Locus 5541

Sequence ID dm3.chr3LHet
Location 438,804 – 438,956
Length 152
Max. P 0.994077
window7605 window7606 window7607 window7608

overview

Window 5

Location 438,804 – 438,919
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.39
Shannon entropy 0.18306
G+C content 0.53630
Mean single sequence MFE -43.70
Consensus MFE -32.16
Energy contribution -32.32
Covariance contribution 0.16
Combinations/Pair 1.11
Mean z-score -3.50
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.67
SVM RNA-class probability 0.994077
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 438804 115 + 2555491
UGUGGCGCCCAGACUGAAGCCCGG-----UCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUAAAACU
.(((..(((.((((((.....)))-----))))))..)))((((..............))))........(((.(...(((((((((....)))))))))...).)))............ ( -40.44, z-score =  -3.32, R)
>droSim1.chr2h_random 682888 115 + 3178526
UGUGGCGCCCAGACUGAAGCCCGG-----UCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGCCACACUGGAACU
(((((((((.((((((.....)))-----)))))).((.(((.(((...((((.((.......)))))))))))))).(((((((((....)))))))))......))))))........ ( -43.80, z-score =  -3.26, R)
>droSec1.super_163 39661 115 + 51592
UGUGGCGCCCAGACUGAAGCCCGG-----UCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGGCUCACUGGAACU
........((((..(((.((((((-----((((((.....((((..............))))....((((.....))))..((((((....))))))))))))))))))))))))).... ( -47.04, z-score =  -3.84, R)
>droYak2.chrU 21900759 119 + 28119190
UGUGGCGCCCAGACUAAAGCCCAGCCCAGUCUGGCAAUACGGCGUAAACAAGUACUAACGCCAAGACCUGUCCUAGAGGACGACAUCUUCUGAUGUCGUCAGACUGGUCACUCUCGACA-
((.(((............)))))(.((((((((((.....(((((............))))).......((((....))))((((((....)))))))))))))))).)..........- ( -44.30, z-score =  -3.48, R)
>droEre2.scaffold_4929 4656536 114 - 26641161
UGUGGCGCCCAGACUAAAGCCCAG-----UCUGGCAACACGGCGUAAGCAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGUCACUCUCGACU-
.(((..(((.(((((.......))-----))))))..)))(((((.((......)).)))))..((((..((......(((((((((....))))))))).))..))))..........- ( -42.90, z-score =  -3.60, R)
>consensus
UGUGGCGCCCAGACUGAAGCCCGG_____UCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGUCACACUCGAACU
.(((((..((((......(((.((......))))).....((((..............))))..........))))..(((((((((....)))))))))......)))))......... (-32.16 = -32.32 +   0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 438,804 – 438,919
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.39
Shannon entropy 0.18306
G+C content 0.53630
Mean single sequence MFE -46.15
Consensus MFE -34.68
Energy contribution -34.48
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -3.02
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.09
SVM RNA-class probability 0.982033
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 438804 115 - 2555491
AGUUUUAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGA-----CCGGGCUUCAGUCUGGGCGCCACA
.......((((((((((.(((((((((((....)))))))(((....)))..(((((.(((((((................))))))))))-----)).....)))).))))))).))). ( -45.49, z-score =  -3.64, R)
>droSim1.chr2h_random 682888 115 - 3178526
AGUUCCAGUGUGGCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGA-----CCGGGCUUCAGUCUGGGCGCCACA
.......(((((.((((.(((((((((((....)))))))(((....)))..(((((.(((((((................))))))))))-----)).....)))).)))).)).))). ( -43.59, z-score =  -2.29, R)
>droSec1.super_163 39661 115 - 51592
AGUUCCAGUGAGCCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGA-----CCGGGCUUCAGUCUGGGCGCCACA
.......(((.((((((.(((((((((((....)))))))(((....)))..(((((.(((((((................))))))))))-----)).....)))).))))))..))). ( -47.49, z-score =  -3.73, R)
>droYak2.chrU 21900759 119 - 28119190
-UGUCGAGAGUGACCAGUCUGACGACAUCAGAAGAUGUCGUCCUCUAGGACAGGUCUUGGCGUUAGUACUUGUUUACGCCGUAUUGCCAGACUGGGCUGGGCUUUAGUCUGGGCGCCACA
-..........((((.(((((((((((((....))))))))).....)))).)))).((((((((((((...........))))))(((((((((((...)).))))))))))))))).. ( -47.30, z-score =  -2.17, R)
>droEre2.scaffold_4929 4656536 114 + 26641161
-AGUCGAGAGUGACCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACUUGCUUACGCCGUGUUGCCAGA-----CUGGGCUUUAGUCUGGGCGCCACA
-.(((.(((.(((((((((((((((((((....)))))))))..........(((..((((((.(((....))).))))))....))))))-----))))...))).))).)))...... ( -46.90, z-score =  -3.28, R)
>consensus
AGUUCCAGUGUGACCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGA_____CCGGGCUUCAGUCUGGGCGCCACA
...........((((..((((((((((((....))))))))).....)))..))))..((((..((......))..))))(((.((((.........(((((....))))))))).))). (-34.68 = -34.48 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 438,839 – 438,956
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.15
Shannon entropy 0.22664
G+C content 0.48983
Mean single sequence MFE -34.37
Consensus MFE -26.86
Energy contribution -27.78
Covariance contribution 0.92
Combinations/Pair 1.14
Mean z-score -2.67
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979647
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 438839 117 + 2555491
GGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUAAAACUUCAGCUCCGC-GCGCAACAAGCUUACGGCA--UAAAACAA
.(((.....((((.((.......)))))).....(((((((((((((....)))))))))...(((((...........))))))))).)-)).......((.....)).--........ ( -29.80, z-score =  -2.28, R)
>droSim1.chr2h_random 682923 119 + 3178526
GGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGCCACACUGGAACUUCAACGCCGC-GCGCAACAAGCUUACUUUAAUCUAAACAA
((((.....((((.((.......))))))....((((((((((((((....)))))))))...(..(.....)..)..))))).))))..-((.......)).................. ( -31.10, z-score =  -2.41, R)
>droSec1.super_163 39696 118 + 51592
GGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGGCUCACUGGAACUUCAGCUCCGCCGCGCAACAAGCUUACGGCA--UAAAACAA
((((..............))))..........(((((((((((((((....)))))))))...(..(.....)..)..))))))....((((.((.....))...)))).--........ ( -35.74, z-score =  -2.53, R)
>droYak2.chrU 21900799 118 + 28119190
GGCGUAAACAAGUACUAACGCCAAGACCUGUCCUAGAGGACGACAUCUUCUGAUGUCGUCAGACUGGUCACUCUCGA-CAUUAGCUGCGCCGCGAAACAAGCUUACGGCA-UCAAAUUAA
(((((............)))))..((((.(((......(((((((((....))))))))).))).))))........-..........((((..(.......)..)))).-......... ( -37.40, z-score =  -2.91, R)
>droEre2.scaffold_4929 4656571 118 - 26641161
GGCGUAAGCAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGUCACUCUCGA-CUUCAGCCUUGCCGCGCAACAAGCUUACGGCA-UCAAAUUAA
(((((.((......)).)))))..........(((((((((((((((....))))))))).((....))........-))))))...(((((.((.....))...)))))-......... ( -37.80, z-score =  -3.23, R)
>consensus
GGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGUCACACUCGAACUUCAGCUCCGCCGCGCAACAAGCUUACGGCA_UCAAAACAA
((((..............))))..........(((((((((((((((....)))))))))...((((.....))))..))))))....((((.((.....))...))))........... (-26.86 = -27.78 +   0.92)

