Locus 11113

Sequence ID dm3.chr3R
Location 18,751,643 – 18,751,733
Length 90
Max. P 0.933675
window15265 window15266

overview

Window 5

Location 18,751,643 – 18,751,733
Length 90
Sequences 7
Columns 107
Reading direction forward
Mean pairwise identity 67.51
Shannon entropy 0.62373
G+C content 0.48764
Mean single sequence MFE -28.45
Consensus MFE -12.74
Energy contribution -14.61
Covariance contribution 1.86
Combinations/Pair 1.20
Mean z-score -1.26
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.801075
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18751643 90 + 27905053
------------CGCACUUCCUGCAAGGAUAUCAAUUGGGCCAAAAAG---AUUGCUGGCCGAGGAU--GGCGUACAUGGCAUACAUGGCGUAUGCUCGAUAUCUGC
------------.(((.....)))..(((((((.....(((((.....---.....)))))(((.((--(.(((.((((.....)))))))))).)))))))))).. ( -31.20, z-score =  -1.86, R)
>droAna3.scaffold_13340 11127199 91 - 23697760
AGCACUUCUCCGCCACCAUUCGGAGGGGAUAUCAAUCAGGC-AAAAAG---AUUGGUUACCGACAGC------------GCAUACAUGGCGUAUGCUUGAUAUCUCC
....((((((((........))))))))......(((((((-(.....---.((((...))))..((------------((.......)))).))))))))...... ( -26.00, z-score =  -1.52, R)
>droEre2.scaffold_4820 1153355 90 - 10470090
------------CUGUACUGCAGCAAGGAUAUCAAUUGGGCCAAAACG---AUUGCUGGCCGAGUGC--GGCGUACAUGGCAUACAUGGCGUAUACUCGAUAUCUGC
------------(((.....)))...(((((((.....(((((.....---.....)))))(((((.--.((((.((((.....)))))))).)))))))))))).. ( -31.10, z-score =  -1.80, R)
>droYak2.chr3R 19608934 92 + 28832112
------------CGUACUUCCUGCAAGGAUAUCAAUUGGGCCAAAAUG---AUUGCUGGCCGAGUAUAUGGCGUACAUGGCAUACAUGGCGUAUACUCAAUAUCUGC
------------.(((.....)))..((((((......(((((.....---.....)))))(((((((((.....((((.....)))).))))))))).)))))).. ( -26.10, z-score =  -0.87, R)
>droSec1.super_0 19116448 102 + 21120651
CGCACUUCCUUCCUUCCUUCCUGCAAGGAUAUCAAUUGGGCCAAAAAG---AUUGCUGGACAAGCAU--GGCGUACAUGGCAUACAUGGCGUAUGCUCGAUAUCUGC
.(((.................)))..(((((((...((.((((.....---..((((.....)))))--))).))...(((((((.....))))))).))))))).. ( -25.64, z-score =   0.21, R)
>droSim1.chr3R 18562727 90 + 27517382
------------CGCACUUCCUGCAAGGAUAUCAAUUGGGCCAAAAAG---AUUGCUGGCCAAGCAU--GGCGUACAUGGCAUACAUGGCGUAUGCUCGAUAUCUGC
------------.(((.....)))..(((((((.....(((((.....---.....))))).(((((--(.(((.((((.....))))))))))))).))))))).. ( -31.20, z-score =  -1.83, R)
>droWil1.scaffold_181089 11087977 100 - 12369635
AGAACUUCUCUGAUAUCUCUCU----GGAUAUCAAUCAGGCGAAAGUGGGCAUUCCUUGCCUAUUUA-UGACUCAUGUCACAUGAACUGGGGGUACUCGUGAGCU--
((.(((((..((((((((....----))))))))..(((....(((((((((.....))))))))).-((((....))))......)))))))).))(....)..-- ( -27.90, z-score =  -1.14, R)
>consensus
____________CGAACUUCCUGCAAGGAUAUCAAUUGGGCCAAAAAG___AUUGCUGGCCGAGUAU__GGCGUACAUGGCAUACAUGGCGUAUGCUCGAUAUCUGC
..........................(((((((.....(((((.............))))).........((((.((((.....))))))))......))))))).. (-12.74 = -14.61 +   1.86)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,751,643 – 18,751,733
