Locus 13304

Sequence ID dm3.chrX
Location 5,717,442 – 5,717,584
Length 142
Max. P 0.936604
window18304 window18305 window18306 window18307

overview

Window 4

Location 5,717,442 – 5,717,547
Length 105
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 70.80
Shannon entropy 0.52928
G+C content 0.42736
Mean single sequence MFE -28.55
Consensus MFE -16.67
Energy contribution -16.37
Covariance contribution -0.30
Combinations/Pair 1.45
Mean z-score -1.47
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.36
SVM RNA-class probability 0.930706
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5717442 105 + 22422827
--GAAAUGGGGAAAAUGCGUCAGUUAGUCGAGUUGAGGUGUGUUGACACAUCGUUUAGGCCAAUUUGCGAAUUUU------GUUGCAAAUCUGCCAGAGACUUCAUUUUCCAA
--.......((((((((.(((...............((((((....)))))).....(((..((((((((.....------.))))))))..)))...)))..)))))))).. ( -33.50, z-score =  -2.70, R)
>droEre2.scaffold_4690 3066281 103 + 18748788
---AAAAUGGCUAAAUGCGUCAGUUGGC-----UGAGGUGUGUUGACACUUCGUUUAGGCCAAUUUGCGACUUUCUGUUGGCUUGCAAAUCUGCCCAGGACUUCAU--UCCAA
---....(((...(((((((.(((((((-----((((((((....))))))).....)))))))).)))...(((((..(((..........))))))))...)))--)))). ( -29.40, z-score =  -0.83, R)
>droYak2.chrX 19015697 99 - 21770863
---AAAUGCGAAAAGUGCGUCAGUUAGU-----UGAGGUGUGUUGACACAUCGUUUAGGCCAAUUUGCAAAUUUU------CUUGCAAAUCUGCCAGAGACUUUAUGCUCCAA
---....(((.(((((.(.((.......-----...((((((....)))))).....(((..((((((((.....------.))))))))..))).)))))))).)))..... ( -28.00, z-score =  -1.88, R)
>droSec1.super_4 5131171 100 - 6179234
--GAAAUGGGGAAAAUAUGUCAGUUAGU-----UGAGGUGUGUUGACACAUCGUUUAGGCCAAUUUGCGAGUUUU------GUUGCAAAUCUGCCAGAGACUUCAUAUUCCAA
--.......(((..(((((..((((...-----...((((((....)))))).....(((..((((((((.....------.))))))))..)))...)))).)))))))).. ( -28.60, z-score =  -2.10, R)
>droSim1.chrX 4456271 100 + 17042790
--GAAAUGGGGAAAAUGCGUCAGUUAGU-----UGAGGUGUGUUGACACAUCGUUUAGGCCAAUUUGCGAAUUUU------GUUGCAAAUCUGCCAGAGACUUCAUAUUCCAA
--.......((((.(((.(((.......-----...((((((....)))))).....(((..((((((((.....------.))))))))..)))...)))..))).)))).. ( -30.00, z-score =  -2.24, R)
>dp4.chrXL_group1a 7059313 99 - 9151740
CAUAGCCAGAAACAGAGUGUAGGACUGC-----AGGAAUGUGCUGACGCGUCGUUUGGGACAAUCAGGGUUAAUC----GGAGUUCGAUUCCUUAAGGACUCUUACAA-----
..(((((.........((((((.((...-----......)).)).))))(((......)))......)))))...----(((((((..........))))))).....----- ( -21.80, z-score =   0.91, R)
>consensus
__GAAAUGGGGAAAAUGCGUCAGUUAGU_____UGAGGUGUGUUGACACAUCGUUUAGGCCAAUUUGCGAAUUUU______GUUGCAAAUCUGCCAGAGACUUCAUAUUCCAA
..................(((...............((((((....)))))).....(((..((((((((............))))))))..)))...)))............ (-16.67 = -16.37 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,717,442 – 5,717,547
Length 105
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 70.80
Shannon entropy 0.52928
G+C content 0.42736
Mean single sequence MFE -23.31
Consensus MFE -11.79
Energy contribution -13.12
Covariance contribution 1.34
Combinations/Pair 1.21
