Locus 9778

Sequence ID dm3.chr3R
Location 8,895,101 – 8,895,237
Length 136
Max. P 0.966838
window13410 window13411 window13412 window13413

overview

Window 0

Location 8,895,101 – 8,895,203
Length 102
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 86.11
Shannon entropy 0.23564
G+C content 0.47509
Mean single sequence MFE -29.84
Consensus MFE -22.70
Energy contribution -22.50
Covariance contribution -0.20
Combinations/Pair 1.08
Mean z-score -1.94
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.810577
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8895101 102 + 27905053
AUCAAAAAGCAUAUUGAAAUUGGGUUAAUGUACGGAUACGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAU------CCACAUCCGCAUCCAGUUGGUAUGGU
.........(((((..(...(((((..((((..(((((((((.(((.((.....)).)))...)))))))))....------..))))....))))).)..))))).. ( -30.20, z-score =  -1.48, R)
>droEre2.scaffold_4770 4993353 79 - 17746568
AUCAAAAAGCAUAUUGAAAUUGGGUUAAUGUACGGAUACGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAU------CCA-----------------------
.((((........)))).....((...((((..(((((((((.(((.((.....)).)))...)))))))))))))------)).----------------------- ( -22.70, z-score =  -1.83, R)
>droYak2.chr3R 13191698 96 + 28832112
AUCAAAAAGCAUAUUGAAAUUGGGUUAAUGUACGGAUACGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAU------CCACAUCC------AGUUGGCCUGGU
.((((........)))).((..(((((((....((((..((((((.....))).(((((((....)))))))...)------))..))))------.)))))))..)) ( -29.70, z-score =  -1.66, R)
>droSec1.super_0 8019048 96 - 21120651
AUCAAAAAGCAUAUUGAAAUUGGGUUAAUGUACGGAUGCGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAU------CCGCACCC------AGUUGGUAUGGU
.........(((((..(...(((((..((((..(((((((((.(((.((.....)).)))...)))))))))))))------....))))------).)..))))).. ( -34.50, z-score =  -2.75, R)
>droSim1.chr3R 14989836 102 - 27517382
AUCAAAAAGCAUAUUGAAAUUGGGUUAAUGUACGGAAACGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAUCCACAUCCGCACCC------AGUUGGUAUGGU
.........(((((..(...(((((..((((..(....)((((((.....))).(((((((....)))))))...)))))))....))))------).)..))))).. ( -32.10, z-score =  -2.00, R)
>consensus
AUCAAAAAGCAUAUUGAAAUUGGGUUAAUGUACGGAUACGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAU______CCACACCC______AGUUGGUAUGGU
.((((........))))...(((....((((..(((((((((.(((.((.....)).)))...)))))))))))))......)))....................... (-22.70 = -22.50 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,895,101 – 8,895,203
Length 102
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 86.11
Shannon entropy 0.23564
G+C content 0.47509
Mean single sequence MFE -28.36
Consensus MFE -21.50
Energy contribution -21.90
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.617230
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8895101 102 - 27905053
ACCAUACCAACUGGAUGCGGAUGUGG------AUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCGUAUCCGUACAUUAACCCAAUUUCAAUAUGCUUUUUGAU
............(((((((((...((------((((((........))))))))((.(.....))))))))))))................((((........)))). ( -28.60, z-score =  -1.10, R)
>droEre2.scaffold_4770 4993353 79 + 17746568
-----------------------UGG------AUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCGUAUCCGUACAUUAACCCAAUUUCAAUAUGCUUUUUGAU
-----------------------..(------(((((((((((((...(((.((.....)).))).)))))))))..))))).........((((........)))). ( -23.50, z-score =  -2.21, R)
>droYak2.chr3R 13191698 96 - 28832112
ACCAGGCCAACU------GGAUGUGG------AUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCGUAUCCGUACAUUAACCCAAUUUCAAUAUGCUUUUUGAU
.((((.....))------))..((.(------(((((((((((((...(((.((.....)).))).)))))))))..))))).))......((((........)))). ( -30.10, z-score =  -1.93, R)
>droSec1.super_0 8019048 96 + 21120651
ACCAUACCAACU------GGGUGCGG------AUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCGCAUCCGUACAUUAACCCAAUUUCAAUAUGCUUUUUGAU