alignment

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secondary structure

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dotplot

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Window 8

Location 438,839 – 438,956
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.15
Shannon entropy 0.22664
G+C content 0.48983
Mean single sequence MFE -38.26
Consensus MFE -27.14
Energy contribution -28.22
Covariance contribution 1.08
Combinations/Pair 1.18
Mean z-score -2.01
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.699247
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 438839 117 - 2555491
UUGUUUUA--UGCCGUAAGCUUGUUGCGC-GCGGAGCUGAAGUUUUAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCC
........--..((((..((.....))..-)))).((.((((...(((.(((........(((((((((....)))))))))(.((((((....)))))).)....)))))).)))))). ( -32.10, z-score =  -0.83, R)
>droSim1.chr2h_random 682923 119 - 3178526
UUGUUUAGAUUAAAGUAAGCUUGUUGCGC-GCGGCGUUGAAGUUCCAGUGUGGCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCC
..............(.((((..((.((((-((.((((((......)))))).))......(((((((((....)))))))))...(((((....)))))))))....))..)))).)... ( -30.60, z-score =  -0.10, R)
>droSec1.super_163 39696 118 - 51592
UUGUUUUA--UGCCGUAAGCUUGUUGCGCGGCGGAGCUGAAGUUCCAGUGAGCCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCC
........--.(((((..((.....)))))))(((((....))))).(((((..(((...(((((((((....)))))))))(.((((((....)))))).).......)))..))))). ( -42.60, z-score =  -3.15, R)
>droYak2.chrU 21900799 118 - 28119190
UUAAUUUGA-UGCCGUAAGCUUGUUUCGCGGCGCAGCUAAUG-UCGAGAGUGACCAGUCUGACGACAUCAGAAGAUGUCGUCCUCUAGGACAGGUCUUGGCGUUAGUACUUGUUUACGCC
......((.-(((((((((....))).))))))))(((((((-((((((.(..((((...(((((((((....)))))))))..)).))...).)))))))))))))............. ( -43.90, z-score =  -3.18, R)
>droEre2.scaffold_4929 4656571 118 + 26641161
UUAAUUUGA-UGCCGUAAGCUUGUUGCGCGGCAAGGCUGAAG-UCGAGAGUGACCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACUUGCUUACGCC
.........-...(((((((..((...(((.(((((((....-((..(((.((....)).(((((((((....))))))))))))..))...))))))).)))....))..))))))).. ( -42.10, z-score =  -2.79, R)
>consensus
UUGUUUUGA_UGCCGUAAGCUUGUUGCGCGGCGGAGCUGAAGUUCCAGUGUGACCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCC
..........((((((..((.....))))))))..............((((((.(((...(((((((((....)))))))))(.((((((....)))))).).......))).)))))). (-27.14 = -28.22 +   1.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:50:24 2011