.......((((((((....(((.(((((((((((....))))...))))))))))......((((((....))))))))))))...(((((((.......))))))).)). ( -20.30, z-score =  -0.95, R)
>droSec1.super_0 18012524 109 - 21120651
UUUGUAACCAUAUAUCGUCGGGAUCAAAGUGGUUCGAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUUGUAAUAUAUACAC--UAUUUUAAAUGAAGAAGUAUGUGC
........(((((.((.(((((.(((((((((.((....))..))))))))))))..((((((((((....)))))).))))...--..........)).)).)))))... ( -26.20, z-score =  -2.35, R)
>droSim1.chr3R 17445812 109 - 27517382
UUUGUAACCAUAUAUCGUCGGGAUCAAAGUGCUUCGAAAGGCUUCACUUUGACCUUUUAAAGUUGCAUAUUUGUAAUAUAUACAA--UAUUUUAAAUGAAGAAGUAUAUGC
........(((((((..(((((.((((((((..((....))...)))))))))))......((((((....))))))........--.............)).))))))). ( -24.00, z-score =  -2.21, R)
>consensus
UUUGUAACCAUAUAUCGUCGGGAUCAAAGUGCUUCGAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUUGUAAUAUAUACAC__UAUUUUAAAUGAAGAAGUAUAUGC
........(((((((..(((((.((((((((..((....))...)))))))))))......((((((....)))))).......................)).))))))). (-20.72 = -20.17 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,640,271 – 17,640,391
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Shannon entropy 0.03826
G+C content 0.36111
Mean single sequence MFE -22.74
Consensus MFE -21.89
Energy contribution -21.89
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.797485
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17640271 120 + 27905053
UAUAUUACAAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUGAAAGCACUUUGAUCCCAACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCA
((((((.....((((....))))...((((((((((...(....)....)))))))))).....))))))((((....((((.(((((..((....))..))))).))))...))))... ( -22.70, z-score =  -1.42, R)
>droSec1.super_0 18012553 120 + 21120651
UAUAUUACAAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUCGAACCACUUUGAUCCCGACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCA
((((((.....((((....))))...((((((((((.............)))))))))).....))))))((((....((((.(((((..((....))..))))).))))...))))... ( -22.72, z-score =  -1.68, R)
>droSim1.chr3R 17445841 120 + 27517382
UAUAUUACAAAUAUGCAACUUUAAAAGGUCAAAGUGAAGCCUUUCGAAGCACUUUGAUCCCGACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCA
..........................((((((((((...(.....)...))))))))))...........((((....((((.(((((..((....))..))))).))))...))))... ( -22.80, z-score =  -1.33, R)
>consensus
UAUAUUACAAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUCGAAGCACUUUGAUCCCGACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCA
..........................((((((((((.............))))))))))...........((((....((((.(((((..((....))..))))).))))...))))... (-21.89 = -21.89 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,640,271 – 17,640,391
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Shannon entropy 0.03826
G+C content 0.36111
Mean single sequence MFE -31.67
Consensus MFE -30.09
Energy contribution -29.87
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.23
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.71
SVM RNA-class probability 0.962862
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17640271 120 - 27905053
UGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUUGGGAUCAAAGUGCUUUCAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUUGUAAUAUA
((((.(((..((((.(((((..((....))..))))).))))))).))))((((.....(((.(((((((((((....))))...))))))))))..))))((((((....))))))... ( -29.50, z-score =  -1.61, R)
>droSec1.super_0 18012553 120 - 21120651
UGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUCGGGAUCAAAGUGGUUCGAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUUGUAAUAUA
((((.(((..((((.(((((..((....))..))))).))))))).)))).........(((.(((((((((.((....))..))))))))))))......((((((....))))))... ( -33.60, z-score =  -2.80, R)
>droSim1.chr3R 17445841 120 - 27517382
UGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUCGGGAUCAAAGUGCUUCGAAAGGCUUCACUUUGACCUUUUAAAGUUGCAUAUUUGUAAUAUA
