Locus 13309

Sequence ID dm3.chrX
Location 5,726,135 – 5,726,298
Length 163
Max. P 0.999191
window18312 window18313 window18314 window18315 window18316 window18317

overview

Window 2

Location 5,726,135 – 5,726,243
Length 108
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 75.00
Shannon entropy 0.43526
G+C content 0.59720
Mean single sequence MFE -44.84
Consensus MFE -36.42
Energy contribution -37.46
Covariance contribution 1.04
Combinations/Pair 1.15
Mean z-score -3.23
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.70
SVM RNA-class probability 0.999191
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5726135 108 + 22422827
--------UUUCCAUUGCUACUUUUGAUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACUACCUCCCG---AUUGGAAGUUCGCAUACUAACUGUAUGCGCUGCCGCCGGCGGCG
--------........(((................(((((.......))))).(((((((((((.((.....---...)).))).(((((((.....)))))))..)))))))).))). ( -43.90, z-score =  -4.59, R)
>droSim1.chrX 4465015 109 + 17042790
--------UUUCCGUUGCUACUUUUAUUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACCACACCCGAG--AUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCG
--------....((((((.................(((((.......)))))..((((((((..((.((((..--..)))).)).(((((((.....))))))).)))))))))))))) ( -50.20, z-score =  -4.73, R)
>droSec1.super_4 5139713 108 - 6179234
--------UUUCCGUUGCUACUUUUAUUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACCACACCCGA---AUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCG
--------....((((((.................(((((.......)))))..((((((((..((.((((.---..)))).)).(((((((.....))))))).)))))))))))))) ( -48.00, z-score =  -4.32, R)
>droYak2.chrX 19025693 113 - 21770863
UGUAUCCAU-UUCCAUGCUACUUUA-----CUUCACCGGGAUUCGAACCCGGACCGGCGGCACUACUCCGCUCCGUUUGGGAGCUCGGAGUCCAACCAACUGUGCUGCCGCCGGCGGCG
.........-......(((......-----.....(((((.......))))).(((((((((..((((((((((.....)))))..))))).((......))...))))))))).))). ( -44.50, z-score =  -2.63, R)
>droEre2.scaffold_4690 3074836 111 + 18748788
CGUGUCUGUGUUCCAUGCUACUUUUAC---UUUCACCGGGACUCGAACCCGGACCGGCGGCUCUACUCCG-----UGUGGGCAGUCGGAGCCUAACUACCUGGACUACCGCCGGCGGCG
................(((........---.....(((((.......))))).((((((((((((((((.-----....)).))).)))))).........((....))))))).))). ( -37.60, z-score =   0.13, R)
>consensus
________UUUCCCUUGCUACUUUUAUUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACUACACCCCA___AUUGGGAGUUCGCAUACUAACUGUAUGCGCUGCCGCCGGCGGCG
................(((................(((((.......))))).(((((((((.....(((........)))....(((((((.....))))))).))))))))).))). (-36.42 = -37.46 +   1.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,726,135 – 5,726,243
Length 108
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 75.00
Shannon entropy 0.43526
G+C content 0.59720
Mean single sequence MFE -48.00
Consensus MFE -39.52
Energy contribution -39.44
Covariance contribution -0.08
Combinations/Pair 1.28
Mean z-score -2.99
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.51
SVM RNA-class probability 0.998826
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5726135 108 - 22422827
CGCCGCCGGCGGCAGCGCAUACAGUUAGUAUGCGAACUUCCAAU---CGGGAGGUAGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAUCAAAAGUAGCAAUGGAAA--------
((((((((((((((.(((((((.....))))))).((((((...---..))))))..))))))))))..(((.......)))))))..(((((.....)))))........-------- ( -50.70, z-score =  -4.95, R)
>droSim1.chrX 4465015 109 - 17042790
CGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAU--CUCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAUAAAAGUAGCAACGGAAA--------
