Locus 12080

Sequence ID dm3.chr3R
Location 25,540,940 – 25,541,070
Length 130
Max. P 0.563877
window16607 window16608 window16609

overview

Window 7

Location 25,540,940 – 25,541,032
Length 92
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 81.44
Shannon entropy 0.30005
G+C content 0.47437
Mean single sequence MFE -29.65
Consensus MFE -20.16
Energy contribution -21.85
Covariance contribution 1.69
Combinations/Pair 1.15
Mean z-score -1.64
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.563877
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25540940 92 - 27905053
UCCCUCCUGGGAUUGGCCUUAUCCCAGGAUCGAAAUGAUACGGAGUGGAUCCAAAGUCAGAAGGAUCGUGAGUAGUUUAGGCUGCCUUUUCA-
((..(((((((((.......)))))))))..))........((((.((((((..........)))))....(((((....)))))).)))).- ( -27.00, z-score =  -0.17, R)
>droYak2.chr3R 7903545 93 + 28832112
UCCCUCCUGGGAAUGGCUGUCUCCCAGAAUAGAACUGAAGCGGAAAGGCAGAAAACUCAGGAGGAAUGUAAGUUGUUUAAACUUCCUUUUUUA
..(((((((((.....(((((((((((.......)))....)))..)))))....)))))))))...(.(((((.....))))).)....... ( -26.90, z-score =  -1.07, R)
>droSec1.super_4 4395051 92 - 6179234
UCCCUCCUGGGAUUGGCCGUAUCCCAGGAUCGAAAUAGUACGGAGUGGAUGAAAAGUCAGAAGGAUCGUGAGUAGUUUAAGCUGUCUUUUCA-
(((((((((((((.......)))))))))(((........))).).)))(((((((.(((...((.(....)....))...))).)))))))- ( -29.00, z-score =  -1.87, R)
>droSim1.chr3R 25213518 92 - 27517382
UCCCUCCUGGGAUUGGCCGUAUCCCAGGACCGAAAUAGUCCGGAGUGGAAGAAAAGUCAGAUGGAGCGUGAGUAGUUUAAGCUGCCUUUUCA-
(((((((((((((.......))))))((((.......)))))))).))).((((((.(((...((((.......))))...))).)))))).- ( -35.70, z-score =  -3.44, R)
>consensus
UCCCUCCUGGGAUUGGCCGUAUCCCAGGAUCGAAAUAAUACGGAGUGGAAGAAAAGUCAGAAGGAUCGUGAGUAGUUUAAGCUGCCUUUUCA_
..(((((((((((.......)))))))))(((........)))...))..((((((.(((...((((.......))))...))).)))))).. (-20.16 = -21.85 +   1.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 25,540,965 – 25,541,070
Length 105
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 67.21
Shannon entropy 0.55791
G+C content 0.50286
Mean single sequence MFE -32.74
Consensus MFE -15.91
Energy contribution -17.07
Covariance contribution 1.16
Combinations/Pair 1.35
Mean z-score -1.07
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.547109
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25540965 105 + 27905053
------------GAUCCUUCUGACUUUGGAUCCACUCCGUAUCAUUUCGAUCCUGGGAUAAGGCCAAUCCCAGGAGGGAAGCCAAUACGACCAAGAGGAGAAAUAGCGGAGUCUUCA
------------(((((..........))))).(((((((...(((((..(((((((((.......)))))))))((....)).......((....)).))))).)))))))..... ( -36.90, z-score =  -2.01, R)
>droEre2.scaffold_4784 12459336 105 - 25762168
UUGGAAUUGGAAAUUUGACCGGAGGUUUCUUUUGCCACGGCCAAGUCCAAGACUGGA------CCAAACCGACUAUGCAAACGAG---AACCAGGAGAAGUGAUAC---AGCUUUCA
.((((((((...((((..((...((((((.(((((..(((....(((((....))))------)....))).....))))).)))---.))).))..))))....)---)).))))) ( -24.50, z-score =  -0.19, R)
>droYak2.chr3R 7903571 105 - 28832112
------------AUUCCUCCUGAGUUUUCUGCCUUUCCGCUUCAGUUCUAUUCUGGGAGACAGCCAUUCCCAGGAGGGAGGCCAAUAUGACCAAGAGGAGGAACACCUGGGUCUUCA
------------.((((((.((.(((....((((..(.((....))....(((((((((.......))))))))))..))))......))))).))))))(((.((....)).))). ( -33.00, z-score =   0.30, R)