((((.(((..((((.(((((..((....))..))))).))))))).)))).........(((.((((((((..((....))...)))))))))))......((((((....))))))... ( -31.90, z-score =  -2.29, R)
>consensus
UGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUCGGGAUCAAAGUGCUUCGAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUUGUAAUAUA
((((.(((..((((.(((((..((....))..))))).))))))).)))).........(((.((((((((..((....))...)))))))))))......((((((....))))))... (-30.09 = -29.87 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,640,279 – 17,640,399
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Shannon entropy 0.04591
G+C content 0.40000
Mean single sequence MFE -23.27
Consensus MFE -22.63
Energy contribution -22.41
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.11
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.621175
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17640279 120 + 27905053
AAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUGAAAGCACUUUGAUCCCAACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCACCCACUGG
..................((((((((((...(....)....))))))))))(((........((((....((((.(((((..((....))..))))).))))...))))........))) ( -22.99, z-score =  -1.08, R)
>droSec1.super_0 18012561 120 + 21120651
AAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUCGAACCACUUUGAUCCCGACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCAUCCACUGG
..................((((((((((.............))))))))))(((..(((...((((....((((.(((((..((....))..))))).))))...))))..)))...))) ( -23.52, z-score =  -1.32, R)
>droSim1.chr3R 17445849 120 + 27517382
AAAUAUGCAACUUUAAAAGGUCAAAGUGAAGCCUUUCGAAGCACUUUGAUCCCGACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCACCCACUGG
..................((((((((((...(.....)...))))))))))...........((((....((((.(((((..((....))..))))).))))...))))(((.....))) ( -23.30, z-score =  -0.92, R)
>consensus
AAAUAUGCAACUAUAAAAGGUCAAAGUGAAGCCUUUCGAAGCACUUUGAUCCCGACGAUAUAUGGUUACAAAUGUCAAAGUAACGAAUGUACCUUUGCCAUUACUGCCACCACCCACUGG
..................((((((((((.............))))))))))(((........((((....((((.(((((..((....))..))))).))))...))))........))) (-22.63 = -22.41 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,640,279 – 17,640,399
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Shannon entropy 0.04591
G+C content 0.40000
Mean single sequence MFE -31.00
Consensus MFE -29.91
Energy contribution -29.47
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.24
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.660279
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17640279 120 - 27905053
CCAGUGGGUGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUUGGGAUCAAAGUGCUUUCAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUU
...(..((((((.(((..((((.(((((..((....))..))))).))))))).)))))........(((.(((((((((((....))))...)))))))))).......)..)...... ( -28.40, z-score =  -0.43, R)
>droSec1.super_0 18012561 120 - 21120651
CCAGUGGAUGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUCGGGAUCAAAGUGGUUCGAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUU
...(..((((((.(((..((((.(((((..((....))..))))).))))))).)))))........(((.(((((((((.((....))..)))))))))))).......)..)...... ( -33.00, z-score =  -1.93, R)
>droSim1.chr3R 17445849 120 - 27517382
CCAGUGGGUGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUCGGGAUCAAAGUGCUUCGAAAGGCUUCACUUUGACCUUUUAAAGUUGCAUAUUU
...(..((((((.(((..((((.(((((..((....))..))))).))))))).)))))........(((.((((((((..((....))...))))))))))).......)..)...... ( -31.60, z-score =  -1.34, R)
>consensus
CCAGUGGGUGGUGGCAGUAAUGGCAAAGGUACAUUCGUUACUUUGACAUUUGUAACCAUAUAUCGUCGGGAUCAAAGUGCUUCGAAAGGCUUCACUUUGACCUUUUAUAGUUGCAUAUUU
...(..((((((.(((..((((.(((((..((....))..))))).))))))).)))))........(((.((((((((..((....))...))))))))))).......)..)...... (-29.91 = -29.47 +  -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 Wed Apr 20 00:33:26 2011