Mean z-score -1.77
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.936604
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5717442 105 - 22422827
UUGGAAAAUGAAGUCUCUGGCAGAUUUGCAAC------AAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAACUCGACUAACUGACGCAUUUUCCCCAUUUC--
..((((((((..(((...(((.(((((((...------.......))))))).))).....((.((((....)))).)).............))).)))))))).......-- ( -27.70, z-score =  -3.47, R)
>droEre2.scaffold_4690 3066281 103 - 18748788
UUGGA--AUGAAGUCCUGGGCAGAUUUGCAAGCCAACAGAAAGUCGCAAAUUGGCCUAAACGAAGUGUCAACACACCUCA-----GCCAACUGACGCAUUUAGCCAUUUU---
..(((--(((..(((.(((((.(((((((................))))))).)))))...((.((((....)))).)).-----.......)))((.....))))))))--- ( -23.09, z-score =  -0.06, R)
>droYak2.chrX 19015697 99 + 21770863
UUGGAGCAUAAAGUCUCUGGCAGAUUUGCAAG------AAAAUUUGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCA-----ACUAACUGACGCACUUUUCGCAUUU---
.....((..(((((....(((.((((((((((------....)))))))))).)))........((((((..........-----......)))))))))))..))....--- ( -25.29, z-score =  -2.17, R)
>droSec1.super_4 5131171 100 + 6179234
UUGGAAUAUGAAGUCUCUGGCAGAUUUGCAAC------AAAACUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCA-----ACUAACUGACAUAUUUUCCCCAUUUC--
..((((((((.(((....(((.(((((((...------.......))))))).))).....((.((((....)))).)).-----....)))..)))))..))).......-- ( -21.90, z-score =  -2.35, R)
>droSim1.chrX 4456271 100 - 17042790
UUGGAAUAUGAAGUCUCUGGCAGAUUUGCAAC------AAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCA-----ACUAACUGACGCAUUUUCCCCAUUUC--
..((((.(((..(((...(((.(((((((...------.......))))))).))).....((.((((....)))).)).-----.......))).))).)))).......-- ( -24.40, z-score =  -2.72, R)
>dp4.chrXL_group1a 7059313 99 + 9151740
-----UUGUAAGAGUCCUUAAGGAAUCGAACUCC----GAUUAACCCUGAUUGUCCCAAACGACGCGUCAGCACAUUCCU-----GCAGUCCUACACUCUGUUUCUGGCUAUG
-----.......((((....((((((((.....)----))......(((((((((......)))).)))))....)))))-----((((.........))))....))))... ( -17.50, z-score =   0.14, R)
>consensus
UUGGAAUAUGAAGUCUCUGGCAGAUUUGCAAC______AAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCA_____ACUAACUGACGCAUUUUCCCCAUUUC__
..................(((.(((((((................))))))).))).....(((((((((.....................)))))))))............. (-11.79 = -13.12 +   1.34)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,717,480 – 5,717,584
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 87.54
Shannon entropy 0.20228
G+C content 0.37736
Mean single sequence MFE -22.28
Consensus MFE -16.99
Energy contribution -17.55
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.71
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.531437
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5717480 104 + 22422827
UGUUGACACAUCGUUUAGGCCAAUUUGCGAAUUUUGUUGCAAAUCUGCCAGAGACUUCAUUUUCCAAAAGUCUUGCAUAUGAGAACUUGAUUUCCUUUUCAACA
.(((((....((((...(((..((((((((......))))))))..))).(((((((..........)))))))....))))(((......)))....))))). ( -23.20, z-score =  -1.57, R)
