Locus 2008

Sequence ID dm3.chr2L
Location 15,499,478 – 15,499,635
Length 157
Max. P 0.906454
window2759 window2760

overview

Window 9

Location 15,499,478 – 15,499,568
Length 90
Sequences 7
Columns 99
Reading direction forward
Mean pairwise identity 63.93
Shannon entropy 0.65368
G+C content 0.42995
Mean single sequence MFE -19.81
Consensus MFE -5.21
Energy contribution -5.69
Covariance contribution 0.47
Combinations/Pair 1.42
Mean z-score -1.91
Structure conservation index 0.26
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.511328
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15499478 90 + 23011544
GACGAAACGAAAAUAACGAGCU-AAAAGGCCAUAAAAAUUGGCCAAAAAU---GUGGUUCCAUA-----GCUGGUUCCAUUCACCCUCUCGCUCGCUCU
................(((((.-....(((((.......)))))......---((((..(((..-----..)))..))))..........))))).... ( -24.50, z-score =  -3.18, R)
>droEre2.scaffold_4929 7245154 90 + 26641161
UCCGAAACCAAAAUAACGAGCC-AAAGAGCCAUAAAAAUUGGCCAAAAAUCGCGUGGUGCCACU-----GCUCG---CGCUCUCCCUCUCGCUCGCUCC
................(((((.-..(((((((.......))))........((((((.((....-----)))))---)))......))).))))).... ( -22.70, z-score =  -2.47, R)
>droYak2.chr2L 2493900 87 - 22324452
CCCGAAACCAAAAUAACGAGCC-AAAAAGCCAUAAAAAUUGGCCUAAAAU---GUGGUUCCAUU-----GCUCG---CGCUCACCCUCUCGCUCGCUCU
................(((((.-.....((((.......)))).......---(((((......-----)).))---)............))))).... ( -15.70, z-score =  -1.31, R)
>droSec1.super_3 1752319 87 + 7220098
GCCGAAACCAAAAUAACGAGCU-AUAAAGCCAUAAAAAUUGGCCAAAAAU---AUGGUUCCAUA-----CCUGG---CACACAUUCUCUCGCUCGCUCU
................(((((.-.....((((.......)))).......---(((((.(((..-----..)))---.)).)))......))))).... ( -16.80, z-score =  -2.08, R)
>droSim1.chr2L 15256770 87 + 22036055
GCCGAAACCAAAAUAUCGAGCU-AUAAAGCCAUAAAAAUUGGCCAAAAAU---GUGGUUCCAUA-----GCUGG---CACACACCCUCUCGCUCGCUCU
................(((((.-.....((((.......)))).......---(((((.(((..-----..)))---.)).)))......))))).... ( -18.50, z-score =  -1.57, R)
>droVir3.scaffold_12963 12178254 90 + 20206255
-AAAGAAAGAAAAAAAAAACCACAACUAACAGA-AAGGCGAGGCAA-UUUCGAAUAUGUUUUU------GCUUUUGCCUCUGUUUCUGCUUCUUGUUCU
-....................((((..(.((((-((.(.(((((((-...((((......)))------)...)))))))).)))))).)..))))... ( -21.00, z-score =  -1.81, R)
>droMoj3.scaffold_6500 20895411 97 + 32352404
-AAAAAACGAAAAUAAAAAAGA-AACAAGCGGGCAAGACAAGGCAAAUUUGGAAUAUUUUUUUUUUCACGCUUUUGCUACAGUUUCUGCUUCUUGUUCU
-..................(((-(.((((.(((((((((..((((((..(((((..........))).))..))))))...)))).))))))))))))) ( -19.50, z-score =  -0.96, R)
>consensus
GCCGAAACCAAAAUAACGAGCU_AAAAAGCCAUAAAAAUUGGCCAAAAAU___GUGGUUCCAUA_____GCUGG___CACUCACCCUCUCGCUCGCUCU
................(((((.......((((.......))))..........(((....)))...........................))))).... ( -5.21 =  -5.69 +   0.47)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,499,535 – 15,499,635
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 60.77
Shannon entropy 0.61895
G+C content 0.55776
Mean single sequence MFE -34.65
Consensus MFE -12.80
Energy contribution -13.42
Covariance contribution 0.62
Combinations/Pair 1.42
Mean z-score -1.94
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.906454
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15499535 100 + 23011544
AUAGCUGGUUCCAUUCACCCUCUCGCUCGCUCUUCCAGCCGGCGAAUUAUUGAUUUUGUGUGAGAGCGAGGGAGCGCGCAUAAGAGAGAGGGAGAGAGAG
.............(((.((((((((((.(((.....))).)))..........(((((((((...((......)).)))))))))))))))).))).... ( -34.00, z-score =  -0.54, R)
>droEre2.scaffold_4929 7245214 82 + 26641161
---ACUGCUCGCGCUCUCCCUCUCGCUCGCUCCUCCAGCCGGCGAACCAUUGAUUUUGCGCGAGAGCGUGUGAGUG----CGAGAGAGA-----------
---.((.(((((((((.(((((((((..(((.....)))..(((((........)))))))))))).).).)))))----))))))...----------- ( -36.40, z-score =  -2.32, R)
>droYak2.chr2L 2493957 83 - 22324452
---AUUGCUCGCGCUCACCCUCUCGCUCGCUCUUCCAGCCGGCGAACCAUUCAUUUUGUGGGAGAGCGAGCGAGAG----UGAGAGAGAG----------
---....(((...(((((..((((((((((((((((.....(((((........))))))))))))))))))))))----)))).)))..---------- ( -42.70, z-score =  -4.23, R)
>droMoj3.scaffold_6500 20895477 94 + 32352404
CGCUUUUGCUACAGUUUCUGCUUCUUGUUCUCCUCGUGCCGGUGCUUCAUUGAUUUUGCUUGCAAGUAUGUGUGUG----UGCGAGAGAGCAAGUCCA--
.((....((....))....))..(((((((((.(((..(((((((((((...........)).))))))...)).)----..))))))))))))....-- ( -25.50, z-score =  -0.69, R)
>consensus
___ACUGCUCGCACUCACCCUCUCGCUCGCUCCUCCAGCCGGCGAACCAUUGAUUUUGCGUGAGAGCGAGUGAGUG____UGAGAGAGAG__________
.....................(((((((((((((.(.....(((((........)))))).))))))))))))).......................... (-12.80 = -13.42 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:42:59 2011