Locus 11990

Sequence ID dm3.chr3R
Location 24,967,006 – 24,967,212
Length 206
Max. P 0.990909
window16472 window16473 window16474 window16475 window16476 window16477

overview

Window 2

Location 24,967,006 – 24,967,122
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.37
Shannon entropy 0.29925
G+C content 0.43734
Mean single sequence MFE -32.02
Consensus MFE -23.82
Energy contribution -24.50
Covariance contribution 0.68
Combinations/Pair 1.12
Mean z-score -1.45
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.591870
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24967006 116 - 27905053
CUCCGUUGGGUAGCCACUUGCAACUGGCUGGAUGGGAAGGGUGUUUCCCACUGCCAGUGUCAUCGACUGAAAUA----UAUAUUUAAAUUCGCAAUAUUUCCCAUUCAGAAGUUGUUGCU
......(((....)))...((((((..((((((((((((((.....)))..(((((((.......))))((((.----...))))......)))....))))))))))).)))))).... ( -33.60, z-score =  -1.22, R)
>droSim1.chr3R 24643325 116 - 27517382
CUCCGUUGGGGAGCCACUUGCAACUGUCUGGAUGGGAAGGGUGUUUCCCACUGCCAAUGUCAUCGACUGAAAUA----UAUAUUUAAAUUCGCGAUAUUUCCCAUUCAGAAGUUGUCGGU
((((.....))))..(((.((((((.(((((((((((((((.....))).......(((((..(((...((((.----...))))....))).))))))))))))))))))))))).))) ( -39.50, z-score =  -2.75, R)
>droSec1.super_4 3831578 116 - 6179234
CUCCGUUGGGGAGCCACUUGCAACUGGCUGGAUGGGAAGGGUGUUUCCCACUGCCAAUGUCAUCGACUGAAAUA----UAUAUUUAAAUUCGCGAUAUUUCCCAUUCAGAAGUUGUCGGU
((((.....))))..(((.((((((..((((((((((((((.....))).......(((((..(((...((((.----...))))....))).)))))))))))))))).)))))).))) ( -38.80, z-score =  -2.26, R)
>droEre2.scaffold_4820 7405253 99 + 10470090
-----------------CCACAUCUGGAUGGAUGGGAAGGGUGUUUCCCACAGCCAGUGUCAUCGACUGAAAUA----UAUAUUUAAAUUCGUGGUAUUUCCCAUUCUGAAGUUGUAACU
-----------------..(((.((....(((((((((((.(((.....))).)).((..((.(((...((((.----...))))....)))))..)))))))))))...)).))).... ( -24.70, z-score =  -0.38, R)
>droYak2.chr3R 7300726 107 + 28832112
-------------CUACAUGCAACUAGCUGGAUGAAAAGGGUGUUUCCCACUGCCAGUGUCAUCGACUGAAAUAUACUUAUAUUUAAAUUCGCAAUAUUUCCCAUUCAGAAGCUGUGGCU
-------------(((((.((......(((((((....(((.....)))..(((((((.......))))((((((....))))))......)))........)))))))..))))))).. ( -23.50, z-score =  -0.63, R)
>consensus
CUCCGUUGGG_AGCCACUUGCAACUGGCUGGAUGGGAAGGGUGUUUCCCACUGCCAGUGUCAUCGACUGAAAUA____UAUAUUUAAAUUCGCGAUAUUUCCCAUUCAGAAGUUGUCGCU
...................((((((..((((((((((((((.....)))..(((.((((((...)))..(((((......)))))..))).)))....))))))))))).)))))).... (-23.82 = -24.50 +   0.68)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,967,046 – 24,967,150
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.04
Shannon entropy 0.25746
G+C content 0.49910
Mean single sequence MFE -32.25
Consensus MFE -24.14
Energy contribution -24.70
Covariance contribution 0.56
Combinations/Pair 1.14
Mean z-score -1.84
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.782931
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24967046 104 + 27905053
----UAUAUUUCAGUCGAUGACACUGGCAGUGGGAAACACCCUUCCCAUCCAGCCAGUUGCAAGUGGCUACCCAACGGAGCUCCACUAAAAAACCCGCUAGGUGACUU------------
----........((((..((..((((((.(((((((......)))))))...))))))..))(((((((.((....)))))..)))).....(((.....))))))).------------ ( -30.70, z-score =  -1.88, R)
>droSim1.chr3R 24643365 104 + 27517382
----UAUAUUUCAGUCGAUGACAUUGGCAGUGGGAAACACCCUUCCCAUCCAGACAGUUGCAAGUGGCUCCCCAACGGAGCUCCACUAAAAAACCCGCUGGGUGACUU------------
----.........((((((...))))))((((((((......)))))((((((...(((...(((((((((.....)))))..))))....)))...)))))).))).------------ ( -30.60, z-score =  -1.26, R)
