Locus 1913

Sequence ID dm3.chr2L
Location 14,665,351 – 14,665,462
Length 111
Max. P 0.956948
window2636 window2637 window2638 window2639

overview

Window 6

Location 14,665,351 – 14,665,459
Length 108
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 82.24
Shannon entropy 0.27799
G+C content 0.39359
Mean single sequence MFE -27.56
Consensus MFE -15.99
Energy contribution -15.71
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -2.54
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.863826
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14665351 108 + 23011544
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUUUUUUU-CUUACUUUUCUGUAAGGAAAAAUAAAACAGAAAAAAAAAAACAGAGAGCCAGAGGAACUGUAGUCUC
..((..((((((((.((((((.....(((((((((((((((-(((((......))))))))))).)))))))))....)))))).(.....)...))))))))..)).. ( -33.40, z-score =  -3.57, R)
>droEre2.scaffold_4929 6412606 83 + 26641161
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUU------CUUACUUUUCCGCCAGGAA--------------------AACGGAGAGCCAGAAGAACUGUAGUCUC
..((..(((((((((((.....))))(((((.((((------((...((((((....))))--------------------)).)))))).))))))))))))..)).. ( -25.30, z-score =  -2.08, R)
>droYak2.chr2L 14771431 83 + 22324452
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUU------CUUACUUCACUGCCAGGAA--------------------AACAGAGAGCCAGAAGAACUGUAGUCUC
..((..(((((((....((((.(((.((((((((((------((..(......)..)))))--------------------)))))))))).)))))))))))..)).. ( -23.80, z-score =  -1.51, R)
>droSec1.super_3 938869 96 + 7220098
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUUUUUUUUUUU--CUUACUUUUCUGCAAGAAAAAAUACAA-----------AAACAGAGAGCCAGAGGAACUGUAGUCUC
..((..((((((((.((((....((((((((...((((((--(((.(......).)))))))))...))-----------)))))).))))....))))))))..)).. ( -28.30, z-score =  -3.02, R)
>droSim1.chr2L 14414144 98 + 22036055
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUUUUUUUUUUUUUCUUACUUUUCUGCAAGAAAAAAUACAA-----------AAACAGAGAGCCAGAGGAACUGUAGUCUC
..((..((((((((.((((....((((((((.....(((((((((.(......).)))))))))...))-----------)))))).))))....))))))))..)).. ( -27.00, z-score =  -2.53, R)
>consensus
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUUUUUU__CUUACUUUUCUGCAAGGAAAAAUA_AA___________AAACAGAGAGCCAGAGGAACUGUAGUCUC
..((..(((((((((((.....)))).....................(((((((.............................)))))))......)))))))..)).. (-15.99 = -15.71 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,665,351 – 14,665,459
Length 108
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 82.24
Shannon entropy 0.27799
G+C content 0.39359
Mean single sequence MFE -24.38
Consensus MFE -12.96
Energy contribution -12.44
Covariance contribution -0.52
Combinations/Pair 1.16
Mean z-score -2.57
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.775216
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14665351 108 - 23011544
GAGACUACAGUUCCUCUGGCUCUCUGUUUUUUUUUUUCUGUUUUAUUUUUCCUUACAGAAAAGUAAG-AAAAAAAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
.......(((((((.........(((((((.((((((...(((((((((((......))))))))))-)...)))))).))))))).........)))))))....... ( -27.87, z-score =  -3.30, R)
>droEre2.scaffold_4929 6412606 83 - 26641161
GAGACUACAGUUCUUCUGGCUCUCCGUU--------------------UUCCUGGCGGAAAAGUAAG------AAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
.......((((((((((.(((.((((((--------------------.....))))))..))).))------))........(((.......)))))))))....... ( -19.60, z-score =  -1.09, R)
>droYak2.chr2L 14771431 83 - 22324452
GAGACUACAGUUCUUCUGGCUCUCUGUU--------------------UUCCUGGCAGUGAAGUAAG------AAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
.......((((((((((.((((.(((((--------------------.....))))).).))).))------))........(((.......)))))))))....... ( -18.40, z-score =  -0.42, R)
>droSec1.super_3 938869 96 - 7220098
GAGACUACAGUUCCUCUGGCUCUCUGUUU-----------UUGUAUUUUUUCUUGCAGAAAAGUAAG--AAAAAAAAAAAAAACAGCUAAAAACUGGAACUGCCACCGG
.......(((((((.........((((((-----------((...(((((((((((......)))))--))))))...)))))))).........)))))))....... ( -28.67, z-score =  -4.25, R)
>droSim1.chr2L 14414144 98 - 22036055
GAGACUACAGUUCCUCUGGCUCUCUGUUU-----------UUGUAUUUUUUCUUGCAGAAAAGUAAGAAAAAAAAAAAAAAAACAGCUAAAAACUGGAACUGCCACCGG
.......(((((((.........((((((-----------((.(.(((((((((((......))))))))))).)...)))))))).........)))))))....... ( -27.37, z-score =  -3.79, R)
>consensus
GAGACUACAGUUCCUCUGGCUCUCUGUUU___________UU_UAUUUUUCCUUGCAGAAAAGUAAG__AAAAAAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
.......(((((((..(((((.(((((...........................)))))...((..................)))))))......)))))))....... (-12.96 = -12.44 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,665,351 – 14,665,462