..((((((((((((.(((((((.....))))))..((.((((..--..)))).))).))))))))))(((((.......)))))....((((.......))))...))...-------- ( -51.50, z-score =  -3.70, R)
>droSec1.super_4 5139713 108 + 6179234
CGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAU---UCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAUAAAAGUAGCAACGGAAA--------
..((((((((((((.(((((((.....))))))..((.((((..---.)))).))).))))))))))(((((.......)))))....((((.......))))...))...-------- ( -49.30, z-score =  -3.18, R)
>droYak2.chrX 19025693 113 + 21770863
CGCCGCCGGCGGCAGCACAGUUGGUUGGACUCCGAGCUCCCAAACGGAGCGGAGUAGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAG-----UAAAGUAGCAUGGAA-AUGGAUACA
((((((((((((((...(((....))).(((((..(((((.....))))))))))..))))))))))..(((.......)))))))...-----....(((.(((....-)))..))). ( -49.70, z-score =  -2.61, R)
>droEre2.scaffold_4690 3074836 111 - 18748788
CGCCGCCGGCGGUAGUCCAGGUAGUUAGGCUCCGACUGCCCACA-----CGGAGUAGAGCCGCCGGUCCGGGUUCGAGUCCCGGUGAAA---GUAAAAGUAGCAUGGAACACAGACACG
((((((((((((((.(((.(((((((.(....))))))))....-----.))).)...)))))))))..(((.......)))))))...---......((.(..((.....))..))). ( -38.80, z-score =  -0.53, R)
>consensus
CGCCGCCGGCGGCAGCGCAUACAGUUAGUAUGCGAACUCCCAAU___UCGGGAGUAGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAUAAAAGUAGCAACGGAAA________
.((.((((((((((.(((((((.....))))))).((.(((........))).))..))))))))))(((((.......))))).................))................ (-39.52 = -39.44 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,726,167 – 5,726,283
Length 116
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 78.55
Shannon entropy 0.38208
G+C content 0.62531
Mean single sequence MFE -45.51
Consensus MFE -31.68
Energy contribution -32.68
Covariance contribution 1.00
Combinations/Pair 1.27
Mean z-score -1.56
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.841055
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5726167 116 + 22422827
AUUCGAACCCGGACCGGCGGCACUACCUCCCG---AUUGGAAGUUCGCAUACUAACUGUAUGCGCUGCCGCCGGCGGCGAGGGGUCAGCUCCCAGGGGAUAAACUAGAACCACACCUGC
..(((...(((..(((((((((((.((.....---...)).))).(((((((.....)))))))..))))))))))))))((((....))))((((..................)))). ( -43.77, z-score =  -1.22, R)
>droSim1.chrX 4465047 117 + 17042790
AUUCGAACCCGGACCGGCGGCACCACACCCGAG--AUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCGAGGGGACUCGCUCCAAAGGAUAAACUAGAACCUCACCUCC
.(((......((((((((((((..((.((((..--..)))).)).(((((((.....))))))).)))))))))..(((((....))))))))..((......)).))).......... ( -51.60, z-score =  -3.49, R)
>droSec1.super_4 5139745 116 - 6179234
AUUCGAACCCGGACCGGCGGCACCACACCCGA---AUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCGAGGGGACUCGCUCCAAAGGAUAAACUAGAACCUCACCUCC
.(((......((((((((((((..((.((((.---..)))).)).(((((((.....))))))).)))))))))..(((((....))))))))..((......)).))).......... ( -49.40, z-score =  -3.12, R)
>droYak2.chrX 19025727 119 - 21770863
AUUCGAACCCGGACCGGCGGCACUACUCCGCUCCGUUUGGGAGCUCGGAGUCCAACCAACUGUGCUGCCGCCGGCGGCGAGGAGACAGCGUCCAGGAGCUCAACUAGAACCUCACCUGC
........((((..(((((((((.((((((((((.....)))))..)))))..........))))))))))))).((.((((((..(((........)))...))....)))).))... ( -46.10, z-score =  -0.56, R)
>droEre2.scaffold_4690 3074873 114 + 18748788
ACUCGAACCCGGACCGGCGGCUCUACUCCG-----UGUGGGCAGUCGGAGCCUAACUACCUGGACUACCGCCGGCGGCGAGGUGACAGCGUCCAACUGAUAAACUAGAGCCUCACCUAC
...........(.((((((((((((((((.-----....)).))).)))))).........((....))))))))((.(((((...((.(((.....)))...))...))))).))... ( -36.70, z-score =   0.58, R)
>consensus
AUUCGAACCCGGACCGGCGGCACUACACCCCA___AUUGGGAGUUCGCAUACUAACUGUAUGCGCUGCCGCCGGCGGCGAGGGGACAGCCUCCAAAGGAUAAACUAGAACCUCACCUCC
