Locus 13944

Sequence ID dm3.chrX
Location 10,176,351 – 10,176,478
Length 127
Max. P 0.956084
window19181 window19182 window19183

overview

Window 1

Location 10,176,351 – 10,176,446
Length 95
Sequences 7
Columns 96
Reading direction reverse
Mean pairwise identity 73.29
Shannon entropy 0.52741
G+C content 0.51551
Mean single sequence MFE -24.35
Consensus MFE -15.39
Energy contribution -15.60
Covariance contribution 0.21
Combinations/Pair 1.44
Mean z-score -0.95
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.778413
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10176351 95 - 22422827
GUCACGUGCCAGCGGCUGACGGAAAACAAUUCCA-GCGAGUGCCAACAUUCAGCUGUGGCAUGCCUCAAACUCAAACUCAAACGCAAACUAGAAGU
....(((((((.(((((((.((((.....)))).-((....))......))))))))))))))................................. ( -25.30, z-score =  -1.04, R)
>droSim1.chrX_random 550623 89 - 5698898
GUCACGUGCCAGCGGCUGACGGAAAACAAUUCCA-GCGAGUGCCAACAUUCAGCUGUGGCAUGCCU------CAAACUCAAACGCAAACUAGAAGU
....(((((((.(((((((.((((.....)))).-((....))......))))))))))))))...------........................ ( -25.30, z-score =  -1.09, R)
>droSec1.super_15 879188 89 - 1954846
GUCACGUGCCAGCGGCUGACGGAAAACAAUUCCA-GCGAGUGCCAACAUUCAGCUGUGGCAUGCCU------CAAACUCAAACACAAACUAGAAGU
....(((((((.(((((((.((((.....)))).-((....))......))))))))))))))...------........................ ( -25.30, z-score =  -1.51, R)
>droEre2.scaffold_4690 13796138 89 + 18748788
GUCACGUGCCAGCGGCUGACGGAAAACAAUUCCA-GCGAGUGCCAACAUUCAGCUGUGGCAUGCCU------CAAACUCAAACGCAAACUAGAAGU
....(((((((.(((((((.((((.....)))).-((....))......))))))))))))))...------........................ ( -25.30, z-score =  -1.09, R)
>droAna3.scaffold_13248 1271652 77 + 4840945
GUCACGUGCCGGCGGCUGACGAAAAACAAUUCCA-GCGAGUGCCAACAUUCAGCUGUGGCAUGCCU------CAAACUAGA--GGU----------
....(((((((.(((((((.........((((..-..))))........))))))))))))))(((------(......))--)).---------- ( -26.63, z-score =  -1.76, R)
>droPer1.super_22 326317 85 + 1688296
GUCACGUGCCGCUGGCUGACGAAAAACAAUUCCA-GCGAGUGCCAACAUU---UUGUGGCAUGCCU-----CCACGCUCCA--GAAUACUAGACGA
(((..(..(((((((.((........))...)))-))).)..)....(((---(((..((.((...-----.)).))..))--))))....))).. ( -24.20, z-score =  -1.37, R)
>droMoj3.scaffold_6500 24884087 92 + 32352404
----GGCGUGGCUGGGGGACAAAAGCUGACAGAGCACAUGGGUCAUCAAUUUGCUGCACGUUGGCUGAAACUCAGACUCAAACUCAAAUUCGAAUU
----...((((((.(....)...)))).)).(((....((((((........(((.......)))((.....))))))))..)))........... ( -18.40, z-score =   1.20, R)
>consensus
GUCACGUGCCAGCGGCUGACGGAAAACAAUUCCA_GCGAGUGCCAACAUUCAGCUGUGGCAUGCCU______CAAACUCAAACGCAAACUAGAAGU
....(((((((.(((((((.........((((.....))))........))))))))))))))................................. (-15.39 = -15.60 +   0.21)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,176,378 – 10,176,478
