Locus 11963

Sequence ID dm3.chr3R
Location 24,802,445 – 24,802,536
Length 91
Max. P 0.758201
window16435 window16436

overview

Window 5

Location 24,802,445 – 24,802,536
Length 91
Sequences 11
Columns 100
Reading direction forward
Mean pairwise identity 86.51
Shannon entropy 0.27813
G+C content 0.43856
Mean single sequence MFE -26.75
Consensus MFE -17.65
Energy contribution -18.14
Covariance contribution 0.49
Combinations/Pair 1.12
Mean z-score -2.05
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.758201
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24802445 91 + 27905053
CAACACUCCACAGUUGGCUUAGUGGGAGCUUCCUUUUUUC--------GGC-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((.((.((((..........--------)))-).)).))))))))).(((((((.((((.........)))).))))))) ( -28.80, z-score =  -2.67, R)
>droSim1.chr3R 24486121 91 + 27517382
CAACACUCCACAGUUGGCUUAGUGGGAGCUUCCUUUUUUC--------GGC-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((.((.((((..........--------)))-).)).))))))))).(((((((.((((.........)))).))))))) ( -28.80, z-score =  -2.67, R)
>droSec1.super_4 3664969 91 + 6179234
CAACACUCCACAGUUGGCUUAGUGGGAGCUUCCUUUUUUC--------GGC-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((.((.((((..........--------)))-).)).))))))))).(((((((.((((.........)))).))))))) ( -28.80, z-score =  -2.67, R)
>droYak2.chr3R 7134896 91 - 28832112
CAACACUCCACAGUUGGCUUAGUGGGAGCUUCCUUUUUUC--------GGC-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUAGCCACAUUUUA
.............(((((((((.((.((((..........--------)))-).)).))))))))).(((((((.(((...........))).))))))) ( -29.20, z-score =  -2.82, R)
>droEre2.scaffold_4820 7235654 91 - 10470090
CAACACUCCACAGUUGGCUUAGUGGGAGCUUCCUUUUUUC--------GGC-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((.((.((((..........--------)))-).)).))))))))).(((((((.((((.........)))).))))))) ( -28.80, z-score =  -2.67, R)
>droAna3.scaffold_13340 3931237 91 - 23697760
CAACACUCCACAGUUGGCUUAGUGGGUGCUUCCUUUUUUU--------GGU-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
............((.(((..((((((((((.(((((.(((--------(((-(.......))))))).)))).).))))))))..))..)))))...... ( -27.20, z-score =  -2.20, R)
>dp4.chr2 17559791 96 - 30794189
CAACACUCCACAGUUGGCUUAGUCGGAGGUUGCUGCUUUUU---UCGGGGC-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............((((((((....(((((.(((.(.....---..).)))-.))))))))))))).(((((((.((((.........)))).))))))) ( -29.30, z-score =  -1.39, R)
>droPer1.super_0 7218871 96 + 11822988
CAACACUCCACAGUUGGCUUAGUCGGAGGUUGCUGCUUUUU---UCGGGGC-UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............((((((((....(((((.(((.(.....---..).)))-.))))))))))))).(((((((.((((.........)))).))))))) ( -29.30, z-score =  -1.39, R)
>droMoj3.scaffold_6540 20651504 85 - 34148556
CAACACUCCACAGUUGGCUUAGUCAGGU---------------UUUCUGGUAUGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((..((((---------------..........))))))))))))).(((((((.((((.........)))).))))))) ( -22.80, z-score =  -1.98, R)
>droVir3.scaffold_13047 18227746 85 + 19223366
CAACACUCCACAGUUGGCUUAGUCAGGU---------------UUUUUGGUAUGCCUUUAAGCCAAAUAAAGUGCGCCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((..((((---------------..........))))))))))))).(((((((.(..((.........))).))))))) ( -17.10, z-score =  -0.30, R)
>droGri2.scaffold_15074 1282120 100 - 7742996
CAACACUCCACAGUUGGCUUAGUCAGGUAUUUUUUUGUUUUUGUUUUUGGUAUGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((..((((((.....................))))))))))))))).(((((((.((((.........)))).))))))) ( -24.10, z-score =  -1.77, R)
>consensus
CAACACUCCACAGUUGGCUUAGUGGGAGCUUCCUUUUUUC________GGC_UGCCUUUAAGCCAAAUAAAGUGCGGCGCUUAAUCUUUGCCACAUUUUA