.(((...((((..(((((((((.....(((........)))....(((((((.....))))))).)))))))))))).).((((.....)))).............))).......... (-31.68 = -32.68 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,726,167 – 5,726,283
Length 116
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 78.55
Shannon entropy 0.38208
G+C content 0.62531
Mean single sequence MFE -52.44
Consensus MFE -42.25
Energy contribution -42.29
Covariance contribution 0.04
Combinations/Pair 1.31
Mean z-score -2.01
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.13
SVM RNA-class probability 0.983237
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5726167 116 - 22422827
GCAGGUGUGGUUCUAGUUUAUCCCCUGGGAGCUGACCCCUCGCCGCCGGCGGCAGCGCAUACAGUUAGUAUGCGAACUUCCAAU---CGGGAGGUAGUGCCGCCGGUCCGGGUUCGAAU
...((((.((...((((...(((....)))))))...)).))))((((((((((.(((((((.....))))))).((((((...---..))))))..))))))))))............ ( -52.90, z-score =  -2.67, R)
>droSim1.chrX 4465047 117 - 17042790
GGAGGUGAGGUUCUAGUUUAUCCUUUGGAGCGAGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAU--CUCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAU
((((((((((..((.((((........)))).))...))))))).(((((((((.(((((((.....))))))..((.((((..--..)))).))).)))))))))))).......... ( -58.00, z-score =  -3.44, R)
>droSec1.super_4 5139745 116 + 6179234
GGAGGUGAGGUUCUAGUUUAUCCUUUGGAGCGAGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAU---UCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAU
((((((((((..((.((((........)))).))...))))))).(((((((((.(((((((.....))))))..((.((((..---.)))).))).)))))))))))).......... ( -55.80, z-score =  -3.03, R)
>droYak2.chrX 19025727 119 + 21770863
GCAGGUGAGGUUCUAGUUGAGCUCCUGGACGCUGUCUCCUCGCCGCCGGCGGCAGCACAGUUGGUUGGACUCCGAGCUCCCAAACGGAGCGGAGUAGUGCCGCCGGUCCGGGUUCGAAU
...(((((((..(..(((.((...)).)))...)...)))))))((((((((((...(((....))).(((((..(((((.....))))))))))..))))))))))............ ( -51.30, z-score =  -0.54, R)
>droEre2.scaffold_4690 3074873 114 - 18748788
GUAGGUGAGGCUCUAGUUUAUCAGUUGGACGCUGUCACCUCGCCGCCGGCGGUAGUCCAGGUAGUUAGGCUCCGACUGCCCACA-----CGGAGUAGAGCCGCCGGUCCGGGUUCGAGU
(.((((((((((((((........))))).))).)))))))(((((((((((((.(((.(((((((.(....))))))))....-----.))).)...)))))))))...)))...... ( -44.20, z-score =  -0.38, R)
>consensus
GCAGGUGAGGUUCUAGUUUAUCCCUUGGACGCUGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGUUAGUAUGCGAACUCCCAAU___UCGGGAGUAGUGCCGCCGGUCCGGGUUCGAAU
...(((((((((((((........)))))).......)))))))((((((((((.(((((((.....))))))).((.(((........))).))..))))))))))............ (-42.25 = -42.29 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,726,182 – 5,726,298
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.11
Shannon entropy 0.49175
G+C content 0.59738
Mean single sequence MFE -42.53
Consensus MFE -21.95
Energy contribution -22.91
Covariance contribution 0.96
Combinations/Pair 1.36
Mean z-score -1.31
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.587794
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5726182 116 + 22422827
---GGCGGCACUACCUCCCG-AUUGGAAGUUCGCAUACUAACUGUAUGCGCUGCCGCCGGCGGCGAGGGGUCAGCUCCCAGGGGAUAAACUAGAACCACACCUGCUUCGAUUGACAGAUU
---(((((((((.((.....-...)).))).(((((((.....)))))))..))))))(((((....((.((((.(((....)))....)).)).))....))))).............. ( -38.50, z-score =  -0.43, R)
>droSim1.chrX 4465062 117 + 17042790
---GGCGGCACCACACCCGAGAUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCGAGGGGACUCGCUCCAAAGGAUAAACUAGAACCUCACCUCCUUCGAUUGACAGAGU
---(((((((..((.((((....)))).)).(((((((.....))))))).)))))))((.((((((....)))))))).(((((.................)))))............. ( -48.73, z-score =  -2.97, R)
>droSec1.super_4 5139760 116 - 6179234