Length 100
Sequences 7
Columns 106
Reading direction forward
Mean pairwise identity 81.32
Shannon entropy 0.37064
G+C content 0.50259
Mean single sequence MFE -28.91
Consensus MFE -23.58
Energy contribution -24.10
Covariance contribution 0.52
Combinations/Pair 1.26
Mean z-score -0.84
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.565657
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10176378 100 + 22422827
UUGAGGCAUGCCACAGCUGAAUGUUGGCACUCGCUGGAAUUGUUUUCCGUCAGCCGCUGGCACGUGACUUUCGUCAUUCACUUGAUGGCAUUUCAUUUCA------
....((.(((((((((.((((((.(((.(.((((.((((.....))))(((((...)))))..)))).).))).)))))).))).)))))).))......------ ( -31.60, z-score =  -1.36, R)
>droSim1.chrX_random 550644 100 + 5698898
UUGAGGCAUGCCACAGCUGAAUGUUGGCACUCGCUGGAAUUGUUUUCCGUCAGCCGCUGGCACGUGACUUUCGUCAUUCACUUGAUGGCAUUUCAUUUCA------
....((.(((((((((.((((((.(((.(.((((.((((.....))))(((((...)))))..)))).).))).)))))).))).)))))).))......------ ( -31.60, z-score =  -1.36, R)
>droSec1.super_15 879209 100 + 1954846
UUGAGGCAUGCCACAGCUGAAUGUUGGCACUCGCUGGAAUUGUUUUCCGUCAGCCGCUGGCACGUGACUUUCGUCAUUCACUUGAUGGCAUUUCAUUUCA------
....((.(((((((((.((((((.(((.(.((((.((((.....))))(((((...)))))..)))).).))).)))))).))).)))))).))......------ ( -31.60, z-score =  -1.36, R)
>droYak2.chrX 18749555 106 + 21770863
UUGAGGCAUGCCACAGCUGAAUGUUGGCACUCGCUGGAAUUGUUUUCCGUCAGCCGCUGGCACGUGACUUUCGUCAUUCACUUGAUGGCAUUUCAUUUCAUUCAGA
....((.(((((((((.((((((.(((.(.((((.((((.....))))(((((...)))))..)))).).))).)))))).))).)))))).))............ ( -31.60, z-score =  -0.92, R)
>droEre2.scaffold_4690 13796159 100 - 18748788
UUGAGGCAUGCCACAGCUGAAUGUUGGCACUCGCUGGAAUUGUUUUCCGUCAGCCGCUGGCACGUGACUUUCGUCAUUCACUUGAUGGCAUUUCAUUCCA------
....((.(((((((((.((((((.(((.(.((((.((((.....))))(((((...)))))..)))).).))).)))))).))).)))))).))......------ ( -31.60, z-score =  -1.22, R)
>droAna3.scaffold_13248 1271665 96 - 4840945
----GGCAUGCCACAGCUGAAUGUUGGCACUCGCUGGAAUUGUUUUUCGUCAGCCGCCGGCACGUGACUUUCGUCAUUCACUUGAUGGCAUUUCAUUUCA------
----((.(((((((((.(((.(((((((....(((((((......)))..)))).))))))).(((((....)))))))).))).)))))).))......------ ( -31.10, z-score =  -1.88, R)
>droMoj3.scaffold_6500 24884114 97 - 32352404
UUCAGCCAACGUGCAGCAAAUUGAUG--ACCCAUGUGCUCUGUCAGCUUUUGUCCCCCAGC-CACGCCUCUCGCCCCAUUAUAGCUCGCAGUCCGAGUGC------
...(((..(((.(.((((...((...--...))..))))))))..))).............-.....................(((((.....)))))..------ ( -13.30, z-score =   2.19, R)
>consensus
UUGAGGCAUGCCACAGCUGAAUGUUGGCACUCGCUGGAAUUGUUUUCCGUCAGCCGCUGGCACGUGACUUUCGUCAUUCACUUGAUGGCAUUUCAUUUCA______
....((.(((((((((.((((((.(((.(.((((.((((.....))))(((((...)))))..)))).).))).)))))).))).)))))).))............ (-23.58 = -24.10 +   0.52)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,176,378 – 10,176,478
