Locus 13347

Sequence ID dm3.chrX
Location 5,971,207 – 5,971,363
Length 156
Max. P 0.997642
window18371 window18372 window18373 window18374

overview

Window 1

Location 5,971,207 – 5,971,323
Length 116
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 77.03
Shannon entropy 0.37910
G+C content 0.42263
Mean single sequence MFE -28.62
Consensus MFE -24.50
Energy contribution -25.02
Covariance contribution 0.52
Combinations/Pair 1.11
Mean z-score -2.76
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.11
SVM RNA-class probability 0.997468
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5971207 116 + 22422827
UAAAAACAAAAAUGUAAUAAGAAAAUCCAAAGAUAUGUCCGUGAUUUCU-CUAUGUGCAUCAGACUUUGGCGCUGAUUUACCGGAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUG
.........................................((((((.(-(.(((.((..(.(((((((((((((......)))..)))))))))).)..))))))))))))).... ( -27.50, z-score =  -2.60, R)
>droEre2.scaffold_4690 14950264 93 + 18748788
------------------------UUAUUAUGACAAAGCCUUAAUUUUUUCUAUGUGCAUCAGACUUUGGCGCUGAUUUAUCGGAUCGCCAAAGUUCGUUGCCGUGAAAGUCAAUUG
------------------------......(((((((.......)))((((.(((.(((.(..(((((((((((((....))))..)))))))))..).)))))))))))))).... ( -26.80, z-score =  -3.16, R)
>droYak2.chrX 1980696 93 + 21770863
-----------------------AUACCAAUGAUAUGGCCCUGAUUUCG-CAAUGUGCAUCAGACUUUGGCGCUGAUUUAGCGGGUCGCCAAAGUCCGUUGCCGUGAAAGUCAAUCG
-----------------------........(((.((((.....(((((-(...(.(((.(.(((((((((((((......)))..)))))))))).).))))))))))))))))). ( -28.70, z-score =  -1.53, R)
>droSec1.super_4 5383884 109 - 6179234
-------UAAAAAGUAAUGAGAAAAUCCAAAGAUAUAUCCGUGAUUUCU-CUACGUGCGUCAGACUUUGGCGCUGAUUUACCGAAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUG
-------...........((((((...((..((....))..)).)))))-)((((.(((.(.((((((((((.((......))...)))))))))).).)))))))........... ( -30.40, z-score =  -3.69, R)
>droSim1.chrX 4695510 109 + 17042790
-------UAAAGAGUAAUGAGAAAAUCCAUAGAUAUAUCCGUGAUUUUU-CUAUGUGCAUCAGACUUUGGCGCUGAUUUACCGGAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUG
-------..........((((((((..((..((....))..))..))))-)((((.((..(.(((((((((((((......)))..)))))))))).)..))))))....))).... ( -29.70, z-score =  -2.79, R)
>consensus
________AAA__GUAAU_AGAAAAUCCAAAGAUAUAUCCGUGAUUUCU_CUAUGUGCAUCAGACUUUGGCGCUGAUUUACCGGAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUG
.........................................((((((....((((.(((.(.(((((((((((((......)))..)))))))))).).))))))).)))))).... (-24.50 = -25.02 +   0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,971,207 – 5,971,323
Length 116
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 77.03
Shannon entropy 0.37910
G+C content 0.42263
Mean single sequence MFE -29.11
Consensus MFE -22.88
Energy contribution -22.68
Covariance contribution -0.20
Combinations/Pair 1.13
Mean z-score -2.87
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.15
SVM RNA-class probability 0.997642
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5971207 116 - 22422827
CAAUUGACUUUCACGGCGACGGACUUUGGCGAUCCGGUAAAUCAGCGCCAAAGUCUGAUGCACAUAG-AGAAAUCACGGACAUAUCUUUGGAUUUUCUUAUUACAUUUUUGUUUUUA
