Locus 14058

Sequence ID dm3.chrX
Location 10,881,475 – 10,881,596
Length 121
Max. P 0.930480
window19331 window19332 window19333 window19334

overview

Window 1

Location 10,881,475 – 10,881,589
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.99
Shannon entropy 0.31967
G+C content 0.48254
Mean single sequence MFE -32.18
Consensus MFE -22.39
Energy contribution -22.32
Covariance contribution -0.08
Combinations/Pair 1.29
Mean z-score -2.12
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.35
SVM RNA-class probability 0.930480
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10881475 114 + 22422827
-GCUGCAUUAUCGUUAUUGCCCAGAAUUCUGCAUAAGUCGGGCCAAUUCGCACGACAUUGCCUCACAGCUAAUCCCGCAGAACAAAGCAGC----CGGCAGUAACAGUUACUG-CCAAAA
-(((((......((....))......((((((....((((.((......)).))))...((......)).......))))))....)))))----.(((((((.....)))))-)).... ( -35.20, z-score =  -3.07, R)
>droAna3.scaffold_13417 5902499 102 - 6960332
GGUUGCAUUAUAGUUAUAGC-------UUCGUGAGAGUGGAG-------GUCCUAGAUC-CUUCAGAGU--AUCCU-UAGAACAAAGUAACAGUUUGGCAGGCAAAGUUUCUGGCCAAAA
.(((((..............-------(((....)))(((((-------(........)-)))))....--.....-.........)))))..(((((((((.......))).)))))). ( -22.40, z-score =   0.21, R)
>droEre2.scaffold_4690 14501993 114 - 18748788
-GCUGCAUUAUCGUUAUUGCCCGGAAUUCUGCAUAAGCCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGCAGAACAAAGCAGC----CGGCAGUAACAGUUACUG-CCAAAA
-(((((....(((........)))..((((((((.((((((((....((....))....)))))...))).))...))))))....)))))----.(((((((.....)))))-)).... ( -35.30, z-score =  -2.09, R)
>droYak2.chrX 10528046 114 - 21770863
-GCUGCAUUAUCGUUAUUGCCCAGAAUUCAGCAUAAGUCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGUGGAACAAAGCAGC----CGGCAGUAACAGUUACUG-CCAAAA
-(((((......(((..(((..........)))...(((((((....((....))....))))))))))...(((...))).....)))))----.(((((((.....)))))-)).... ( -34.10, z-score =  -2.28, R)
>droSec1.super_15 1583473 114 + 1954846
-GCUGCAUUAUCGUUAUUGCCCAGAAUUCUGCAUAAGUCGAGCCAAUUCGCACGAUAUCGCCUGACAGCUAAUCCCGUAGAACAAAGCAGC----CGGCAGUAACAGUUACUG-CCAAAA
-(((((......((....))......((((((....((((.((......)).))))...((......)).......))))))....)))))----.(((((((.....)))))-)).... ( -31.30, z-score =  -2.62, R)
>droSim1.chrX 8434774 114 + 17042790
-GCUGCAUUAUCGUUAUUGCCCAGAAUUCUGCAUAAGUCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGUAGAACAAAGCAGC----CGGCAGUAACAGUUACUG-CCAAAA
-(((((......((....))......((((((....(((((((....((....))....))))))).(.......)))))))....)))))----.(((((((.....)))))-)).... ( -34.80, z-score =  -2.85, R)
>consensus
_GCUGCAUUAUCGUUAUUGCCCAGAAUUCUGCAUAAGUCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGUAGAACAAAGCAGC____CGGCAGUAACAGUUACUG_CCAAAA
.(((((......((....))......((((((....((((.((......)).))))...((......)).......))))))....))))).....(((((((.....))))).)).... (-22.39 = -22.32 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,881,475 – 10,881,589
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.99
Shannon entropy 0.31967
G+C content 0.48254
Mean single sequence MFE -35.65
Consensus MFE -25.90
Energy contribution -26.21
Covariance contribution 0.31
Combinations/Pair 1.28
Mean z-score -1.40
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.595065
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10881475 114 - 22422827