Length 100
Sequences 7
Columns 106
Reading direction reverse
Mean pairwise identity 81.32
Shannon entropy 0.37064
G+C content 0.50259
Mean single sequence MFE -31.53
Consensus MFE -25.15
Energy contribution -25.30
Covariance contribution 0.15
Combinations/Pair 1.29
Mean z-score -1.75
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956084
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10176378 100 - 22422827
------UGAAAUGAAAUGCCAUCAAGUGAAUGACGAAAGUCACGUGCCAGCGGCUGACGGAAAACAAUUCCAGCGAGUGCCAACAUUCAGCUGUGGCAUGCCUCAA
------.....(((................((((....))))(((((((.(((((((.((((.....)))).((....))......))))))))))))))..))). ( -32.80, z-score =  -2.36, R)
>droSim1.chrX_random 550644 100 - 5698898
------UGAAAUGAAAUGCCAUCAAGUGAAUGACGAAAGUCACGUGCCAGCGGCUGACGGAAAACAAUUCCAGCGAGUGCCAACAUUCAGCUGUGGCAUGCCUCAA
------.....(((................((((....))))(((((((.(((((((.((((.....)))).((....))......))))))))))))))..))). ( -32.80, z-score =  -2.36, R)
>droSec1.super_15 879209 100 - 1954846
------UGAAAUGAAAUGCCAUCAAGUGAAUGACGAAAGUCACGUGCCAGCGGCUGACGGAAAACAAUUCCAGCGAGUGCCAACAUUCAGCUGUGGCAUGCCUCAA
------.....(((................((((....))))(((((((.(((((((.((((.....)))).((....))......))))))))))))))..))). ( -32.80, z-score =  -2.36, R)
>droYak2.chrX 18749555 106 - 21770863
UCUGAAUGAAAUGAAAUGCCAUCAAGUGAAUGACGAAAGUCACGUGCCAGCGGCUGACGGAAAACAAUUCCAGCGAGUGCCAACAUUCAGCUGUGGCAUGCCUCAA
...........(((................((((....))))(((((((.(((((((.((((.....)))).((....))......))))))))))))))..))). ( -32.80, z-score =  -1.95, R)
>droEre2.scaffold_4690 13796159 100 + 18748788
------UGGAAUGAAAUGCCAUCAAGUGAAUGACGAAAGUCACGUGCCAGCGGCUGACGGAAAACAAUUCCAGCGAGUGCCAACAUUCAGCUGUGGCAUGCCUCAA
------.((.....................((((....))))(((((((.(((((((.((((.....)))).((....))......)))))))))))))))).... ( -33.10, z-score =  -2.03, R)
>droAna3.scaffold_13248 1271665 96 + 4840945
------UGAAAUGAAAUGCCAUCAAGUGAAUGACGAAAGUCACGUGCCGGCGGCUGACGAAAAACAAUUCCAGCGAGUGCCAACAUUCAGCUGUGGCAUGCC----
------.........((((((....(((..((((....))))..)))((((.((((..(((......)))))))(((((....))))).))))))))))...---- ( -30.20, z-score =  -2.01, R)
>droMoj3.scaffold_6500 24884114 97 + 32352404
------GCACUCGGACUGCGAGCUAUAAUGGGGCGAGAGGCGUG-GCUGGGGGACAAAAGCUGACAGAGCACAUGGGU--CAUCAAUUUGCUGCACGUUGGCUGAA
------(((.......))).(((((...((.((((((..(.(((-(((.(....)....(((.....))).....)))--))))..)))))).))...)))))... ( -26.20, z-score =   0.83, R)
>consensus
______UGAAAUGAAAUGCCAUCAAGUGAAUGACGAAAGUCACGUGCCAGCGGCUGACGGAAAACAAUUCCAGCGAGUGCCAACAUUCAGCUGUGGCAUGCCUCAA
..............................((((....))))(((((((.(((((((.((((.....)))).....((....))..))))))))))))))...... (-25.15 = -25.30 +   0.15)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:30:44 2011