...............(((.((((((((((((..............)))))))))))).)))....((-((((.(((.(((....))).))).))))))................... ( -29.34, z-score =  -2.50, R)
>droEre2.scaffold_4690 14950264 93 - 18748788
CAAUUGACUUUCACGGCAACGAACUUUGGCGAUCCGAUAAAUCAGCGCCAAAGUCUGAUGCACAUAGAAAAAAUUAAGGCUUUGUCAUAAUAA------------------------
........((((...(((.((.(((((((((....((....))..))))))))).)).))).....))))..((((.(((...))).))))..------------------------ ( -20.00, z-score =  -1.47, R)
>droYak2.chrX 1980696 93 - 21770863
CGAUUGACUUUCACGGCAACGGACUUUGGCGACCCGCUAAAUCAGCGCCAAAGUCUGAUGCACAUUG-CGAAAUCAGGGCCAUAUCAUUGGUAU-----------------------
...((((.((((.(((((.((((((((((((..............)))))))))))).)))....))-.)))))))).((((......))))..----------------------- ( -31.14, z-score =  -2.81, R)
>droSec1.super_4 5383884 109 + 6179234
CAAUUGACUUUCACGGCGACGGACUUUGGCGAUUCGGUAAAUCAGCGCCAAAGUCUGACGCACGUAG-AGAAAUCACGGAUAUAUCUUUGGAUUUUCUCAUUACUUUUUA-------
............((((((.((((((((((((..............)))))))))))).))).))).(-(((((((.((((......)))))).))))))...........------- ( -35.14, z-score =  -4.48, R)
>droSim1.chrX 4695510 109 - 17042790
CAAUUGACUUUCACGGCGACGGACUUUGGCGAUCCGGUAAAUCAGCGCCAAAGUCUGAUGCACAUAG-AAAAAUCACGGAUAUAUCUAUGGAUUUUCUCAUUACUCUUUA-------
...............(((.((((((((((((..............)))))))))))).)))....((-((((.(((..((....))..))).))))))............------- ( -29.94, z-score =  -3.07, R)
>consensus
CAAUUGACUUUCACGGCGACGGACUUUGGCGAUCCGGUAAAUCAGCGCCAAAGUCUGAUGCACAUAG_AGAAAUCACGGAUAUAUCUUUGGAUUUUCU_AUUAC__UUU________
...............(((.((((((((((((..............)))))))))))).)))........................................................ (-22.88 = -22.68 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,971,247 – 5,971,363
Length 116
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 86.43
Shannon entropy 0.24520
G+C content 0.45825
Mean single sequence MFE -36.52
Consensus MFE -27.98
Energy contribution -28.34
Covariance contribution 0.36
Combinations/Pair 1.14
Mean z-score -2.92
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.43
SVM RNA-class probability 0.990707
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5971247 116 + 22422827
GUGAUUUCU-CUAUGUGCAUCAGACUUUGGCGCUGAUUUACCGGAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUGUAUUGGUUGACCCCUUCGCAAAGUAUCUGGAUAUACAUAU
.........-.((((((.(((.(((((((((((((......)))..)))))))))).......(((((.(((((((.....)))))))...)))))..........))).)))))). ( -34.70, z-score =  -2.53, R)
>droEre2.scaffold_4690 14950280 107 + 18748788
UUAAUUUUUUCUAUGUGCAUCAGACUUUGGCGCUGAUUUAUCGGAUCGCCAAAGUUCGUUGCCGUGAAAGUCAAUUGUAUUGGUUGACCCCACCGCCAAGUAUAUAC----------
...........(((((((....((((((((((((((....))))..))))))))))....((.(((...(((((((.....)))))))..))).))...))))))).---------- ( -32.40, z-score =  -3.58, R)
>droYak2.chrX 1980713 116 + 21770863
CUGAUUUCG-CAAUGUGCAUCAGACUUUGGCGCUGAUUUAGCGGGUCGCCAAAGUCCGUUGCCGUGAAAGUCAAUCGUAUUGGCUGACCCCUGCGCCAAGCAUCUGGUUAUACAUAU
.........-..(((((.((((((.((((((((......((.((((((((((...(.((((.(......).)))).)..))))).)))))))))))))))..))))))..))))).. ( -38.40, z-score =  -1.77, R)
>droSec1.super_4 5383917 116 - 6179234
GUGAUUUCU-CUACGUGCGUCAGACUUUGGCGCUGAUUUACCGAAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUGUAUGGGUUGACCCCUUCGCCGAGAAUAUGGAUAUACAUAU
