Locus 1925

Sequence ID dm3.chr2L
Location 14,789,864 – 14,789,921
Length 57
Max. P 0.962048
window2657 window2658

overview

Window 7

Location 14,789,864 – 14,789,921
Length 57
Sequences 10
Columns 62
Reading direction forward
Mean pairwise identity 77.69
Shannon entropy 0.47734
G+C content 0.52346
Mean single sequence MFE -17.57
Consensus MFE -10.84
Energy contribution -10.66
Covariance contribution -0.18
Combinations/Pair 1.18
Mean z-score -1.56
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.28
SVM RNA-class probability 0.921317
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14789864 57 + 23011544
-----UCCACCAGAGGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUAGCACCGAAGGCUCC
-----(((......)))((.((((..(((..((((((....))))))))).....)))))). ( -18.90, z-score =  -2.35, R)
>droSim1.chr2L 14540173 57 + 22036055
-----UCCACCAGAGGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUAGCACCGAAGGCUCC
-----(((......)))((.((((..(((..((((((....))))))))).....)))))). ( -18.90, z-score =  -2.35, R)
>droSec1.super_3 1066883 57 + 7220098
-----UCCACCAGAGGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUAGCACCGAAGGCUCC
-----(((......)))((.((((..(((..((((((....))))))))).....)))))). ( -18.90, z-score =  -2.35, R)
>droYak2.chr2L 14898916 57 + 22324452
-----UCCACCAGGGGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUGCUACCGAAGUCCGC
-----(((......)))(((.....(((...((((((....)))))))))......)))... ( -14.20, z-score =   0.17, R)
>droEre2.scaffold_4929 6537083 56 + 26641161
-----UCCACCAGAGGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUAGCACCGAAGGCUC-
-----(((......)))...((((..(((..((((((....))))))))).....))))..- ( -18.40, z-score =  -2.24, R)
>droAna3.scaffold_12916 15120159 57 - 16180835
-----UCUGCCCGAAGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUGGCACCGAGGCUUUC
-----..........((((.((((..(((..((((((....)))))))))....)))))))) ( -19.70, z-score =  -1.90, R)
>droWil1.scaffold_180764 3238689 56 + 3949147
UGAAAUACCCAUGGAGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUGCAAACUAG------
...........((.((...(((((((((......))..))))))))).))......------ ( -11.90, z-score =  -1.03, R)
>droVir3.scaffold_12963 15259968 57 - 20206255
-----UAUGCUGUAGGAGCUGCCUAAGCUUAAGUGCCAUUAGGCACUGCAACUGAAGGCUCC
-----.........((((((.....((....((((((....))))))....))...)))))) ( -20.20, z-score =  -1.32, R)
>droMoj3.scaffold_6500 23520538 57 - 32352404
-----UGGGAGCUGGGAGCUGCCUAAGCUUAAGUGCCAUUAGGCAUUGCAACUGAAGGCUCC
-----..((((((..(((((.....))))).((((((....)))))).........)))))) ( -21.70, z-score =  -1.17, R)
>droGri2.scaffold_15252 541619 54 + 17193109
--------UGUGCAGAGGAUGCCUAAGCUUAAGUGCCAUUAGGCACUGAAACUGAAGACUAC
--------....(((.((.(((((((((......))..)))))))))....)))........ ( -12.90, z-score =  -1.08, R)
>consensus
_____UCCACCAGAGGAGAUGCCUAAGCUUAAGUGCCAUUAGGCACUGGCACCGAAGGCUCC
................((.(((((((((......))..)))))))))............... (-10.84 = -10.66 +  -0.18)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 8

Location 14,789,864 – 14,789,921
Length 57
Sequences 10
Columns 62
Reading direction reverse
Mean pairwise identity 77.69
Shannon entropy 0.47734
G+C content 0.52346
Mean single sequence MFE -20.55
Consensus MFE -12.49
Energy contribution -12.42
Covariance contribution -0.07
Combinations/Pair 1.17
Mean z-score -1.82
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.70
SVM RNA-class probability 0.962048
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14789864 57 - 23011544
GGAGCCUUCGGUGCUAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCCUCUGGUGGA-----
...((((..(((...((((((....))))))...))).))))...(((......)))----- ( -21.90, z-score =  -1.61, R)
>droSim1.chr2L 14540173 57 - 22036055
GGAGCCUUCGGUGCUAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCCUCUGGUGGA-----
...((((..(((...((((((....))))))...))).))))...(((......)))----- ( -21.90, z-score =  -1.61, R)
>droSec1.super_3 1066883 57 - 7220098
GGAGCCUUCGGUGCUAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCCUCUGGUGGA-----
...((((..(((...((((((....))))))...))).))))...(((......)))----- ( -21.90, z-score =  -1.61, R)
>droYak2.chr2L 14898916 57 - 22324452
GCGGACUUCGGUAGCAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCCCCUGGUGGA-----
((..((....)).))((((((....))))))..........((((......))))..----- ( -17.80, z-score =  -0.14, R)
>droEre2.scaffold_4929 6537083 56 - 26641161
-GAGCCUUCGGUGCUAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCCUCUGGUGGA-----
-..((((..(((...((((((....))))))...))).))))...(((......)))----- ( -21.90, z-score =  -2.02, R)
>droAna3.scaffold_12916 15120159 57 + 16180835
GAAAGCCUCGGUGCCAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCUUCGGGCAGA-----
....((((.((((((((((((....))))))........)))))).....))))...----- ( -22.00, z-score =  -1.97, R)
>droWil1.scaffold_180764 3238689 56 - 3949147
------CUAGUUUGCAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCUCCAUGGGUAUUUCA
------((((((((.((((((....))))))))))).)))....(((.....)))....... ( -15.70, z-score =  -1.40, R)
>droVir3.scaffold_12963 15259968 57 + 20206255
GGAGCCUUCAGUUGCAGUGCCUAAUGGCACUUAAGCUUAGGCAGCUCCUACAGCAUA-----
((((((((.((((..((((((....))))))..)))).)))..))))).........----- ( -22.60, z-score =  -2.25, R)
>droMoj3.scaffold_6500 23520538 57 + 32352404
GGAGCCUUCAGUUGCAAUGCCUAAUGGCACUUAAGCUUAGGCAGCUCCCAGCUCCCA-----
(((((....((((((..((((....))))((.......))))))))....)))))..----- ( -21.10, z-score =  -1.96, R)
>droGri2.scaffold_15252 541619 54 - 17193109
GUAGUCUUCAGUUUCAGUGCCUAAUGGCACUUAAGCUUAGGCAUCCUCUGCACA--------
...((((..(((((.((((((....)))))).))))).))))............-------- ( -18.70, z-score =  -3.63, R)
>consensus
GGAGCCUUCGGUGCCAGUGCCUAAUGGCACUUAAGCUUAGGCAUCUCCUCUGGUGGA_____
.....(((.(((...((((((....))))))...))).)))..................... (-12.49 = -12.42 +  -0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:41:33 2011