.(((.......)------))((((((------(((((((..((((......))))....((...)))))))))))))))............((((........)))). ( -30.10, z-score =  -2.16, R)
>droSim1.chr3R 14989836 102 + 27517382
ACCAUACCAACU------GGGUGCGGAUGUGGAUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCGUUUCCGUACAUUAACCCAAUUUCAAUAUGCUUUUUGAU
...........(------((((...((((((....((((.(((((...(((.((.....)).))).))))).)))))))))).)))))...((((........)))). ( -29.50, z-score =  -0.99, R)
>consensus
ACCAUACCAACU______GGAUGUGG______AUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCGUAUCCGUACAUUAACCCAAUUUCAAUAUGCUUUUUGAU
........................((......(((((((((((((...(((.((.....)).))).)))))))))..))))....))....((((........)))). (-21.50 = -21.90 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,895,139 – 8,895,237
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 91.70
Shannon entropy 0.11244
G+C content 0.57943
Mean single sequence MFE -39.43
Consensus MFE -34.70
Energy contribution -36.03
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.77
SVM RNA-class probability 0.966838
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8895139 98 + 27905053
CGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAUCCACAUCCGCAUCCAGUUGGUAUGGUAUGGUACGGUCUGUCCUGGUCUGGUGGUGUCCUU
.(((.((.(((((.((((((...((.(((((.(((...(((.(((.((.....)).))).)))..)))))))).)))))).)).))))).)).))).. ( -41.60, z-score =  -2.57, R)
>droSec1.super_0 8019086 87 - 21120651
CGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAUCC------GCACCCAGUUGGUAUGGUAUGGU-----CUGUCCUGGUCUGGUGGUGUCCUU
.(((.((.(((((.(((((((((....))))))).(((((------(.(((.....))).))).)))..-----.......)).))))).)).))).. ( -37.70, z-score =  -2.56, R)
>droSim1.chr3R 14989874 93 - 27517382
CGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAUCCACAUCCGCACCCAGUUGGUAUGGUAUGGU-----CUGUCCUGGUCUGGUGGUGUCCUU
.(((.((.(((((.(((((((((....)))))))(((..(.((((((.(((.....))).))).)))).-----.)))...)).))))).)).))).. ( -39.00, z-score =  -2.30, R)
>consensus
CGGAGGCAACCAGUCCGGAUGCGAGUCCGUAUCCACAUCCACAUCCGCACCCAGUUGGUAUGGUAUGGU_____CUGUCCUGGUCUGGUGGUGUCCUU
.(((.((.(((((.(((((((((....))))))).((((((.(((.((.....)).))).))).)))..............)).))))).)).))).. (-34.70 = -36.03 +   1.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,895,139 – 8,895,237
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 91.70
Shannon entropy 0.11244
G+C content 0.57943
Mean single sequence MFE -33.87
Consensus MFE -27.52
Energy contribution -27.30
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.00
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.686667
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8895139 98 - 27905053
AAGGACACCACCAGACCAGGACAGACCGUACCAUACCAUACCAACUGGAUGCGGAUGUGGAUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCG
..(((..(.(((((.((.(((..(((((((((((((((((((..........)).))))).))))).)))))..))...))))).))))).)..))). ( -36.90, z-score =  -2.62, R)
>droSec1.super_0 8019086 87 + 21120651
AAGGACACCACCAGACCAGGACAG-----ACCAUACCAUACCAACUGGGUGC------GGAUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCG
..(((..(.(((((....((....-----.))............((((((((------(..(.((....)).)..))))))))).))))).)..))). ( -31.00, z-score =  -1.87, R)
>droSim1.chr3R 14989874 93 + 27517382
AAGGACACCACCAGACCAGGACAG-----ACCAUACCAUACCAACUGGGUGCGGAUGUGGAUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCG
..(((..(.(((((.((...(((.-----.(((((((.((((.....)))).)).))))).)))((((.((....)).)))))).))))).)..))). ( -33.70, z-score =  -1.51, R)
>consensus
AAGGACACCACCAGACCAGGACAG_____ACCAUACCAUACCAACUGGGUGCGGAUGUGGAUGUGGAUACGGACUCGCAUCCGGACUGGUUGCCUCCG
..(((..(.(((((.((..............(((.(((.......)))))).......((((((((........)))))))))).))))).)..))). (-27.52 = -27.30 +  -0.22)

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 00:10:55 2011