.....((((-(((((.(((.(.((((((((((.((......))...)))))))))).).)))))))...(((((((.....))))))).........)))))((((......)))). ( -37.50, z-score =  -2.81, R)
>droSim1.chrX 4695543 116 + 17042790
GUGAUUUUU-CUAUGUGCAUCAGACUUUGGCGCUGAUUUACCGGAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUGUAUUGGUUGACCCCUUCGCCAAGCAUAUGGAUAUACAUAU
(((.....(-((((((((....(((((((((((((......)))..)))))))))).......(((((.(((((((.....)))))))...)))))...)))))))))....))).. ( -39.60, z-score =  -3.89, R)
>consensus
GUGAUUUCU_CUAUGUGCAUCAGACUUUGGCGCUGAUUUACCGGAUCGCCAAAGUCCGUCGCCGUGAAAGUCAAUUGUAUUGGUUGACCCCUUCGCCAAGCAUAUGGAUAUACAUAU
...........((((.(((.(.(((((((((((((......)))..)))))))))).).)))))))...(((((((.....)))))))............................. (-27.98 = -28.34 +   0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,971,247 – 5,971,363
Length 116
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 86.43
Shannon entropy 0.24520
G+C content 0.45825
Mean single sequence MFE -35.24
Consensus MFE -29.82
Energy contribution -29.46
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -2.87
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.70
SVM RNA-class probability 0.994479
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5971247 116 - 22422827
AUAUGUAUAUCCAGAUACUUUGCGAAGGGGUCAACCAAUACAAUUGACUUUCACGGCGACGGACUUUGGCGAUCCGGUAAAUCAGCGCCAAAGUCUGAUGCACAUAG-AGAAAUCAC
.(((((................((..((((((((.........))))))))..))(((.((((((((((((..............)))))))))))).))))))))(-(....)).. ( -34.64, z-score =  -2.94, R)
>droEre2.scaffold_4690 14950280 107 - 18748788
----------GUAUAUACUUGGCGGUGGGGUCAACCAAUACAAUUGACUUUCACGGCAACGAACUUUGGCGAUCCGAUAAAUCAGCGCCAAAGUCUGAUGCACAUAGAAAAAAUUAA
----------((((.......((.((((((((((.........))))).))))).))..((.(((((((((....((....))..))))))))).))))))................ ( -28.50, z-score =  -2.33, R)
>droYak2.chrX 1980713 116 - 21770863
AUAUGUAUAACCAGAUGCUUGGCGCAGGGGUCAGCCAAUACGAUUGACUUUCACGGCAACGGACUUUGGCGACCCGCUAAAUCAGCGCCAAAGUCUGAUGCACAUUG-CGAAAUCAG
...(((((...(((((..((((((((((((((.(((((...((.......)).((....))....)))))))))).))......))))))).)))))))))).....-......... ( -39.70, z-score =  -2.87, R)
>droSec1.super_4 5383917 116 + 6179234
AUAUGUAUAUCCAUAUUCUCGGCGAAGGGGUCAACCCAUACAAUUGACUUUCACGGCGACGGACUUUGGCGAUUCGGUAAAUCAGCGCCAAAGUCUGACGCACGUAG-AGAAAUCAC
.((((......))))(((((.(((..(((.....)))..................(((.((((((((((((..............)))))))))))).))).))).)-))))..... ( -39.34, z-score =  -3.75, R)
>droSim1.chrX 4695543 116 - 17042790
AUAUGUAUAUCCAUAUGCUUGGCGAAGGGGUCAACCAAUACAAUUGACUUUCACGGCGACGGACUUUGGCGAUCCGGUAAAUCAGCGCCAAAGUCUGAUGCACAUAG-AAAAAUCAC
.(((((....(((......)))((..((((((((.........))))))))..))(((.((((((((((((..............)))))))))))).)))))))).-......... ( -34.04, z-score =  -2.47, R)
>consensus
AUAUGUAUAUCCAUAUACUUGGCGAAGGGGUCAACCAAUACAAUUGACUUUCACGGCGACGGACUUUGGCGAUCCGGUAAAUCAGCGCCAAAGUCUGAUGCACAUAG_AGAAAUCAC
......................((..((((((((.........))))))))..))(((.((((((((((((..............)))))))))))).)))................ (-29.82 = -29.46 +  -0.36)

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 01:19:36 2011