.............(((((((((.(((......))).............((....)).))))))))).(((((((.((((.........)))).))))))) (-17.65 = -18.14 +   0.49)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 24,802,445 – 24,802,536
Length 91
Sequences 11
Columns 100
Reading direction reverse
Mean pairwise identity 86.51
Shannon entropy 0.27813
G+C content 0.43856
Mean single sequence MFE -25.03
Consensus MFE -19.27
Energy contribution -19.16
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -1.33
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr3R 24802445 91 - 27905053
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-GCC--------GAAAAAAGGAAGCUCCCACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((..((.(-((.--------...........))).))..))))))))..))))))))).. ( -26.60, z-score =  -1.43, R)
>droSim1.chr3R 24486121 91 - 27517382
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-GCC--------GAAAAAAGGAAGCUCCCACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((..((.(-((.--------...........))).))..))))))))..))))))))).. ( -26.60, z-score =  -1.43, R)
>droSec1.super_4 3664969 91 - 6179234
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-GCC--------GAAAAAAGGAAGCUCCCACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((..((.(-((.--------...........))).))..))))))))..))))))))).. ( -26.60, z-score =  -1.43, R)
>droYak2.chr3R 7134896 91 + 28832112
UAAAAUGUGGCUAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-GCC--------GAAAAAAGGAAGCUCCCACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((..((.(-((.--------...........))).))..))))))))..))))))))).. ( -26.50, z-score =  -1.34, R)
>droEre2.scaffold_4820 7235654 91 + 10470090
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-GCC--------GAAAAAAGGAAGCUCCCACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((..((.(-((.--------...........))).))..))))))))..))))))))).. ( -26.60, z-score =  -1.43, R)
>droAna3.scaffold_13340 3931237 91 + 23697760
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-ACC--------AAAAAAAGGAAGCACCCACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((...((.-.((--------.......))..))......))))))))..))))))))).. ( -24.80, z-score =  -1.39, R)
>dp4.chr2 17559791 96 + 30794189
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-GCCCCGA---AAAAAGCAGCAACCUCCGACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((.(((..-((..(..---.....)..))..))).....))))))))..))))))))).. ( -24.10, z-score =  -0.37, R)
>droPer1.super_0 7218871 96 - 11822988
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA-GCCCCGA---AAAAAGCAGCAACCUCCGACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((.(((..-((..(..---.....)..))..))).....))))))))..))))))))).. ( -24.10, z-score =  -0.37, R)
>droMoj3.scaffold_6540 20651504 85 + 34148556
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCAUACCAGAAA---------------ACCUGACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((.(((...........---------------.)))...))))))))..))))))))).. ( -23.30, z-score =  -1.80, R)
>droVir3.scaffold_13047 18227746 85 - 19223366
UAAAAUGUGGCAAAGAUUAAGCGGCGCACUUUAUUUGGCUUAAAGGCAUACCAAAAA---------------ACCUGACUAAGCCAACUGUGGAGUGUUG
......((.((.........)).))(((((((((((((((((.(((...........---------------.)))...))))))))..))))))))).. ( -23.70, z-score =  -1.90, R)
>droGri2.scaffold_15074 1282120 100 + 7742996
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCAUACCAAAAACAAAAACAAAAAAAUACCUGACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((.(((...........................)))...))))))))..))))))))).. ( -22.43, z-score =  -1.68, R)
>consensus
UAAAAUGUGGCAAAGAUUAAGCGCCGCACUUUAUUUGGCUUAAAGGCA_GCC________GAAAAAAGGAAGCUCCCACUAAGCCAACUGUGGAGUGUUG
........(((...........)))(((((((((((((((((..((............................))...))))))))..))))))))).. (-19.27 = -19.16 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:52:58 2011