Length 111
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 82.75
Shannon entropy 0.27054
G+C content 0.41246
Mean single sequence MFE -29.70
Consensus MFE -17.73
Energy contribution -17.45
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -2.87
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.64
SVM RNA-class probability 0.956948
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14665351 111 + 23011544
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUUUUUUU-CUUACUUUUCUGUAAGGAAAAAUAAAACAGAAAAAAAAAAACAGAGAGCCAGAGGAACUGUAGUCUCCGC
.(((..((((((((.((((((.....(((((((((((((((-(((((......))))))))))).)))))))))....)))))).(.....)...)))))))).....))). ( -35.30, z-score =  -3.82, R)
>droEre2.scaffold_4929 6412606 86 + 26641161
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUU------CUUACUUUUCCGCCAGGAAAA--------------------CGGAGAGCCAGAAGAACUGUAGUCUCCGC
.(((..(((((((((((.....))))(((((.((((------((...((((((....))))))--------------------.)))))).)))))))))))).....))). ( -27.20, z-score =  -2.26, R)
>droYak2.chr2L 14771431 86 + 22324452
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUU------CUUACUUCACUGCCAGGAAAA--------------------CAGAGAGCCAGAAGAACUGUAGUCUCCGC
.(((.(((.....((((((((.(((.((((((((((------((..(......)..)))))))--------------------))))))))...))))))))..))).))). ( -26.90, z-score =  -2.23, R)
>droSec1.super_3 938869 99 + 7220098
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUUUUUUUUUUU--CUUACUUUUCUGCAAGAAAAAAUACAA-----------AAACAGAGAGCCAGAGGAACUGUAGUCUCCGC
.(((..((((((((.((((....((((((((...((((((--(((.(......).)))))))))...))-----------)))))).))))....)))))))).....))). ( -30.20, z-score =  -3.25, R)
>droSim1.chr2L 14414144 101 + 22036055
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUUUUUUUUUUUUUCUUACUUUUCUGCAAGAAAAAAUACAA-----------AAACAGAGAGCCAGAGGAACUGUAGUCUCCGC
.(((..((((((((.((((....((((((((.....(((((((((.(......).)))))))))...))-----------)))))).))))....)))))))).....))). ( -28.90, z-score =  -2.80, R)
>consensus
CCGGUGGCAGUUCCAGUUUUUAGCUGUUUUGUUUUUUUUU__CUUACUUUUCUGCAAGGAAAAAUA_AA___________AAACAGAGAGCCAGAGGAACUGUAGUCUCCGC
.(((..(((((((((((.....)))).....................(((((((.............................)))))))......))))))).....))). (-17.73 = -17.45 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,665,351 – 14,665,462
Length 111
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 82.75
Shannon entropy 0.27054
G+C content 0.41246
Mean single sequence MFE -27.17
Consensus MFE -15.28
Energy contribution -15.36
Covariance contribution 0.08
Combinations/Pair 1.11
Mean z-score -2.79
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.912607
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14665351 111 - 23011544
GCGGAGACUACAGUUCCUCUGGCUCUCUGUUUUUUUUUUUCUGUUUUAUUUUUCCUUACAGAAAAGUAAG-AAAAAAAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
.(((.(....(((((((.........(((((((.((((((...(((((((((((......))))))))))-)...)))))).))))))).........))))))).).))). ( -30.47, z-score =  -3.50, R)
>droEre2.scaffold_4929 6412606 86 - 26641161
GCGGAGACUACAGUUCUUCUGGCUCUCCG--------------------UUUUCCUGGCGGAAAAGUAAG------AAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
(((((((...(((.....)))..))))))--------------------).....((((((....((...------....))....(((.......)))...)))))).... ( -22.20, z-score =  -1.23, R)
>droYak2.chr2L 14771431 86 - 22324452
GCGGAGACUACAGUUCUUCUGGCUCUCUG--------------------UUUUCCUGGCAGUGAAGUAAG------AAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
(((((((...(((.....)))..))))))--------------------).....(((((((..(((...------...................)))...))))))).... ( -21.95, z-score =  -0.96, R)
>droSec1.super_3 938869 99 - 7220098
GCGGAGACUACAGUUCCUCUGGCUCUCUGUUU-----------UUGUAUUUUUUCUUGCAGAAAAGUAAG--AAAAAAAAAAAAAACAGCUAAAAACUGGAACUGCCACCGG
.(((.(....(((((((.........((((((-----------((...(((((((((((......)))))--))))))...)))))))).........))))))).).))). ( -31.27, z-score =  -4.31, R)
>droSim1.chr2L 14414144 101 - 22036055
GCGGAGACUACAGUUCCUCUGGCUCUCUGUUU-----------UUGUAUUUUUUCUUGCAGAAAAGUAAGAAAAAAAAAAAAAAAACAGCUAAAAACUGGAACUGCCACCGG
.(((.(....(((((((.........((((((-----------((.(.(((((((((((......))))))))))).)...)))))))).........))))))).).))). ( -29.97, z-score =  -3.93, R)
>consensus
GCGGAGACUACAGUUCCUCUGGCUCUCUGUUU___________UU_UAUUUUUCCUUGCAGAAAAGUAAG__AAAAAAAAACAAAACAGCUAAAAACUGGAACUGCCACCGG
(((((((...(((.....)))..)))))..........................(((((......)))))..................))......((((........)))) (-15.28 = -15.36 +   0.08)

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 21:41:17 2011