Locus 12960

Sequence ID dm3.chrX
Location 3,613,778 – 3,613,938
Length 160
Max. P 0.981818
window17814 window17815 window17816

overview

Window 4

Location 3,613,778 – 3,613,898
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.86
Shannon entropy 0.24920
G+C content 0.57356
Mean single sequence MFE -48.85
Consensus MFE -38.79
Energy contribution -38.48
Covariance contribution -0.31
Combinations/Pair 1.26
Mean z-score -2.58
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.09
SVM RNA-class probability 0.981818
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3613778 120 + 22422827
GAGGUGGGUGUGAUCGCUAAGGCUGGUGGGUGUACUCGCUUUGCUGGUUGAUGUACUCGAUAGGCGAGCGAGCGAGUUGUGCACUCGCUGGCGAGCGGUUUAAGUAUCCGAUAACUAUGG
.((.((((((.(((((((...((..((((((((((((((((((((.(((((.....))))).))))...))))))))...))))))))..)).)))))))....))))))....)).... ( -51.10, z-score =  -3.71, R)
>droSim1.chrX 2652958 120 + 17042790
GAGGUGGGUGUGAUCGCUAAGGCUGGUGGGUGUACUCGCCAAGCUGGUGGAUGUACUCGAUAGGCGAGCGAGCGAGUCGUGCACUCGCUGGCGAGCGGUUUAAGUUACCGGUAGCUAUAG
..(((((.(..(((((((...((..((((((((((((((...(((.((..((.......))..)).)))..))))))...))))))))..)).)))))))..).)))))........... ( -49.20, z-score =  -2.04, R)
>droSec1.super_4 3096042 120 - 6179234
GAGGUGGGUGUGAUCGCUAAGGCUGGUGGGUGUACUCGCCAAGCUGGUGGAUGUACUCGAUAGGCGAGCGAGAGAGUCGUGCACUCGCUGGCGAGCGGUUUAAGUUACCGGUAGCUAUGG
..(((((.(..(((((((...((..((((((((((.((((.....))))(((...((((.........))))...)))))))))))))..)).)))))))..).)))))........... ( -48.90, z-score =  -2.37, R)
>droEre2.scaffold_4690 1010188 116 + 18748788
GAGGUGGGUGUCGUCGCUAAGGUCGGUAGGUGUACUGGCUAAGCUGGUGCAUGUACUCGGUGGGCGAGCGA----UUCGUGCAUUCGCUGGUACGCGGUGUAUGUCCUCGCUAAAUGUGG
..((((((.(((((((((....((((((.((((((..((...))..)))))).))).)))..))))).)))----).(((((((.(((......))))))))))..))))))........ ( -46.20, z-score =  -2.19, R)
>consensus
GAGGUGGGUGUGAUCGCUAAGGCUGGUGGGUGUACUCGCCAAGCUGGUGGAUGUACUCGAUAGGCGAGCGAGCGAGUCGUGCACUCGCUGGCGAGCGGUUUAAGUUACCGGUAACUAUGG
..(((((....(((((((...(((((((((((((((((((...(.((((....)))).)...))))))(((.....)))))))))))))))).)))))))....)))))........... (-38.79 = -38.48 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,613,778 – 3,613,898
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.86
Shannon entropy 0.24920
G+C content 0.57356
Mean single sequence MFE -29.05
Consensus MFE -17.88
Energy contribution -21.50
Covariance contribution 3.62
Combinations/Pair 1.07
Mean z-score -2.36
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.774059
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3613778 120 - 22422827
CCAUAGUUAUCGGAUACUUAAACCGCUCGCCAGCGAGUGCACAACUCGCUCGCUCGCCUAUCGAGUACAUCAACCAGCAAAGCGAGUACACCCACCAGCCUUAGCGAUCACACCCACCUC
.....((.(((.............((((((.(((((((.....))))))).(((((.....)))))...............))))))..........((....))))).))......... ( -28.80, z-score =  -2.95, R)
>droSim1.chrX 2652958 120 - 17042790
CUAUAGCUACCGGUAACUUAAACCGCUCGCCAGCGAGUGCACGACUCGCUCGCUCGCCUAUCGAGUACAUCCACCAGCUUGGCGAGUACACCCACCAGCCUUAGCGAUCACACCCACCUC
