Locus 4073

Sequence ID dm3.chr2R
Location 10,207,555 – 10,207,717
Length 162
Max. P 0.938747
window5582 window5583

overview

Window 2

Location 10,207,555 – 10,207,717
Length 162
Sequences 5
Columns 176
Reading direction forward
Mean pairwise identity 76.73
Shannon entropy 0.40559
G+C content 0.45989
Mean single sequence MFE -53.88
Consensus MFE -30.46
Energy contribution -30.74
Covariance contribution 0.28
Combinations/Pair 1.23
Mean z-score -2.18
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.42
SVM RNA-class probability 0.938747
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10207555 162 + 21146708
UGUCAUCCGGCAGCAGCCAGCUGGAGGAUCGGAUUGGAUCGGAUC-----GCAUCCUCAAC------GCUGGAAAAACAGAAAGUGAC-CGAGUGAAAGAUUUU-UGGCUUUCUAAUUGGAUCUGUGCCGGGUGACUCUUUUUUGCUCAGAUUUUUUGU-GGUAUCUUGGUAUCUG
.(((((((((((.((((((((..((((((.(((((......))))-----.)))))))...------)))))...............(-(((..(((((.....-...)))))...))))..)))))))))))))).......((((.((((.......-...)))).)))).... ( -56.10, z-score =  -2.13, R)
>droAna3.scaffold_13266 14556558 168 + 19884421
UGUCAUCCAGCAGCCGGAGGAUCCAGCUCUGACUCUGACCACAUCCUCUUCUACUCGCGGCUUCUUGGCUGGAAAAACAGAAAGUGAUGUGAGUGAAAGAUUUUUCGGCUUUCUAAUUGGGUCCGAAAUGG-UGACUUUUUUUCUUGCCAAUUUCUUAA-GACAUUUCUU------
((((((((((.(((((((((((((((........)))((((((((((.((((..((.(((((....))))))).....)))))).)))))).))....))))))))))))......))))))..(((((((-..(.........)..)).)))))....-))))......------ ( -47.00, z-score =  -0.64, R)
>droYak2.chr2R 10145199 148 + 21139217
UGUCAUCCGGCA---GCCAGCUGGAGGAUCGCAUCGGAUC---------------CUCAAC------GCUGGAAAAACAGAAAGUGAC-CGAGUGAAAGAUUUU-CGGCUUUCUAAUUGGAUCUGUGCCGGGUGACUCUUUUUUGCUCAGAUUUUU-GU-GGUAUCUUUGUAUCUU
.((((((((((.---.(((((..(((((((......))))---------------)))...------)))))....(((((......(-(((..(((((.....-...)))))...)))).))))))))))))))).......(((..((((....-..-...))))..))).... ( -54.50, z-score =  -3.39, R)
>droSec1.super_1 7714449 155 + 14215200
UGUCAUCCGGCA---GCCAGCUGGAGGAUCGGAUCGGAUC----------GCAUCCUCAAC------GCUGGAAAAACAGAAAGUGAA-CGAGUGAAAGAUUUU-CGGCUUUCUAAUUGGAUCUUUGCCGGGUGACUCUUUUUUGCUCAGAUUUUUUUUAGGUAUCUUGGUAUCUG
.(((((((((((---((((((..(((((((((......))----------).))))))...------)))))......(((((((...-((((.........))-)))))))))..........))))))))))))......................(((((((....))))))) ( -53.00, z-score =  -2.49, R)
>droSim1.chr2R 8970167 165 + 19596830
UGUCAUCCGGCA---GCCAGCUGGAGGAUCGGGUCGGAUCGGAUCGGAUCGCAUCCUCAAC------GCUGGAAAAACAGAAAGUGAA-CGAGUGAAAGAUUUU-CGGCUUUCUAAUUGGAUCUGUGCCGGGUGACUCUUUUUUGCUCAGAUUUUUUUGAGGUAUCUUGGUAUCUG
.(((((((((((---.(((((..((((((.(((((.(((...))).)))).)))))))...------)))))......(((((((...-((((.........))-)))))))))...........))))))))))).........((((((....))))))((((....))))... ( -58.80, z-score =  -2.24, R)
>consensus
UGUCAUCCGGCA___GCCAGCUGGAGGAUCGGAUCGGAUC__AUC_____GCAUCCUCAAC______GCUGGAAAAACAGAAAGUGAA_CGAGUGAAAGAUUUU_CGGCUUUCUAAUUGGAUCUGUGCCGGGUGACUCUUUUUUGCUCAGAUUUUUUGU_GGUAUCUUGGUAUCUG
.(((((((((((....((....))..........((((((............................(((......))).........(((..(((((.........)))))...)))))))))))))))))))).......((((.((((.((.....)).)))).)))).... (-30.46 = -30.74 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,207,555 – 10,207,717
