Locus 12872

Sequence ID dm3.chrX
Location 2,868,407 – 2,868,645
Length 238
Max. P 0.980831
window17696 window17697 window17698 window17699

overview

Window 6

Location 2,868,407 – 2,868,525
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Shannon entropy 0.11106
G+C content 0.47120
Mean single sequence MFE -33.14
Consensus MFE -30.16
Energy contribution -30.04
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.34
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.614542
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2868407 118 + 22422827
CAGAUUGAGAUAAAGUAGGAGAAUUGGCCGUCAAGAGGUCAAUGCUGUCGGGACAGCAGCUGUUCACCA--AUCUCUCCUCCUUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAU
..(..((.((..(((.(((((((((((((.......)))))))(((((....)))))............--...)))))).)))..)).))..)....((((.((......)).)))).. ( -32.70, z-score =  -1.08, R)
>droSim1.chrX 2010822 120 + 17042790
CAGAUUGAGAUAAAGUAGGAGAAUUGGCCGUCAAGAGGUCAAUGCUGUCGGGACAGCAGCUGUUCACCAGCAUCUCUCCUCCUUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAU
..(..((.((..(((.(((((((((((((.......)))))))((((...((((((...))))))..))))...)))))).)))..)).))..)....((((.((......)).)))).. ( -37.20, z-score =  -2.08, R)
>droSec1.super_10 2609631 120 + 3036183
CAGAUUGAGAUAAAGUAGGAGAAUUGGCCGUCAAGAGGUCAAUGCUGUCGGGACAGCAGCUGUUCACCACCAGCUCUCCUCUUUUUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAU
......((((.((((.(((((((((((((.......)))))))(((((....))))).((((........))))))))))))))))))..........((((.((......)).)))).. ( -36.60, z-score =  -2.06, R)
>droYak2.chrX 16276351 117 - 21770863
CAGAUUAAGAUAAAGUAGGAGAAUUGGCCGUCAAGAGGUCAAUGCUGUCGGGACAGCAGCUGUUCACUAU---CUCUCCUCCUUCCUCGCACCCACAAUUCUUCUCAUUUUGGUAGAAAU
........((..(((.(((((((((((((.......)))))))(((((....))))).............---.)))))).)))..))..........((((.((......)).)))).. ( -29.20, z-score =  -0.57, R)
>droEre2.scaffold_4690 293755 117 + 18748788
CAGAUUGAGAUAAAGUAGGAGAAUUGGCCGUCAAGAGGUCAAUGCUGUCGGUACAGCAGCUGUUCUCCAU---UUCUCCUCCCUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAU
.(((..(((...((((.((((((((((((.......))))).((((((....))))))...)))))))))---))...)))..)))............((((.((......)).)))).. ( -30.00, z-score =  -0.93, R)
>consensus
CAGAUUGAGAUAAAGUAGGAGAAUUGGCCGUCAAGAGGUCAAUGCUGUCGGGACAGCAGCUGUUCACCAU_A_CUCUCCUCCUUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAU
........((..(((.(((((((((((((.......)))))))(((((....))))).................)))))).)))..))..........((((.((......)).)))).. (-30.16 = -30.04 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,868,485 – 2,868,605
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.25
Shannon entropy 0.10374
G+C content 0.46969
Mean single sequence MFE -38.47
Consensus MFE -33.95
Energy contribution -36.03
Covariance contribution 2.08
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.47
SVM RNA-class probability 0.941192
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2868485 120 + 22422827
CCUUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAUCUGCAGUCUUUCUUCCGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUACAGAGCAAUUUGAGUA
((((((..(((.......((((.((......)).)))).((..(((((........)))))..)).))).))))))(((.((.((((.(((.....))))))).)).))).......... ( -39.00, z-score =  -2.69, R)