>droSec1.super_4 3831618 104 + 6179234
----UAUAUUUCAGUCGAUGACAUUGGCAGUGGGAAACACCCUUCCCAUCCAGCCAGUUGCAAGUGGCUCCCCAACGGAGCUCCACUAAAAAACCCGCUGGGUGACUU------------
----........((((..((..((((((.(((((((......)))))))...))))))..))(((((((((.....)))))..)))).....((((...)))))))).------------ ( -34.40, z-score =  -2.29, R)
>droYak2.chr3R 7300766 107 - 28832112
UAAGUAUAUUUCAGUCGAUGACACUGGCAGUGGGAAACACCCUUUUCAUCCAGCUAGUUGCAUGU-------------AGAUCCACUAAAAAACCCGCUGGGUGACUUGGGUGAGCUUAG
(((((.(((((((((.......))))).)))).....(((((...(((((((((..(((.....(-------------((.....)))...)))..)))))))))...))))).))))). ( -33.30, z-score =  -1.94, R)
>consensus
____UAUAUUUCAGUCGAUGACACUGGCAGUGGGAAACACCCUUCCCAUCCAGCCAGUUGCAAGUGGCUCCCCAACGGAGCUCCACUAAAAAACCCGCUGGGUGACUU____________
............((((..((..((((((.(((((((......)))))))...))))))..)).(..(((((.....)))))..)........(((.....)))))))............. (-24.14 = -24.70 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,967,082 – 24,967,187
Length 105
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 95.56
Shannon entropy 0.06122
G+C content 0.52381
Mean single sequence MFE -29.47
Consensus MFE -23.14
Energy contribution -24.14
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734147
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24967082 105 + 27905053
CCUUCCCAUCCAGCCAGUUGCAAGUGGCUACCCAACGGAGCUCCACUAAAAAACCCGCUAGGUGACUUAAGCUUAUAUUUAAGUCGCCGCGUAAGCCAGCCAUUA
............((.....)).(((((((.......((....))................(((((((((((......)))))))))))((....)).))))))). ( -28.50, z-score =  -2.35, R)
>droSim1.chr3R 24643401 105 + 27517382
CCUUCCCAUCCAGACAGUUGCAAGUGGCUCCCCAACGGAGCUCCACUAAAAAACCCGCUGGGUGACUUAAGCUUAUAGUCCAGUCGCCGCGUAAGCCAGUCAUUA
..........(((...(((...(((((((((.....)))))..))))....)))...)))(((((((...((.....))..)))))))((....))......... ( -28.70, z-score =  -1.96, R)
>droSec1.super_4 3831654 105 + 6179234
CCUUCCCAUCCAGCCAGUUGCAAGUGGCUCCCCAACGGAGCUCCACUAAAAAACCCGCUGGGUGACUUAAGCUUAUAUUCAAGUCGCCGCGUAAGCCAGCCAUUA
..........((((..(((...(((((((((.....)))))..))))....)))..))))((((((((............))))))))((....))......... ( -31.20, z-score =  -2.81, R)
>consensus
CCUUCCCAUCCAGCCAGUUGCAAGUGGCUCCCCAACGGAGCUCCACUAAAAAACCCGCUGGGUGACUUAAGCUUAUAUUCAAGUCGCCGCGUAAGCCAGCCAUUA
......((((((((..(((...(((((((((.....)))))..))))....)))..))))))))......((((((..............))))))......... (-23.14 = -24.14 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,967,082 – 24,967,187
Length 105
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 95.56
Shannon entropy 0.06122
G+C content 0.52381
Mean single sequence MFE -35.58
Consensus MFE -34.07
Energy contribution -34.30
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -1.08
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.570089
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24967082 105 - 27905053
UAAUGGCUGGCUUACGCGGCGACUUAAAUAUAAGCUUAAGUCACCUAGCGGGUUUUUUAGUGGAGCUCCGUUGGGUAGCCACUUGCAACUGGCUGGAUGGGAAGG
......(..(((...((((((((((((........)))))))((((((((((((((.....))))).))))))))).)))....))....)))..)......... ( -36.30, z-score =  -1.47, R)
>droSim1.chr3R 24643401 105 - 27517382
UAAUGACUGGCUUACGCGGCGACUGGACUAUAAGCUUAAGUCACCCAGCGGGUUUUUUAGUGGAGCUCCGUUGGGGAGCCACUUGCAACUGUCUGGAUGGGAAGG
....(((..((....(.(((((((..............)))).(((((((((((((.....))))).))))))))..))).)..))....)))............ ( -32.24, z-score =  -0.08, R)
>droSec1.super_4 3831654 105 - 6179234
