Locus 9241

Sequence ID dm3.chr3R
Location 5,149,045 – 5,149,165
Length 120
Max. P 0.981601
window12666 window12667 window12668

overview

Window 6

Location 5,149,045 – 5,149,136
Length 91
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 71.56
Shannon entropy 0.50649
G+C content 0.50556
Mean single sequence MFE -16.42
Consensus MFE -8.92
Energy contribution -10.76
Covariance contribution 1.84
Combinations/Pair 1.06
Mean z-score -1.74
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.36
SVM RNA-class probability 0.931551
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5149045 91 + 27905053
UGAUGACCGUAUUUGUUUACGUGCCUCGGUCGACCCUCA-AAACAAUGGACUGCCAUUGUUUUUAGUUUUCCCACCCCGCUUCACCCCUCGC
(((((((((....((....)).....))))))...((.(-(((((((((....)))))))))).))...............)))........ ( -19.40, z-score =  -1.93, R)
>droAna3.scaffold_13340 18801126 82 - 23697760
--------GUAUUUGUUAACGUGCCUGAACCGACCCCCCUAGACAAUAGACCUCCAUUGUUUUUCUGGUUUGCCAGCCCCUACCCCCACC--
--------............(((.................(((((((.(....).)))))))..((((....))))..........))).-- (  -9.50, z-score =  -0.46, R)
>droEre2.scaffold_4770 1288148 87 - 17746568
UGAUGACCGUAUUUGUUUACGUGCCUCGGCCGACCCUCC-AAACAAUGGACUGCCAUUGUUUUAGCUCCUCCAGUU----UUUCCUCCCCGC
.((.(..((((......))))..).))((..((.(....-(((((((((....)))))))))..).))..))....----............ ( -15.40, z-score =  -0.68, R)
>droYak2.chr3R 9195171 77 + 28832112
UGAUGACCGUAUUUGUUUACGUGCCUGCGUCGACCCUCA-AAACAAUGGACUGCCAUUGUUUUUGCU--------------UUCCUCCCCGC
.((.((..(((...(((.((((....)))).)))....(-(((((((((....))))))))))))).--------------.)).))..... ( -16.70, z-score =  -2.26, R)
>droSim1.chr3R 11345445 78 - 27517382
UGAUGACCGUAUUUGUUUACGUGCCUCGGUCGACCCUCA-AAACAAUGGACUGCCAUUGUUUUUAGU-------------UUCCCCCCUCGC
.((.(..((((......))))..).))((..((..((.(-(((((((((....)))))))))).)).-------------.))..))..... ( -21.10, z-score =  -3.36, R)
>consensus
UGAUGACCGUAUUUGUUUACGUGCCUCGGUCGACCCUCA_AAACAAUGGACUGCCAUUGUUUUUACU__U__________UUCCCCCCCCGC
...((((((....((....)).....))))))........(((((((((....))))))))).............................. ( -8.92 = -10.76 +   1.84)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,149,045 – 5,149,136
Length 91
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 71.56
Shannon entropy 0.50649
G+C content 0.50556
Mean single sequence MFE -24.16
Consensus MFE -11.42
Energy contribution -11.86
Covariance contribution 0.44
Combinations/Pair 1.17
Mean z-score -2.43
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.08
SVM RNA-class probability 0.981601
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5149045 91 - 27905053
GCGAGGGGUGAAGCGGGGUGGGAAAACUAAAAACAAUGGCAGUCCAUUGUUU-UGAGGGUCGACCGAGGCACGUAAACAAAUACGGUCAUCA
......(((((.((..(((.((....((.((((((((((....)))))))))-).))..)).)))...)).((((......)))).))))). ( -26.80, z-score =  -2.03, R)
>droAna3.scaffold_13340 18801126 82 + 23697760
--GGUGGGGGUAGGGGCUGGCAAACCAGAAAAACAAUGGAGGUCUAUUGUCUAGGGGGGUCGGUUCAGGCACGUUAACAAAUAC--------
--(.(((.(((..((((((((...((......(((((((....))))))).....)).))))))))..)).).))).)......-------- ( -23.10, z-score =  -2.76, R)
