Locus 4174

Sequence ID dm3.chr2R
Location 10,970,532 – 10,970,632
Length 100
Max. P 0.992836
window5724 window5725

overview

Window 4

Location 10,970,532 – 10,970,632
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 85.49
Shannon entropy 0.26196
G+C content 0.55214
Mean single sequence MFE -35.15
Consensus MFE -22.40
Energy contribution -22.79
Covariance contribution 0.39
Combinations/Pair 1.22
Mean z-score -3.37
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.57
SVM RNA-class probability 0.992836
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10970532 100 + 21146708
UUCUCGAUUCAAUUCCGAGUUUUCUUAGCCAGUGGCAGGUCCUGGUC-------CUUGUCCUAGUCCC------AGUCGUAGUCGUAGUCCUCUGGCCCUGCCGCUUGGCAAC
..((((.........))))........((((((((((((..((((..-------((......))..))------)).....((((........)))))))))))).))))... ( -34.10, z-score =  -3.90, R)
>droEre2.scaffold_4845 7699142 101 - 22589142
UUCUCGAUUCAAUUCCGAGUUUUCUUAGCCAGUGGCAGGACCUGGUC-------CUUGUCCCAGUCCCC-----AGUCCUAGUCGUAGUCCUGUGGCCCUGCCGCUUGGCAAC
..((((.........))))........((((((((((((..((((..-------......))))..(((-----((..(((....)))..))).)).)))))))).))))... ( -37.10, z-score =  -4.25, R)
>droYak2.chr2R 10905044 113 + 21139217
UUCUCGAUUCAAUUCCGAGUUUUCUUAGCCAGUGGAAGCUCUUGGUCCCUGGUCCUUGUCCUAGUCCCAGUCGUAGUCGUAGUCGUAGUCCUGUGGCCCUGCCGCUUGGCAAC
..((((((((......((((((((.........)))))))).......((((..((......))..))))..).))))).)).....(((..(((((...)))))..)))... ( -29.80, z-score =  -1.26, R)
>droSec1.super_1 8480267 106 + 14215200
UUCUCGAUUCAAUUCCGAGUUUUCUUAGCCAGUGGCAGGUCCUGGUCC-UGGUCCUUGUCCUAGUCCC------AGUCGUAGUCGUAGUCCUCUGGCCCUGCCGCUUGGCAAC
..((((.........))))........((((((((((((.((.((.((-(((..((......))..))------)).((....))..).))...)).)))))))).))))... ( -37.70, z-score =  -4.19, R)
>droSim1.chr2R 9722776 106 + 19596830
UUCUCGAUUCAAUUCCGAGUUUUCUUAGCCAGUGGCAGGUCCUGGUCC-UGGUCCUUGUCCUAGUCCC------AGUCGUAGUCGUAGUCCUCUGGCCCUGCCGCUUGGCAAC
..((((.........))))........((((((((((((.((.((.((-(((..((......))..))------)).((....))..).))...)).)))))))).))))... ( -37.70, z-score =  -4.19, R)
>droAna3.scaffold_13266 17521995 99 - 19884421
UUCUCGAUUCAAUUCCAAAUUUUCUUAGCCACUGGCAGCCACAGGGCA--------GGUCCUAGUCCU------GAUCAUGGUCCUGGCCCUCUGGUCCUGCCCCUUGGCAAC
...........................((((..((((((((.((((((--------((.((.......------......)).))).))))).)))..)))))...))))... ( -34.52, z-score =  -2.40, R)
>consensus
UUCUCGAUUCAAUUCCGAGUUUUCUUAGCCAGUGGCAGGUCCUGGUCC______CUUGUCCUAGUCCC______AGUCGUAGUCGUAGUCCUCUGGCCCUGCCGCUUGGCAAC
.....(((((......)))))......((((((((((((..((((...............))))...........((((.((........)).)))))))))))).))))... (-22.40 = -22.79 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,970,532 – 10,970,632
Length 100
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 85.49
Shannon entropy 0.26196
G+C content 0.55214
Mean single sequence MFE -35.64
Consensus MFE -20.04
Energy contribution -20.93
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -2.54
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.781670
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10970532 100 - 21146708
GUUGCCAAGCGGCAGGGCCAGAGGACUACGACUACGACU------GGGACUAGGACAAG-------GACCAGGACCUGCCACUGGCUAAGAAAACUCGGAAUUGAAUCGAGAA
...((((.(.((((((.....((........))....((------((..((......))-------..))))..)))))).)))))........(((((.......))))).. ( -32.60, z-score =  -2.53, R)
>droEre2.scaffold_4845 7699142 101 + 22589142
GUUGCCAAGCGGCAGGGCCACAGGACUACGACUAGGACU-----GGGGACUGGGACAAG-------GACCAGGUCCUGCCACUGGCUAAGAAAACUCGGAAUUGAAUCGAGAA
...((((.(.(((((((((.(((..(((....)))..))-----)((..((......))-------..)).))))))))).)))))........(((((.......))))).. ( -43.70, z-score =  -4.65, R)
>droYak2.chr2R 10905044 113 - 21139217
GUUGCCAAGCGGCAGGGCCACAGGACUACGACUACGACUACGACUGGGACUAGGACAAGGACCAGGGACCAAGAGCUUCCACUGGCUAAGAAAACUCGGAAUUGAAUCGAGAA
.(((((....)))))(((((..(((...((....)).......((((..((......))..))))............)))..))))).......(((((.......))))).. ( -28.80, z-score =  -0.51, R)
>droSec1.super_1 8480267 106 - 14215200
GUUGCCAAGCGGCAGGGCCAGAGGACUACGACUACGACU------GGGACUAGGACAAGGACCA-GGACCAGGACCUGCCACUGGCUAAGAAAACUCGGAAUUGAAUCGAGAA
...((((.(.((((((.((...((....((....)).((------((..((......))..)))-)..)).)).)))))).)))))........(((((.......))))).. ( -35.90, z-score =  -2.85, R)
>droSim1.chr2R 9722776 106 - 19596830
GUUGCCAAGCGGCAGGGCCAGAGGACUACGACUACGACU------GGGACUAGGACAAGGACCA-GGACCAGGACCUGCCACUGGCUAAGAAAACUCGGAAUUGAAUCGAGAA
...((((.(.((((((.((...((....((....)).((------((..((......))..)))-)..)).)).)))))).)))))........(((((.......))))).. ( -35.90, z-score =  -2.85, R)
>droAna3.scaffold_13266 17521995 99 + 19884421
GUUGCCAAGGGGCAGGACCAGAGGGCCAGGACCAUGAUC------AGGACUAGGACC--------UGCCCUGUGGCUGCCAGUGGCUAAGAAAAUUUGGAAUUGAAUCGAGAA
...((((...(((((..(((.(((((.(((.((......------.......)).))--------)))))).))))))))..))))........(((.((......)).))). ( -36.92, z-score =  -1.87, R)
>consensus
GUUGCCAAGCGGCAGGGCCAGAGGACUACGACUACGACU______GGGACUAGGACAAG______GGACCAGGACCUGCCACUGGCUAAGAAAACUCGGAAUUGAAUCGAGAA
...((((.(.((((((.((..((..((..................))..)).((..............)).)).)))))).)))))........(((((.......))))).. (-20.04 = -20.93 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:24:11 2011