UAAUGGCUGGCUUACGCGGCGACUUGAAUAUAAGCUUAAGUCACCCAGCGGGUUUUUUAGUGGAGCUCCGUUGGGGAGCCACUUGCAACUGGCUGGAUGGGAAGG
.....((((.......))))(((((((........)))))))..(((((.((((....(((((..((((...))))..)))))...)))).)))))......... ( -38.20, z-score =  -1.70, R)
>consensus
UAAUGGCUGGCUUACGCGGCGACUUGAAUAUAAGCUUAAGUCACCCAGCGGGUUUUUUAGUGGAGCUCCGUUGGGGAGCCACUUGCAACUGGCUGGAUGGGAAGG
......(..(((...((((((((((((........))))))).(((((((((((((.....))))).))))))))..)))....))....)))..)......... (-34.07 = -34.30 +   0.23)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,967,122 – 24,967,212
Length 90
Sequences 3
Columns 90
Reading direction forward
Mean pairwise identity 96.30
Shannon entropy 0.05102
G+C content 0.45185
Mean single sequence MFE -27.00
Consensus MFE -23.12
Energy contribution -25.23
Covariance contribution 2.11
Combinations/Pair 1.06
Mean z-score -3.39
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.45
SVM RNA-class probability 0.990909
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24967122 90 + 27905053
CUCCACUAAAAAACCCGCUAGGUGACUUAAGCUUAUAUUUAAGUCGCCGCGUAAGCCAGCCAUUAAUAUUUUCCAGUCUUAGUGGGUGUG
............(((((((((((((((((((......)))))))))))((....)).......................))))))))... ( -29.80, z-score =  -4.67, R)
>droSim1.chr3R 24643441 90 + 27517382
CUCCACUAAAAAACCCGCUGGGUGACUUAAGCUUAUAGUCCAGUCGCCGCGUAAGCCAGUCAUUAAUAUUUUCCAGUCUUAGUGGGUGUG
............(((((((((((((((...((.....))..)))))))((....)).......................))))))))... ( -25.80, z-score =  -2.88, R)
>droSec1.super_4 3831694 90 + 6179234
CUCCACUAAAAAACCCGCUGGGUGACUUAAGCUUAUAUUCAAGUCGCCGCGUAAGCCAGCCAUUAAUAUUUUCCAGUCUUAGUGGGUGUG
............((((((((((((((((............))))))))((....)).......................))))))))... ( -25.40, z-score =  -2.61, R)
>consensus
CUCCACUAAAAAACCCGCUGGGUGACUUAAGCUUAUAUUCAAGUCGCCGCGUAAGCCAGCCAUUAAUAUUUUCCAGUCUUAGUGGGUGUG
............((((((((((((((((............))))))))((....)).......................))))))))... (-23.12 = -25.23 +   2.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 24,967,122 – 24,967,212
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 96.30
Shannon entropy 0.05102
G+C content 0.45185
Mean single sequence MFE -24.05
Consensus MFE -24.00
Energy contribution -23.89
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.69
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.54
SVM RNA-class probability 0.948617
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24967122 90 - 27905053
CACACCCACUAAGACUGGAAAAUAUUAAUGGCUGGCUUACGCGGCGACUUAAAUAUAAGCUUAAGUCACCUAGCGGGUUUUUUAGUGGAG
.....(((((((((...............((((.(((.....((.(((((((........))))))).)).))).))))))))))))).. ( -24.86, z-score =  -2.10, R)
>droSim1.chr3R 24643441 90 - 27517382
CACACCCACUAAGACUGGAAAAUAUUAAUGACUGGCUUACGCGGCGACUGGACUAUAAGCUUAAGUCACCCAGCGGGUUUUUUAGUGGAG
.....(((((((((...............((((((((((...(((.....).)).))))))..))))((((...)))).))))))))).. ( -21.80, z-score =  -0.97, R)
>droSec1.super_4 3831694 90 - 6179234
CACACCCACUAAGACUGGAAAAUAUUAAUGGCUGGCUUACGCGGCGACUUGAAUAUAAGCUUAAGUCACCCAGCGGGUUUUUUAGUGGAG
.....(((((((((((((............((((.......))))(((((((........)))))))..))))......))))))))).. ( -25.50, z-score =  -2.01, R)
>consensus
CACACCCACUAAGACUGGAAAAUAUUAAUGGCUGGCUUACGCGGCGACUUGAAUAUAAGCUUAAGUCACCCAGCGGGUUUUUUAGUGGAG
.....(((((((((...............((((.(((.....((.(((((((........))))))).)).))).))))))))))))).. (-24.00 = -23.89 +  -0.11)

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 00:53:31 2011