Length 90
Sequences 7
Columns 107
Reading direction reverse
Mean pairwise identity 67.51
Shannon entropy 0.62373
G+C content 0.48764
Mean single sequence MFE -25.70
Consensus MFE -15.48
Energy contribution -16.33
Covariance contribution 0.85
Combinations/Pair 1.26
Mean z-score -0.96
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.933675
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18751643 90 - 27905053
GCAGAUAUCGAGCAUACGCCAUGUAUGCCAUGUACGCC--AUCCUCGGCCAGCAAU---CUUUUUGGCCCAAUUGAUAUCCUUGCAGGAAGUGCG------------
(((((((((((((((((.....))))))..........--......((((((....---....))))))...))))))))..)))..........------------ ( -25.90, z-score =  -1.19, R)
>droAna3.scaffold_13340 11127199 91 + 23697760
GGAGAUAUCAAGCAUACGCCAUGUAUGC------------GCUGUCGGUAACCAAU---CUUUUU-GCCUGAUUGAUAUCCCCUCCGAAUGGUGGCGGAGAAGUGCU
((.((((((((((((((.....))))))------------......(((((.....---....))-)))...))))))))))(((((........)))))....... ( -28.70, z-score =  -1.63, R)
>droEre2.scaffold_4820 1153355 90 + 10470090
GCAGAUAUCGAGUAUACGCCAUGUAUGCCAUGUACGCC--GCACUCGGCCAGCAAU---CGUUUUGGCCCAAUUGAUAUCCUUGCUGCAGUACAG------------
(((((((((((((....((..(((((.....)))))..--))))))((((((....---....)))))).....))))))..)))..........------------ ( -24.60, z-score =  -0.83, R)
>droYak2.chr3R 19608934 92 - 28832112
GCAGAUAUUGAGUAUACGCCAUGUAUGCCAUGUACGCCAUAUACUCGGCCAGCAAU---CAUUUUGGCCCAAUUGAUAUCCUUGCAGGAAGUACG------------
((((((((((((((((.((((((.....))))...))..)))))))((((((....---....)))))).....))))))..)))..........------------ ( -25.30, z-score =  -1.59, R)
>droSec1.super_0 19116448 102 - 21120651
GCAGAUAUCGAGCAUACGCCAUGUAUGCCAUGUACGCC--AUGCUUGUCCAGCAAU---CUUUUUGGCCCAAUUGAUAUCCUUGCAGGAAGGAAGGAAGGAAGUGCG
(((..((((((((((((.....)))))).......(((--(((((.....))))..---.....))))....))))))(((((.(.....).)))))......))). ( -26.21, z-score =   0.32, R)
>droSim1.chr3R 18562727 90 - 27517382
GCAGAUAUCGAGCAUACGCCAUGUAUGCCAUGUACGCC--AUGCUUGGCCAGCAAU---CUUUUUGGCCCAAUUGAUAUCCUUGCAGGAAGUGCG------------
(((((((((((((((((.....))))))((((.....)--)))...((((((....---....))))))...))))))))..)))..........------------ ( -26.60, z-score =  -0.78, R)
>droWil1.scaffold_181089 11087977 100 + 12369635
--AGCUCACGAGUACCCCCAGUUCAUGUGACAUGAGUCA-UAAAUAGGCAAGGAAUGCCCACUUUCGCCUGAUUGAUAUCC----AGAGAGAUAUCAGAGAAGUUCU
--..(((..................((((((....))))-))..(((((((((........)))).)))))..(((((((.----.....))))))))))....... ( -22.60, z-score =  -0.98, R)
>consensus
GCAGAUAUCGAGCAUACGCCAUGUAUGCCAUGUACGCC__AUACUCGGCCAGCAAU___CUUUUUGGCCCAAUUGAUAUCCUUGCAGGAAGUAAG____________
(((((((((((((((((.....))))))..................((((((...........))))))...))))))))..)))...................... (-15.48 = -16.33 +   0.85)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:36:35 2011