Locus 11865

Sequence ID dm3.chr3R
Location 24,267,404 – 24,267,567
Length 163
Max. P 0.968865
window16308 window16309 window16310

overview

Window 8

Location 24,267,404 – 24,267,504
Length 100
Sequences 9
Columns 107
Reading direction forward
Mean pairwise identity 70.32
Shannon entropy 0.60101
G+C content 0.57574
Mean single sequence MFE -33.76
Consensus MFE -15.38
Energy contribution -15.97
Covariance contribution 0.58
Combinations/Pair 1.33
Mean z-score -1.05
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.586633
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24267404 100 + 27905053
----GCGCU-CCUGUUGUUCCUGGGC-CCCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUCGGAGAGUG-
----((.((-((.((((((..(((..-..)))..))))))........(.((((.(((((((....))))))).)))))..((((....)))).....)))).)).- ( -39.90, z-score =  -2.10, R)
>droSim1.chr3R 23955117 100 + 27517382
----GCGCU-CCUGUUGUUCCUGGGC-CCCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGCUGAGUUGGAGAGUG-
----((.((-((.((((((..(((..-..)))..)))))).....(((((((((.(((((((....))))))).))))......(....))))))...)))).)).- ( -37.00, z-score =  -1.15, R)
>droSec1.super_22 870910 100 + 1066717
----GCGCU-CCUGUUAUUCCGGGGC-CCCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUUGGAGAGUG-
----((.((-((....((((((((..-..((((((((.......))))))))((.(((((((....))))))).)))))).((((....)))))))).)))).)).- ( -41.40, z-score =  -2.39, R)
>droYak2.chr3R 6600740 101 - 28832112
----GCGCU-CCUGUUGUUCUUCGGC-CCCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCGCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUAGGUUGGGAU
----.(.(.-(((((..((((((((.-..((((((((.......))))))))((.(((((.(....).))))).)).......))).)))))..).))))..).).. ( -34.10, z-score =  -0.02, R)
>droEre2.scaffold_4820 6697614 100 - 10470090
----GCGCU-CCUGUUGUUCUUGUGC-CCCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCAGCUGGGGGAUGAGUUCGCGUCCGCAGGGAUGAGUAGGUGGGCU-
----((.(.-(((((..((((((((.-.(((((((((.......))))))))((.(((((((....))))))).)).....)..))))))))..).)))).).)).- ( -42.60, z-score =  -2.20, R)
>droAna3.scaffold_13340 17067254 92 + 23697760
----GCGCU-CCUGUUGUUGCU-GCCGUUCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUUGAC-GGGGGAUGAGCCUAC-CCCCCGCAGCUGAGUCUU-------
----..(((-(........(((-((......((((((.......))))))((((.((((((....-.)))))).))))...-.....))))).))))...------- ( -30.00, z-score =  -1.35, R)
>dp4.chr2 20528908 97 - 30794189
CCUCUCGCU-CCUUCAGCUGUUUGCCGCUCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUUGGC-GGGGGACCACUUCGC-UCCCCAGCUCCCAGUUGC-------
.........-....((((((...((((((((((((((.......))))))))..........)))-)(((((.(.....).-))))).))...)))))).------- ( -28.90, z-score =  -0.74, R)
>droPer1.super_0 10216267 97 + 11822988
CCUCUCGCU-CCUUCAGUUGUUUGCCGCUCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUUGGC-GGGGGACCACUUCGC-UCCCCAGCUCCCAGUUGC-------
.((((((((-...(((((..(((((.(((........))).))))...)..)))))......)))-)))))..........-....((((.....)))).------- ( -25.20, z-score =   0.25, R)
>droWil1.scaffold_181089 8937832 87 + 12369635
---CCUGCUACUUGCUACUUCUGCCUCUUUCACUAAUAGCCGUAAUUAGUGGCCGAUCC---AGUUGAGAAUGUAGGGCGUAGGCGGAGGGUA--------------
---...((.....))..((((((((((...(((((((.......)))))))(((..(.(---(........)).).)))).)))))))))...-------------- ( -24.70, z-score =   0.28, R)
>consensus
____GCGCU_CCUGUUGUUCCUGGGC_CCCCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUUGG___G___
....((((.....................((((((((.......))))))))....((((((....)))))).......))))........................ (-15.38 = -15.97 +   0.58)