>droSim1.chrX 2010902 120 + 17042790
CCUUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAUCUGCAGUCUUUCUUCGGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCCGAGCAAUUUGAGUA
((((((..(((.(((((((((...........((((....))))...........)))))))))..))).))))))(((..((((((.(((.....)))))))))..))).......... ( -41.15, z-score =  -2.92, R)
>droSec1.super_10 2609711 117 + 3036183
CUUUUUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAUCU---GUCUUUCUUCGGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCAGAGCAAUUUGAGUA
((((((..(((.((((((((((.((......)).)))).(((---(........))))))))))..))).))))))(((.(((((((.(((.....)))))))))).))).......... ( -38.20, z-score =  -2.58, R)
>droYak2.chrX 16276428 119 - 21770863
CCUUCCUCGCACCCACAAUUCUUCUCAUUUUGGUAGAAAUCUGCAGUCUUUCUUCGGAUUGUGGACUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUGCAG-GCAAUUUGAGUA
....(((.((...((((.(((((((......(((((...((..((((((......))))))..)))))))))))))).)))).((((.(((.....)))))))))))-)........... ( -37.70, z-score =  -1.44, R)
>droEre2.scaffold_4690 293832 120 + 18748788
CCCUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAUCUGCAGUCUUUCUUCGGUUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCCGACCAAUUUGAGUA
.(((((((((((((....((((.((......)).)))).((((((.(((..(....).....))).)).)))).))).))))))))).).((..(((((.......)))))...)).... ( -36.30, z-score =  -1.85, R)
>consensus
CCUUCUUCGCACCCACAAUUCUUCCCGUUUUGGUAGAAAUCUGCAGUCUUUCUUCGGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCAGAGCAAUUUGAGUA
((((((..(((.(((((((((...........((((....))))...........)))))))))..))).))))))(((.(((((((.(((.....)))))))))).))).......... (-33.95 = -36.03 +   2.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,868,485 – 2,868,605
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.25
Shannon entropy 0.10374
G+C content 0.46969
Mean single sequence MFE -35.03
Consensus MFE -30.94
Energy contribution -32.82
Covariance contribution 1.88
Combinations/Pair 1.05
Mean z-score -1.75
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.61
SVM RNA-class probability 0.760386
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2868485 120 - 22422827
UACUCAAAUUGCUCUGUAGAGGACCAUAUGUCGCUCUUCACAGCCCUUCUGGCAUUCCACAAUCGGAAGAAAGACUGCAGAUUUCUACCAAAACGGGAAGAAUUGUGGGUGCGAAGAAGG
..........(((.((.(((((((.....))).)))).)).)))((((((.((((.((((((((....))............((((.((......)).))))))))))))))..)))))) ( -38.50, z-score =  -2.57, R)
>droSim1.chrX 2010902 120 - 17042790
UACUCAAAUUGCUCGGAAGAGGACCAUAUGUCGCUCUUCACAGCCCUUCUGGCAUUCCACAAUCCGAAGAAAGACUGCAGAUUUCUACCAAAACGGGAAGAAUUGUGGGUGCGAAGAAGG
..........(((..(((((((((.....))).))))))..)))((((((.((((.(((((((.(..(((((.........))))).((.....))...).)))))))))))..)))))) ( -38.00, z-score =  -2.50, R)
>droSec1.super_10 2609711 117 - 3036183
UACUCAAAUUGCUCUGAAGAGGACCAUAUGUCGCUCUUCACAGCCCUUCUGGCAUUCCACAAUCCGAAGAAAGAC---AGAUUUCUACCAAAACGGGAAGAAUUGUGGGUGCGAAAAAAG
...((.....(((.((((((((((.....))).))))))).))).......((((.(((((((.(..(((((...---...))))).((.....))...).)))))))))))))...... ( -33.80, z-score =  -2.54, R)
>droYak2.chrX 16276428 119 + 21770863
UACUCAAAUUGC-CUGCAGAGGACCAUAUGUCGCUCUUCACAGCCCUUCUGGCAGUCCACAAUCCGAAGAAAGACUGCAGAUUUCUACCAAAAUGAGAAGAAUUGUGGGUGCGAGGAAGG