---GGCGGCACCACACCCGA-AUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCGAGGGGACUCGCUCCAAAGGAUAAACUAGAACCUCACCUCCUUCGAUUGACAGAGU
---(((((((..((.((((.-..)))).)).(((((((.....))))))).)))))))((.((((((....)))))))).(((((.................)))))............. ( -46.53, z-score =  -2.58, R)
>droYak2.chrX 19025742 119 - 21770863
GGCGGCACUACUCCGCUCCG-UUUGGGAGCUCGGAGUCCAACCAACUGUGCUGCCGCCGGCGGCGAGGAGACAGCGUCCAGGAGCUCAACUAGAACCUCACCUGCUUCGAUUGCCACAAA
((((((((.((((((((((.-....)))))..)))))..........))))))))...((((((((((...(((.((..(((..((.....))..))).)))))))))).)))))..... ( -45.70, z-score =  -1.01, R)
>droEre2.scaffold_4690 3074888 106 + 18748788
-----GGCGGCUCUACUCCG-UGUGGGCAGUCGGAGCCUAACUACCUGGACUACCGCCGGCGGCGAGGUGACAGCGUCCAACUGAUAAACUAGAGCCUCACCUACUUCGAUU--------
-----((((((((((((((.-....)).))).))))))........(((((...((((...)))).(....)...)))))..............)))...............-------- ( -33.20, z-score =   0.45, R)
>consensus
___GGCGGCACUACACCCCG_AUUGGGAGUUCGCAUACUAACUGUAUGCGCUGCCGCCGGCGGCGAGGGGACAGCCUCCAAAGGAUAAACUAGAACCUCACCUCCUUCGAUUGACAGAGU
...(((((((..((.(((......))).)).(((((((.....))))))).)))))))...((.((((...........................)))).)).................. (-21.95 = -22.91 +   0.96)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,726,182 – 5,726,298
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.11
Shannon entropy 0.49175
G+C content 0.59738
Mean single sequence MFE -46.78
Consensus MFE -28.23
Energy contribution -29.39
Covariance contribution 1.16
Combinations/Pair 1.34
Mean z-score -1.77
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.69
SVM RNA-class probability 0.960867
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5726182 116 - 22422827
AAUCUGUCAAUCGAAGCAGGUGUGGUUCUAGUUUAUCCCCUGGGAGCUGACCCCUCGCCGCCGGCGGCAGCGCAUACAGUUAGUAUGCGAACUUCCAAU-CGGGAGGUAGUGCCGCC---
.((((((........))))))(((((....(((..(((....)))...))).....))))).(((((((.(((((((.....))))))).((((((...-..))))))..)))))))--- ( -46.90, z-score =  -2.48, R)
>droSim1.chrX 4465062 117 - 17042790
ACUCUGUCAAUCGAAGGAGGUGAGGUUCUAGUUUAUCCUUUGGAGCGAGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAUCUCGGGUGUGGUGCCGCC---
...............((.(((((((..((.((((........)))).))...))))))).))(((((((.(((((((.....))))))..((.((((....)))).))).)))))))--- ( -51.90, z-score =  -2.93, R)
>droSec1.super_4 5139760 116 + 6179234
ACUCUGUCAAUCGAAGGAGGUGAGGUUCUAGUUUAUCCUUUGGAGCGAGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAU-UCGGGUGUGGUGCCGCC---
...............((.(((((((..((.((((........)))).))...))))))).))(((((((.(((((((.....))))))..((.((((..-.)))).))).)))))))--- ( -49.70, z-score =  -2.49, R)
>droYak2.chrX 19025742 119 + 21770863
UUUGUGGCAAUCGAAGCAGGUGAGGUUCUAGUUGAGCUCCUGGACGCUGUCUCCUCGCCGCCGGCGGCAGCACAGUUGGUUGGACUCCGAGCUCCCAAA-CGGAGCGGAGUAGUGCCGCC
...(((((((((((..((((...(((((.....)))))))))...((((((.((........)).))))))....))))))..(((((..(((((....-.))))))))))...))))). ( -47.70, z-score =  -0.37, R)
>droEre2.scaffold_4690 3074888 106 - 18748788
--------AAUCGAAGUAGGUGAGGCUCUAGUUUAUCAGUUGGACGCUGUCACCUCGCCGCCGGCGGUAGUCCAGGUAGUUAGGCUCCGACUGCCCACA-CGGAGUAGAGCCGCC-----
--------..........(((..(((((((.((..(((((((((.(((..(((((.((((....)))).....)))).)...))))))))))).....)-..)).))))))))))----- ( -37.70, z-score =  -0.59, R)
>consensus
ACUCUGUCAAUCGAAGCAGGUGAGGUUCUAGUUUAUCCCUUGGACGCUGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGUUAGUAUGCGAACUCCCAAU_CGGGGUGUAGUGCCGCC___
..................(((((((((((((........)))))).......)))))))...(((((((.(((((((.....))))))).((.(((......))).))..)))))))... (-28.23 = -29.39 +   1.16)

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 01:18:51 2011