alignment

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secondary structure

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dotplot

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Window 9

Location 24,267,428 – 24,267,537
Length 109
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.77
Shannon entropy 0.35021
G+C content 0.58587
Mean single sequence MFE -43.80
Consensus MFE -32.27
Energy contribution -33.25
Covariance contribution 0.98
Combinations/Pair 1.23
Mean z-score -2.12
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.968865
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24267428 109 + 27905053
CACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUCGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGCUUUGAGAAC
((((.....(((......(.((((.(((((((....))))))).)))))..((((....))))....))).-.))))(((((.((((((....)))))))))))...... ( -48.70, z-score =  -2.83, R)
>droSim1.chr3R 23955141 109 + 27517382
CACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGCUGAGUUGGA-GAGUGGGGGCUCUGGCCUAAGGGCUGGGAUCUGAGAAC
((((.....(((...(((((((((.(((((((....))))))).))))......(....))))))..))).-.)))).(((..(..(((....)))..)..)))...... ( -42.00, z-score =  -1.06, R)
>droSec1.super_22 870934 109 + 1066717
CACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUUGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAAC
((((..(((((.......(.((((.(((((((....))))))).)))))..((((....))))).))))..-.)))).(((..((((((....))))))..)))...... ( -46.80, z-score =  -2.66, R)
>droYak2.chr3R 6600764 110 - 28832112
CACUAAUAGCCGUAAUUAGUGGCUGAUCCCGCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUAGGUUGGGAUUGGGCUACGGCCCAAGGGCUGGGAUCUGAGAAC
(((((((.......)))))))...((((((.(((((...(((....)))..((((....)))).)))))....((.((((((....))))))...))))))))....... ( -44.30, z-score =  -2.21, R)
>droEre2.scaffold_4820 6697638 109 - 10470090
CACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCAGCUGGGGGAUGAGUUCGCGUCCGCAGGGAUGAGUAGGU-GGGCUUGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAAC
(((((((.......)))))))(((.(((((((....))))))).)))...(((((....))))).......-(..((..((..((((((....))))))..))..))..) ( -45.90, z-score =  -1.94, R)
>droAna3.scaffold_13340 17067278 98 + 23697760
CACUAAUAGCCGUAAUUAGUGGCUGAUCCCUUGAC-GGGGGAUGAGCCUACCCCC-CGCAGCUGAGU--------CUUGAGCCCCA--CCAGCUCCCGAGCUCCGUGUGG
.((((((.......))))))((((.((((((....-.)))))).))))......(-((((.(.(((.--------(((((((....--...))))..)))))).)))))) ( -35.10, z-score =  -1.99, R)
>consensus
CACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUGUCCGCAAGGAUGAGUAGGA_GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAAC
(((((((.......)))))))(((.(((((((....))))))).)))...(((((....)))))..............((..(((((((....)))))))..))...... (-32.27 = -33.25 +   0.98)

alignment

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secondary structure

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dotplot

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Window 0

Location 24,267,465 – 24,267,567
Length 102
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 76.76
Shannon entropy 0.41890
G+C content 0.59196
Mean single sequence MFE -41.43
Consensus MFE -21.82
Energy contribution -23.85
Covariance contribution 2.03
Combinations/Pair 1.23
Mean z-score -1.67
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.613886
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24267465 102 + 27905053
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUCGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGCUUUGAGAACUCUUGGGGC------CUCUGACUUUAAUUUAUGCCC----
(((.((((((....((((....))))((((((((-(..........((((((....))))))((((..((....))..))))------)))))))))..)))))).)))---- ( -47.40, z-score =  -2.89, R)
>droSim1.chr3R 23955178 102 + 27517382
GGGGAUGAGUCCGUGUCCGCAAGGCUGAGUUGGA-GAGUGGGGGCUCUGGCCUAAGGGCUGGGAUCUGAGAACUCUUGGGGC------CUCUGACUUUAAUUUAUGCCC----
(((.(((....))).)))....((((((((((((-(..(((((((((..(((....)))..)).((..((....))..))))------))))).)))))))))).))).---- ( -41.20, z-score =  -1.36, R)
>droSec1.super_22 870971 106 + 1066717
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUUGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAACUCUUGGGGC------CUCUGACUUUAAUUUAUGCCCGUGU
(((.(((((((((.((((....))))....)))(-(((((((((((((((((....))))))).((..((....))..))))------)))).))))).)))))).))).... ( -47.40, z-score =  -2.80, R)
>droYak2.chr3R 6600801 104 - 28832112
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUAGGUUGGGAUUGGGCUACGGCCCAAGGGCUGGGAUCUGAGAACUCUUGGGG-----GGCUCUGACUUUAAUUUAUGCCC----
(((.((((((....((((....))))....((((..(..((((((....)))))).((((....((..((....))..)).-----)))))..))))..)))))).)))---- ( -40.30, z-score =  -1.52, R)
>droEre2.scaffold_4820 6697675 108 - 10470090
GGGGAUGAGUUCGCGUCCGCAGGGAUGAGUAGGU-GGGCUUGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAACUCCUGGGGUUGGGGGCUCUGACUUUAAUUUAUGCCC----
(((.(((((((..(((((....)))))..((((.-(..((..((..((((((....))))))..))..))..).))))((((..(.....)..)))).))))))).)))---- ( -45.20, z-score =  -1.40, R)
>droAna3.scaffold_13340 17067314 89 + 23697760
GGGGAUGAGCCUAC-CCCCCGCAGCUGAGU--------CUUGAGCCCCA--CCAGCUCCCGAGCUCCGUGUGGCCCCAGGG---------CUGACUUUAAUUUAUGCCC----
((((..........-.))))(((..(.(((--------((((.(((.((--(.((((....))))..))).)))..)))))---------)).)..........)))..---- ( -27.10, z-score =  -0.03, R)
>consensus
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUAGGA_GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAACUCUUGGGGC______CUCUGACUUUAAUUUAUGCCC____
(((.((((((....((((....))))((((.....((((..((..(((((((....)))))))..))....)))).(((((.......)))))))))..)))))).))).... (-21.82 = -23.85 +   2.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:51:10 2011