>droYak2.chrX 19015729 92 - 21770863
UGUUGACACAUCGUUUAGGCCAAUUUGCAAAUUUUCUUGCAAAUCUGCCAGAGACUUUAUGCUCCAAAAAUGC------------CUUGAUUUUCUUUGCAACA
.((((.((.........(((..((((((((......))))))))..)))(((((.((...((.........))------------...)).))))).)))))). ( -20.60, z-score =  -1.78, R)
>droSec1.super_4 5131204 102 - 6179234
UGUUGACACAUCGUUUAGGCCAAUUUGCGAGUUUUGUUGCAAAUCUGCCAGAGACUUCAUAUUCCAAAAGUCCAGCAUAUGA--ACUUGAUUUCCUUCUCAACA
.(((((......((((((((..((((((((......))))))))..))).(.(((((..........))))))......)))--))..((......))))))). ( -22.60, z-score =  -1.56, R)
>droSim1.chrX 4456304 102 + 17042790
UGUUGACACAUCGUUUAGGCCAAUUUGCGAAUUUUGUUGCAAAUCUGCCAGAGACUUCAUAUUCCAAAAGUCCAGCAUAUGA--ACUUGAUUUCCUUCUCAACA
.(((((......((((((((..((((((((......))))))))..))).(.(((((..........))))))......)))--))..((......))))))). ( -22.70, z-score =  -1.93, R)
>consensus
UGUUGACACAUCGUUUAGGCCAAUUUGCGAAUUUUGUUGCAAAUCUGCCAGAGACUUCAUAUUCCAAAAGUCCAGCAUAUGA__ACUUGAUUUCCUUCUCAACA
.(((((...........(((..((((((((......))))))))..)))...(((((..........)))))..........................))))). (-16.99 = -17.55 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,717,480 – 5,717,584
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 87.54
Shannon entropy 0.20228
G+C content 0.37736
Mean single sequence MFE -24.73
Consensus MFE -21.56
Energy contribution -21.50
Covariance contribution -0.06
Combinations/Pair 1.12
Mean z-score -1.36
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.668355
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5717480 104 - 22422827
UGUUGAAAAGGAAAUCAAGUUCUCAUAUGCAAGACUUUUGGAAAAUGAAGUCUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACA
.(((((...((((......))))(((((.(.(((((((........)))))))..(((.(((((((..........))))))).))).....))))))))))). ( -25.30, z-score =  -1.63, R)
>droYak2.chrX 19015729 92 + 21770863
UGUUGCAAAGAAAAUCAAG------------GCAUUUUUGGAGCAUAAAGUCUCUGGCAGAUUUGCAAGAAAAUUUGCAAAUUGGCCUAAACGAUGUGUCAACA
.((((((......(((...------------........(((((.....).))))(((.((((((((((....)))))))))).))).....))).)).)))). ( -22.40, z-score =  -1.01, R)
>droSec1.super_4 5131204 102 + 6179234
UGUUGAGAAGGAAAUCAAGU--UCAUAUGCUGGACUUUUGGAAUAUGAAGUCUCUGGCAGAUUUGCAACAAAACUCGCAAAUUGGCCUAAACGAUGUGUCAACA
.(((((.(.....(((...(--((((((.(..(....)..).)))))))((....(((.(((((((..........))))))).)))...))))).).))))). ( -25.60, z-score =  -1.39, R)
>droSim1.chrX 4456304 102 - 17042790
UGUUGAGAAGGAAAUCAAGU--UCAUAUGCUGGACUUUUGGAAUAUGAAGUCUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACA
.(((((.(.....(((...(--((((((.(..(....)..).)))))))((....(((.(((((((..........))))))).)))...))))).).))))). ( -25.60, z-score =  -1.40, R)
>consensus
UGUUGAAAAGGAAAUCAAGU__UCAUAUGCUGGACUUUUGGAAUAUGAAGUCUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACA
.(((((.(.....(((...............(((((((........)))))))..(((.(((((((..........))))))).))).....))).).))))). (-21.56 = -21.50 +  -0.06)

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 01:18:43 2011