Locus 4113

Sequence ID dm3.chr2R
Location 10,546,077 – 10,546,148
Length 71
Max. P 0.996978
window5640 window5641

overview

Window 0

Location 10,546,077 – 10,546,148
Length 71
Sequences 7
Columns 71
Reading direction forward
Mean pairwise identity 61.23
Shannon entropy 0.79626
G+C content 0.62083
Mean single sequence MFE -28.21
Consensus MFE -16.84
Energy contribution -14.69
Covariance contribution -2.15
Combinations/Pair 2.18
Mean z-score -0.93
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.52
SVM RNA-class probability 0.992086
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10546077 71 + 21146708
UUCUGGAUUGUGGUGUAUCCACUGGGCGGCGGUGGGCGUGGCACGCCUCGCCCAUCCAGCGAGGAGCAUCC
..((((((.((((.....)))).((((((.((((.((...)).))))))))))))))))............ ( -29.90, z-score =  -0.51, R)
>droAna3.scaffold_13266 5023569 71 - 19884421
GUCGACCUGGUGGUGCAGGAAUCGGUUGGCAGUUGGAACGGCCCUCCUGACCAGCCUGGCGGGCUGCCAAU
(((((((.(((.........)))))))))).(((((..((((((.((.(......).)).))))))))))) ( -27.60, z-score =  -0.02, R)
>droEre2.scaffold_4845 7283902 71 - 22589142
GUGCGGAUUCUCGUGCAUUAACUGGACGGCGGUGGGCGUGGCACGCCUCGCCAGUCCAGCGAGUAGCGCCC
((((.....((((........((((((((((..(((((.....))))))))).))))))))))..)))).. ( -32.40, z-score =  -1.33, R)
>droYak2.chr2R 10477786 71 + 21139217
GUUCGGAUUCUCGUGCAUCAAUUGGACGGCGGUGGGCGUGGCACGCCGCGCCAAUCCAGCAAGUUGCAUCC
....((((.(.(((.((.....)).)))((((..(((((((....)))))))...)).)).....).)))) ( -26.80, z-score =  -0.80, R)
>droSec1.super_1 8065708 71 + 14215200
UUCUGGGUUGUGGUGCAUCCACUGGACGGCGGUUGGCGUGGCACGCCUCGCCCAUCCAGCGAGGAGCACCC
...........(((((.(((.(((((.(((((..((((.....)))))))))..)))))...)))))))). ( -32.70, z-score =  -1.22, R)
>droSim1.chr2R 9309000 71 + 19596830
UUCUGGUUUGUGGUGCAUCCACUGGACGGCGGUGGGCGUGGCACGCCUCGCCCGUCCAGCGAGGAGUACCC
...........(((((.(((.((((((((((..(((((.....))))))).))))))))...)))))))). ( -35.10, z-score =  -1.92, R)
>droGri2.scaffold_15112 4560740 67 - 5172618
GCCGGUAAAACAACGUAUCGUUUGGCCACAAAUGCCUAUACCUUGGGCCAUUUAA--AACAAAUAAUUU--
...(((.((((........)))).)))..(((((((((.....)))).)))))..--............-- ( -13.00, z-score =  -0.73, R)
>consensus
GUCUGGAUUGUGGUGCAUCAACUGGACGGCGGUGGGCGUGGCACGCCUCGCCAAUCCAGCGAGGAGCACCC
............((((.....(((((....((((((((.....)))).))))..)))))......)))).. (-16.84 = -14.69 +  -2.15)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,546,077 – 10,546,148
Length 71
Sequences 7
Columns 71
Reading direction reverse
Mean pairwise identity 61.23
Shannon entropy 0.79626
G+C content 0.62083
Mean single sequence MFE -27.00
Consensus MFE -15.25
Energy contribution -14.91
Covariance contribution -0.34
Combinations/Pair 1.80
Mean z-score -1.34
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.02
SVM RNA-class probability 0.996978
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10546077 71 - 21146708
GGAUGCUCCUCGCUGGAUGGGCGAGGCGUGCCACGCCCACCGCCGCCCAGUGGAUACACCACAAUCCAGAA
((.....))...(((((((((((.((((.....))))......))))).((((.....)))).)))))).. ( -29.00, z-score =  -1.74, R)
>droAna3.scaffold_13266 5023569 71 + 19884421
AUUGGCAGCCCGCCAGGCUGGUCAGGAGGGCCGUUCCAACUGCCAACCGAUUCCUGCACCACCAGGUCGAC
..((((.....))))((.(((((((((((((.((....)).)))......)))))).))))))........ ( -23.80, z-score =  -0.03, R)
>droEre2.scaffold_4845 7283902 71 + 22589142
GGGCGCUACUCGCUGGACUGGCGAGGCGUGCCACGCCCACCGCCGUCCAGUUAAUGCACGAGAAUCCGCAC
..(((...((((((((((.((((.((((.....))))...))))))))))........))))....))).. ( -29.50, z-score =  -1.59, R)
>droYak2.chr2R 10477786 71 - 21139217
GGAUGCAACUUGCUGGAUUGGCGCGGCGUGCCACGCCCACCGCCGUCCAAUUGAUGCACGAGAAUCCGAAC
((((....(.((((.((((((.((((((((.......)).)))))))))))).).))).)...)))).... ( -25.00, z-score =  -1.25, R)
>droSec1.super_1 8065708 71 - 14215200
GGGUGCUCCUCGCUGGAUGGGCGAGGCGUGCCACGCCAACCGCCGUCCAGUGGAUGCACCACAACCCAGAA
.((((((((..(((((((((.((.((((.....))))...)))))))))))))).)))))........... ( -36.60, z-score =  -3.01, R)
>droSim1.chr2R 9309000 71 - 19596830
GGGUACUCCUCGCUGGACGGGCGAGGCGUGCCACGCCCACCGCCGUCCAGUGGAUGCACCACAAACCAGAA
(((((.(((..(((((((((.((.((((.....))))...))))))))))))))))).))........... ( -32.70, z-score =  -2.24, R)
>droGri2.scaffold_15112 4560740 67 + 5172618
--AAAUUAUUUGUU--UUAAAUGGCCCAAGGUAUAGGCAUUUGUGGCCAAACGAUACGUUGUUUUACCGGC
--.......(((((--.....(((((((((((....)).)))).))))))))))...((((......)))) ( -12.40, z-score =   0.52, R)
>consensus
GGAUGCUACUCGCUGGAUGGGCGAGGCGUGCCACGCCCACCGCCGUCCAGUGGAUGCACCACAAUCCAGAC
...........(((((((.((((.((((.....))))...))))))))))).................... (-15.25 = -14.91 +  -0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:23:02 2011