Locus 11381

Sequence ID dm3.chr3R
Location 20,779,234 – 20,779,363
Length 129
Max. P 0.657880
window15643 window15644 window15645

overview

Window 3

Location 20,779,234 – 20,779,328
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 84.87
Shannon entropy 0.26474
G+C content 0.61931
Mean single sequence MFE -24.54
Consensus MFE -19.28
Energy contribution -19.76
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -1.46
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.642487
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20779234 94 + 27905053
GCAGCUGCCCAUCCCCAUCCGCAUCCCCAUCCUCGUCUUUAGUCUGGCCCUCAACCUUGGCCACAGCCCCAGCAUUUGGCCAAAGACAGCAGCC
...(((((............(......)......((((((.((((((((.........)))))..((....))....))).)))))).))))). ( -23.00, z-score =  -1.74, R)
>droSim1.chr3R 20611137 93 + 27517382
GCAGCUGCCCAUCCCCACCC-CAUCACCAUCCUCGUCUUCGGUCUGGCUCUCAGCCUUGGCCCCAGCCCCAGCAUUUGGCCAAAGACAGCAGCC
...(((((............-............((....))(((((((.....)))((((((...((....))....)))))))))).))))). ( -25.90, z-score =  -1.77, R)
>droSec1.super_33 40783 88 + 478481
GCAGCUGCCCAUCCCCA------UCACCAUCCUCGUCUUCGGUCUGGCUCUCAGCCUUGGCCCCAGCCCCAGCAUUUGGCCAAAGACAGCAGCC
...(((((.........------..........((....))(((((((.....)))((((((...((....))....)))))))))).))))). ( -25.90, z-score =  -1.63, R)
>droYak2.chr3R 3111601 94 - 28832112
GCAGCUGCCCAUCCUCAUACUCCAGCUCAGCCUCGGUCUCAGUCUGGCUCUUAGCCUUGGCCACAUCCCCAGCAUUUGGCCAAAGACAGCAGCC
...(((((.............((((......)).)).....(((((((.....)))(((((((.((.......)).))))))))))).))))). ( -25.70, z-score =  -0.67, R)
>droEre2.scaffold_4820 3195357 88 - 10470090
GCAGCUGCCCAUCCUCA------GCCUCAUCCUUCACCUCAGUCCGGCUCUUAGCCUUGGCCACAUCCCCAGCAUUUGGCCAAAGACAGCAGCC
((.((((........))------))................(((.(((.....)))(((((((.((.......)).))))))).))).)).... ( -22.20, z-score =  -1.47, R)
>consensus
GCAGCUGCCCAUCCCCA__C_C_UCCCCAUCCUCGUCUUCAGUCUGGCUCUCAGCCUUGGCCACAGCCCCAGCAUUUGGCCAAAGACAGCAGCC
...(((((..........................(....).(((((((.....)))((((((...............)))))))))).))))). (-19.28 = -19.76 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,779,234 – 20,779,328
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 84.87
Shannon entropy 0.26474
G+C content 0.61931
Mean single sequence MFE -35.10
Consensus MFE -27.39
Energy contribution -27.55
Covariance contribution 0.16
Combinations/Pair 1.14
Mean z-score -1.52
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.657880
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20779234 94 - 27905053
GGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGUGGCCAAGGUUGAGGGCCAGACUAAAGACGAGGAUGGGGAUGCGGAUGGGGAUGGGCAGCUGC
(((((((((((((((((....(((..(((....)))..)))....))))).....)))))..(.((....)).)...........))))))).. ( -33.20, z-score =  -1.08, R)
>droSim1.chr3R 20611137 93 - 27517382
GGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGGGGCCAAGGCUGAGAGCCAGACCGAAGACGAGGAUGGUGAUG-GGGUGGGGAUGGGCAGCUGC
(((((((((((..(.((....(((..(((....)))..))).....((((..(((....)).)..))))....-)).)..)))).))))))).. ( -36.70, z-score =  -1.55, R)
>droSec1.super_33 40783 88 - 478481
GGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGGGGCCAAGGCUGAGAGCCAGACCGAAGACGAGGAUGGUGA------UGGGGAUGGGCAGCUGC
(((((((..((((((((....((....))...))))))))((.(..((((..(((....)).)..))))..------).))....))))))).. ( -36.20, z-score =  -1.91, R)
>droYak2.chr3R 3111601 94 + 28832112
GGCUGCUGUCUUUGGCCAAAUGCUGGGGAUGUGGCCAAGGCUAAGAGCCAGACUGAGACCGAGGCUGAGCUGGAGUAUGAGGAUGGGCAGCUGC
(((((((..(((((((((....(....)...)))))))))((.....((((.((.((.(....))).))))))......))....))))))).. ( -35.30, z-score =  -1.00, R)
>droEre2.scaffold_4820 3195357 88 + 10470090
GGCUGCUGUCUUUGGCCAAAUGCUGGGGAUGUGGCCAAGGCUAAGAGCCGGACUGAGGUGAAGGAUGAGGC------UGAGGAUGGGCAGCUGC
((((((((((((..(((.....((((.....((((....))))....)))).((.......)).....)))------..))))).))))))).. ( -34.10, z-score =  -2.05, R)
>consensus
GGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGUGGCCAAGGCUGAGAGCCAGACUGAAGACGAGGAUGGGGA_G_G__UGGGGAUGGGCAGCUGC
((((((...(((((((((...((....))..))))))))).......(((..((.........................))..))))))))).. (-27.39 = -27.55 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,779,269 – 20,779,363
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 89.89
Shannon entropy 0.18098
G+C content 0.57607
Mean single sequence MFE -37.68
Consensus MFE -30.94
Energy contribution -32.90
Covariance contribution 1.96
Combinations/Pair 1.10
Mean z-score -1.59
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.598760
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20779269 94 - 27905053
GGGUUGGUUGGGGGGCCAGCCAAUGCGAAUUAAUUGGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGUGGCCAAGGUUGAGGGCCAGACUAAAGA
(.(((((((((....))))))))).).......((((((.((..(((((((((...((....))..)))))))))...))))))))........ ( -40.50, z-score =  -2.27, R)
>droSim1.chr3R 20611171 94 - 27517382
GGGUUGGUUGGGGGGCCAGCCAAUGCGAAUUAAUUGGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGGGGCCAAGGCUGAGAGCCAGACCGAAGA
(((((((((((....))))))))).........((((((.((..((((((((....((....))...))))))))...)))))))).))..... ( -39.00, z-score =  -1.05, R)
>droSec1.super_33 40812 94 - 478481
GGGUUGGUUGGGGGGCCAGCCAAUGCGAAUUAAUUGGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGGGGCCAAGGCUGAGAGCCAGACCGAAGA
(((((((((((....))))))))).........((((((.((..((((((((....((....))...))))))))...)))))))).))..... ( -39.00, z-score =  -1.05, R)
>droYak2.chr3R 3111636 89 + 28832112
GGGUUGGUUGGGGGCC-----AAUGCGAAUUAAUUGGCUGCUGUCUUUGGCCAAAUGCUGGGGAUGUGGCCAAGGCUAAGAGCCAGACUGAGAC
(.((((((.....)))-----))).).......(((((..(.(((((..((.....))..))))))..)))))(((.....))).......... ( -33.40, z-score =  -2.05, R)
>droEre2.scaffold_4820 3195386 94 + 10470090
GGGUUGGUUGGGGGCCAGCCGAAUGCGAAUUAAUUGGCUGCUGUCUUUGGCCAAAUGCUGGGGAUGUGGCCAAGGCUAAGAGCCGGACUGAGGU
.(((((((.....))))))).............(((((..(.(((((..((.....))..))))))..)))))(((.....))).......... ( -36.50, z-score =  -1.51, R)
>consensus
GGGUUGGUUGGGGGGCCAGCCAAUGCGAAUUAAUUGGCUGCUGUCUUUGGCCAAAUGCUGGGGCUGUGGCCAAGGCUGAGAGCCAGACUGAAGA
(.(((((((((....))))))))).).......((((((.((..(((((((((...((....))..)))))))))...))))))))........ (-30.94 = -32.90 +   1.96)

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 00:41:53 2011