>droEre2.scaffold_4770 1288148 87 + 17746568
GCGGGGAGGAAA----AACUGGAGGAGCUAAAACAAUGGCAGUCCAUUGUUU-GGAGGGUCGGCCGAGGCACGUAAACAAAUACGGUCAUCA
............----....((..((.((.(((((((((....)))))))))-...)).))..))(((((.((((......))))))).)). ( -23.10, z-score =  -1.16, R)
>droYak2.chr3R 9195171 77 - 28832112
GCGGGGAGGAA--------------AGCAAAAACAAUGGCAGUCCAUUGUUU-UGAGGGUCGACGCAGGCACGUAAACAAAUACGGUCAUCA
(((..((....--------------....((((((((((....)))))))))-).....))..))).(((.((((......))))))).... ( -21.72, z-score =  -2.60, R)
>droSim1.chr3R 11345445 78 + 27517382
GCGAGGGGGGAA-------------ACUAAAAACAAUGGCAGUCCAUUGUUU-UGAGGGUCGACCGAGGCACGUAAACAAAUACGGUCAUCA
.....((..((.-------------.((.((((((((((....)))))))))-).))..))..))(((((.((((......))))))).)). ( -26.10, z-score =  -3.62, R)
>consensus
GCGGGGGGGGAA__________A__ACCAAAAACAAUGGCAGUCCAUUGUUU_UGAGGGUCGACCGAGGCACGUAAACAAAUACGGUCAUCA
...........................((.(((((((((....))))))))).))...(((......))).((((......))))....... (-11.42 = -11.86 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,149,075 – 5,149,165
Length 90
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 70.59
Shannon entropy 0.52501
G+C content 0.49683
Mean single sequence MFE -24.48
Consensus MFE -11.98
Energy contribution -12.98
Covariance contribution 1.00
Combinations/Pair 1.10
Mean z-score -1.25
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.565333
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5149075 90 - 27905053
ACACCUAAUCUACAUCUUGUGCCAUGCCCGCGAGGGGUGAAGCGGGGUGGGAAAACU--AAAAACAAUGGCAGUCCAUUGUUU-UGAGGGUCG
..(((...(((.((((((((..(((.(((....))))))..)))))))))))...((--.((((((((((....)))))))))-).))))).. ( -33.90, z-score =  -2.68, R)
>droAna3.scaffold_13340 18801148 89 + 23697760
ACACAUAAUCUACAUCUUGUACUCUCUUAGGUGGGGGUAGG----GGCUGGCAAACCAGAAAAACAAUGGAGGUCUAUUGUCUAGGGGGGUCG
..................(.((((((((((...........----..((((....))))....(((((((....)))))))))))))))))). ( -22.70, z-score =  -0.45, R)
>droEre2.scaffold_4770 1288178 86 + 17746568
ACACCUAAUCUACAUCUUGUGUGGAGCCCGCGGGGAGGAAA----AACUGGAGGAGC--UAAAACAAUGGCAGUCCAUUGUUU-GGAGGGUCG
..((((..(((((((...)))))))((((.(.((.......----..)).).)).))--..(((((((((....)))))))))-...)))).. ( -24.30, z-score =  -0.30, R)
>droYak2.chr3R 9195201 76 - 28832112
ACACCUAAUCUACAUCUUGUGCCGAGUCCGCGGGGAGGAA--------------AGC--AAAAACAAUGGCAGUCCAUUGUUU-UGAGGGUCG
..((((........((((.(.(((......))).))))).--------------...--.((((((((((....)))))))))-)..)))).. ( -19.00, z-score =  -0.09, R)
>droSim1.chr3R 11345475 69 + 27517382
ACACCUAAUCUACAUCUUG--------CCGCGAGG-------------GGGGAAACU--AAAAACAAUGGCAGUCCAUUGUUU-UGAGGGUCG
..(((.........((((.--------((....))-------------.))))..((--.((((((((((....)))))))))-).))))).. ( -22.50, z-score =  -2.71, R)
>consensus
ACACCUAAUCUACAUCUUGUGCCGAGCCCGCGGGGAGGAA________GGGAAAACC__AAAAACAAUGGCAGUCCAUUGUUU_UGAGGGUCG
..((((........(((((((.......)))))))..........................(((((((((....)))))))))....)))).. (-11.98 = -12.98 +   1.00)

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 00:00:34 2011