>droSec1.super_4 4395076 105 + 6179234
------------GAUCCUUCUGACUUUUCAUCCACUCCGUACUAUUUCGAUCCUGGGAUACGGCCAAUCCCAGGAGGGAAGCCAAUACGACCAAGAGGAGAAACAGCGGAGUCUUCA
------------((...(((((.((((((.(((.((.((((...((((..(((((((((.......)))))))))..))))....))))....)).))))))).)))))))...)). ( -32.40, z-score =  -1.53, R)
>droSim1.chr3R 25213543 105 + 27517382
------------GCUCCAUCUGACUUUUCUUCCACUCCGGACUAUUUCGGUCCUGGGAUACGGCCAAUCCCAGGAGGGAAGCCAAUACGACCAAGAGGAGAAACAGCGGAGUCUUCA
------------(((((..(((......(((((.(((((((((.....)))))((((((.......))))))))))))))).........((....)).....))).)))))..... ( -36.90, z-score =  -1.93, R)
>consensus
____________GAUCCUUCUGACUUUUCUUCCACUCCGGACCAUUUCGAUCCUGGGAUACGGCCAAUCCCAGGAGGGAAGCCAAUACGACCAAGAGGAGAAACAGCGGAGUCUUCA
.....................(((((........((((............(((((((((.......)))))))))((....)).............))))........))))).... (-15.91 = -17.07 +   1.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 25,540,965 – 25,541,070
Length 105
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 67.21
Shannon entropy 0.55791
G+C content 0.50286
Mean single sequence MFE -34.02
Consensus MFE -16.04
Energy contribution -19.28
Covariance contribution 3.24
Combinations/Pair 1.30
Mean z-score -1.13
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.513952
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25540965 105 - 27905053
UGAAGACUCCGCUAUUUCUCCUCUUGGUCGUAUUGGCUUCCCUCCUGGGAUUGGCCUUAUCCCAGGAUCGAAAUGAUACGGAGUGGAUCCAAAGUCAGAAGGAUC------------
.....((((((.((((((...((((((..(((..((((((((....))))..)))).))).))))))..))))))...)))))).(((((..........)))))------------ ( -36.00, z-score =  -1.38, R)
>droEre2.scaffold_4784 12459336 105 + 25762168
UGAAAGCU---GUAUCACUUCUCCUGGUU---CUCGUUUGCAUAGUCGGUUUGG------UCCAGUCUUGGACUUGGCCGUGGCAAAAGAAACCUCCGGUCAAAUUUCCAAUUCCAA
.((((..(---(..........((.((((---.((.(((((.....((((..((------(((......)))))..))))..))))).))))))...)).))..))))......... ( -26.70, z-score =  -0.93, R)
>droYak2.chr3R 7903571 105 + 28832112
UGAAGACCCAGGUGUUCCUCCUCUUGGUCAUAUUGGCCUCCCUCCUGGGAAUGGCUGUCUCCCAGAAUAGAACUGAAGCGGAAAGGCAGAAAACUCAGGAGGAAU------------
.(((.((....)).)))........((((.....))))..(((((((((.....(((((((((((.......)))....)))..)))))....)))))))))...------------ ( -33.60, z-score =  -0.26, R)
>droSec1.super_4 4395076 105 - 6179234
UGAAGACUCCGCUGUUUCUCCUCUUGGUCGUAUUGGCUUCCCUCCUGGGAUUGGCCGUAUCCCAGGAUCGAAAUAGUACGGAGUGGAUGAAAAGUCAGAAGGAUC------------
.....(((((((((((((...((((((..((((.((((((((....))))..)))))))).))))))..)))))))..)))))).(((.....))).........------------ ( -36.50, z-score =  -1.63, R)
>droSim1.chr3R 25213543 105 - 27517382
UGAAGACUCCGCUGUUUCUCCUCUUGGUCGUAUUGGCUUCCCUCCUGGGAUUGGCCGUAUCCCAGGACCGAAAUAGUCCGGAGUGGAAGAAAAGUCAGAUGGAGC------------
......(((((((((((((((((((((..((((.((((((((....))))..)))))))).))))))(((........)))...)).)))))...))).))))).------------ ( -37.30, z-score =  -1.44, R)
>consensus
UGAAGACUCCGCUGUUUCUCCUCUUGGUCGUAUUGGCUUCCCUCCUGGGAUUGGCCGUAUCCCAGGAUCGAAAUAGUACGGAGUGGAAGAAAAGUCAGAAGGAAC____________
.....((((((.((((((...((((((......(((((((((....))))..)))))....))))))..))))))...))))))................................. (-16.04 = -19.28 +   3.24)

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 00:55:21 2011