(((..(((...(((.......)))((((((((((((((.....))))))..(((((.....))))).............)))))))).........)))..)))................ ( -34.90, z-score =  -3.03, R)
>droSec1.super_4 3096042 120 + 6179234
CCAUAGCUACCGGUAACUUAAACCGCUCGCCAGCGAGUGCACGACUCUCUCGCUCGCCUAUCGAGUACAUCCACCAGCUUGGCGAGUACACCCACCAGCCUUAGCGAUCACACCCACCUC
.....((((..(((.......)))((((((((((((((.....))))....(((((.....)))))..........)).))))))))..............))))............... ( -32.20, z-score =  -2.83, R)
>droEre2.scaffold_4690 1010188 116 - 18748788
CCACAUUUAGCGAGGACAUACACCGCGUACCAGCGAAUGCACGAA----UCGCUCGCCCACCGAGUACAUGCACCAGCUUAGCCAGUACACCUACCGACCUUAGCGACGACACCCACCUC
...........((((........(((......)))..........----(((.((((....((.(((..((.((..((...))..)).))..)))))......)))))))......)))) ( -20.30, z-score =  -0.65, R)
>consensus
CCAUAGCUACCGGUAACUUAAACCGCUCGCCAGCGAGUGCACGACUCGCUCGCUCGCCUAUCGAGUACAUCCACCAGCUUAGCGAGUACACCCACCAGCCUUAGCGAUCACACCCACCUC
.....((((..((((.....))))(((((((((((((((.......)))))(((((.....)))))..........)).))))))))..............))))............... (-17.88 = -21.50 +   3.62)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,613,818 – 3,613,938
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.25
Shannon entropy 0.30903
G+C content 0.54842
Mean single sequence MFE -46.42
Consensus MFE -31.77
Energy contribution -33.65
Covariance contribution 1.88
Combinations/Pair 1.20
Mean z-score -1.67
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.628923
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3613818 120 + 22422827
UUGCUGGUUGAUGUACUCGAUAGGCGAGCGAGCGAGUUGUGCACUCGCUGGCGAGCGGUUUAAGUAUCCGAUAACUAUGGUUGGUGCACACGCUAAGUAACAAGUGACCGCUAAACUGCU
(((((.(((((.....))))).)))))((.(((((((.....))))))).)).(((((((((.(((.(((((.......))))))))...((((........)))).....))))))))) ( -41.80, z-score =  -1.22, R)
>droSim1.chrX 2652998 120 + 17042790
AAGCUGGUGGAUGUACUCGAUAGGCGAGCGAGCGAGUCGUGCACUCGCUGGCGAGCGGUUUAAGUUACCGGUAGCUAUAGGUGGUGCACUCGCUAAGUAACAAGUGACCGCCAAACCGCU
..((..(((..(((((..(((..((......))..))))))))..)))..)).((((((((.(((((....)))))...((((((.((((.(........).)))))))))))))))))) ( -49.40, z-score =  -2.06, R)
>droSec1.super_4 3096082 120 - 6179234
AAGCUGGUGGAUGUACUCGAUAGGCGAGCGAGAGAGUCGUGCACUCGCUGGCGAGCGGUUUAAGUUACCGGUAGCUAUGGGUGGUGCACUCGCUAAGUAACAAGUGACCGCCAAACCGCC
..((..(((..(((((......(((...(....).))))))))..)))..))..(((((((.(((((....)))))...((((((.((((.(........).))))))))))))))))). ( -46.50, z-score =  -1.59, R)
>droEre2.scaffold_4690 1010228 116 + 18748788
AAGCUGGUGCAUGUACUCGGUGGGCGAGCGAU----UCGUGCAUUCGCUGGUACGCGGUGUAUGUCCUCGCUAAAUGUGGUUUGUGCGCUCGCUGCAUUGCAUGUGAUUGCCAAACCGCG
..(((((((....))).)))).((((((.((.----.(((((((.(((......))))))))))))))))))....((((((((.(((.(((((((...))).)))).))))))))))). ( -48.00, z-score =  -1.79, R)
>consensus
AAGCUGGUGGAUGUACUCGAUAGGCGAGCGAGCGAGUCGUGCACUCGCUGGCGAGCGGUUUAAGUUACCGGUAACUAUGGGUGGUGCACUCGCUAAGUAACAAGUGACCGCCAAACCGCU
..((..(((..((((((((.....))))(((.....)))))))..)))..)).((((((((.(((((....)))))...((((((.((((.(........).)))))))))))))))))) (-31.77 = -33.65 +   1.88)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:12:01 2011