Locus 4427

Sequence ID dm3.chr2R
Location 12,971,515 – 12,971,652
Length 137
Max. P 0.982667
window6060 window6061 window6062

overview

Window 0

Location 12,971,515 – 12,971,620
Length 105
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 94.58
Shannon entropy 0.10130
G+C content 0.46720
Mean single sequence MFE -30.52
Consensus MFE -29.78
Energy contribution -30.06
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -2.14
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.11
SVM RNA-class probability 0.982667
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12971515 105 + 21146708
AAAAGUUCCCCAAGUCUGGGGCCUAACAAGUGCAGCAUUGUCGUUCCAAUUGGACGGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUAU--
....((((((((....)))))...))).(((((....(((((((.(((.(((((.((.....)))))))..)))..)))))))..)))))...............-- ( -31.10, z-score =  -2.30, R)
>droEre2.scaffold_4845 9718007 107 - 22589142
AAAAGUUCUCCAAGUCUGGGGCCUAACAAGUGCAGCAUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUAUACAUAC
....((((((((....)))))...))).(((((....(((((((.((((((.((.(((....))))).))))))..)))))))..)))))................. ( -29.20, z-score =  -2.13, R)
>droYak2.chr2R 2644090 107 - 21139217
AAAAGUUCCCCAAGUCUGGGGCCUAACAAGUGCAGCAUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAUGUGGCUGCGCCAAACGCACUCUUCUAUAUAAAUAUAU
....((((((((....)))))...)))..(((((((...(((..(((....)))..))).(((.......))))))))))........................... ( -27.20, z-score =  -1.10, R)
>droSec1.super_1 10482329 107 + 14215200
AAAAGUUCCCCAAGUCUGGGGCCUAACAAGUGCAGCAUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUACUA
....((((((((....)))))...))).(((((....(((((((.((((((.((.(((....))))).))))))..)))))))..)))))................. ( -32.20, z-score =  -2.67, R)
>droSim1.chr2R 11709231 107 + 19596830
AAAAGUUCCCCAGGUCUGGGGCCUAACAAGUGCAGCAUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUACUA
....((((((((....)))))...))).(((((....(((((((.((((((.((.(((....))))).))))))..)))))))..)))))................. ( -32.90, z-score =  -2.47, R)
>consensus
AAAAGUUCCCCAAGUCUGGGGCCUAACAAGUGCAGCAUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUAUAA
....((((((((....)))))...))).(((((....(((((((.((((((.((.(((....))))).))))))..)))))))..)))))................. (-29.78 = -30.06 +   0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,971,551 – 12,971,652
Length 101
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 86.52
Shannon entropy 0.22394
G+C content 0.39302
Mean single sequence MFE -25.66
Consensus MFE -18.80
Energy contribution -20.93
Covariance contribution 2.13
Combinations/Pair 1.15
Mean z-score -2.58
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.952115
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12971551 101 + 21146708
AUUGUCGUUCCAAUUGGACGGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUA----UGUAU------GUAUACUACAAGUAAACUGCAUUCUGCA
.(((((((.(((.(((((.((.....)))))))..)))..)))))))..(((......(((((((...----.))))------)))(((.....)))...)))........ ( -25.40, z-score =  -2.20, R)
>droYak2.chr2R 2644126 111 - 21139217
AUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAUGUGGCUGCGCCAAACGCACUCUUCUAUAUAAAUAUAUAUACGAGUAUACACAUACUACUUGUAUACUGCAUUCUGCA
.(((.(((.((((...((.(((....)))))...))))..))).)))..(((......((((((....))))))..((((((((.........))))))))......))). ( -22.90, z-score =  -1.29, R)
>droSec1.super_1 10482365 105 + 14215200
AUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUACUAGUAUAU------AUAUACUACAAGUAAACUGCAUUCUGCA
.(((((((.((((((.((.(((....))))).))))))..)))))))..(((......(((((((......))))))------)..(((.....)))...)))........ ( -26.40, z-score =  -3.15, R)
>droSim1.chr2R 11709267 111 + 19596830
AUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUACUAGUAUAUAAAUAUAUAUACUACAAGUAAACUGCAUUCUGCA
.(((((((.((((((.((.(((....))))).))))))..)))))))..(((..........(((....(((((((((....)))))))))...)))..........))). ( -27.95, z-score =  -3.70, R)
>consensus
AUUGUCGUUCCAUUUGGACAGGCUCACCUUCAAAGUGGCUGCGACAAACGCACUCUUCUAUAUACAUACUAGUAUAU______AUAUACUACAAGUAAACUGCAUUCUGCA
.(((((((.((((((.((.(((....))))).))))))..)))))))..(((..........(((....(((((((((....)))))))))...)))..........))). (-18.80 = -20.93 +   2.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,971,551 – 12,971,652
Length 101
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 86.52
Shannon entropy 0.22394
G+C content 0.39302
Mean single sequence MFE -29.00
Consensus MFE -20.29
Energy contribution -23.10
Covariance contribution 2.81
Combinations/Pair 1.14
Mean z-score -1.98
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.629764
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12971551 101 - 21146708
UGCAGAAUGCAGUUUACUUGUAGUAUAC------AUACA----UAUGUAUAUAGAAGAGUGCGUUUGUCGCAGCCACUUUGAAGGUGAGCCCGUCCAAUUGGAACGACAAU
....(((((((.(((.((....((((((------((...----.)))))))))).))).)))))))((((..((((((.....)))).))...(((....))).))))... ( -27.80, z-score =  -2.13, R)
>droYak2.chr2R 2644126 111 + 21139217
UGCAGAAUGCAGUAUACAAGUAGUAUGUGUAUACUCGUAUAUAUAUUUAUAUAGAAGAGUGCGUUUGGCGCAGCCACAUUGAAGGUGAGCCUGUCCAAAUGGAACGACAAU
....((((((.(((((((.......)))))))((((.((((((....))))))...))))))))))(((...(((........)))..)))..(((....)))........ ( -27.90, z-score =  -1.10, R)
>droSec1.super_1 10482365 105 - 14215200
UGCAGAAUGCAGUUUACUUGUAGUAUAU------AUAUACUAGUAUGUAUAUAGAAGAGUGCGUUUGUCGCAGCCACUUUGAAGGUGAGCCUGUCCAAAUGGAACGACAAU
....(((((((.(((.((....((((((------((((....)))))))))))).))).)))))))((((...(((.((((.(((....)))...)))))))..))))... ( -29.70, z-score =  -2.32, R)
>droSim1.chr2R 11709267 111 - 19596830
UGCAGAAUGCAGUUUACUUGUAGUAUAUAUAUUUAUAUACUAGUAUGUAUAUAGAAGAGUGCGUUUGUCGCAGCCACUUUGAAGGUGAGCCUGUCCAAAUGGAACGACAAU
....(((((((.(((.((....(((((((((((........))))))))))))).))).)))))))((((...(((.((((.(((....)))...)))))))..))))... ( -30.60, z-score =  -2.37, R)
>consensus
UGCAGAAUGCAGUUUACUUGUAGUAUAU______AUAUACUAGUAUGUAUAUAGAAGAGUGCGUUUGUCGCAGCCACUUUGAAGGUGAGCCUGUCCAAAUGGAACGACAAU
....(((((((.(((.((....(((((((((((........))))))))))))).))).)))))))((((..((((((.....)))).))...(((....))).))))... (-20.29 = -23.10 +   2.81)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:28:55 2011