Length 162
Sequences 5
Columns 176
Reading direction reverse
Mean pairwise identity 76.73
Shannon entropy 0.40559
G+C content 0.45989
Mean single sequence MFE -44.22
Consensus MFE -24.52
Energy contribution -23.68
Covariance contribution -0.84
Combinations/Pair 1.27
Mean z-score -2.16
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.915558
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10207555 162 - 21146708
CAGAUACCAAGAUACC-ACAAAAAAUCUGAGCAAAAAAGAGUCACCCGGCACAGAUCCAAUUAGAAAGCCA-AAAAUCUUUCACUCG-GUCACUUUCUGUUUUUCCAGC------GUUGAGGAUGC-----GAUCCGAUCCAAUCCGAUCCUCCAGCUGGCUGCUGCCGGAUGACA
(((((...........-.......)))))...........((((.(((((((((.......(((((((((.-..............)-)...))))))).....(((((------...(((((((.-----(((........)))).))))))..)))))))).)))))).)))). ( -45.23, z-score =  -2.52, R)
>droAna3.scaffold_13266 14556558 168 - 19884421
------AAGAAAUGUC-UUAAGAAAUUGGCAAGAAAAAAAGUCA-CCAUUUCGGACCCAAUUAGAAAGCCGAAAAAUCUUUCACUCACAUCACUUUCUGUUUUUCCAGCCAAGAAGCCGCGAGUAGAAGAGGAUGUGGUCAGAGUCAGAGCUGGAUCCUCCGGCUGCUGGAUGACA
------..((((((((-..........)))).............-...((((((..............))))))....))))...((((((..((((((...((((.((......)).).)))))))))..))))))((((...((((((((((.....)))))).)))).)))). ( -42.74, z-score =  -0.02, R)
>droYak2.chr2R 10145199 148 - 21139217
AAGAUACAAAGAUACC-AC-AAAAAUCUGAGCAAAAAAGAGUCACCCGGCACAGAUCCAAUUAGAAAGCCG-AAAAUCUUUCACUCG-GUCACUUUCUGUUUUUCCAGC------GUUGAG---------------GAUCCGAUGCGAUCCUCCAGCUGGC---UGCCGGAUGACA
.........((((...-..-....))))............((((.((((((..........((((((((((-(...........)))-)...))))))).....(((((------...(((---------------((((......)))))))..))))).---)))))).)))). ( -45.60, z-score =  -3.35, R)
>droSec1.super_1 7714449 155 - 14215200
CAGAUACCAAGAUACCUAAAAAAAAUCUGAGCAAAAAAGAGUCACCCGGCAAAGAUCCAAUUAGAAAGCCG-AAAAUCUUUCACUCG-UUCACUUUCUGUUUUUCCAGC------GUUGAGGAUGC----------GAUCCGAUCCGAUCCUCCAGCUGGC---UGCCGGAUGACA
(((((...................)))))...........((((.((((((..........(((((((.((-(...........)))-....))))))).....(((((------...((((((.(----------(........))))))))..))))).---)))))).)))). ( -43.41, z-score =  -2.79, R)
>droSim1.chr2R 8970167 165 - 19596830
CAGAUACCAAGAUACCUCAAAAAAAUCUGAGCAAAAAAGAGUCACCCGGCACAGAUCCAAUUAGAAAGCCG-AAAAUCUUUCACUCG-UUCACUUUCUGUUUUUCCAGC------GUUGAGGAUGCGAUCCGAUCCGAUCCGACCCGAUCCUCCAGCUGGC---UGCCGGAUGACA
...............((((........)))).........((((.((((((..........(((((((.((-(...........)))-....))))))).....(((((------...((((((.((.((.(((...))).))..))))))))..))))).---)))))).)))). ( -44.10, z-score =  -2.09, R)
>consensus
CAGAUACCAAGAUACC_AAAAAAAAUCUGAGCAAAAAAGAGUCACCCGGCACAGAUCCAAUUAGAAAGCCG_AAAAUCUUUCACUCG_GUCACUUUCUGUUUUUCCAGC______GUUGAGGAUGC_____GAU__GAUCCGAUCCGAUCCUCCAGCUGGC___UGCCGGAUGACA
........................................((((.((((((..((((....(((((((........................)))))))...(((((((......)))).))).............))))............((....))....)))))).)))). (-24.52 = -23.68 +  -0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:22:15 2011