UUUUGG-CAGUAACUGUUACUGCCG----GCUGCUUUGUUCUGCGGGAUUAGCUGUGAGGCAAUGUCGUGCGAAUUGGCCCGACUUAUGCAGAAUUCUGGGCAAUAACGAUAAUGCAGC-
...(((-(((((.....))))))))----(((((.((((..(((((......)))))..))))((((((....((((.((.((.((......)).)).)).)))).))))))..)))))- ( -38.60, z-score =  -1.45, R)
>droAna3.scaffold_13417 5902499 102 + 6960332
UUUUGGCCAGAAACUUUGCCUGCCAAACUGUUACUUUGUUCUA-AGGAU--ACUCUGAAG-GAUCUAGGAC-------CUCCACUCUCACGAA-------GCUAUAACUAUAAUGCAACC
.((((((.((.........))))))))..((((((((((....-.((((--.((....))-.)))).((..-------..))......)))))-------)...))))............ ( -14.80, z-score =   1.04, R)
>droEre2.scaffold_4690 14501993 114 + 18748788
UUUUGG-CAGUAACUGUUACUGCCG----GCUGCUUUGUUCUGCGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGGCUUAUGCAGAAUUCCGGGCAAUAACGAUAAUGCAGC-
...(((-(((((.....))))))))----(((((.(((((.((((.(((..(((....)))...))).)))).....((((((...((.....)).))))))......))))).)))))- ( -43.30, z-score =  -1.97, R)
>droYak2.chrX 10528046 114 + 21770863
UUUUGG-CAGUAACUGUUACUGCCG----GCUGCUUUGUUCCACGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGACUUAUGCUGAAUUCUGGGCAAUAACGAUAAUGCAGC-
...(((-(((((.....))))))))----(((((.(((((((.((((((((((.(((.(((.(..((....))..).))).)))....)))).))))))))....)))))....)))))- ( -41.90, z-score =  -2.59, R)
>droSec1.super_15 1583473 114 - 1954846
UUUUGG-CAGUAACUGUUACUGCCG----GCUGCUUUGUUCUACGGGAUUAGCUGUCAGGCGAUAUCGUGCGAAUUGGCUCGACUUAUGCAGAAUUCUGGGCAAUAACGAUAAUGCAGC-
....((-(((((.....)))))))(----((.(((..((((....)))).))).)))..(((.((((((....((((.((.((.((......)).)).)).)))).)))))).)))...- ( -36.70, z-score =  -1.74, R)
>droSim1.chrX 8434774 114 - 17042790
UUUUGG-CAGUAACUGUUACUGCCG----GCUGCUUUGUUCUACGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGACUUAUGCAGAAUUCUGGGCAAUAACGAUAAUGCAGC-
....((-(((((.....)))))))(----((.(((..((((....)))).))).)))..(((.((((((....((((.((.((.((......)).)).)).)))).)))))).)))...- ( -38.60, z-score =  -1.71, R)
>consensus
UUUUGG_CAGUAACUGUUACUGCCG____GCUGCUUUGUUCUACGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGACUUAUGCAGAAUUCUGGGCAAUAACGAUAAUGCAGC_
....((.(((((.....))))))).....(((((.(((((..((((......))))..)))))((((((........(((((...............)))))....))))))..))))). (-25.90 = -26.21 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,881,496 – 10,881,596
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 95.02
Shannon entropy 0.08824
G+C content 0.50299
Mean single sequence MFE -27.84
Consensus MFE -24.92
Energy contribution -25.32
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -1.86
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.850289
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10881496 100 + 22422827
AGAAUUCUGCAUAAGUCGGGCCAAUUCGCACGACAUUGCCUCACAGCUAAUCCCGCAGAACAAAGCAGCCGGCAGUAACAGUUACUGCCAAAAGUUUCGG-
.(((((((((....((((.((......)).))))...((......)).......))))))..........(((((((.....)))))))......)))..- ( -28.20, z-score =  -2.28, R)
>droEre2.scaffold_4690 14502014 100 - 18748788
GGAAUUCUGCAUAAGCCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGCAGAACAAAGCAGCCGGCAGUAACAGUUACUGCCAAAAGUUUCGG-
((((((((((((.((((((((....((....))....)))))...))).))...)))))...........(((((((.....)))))))....)))))..- ( -27.70, z-score =  -1.20, R)