...........(-(((((((((((.....))).)))(((((((..(((((.((((((...............))))))((....)).........)))))..)))))))))).))).... ( -29.76, z-score =   0.08, R)
>droEre2.scaffold_4690 293832 120 - 18748788
UACUCAAAUUGGUCGGAAGAGGACCAUAUGUCGCUCUUCACAGCCCUUCUGGCAUUCCACAAACCGAAGAAAGACUGCAGAUUUCUACCAAAACGGGAAGAAUUGUGGGUGCGAAGAGGG
..........(((.((((((((((.....))).)))))).).)))(((((.((((.((((((.....(((((.........))))).((.....))......))))))))))..))))). ( -35.10, z-score =  -1.24, R)
>consensus
UACUCAAAUUGCUCUGAAGAGGACCAUAUGUCGCUCUUCACAGCCCUUCUGGCAUUCCACAAUCCGAAGAAAGACUGCAGAUUUCUACCAAAACGGGAAGAAUUGUGGGUGCGAAGAAGG
..........(((.((((((((((.....))).))))))).)))((((((.(((.((((((((.(..(((((.........))))).((......))..).)))))))))))..)))))) (-30.94 = -32.82 +   1.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,868,525 – 2,868,645
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.58
Shannon entropy 0.13468
G+C content 0.46470
Mean single sequence MFE -41.68
Consensus MFE -32.20
Energy contribution -33.76
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -3.13
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.06
SVM RNA-class probability 0.980831
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2868525 120 + 22422827
CUGCAGUCUUUCUUCCGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUACAGAGCAAUUUGAGUAAAAAGUCCAAAUCUGUGGCUUGACAAAACGGCGGAAAUCC
(..(((((........)))))..)..((((.(((..(((.((.((((.(((.....))))))).)).)))..)))..((...(((((((....)).))))).)).....))))....... ( -35.90, z-score =  -1.58, R)
>droSim1.chrX 2010942 120 + 17042790
CUGCAGUCUUUCUUCGGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCCGAGCAAUUUGAGUAAAAAGACCAAAUCUGUGGCUUGACAAAACGGAGGAAGUCC
.....(.(((((((((..((((.((..((((..((((((..((((((.(((.....)))))))))..)))..((((.((......))))))))).)))))).))))..))))))))).). ( -40.60, z-score =  -2.55, R)
>droSec1.super_10 2609751 117 + 3036183
---CUGUCUUUCUUCGGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCAGAGCAAUUUGAGUAAAAAGUUCAAAUCUGUGGCUUGACAAAACGGAGGAAGUCC
---..(.(((((((((..((((.((..((((..((((((.(((((((.(((.....)))))))))).)))..((((((.......))))))))).)))))).))))..))))))))).). ( -45.50, z-score =  -4.52, R)
>droYak2.chrX 16276468 119 - 21770863
CUGCAGUCUUUCUUCGGAUUGUGGACUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUGCAG-GCAAUUUGAGUAAAAAGUCUAAAUCUUUGGCUUGACAAAACGAAGGAAGUCC
.....(.(((((((((((((.((((((((((((..(.((((..((((.(((.....)))))))))))-.)..)))).))....))))))))))((((......)))).))))))))).). ( -38.20, z-score =  -1.96, R)
>droEre2.scaffold_4690 293872 120 + 18748788
CUGCAGUCUUUCUUCGGUUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCCGACCAAUUUGAGUAAAAACUCGAAAUCUCUGGCUUGACAAAACGAAGGAAGUCC
.....(.(((((((((.(((((.((..((((((..((.((.((((((.(((.....))))))))))).))..(((((((....)))))))...)))))))).))))).))))))))).). ( -48.20, z-score =  -5.02, R)
>consensus
CUGCAGUCUUUCUUCGGAUUGUGGAAUGCCAGAAGGGCUGUGAAGAGCGACAUAUGGUCCUCUUCAGAGCAAUUUGAGUAAAAAGUCCAAAUCUGUGGCUUGACAAAACGGAGGAAGUCC
.....(.(((((((((..((((.((..(((((((..(((.(((((((.(((.....)))))))))).)))..)))((..............))..)))))).))))..))))))))).). (-32.20 = -33.76 +   1.56)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:10:25 2011