>droYak2.chrX 10528067 101 - 21770863
AGAAUUCAGCAUAAGUCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGUGGAACAAAGCAGCCGGCAGUAACAGUUACUGCCAAAAGUUUUGGG
.......(((....(((((((....((....))....))))))).)))..(((...))).((((((....(((((((.....)))))))....)))))).. ( -29.50, z-score =  -1.67, R)
>droSec1.super_15 1583494 100 + 1954846
AGAAUUCUGCAUAAGUCGAGCCAAUUCGCACGAUAUCGCCUGACAGCUAAUCCCGUAGAACAAAGCAGCCGGCAGUAACAGUUACUGCCAAAACUUUCGG-
.(((((((((....((((.((......)).))))...((......)).......))))))..........(((((((.....)))))))......)))..- ( -24.30, z-score =  -1.61, R)
>droSim1.chrX 8434795 100 + 17042790
AGAAUUCUGCAUAAGUCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGUAGAACAAAGCAGCCGGCAGUAACAGUUACUGCCAAAAGUUUCGG-
.(((..((((....(((((((....((....))....)))))))..(((......)))......))))..(((((((.....)))))))......)))..- ( -29.50, z-score =  -2.53, R)
>consensus
AGAAUUCUGCAUAAGUCGGGCCAAUUCGCACGACAUCGCCUGACAGCUAAUCCCGUAGAACAAAGCAGCCGGCAGUAACAGUUACUGCCAAAAGUUUCGG_
.(((..((((....(((((((....((....))....))))))).((.......))........))))..(((((((.....)))))))......)))... (-24.92 = -25.32 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,881,496 – 10,881,596
Length 100
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 95.02
Shannon entropy 0.08824
G+C content 0.50299
Mean single sequence MFE -32.00
Consensus MFE -29.70
Energy contribution -29.78
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.32
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.648058
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10881496 100 - 22422827
-CCGAAACUUUUGGCAGUAACUGUUACUGCCGGCUGCUUUGUUCUGCGGGAUUAGCUGUGAGGCAAUGUCGUGCGAAUUGGCCCGACUUAUGCAGAAUUCU
-..(((....(((((((((.....)))))))))((((.((((..(((((......)))))..)))).((((.((......)).))))....))))..))). ( -32.50, z-score =  -1.48, R)
>droEre2.scaffold_4690 14502014 100 + 18748788
-CCGAAACUUUUGGCAGUAACUGUUACUGCCGGCUGCUUUGUUCUGCGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGGCUUAUGCAGAAUUCC
-.((((.(..(((((((((.....)))))))))..).))))(((((((.....(((((...(((.(..((....))..).))))))))..))))))).... ( -32.90, z-score =  -0.83, R)
>droYak2.chrX 10528067 101 + 21770863
CCCAAAACUUUUGGCAGUAACUGUUACUGCCGGCUGCUUUGUUCCACGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGACUUAUGCUGAAUUCU
............(((((((.....)))))))(((.(((..((((....)))).))).))).((((..((((.((......)).))))...))))....... ( -31.90, z-score =  -1.55, R)
>droSec1.super_15 1583494 100 - 1954846
-CCGAAAGUUUUGGCAGUAACUGUUACUGCCGGCUGCUUUGUUCUACGGGAUUAGCUGUCAGGCGAUAUCGUGCGAAUUGGCUCGACUUAUGCAGAAUUCU
-.(....)....(((((((.....)))))))(((.(((..((((....)))).))).)))..((((..(((.((......)).)))..).)))........ ( -29.90, z-score =  -0.95, R)
>droSim1.chrX 8434795 100 - 17042790
-CCGAAACUUUUGGCAGUAACUGUUACUGCCGGCUGCUUUGUUCUACGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGACUUAUGCAGAAUUCU
-..(((......(((((((.....)))))))(((.(((..((((....)))).))).)))..(((..((((.((......)).))))...)))....))). ( -32.80, z-score =  -1.79, R)
>consensus
_CCGAAACUUUUGGCAGUAACUGUUACUGCCGGCUGCUUUGUUCUACGGGAUUAGCUGUCAGGCGAUGUCGUGCGAAUUGGCCCGACUUAUGCAGAAUUCU
............(((((((.....)))))))(((.(((..((((....)))).))).)))..(((..((((.((......)).))))...)))........ (-29.70 = -29.78 +   0.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:32:49 2011