Locus 11250

Sequence ID dm3.chr3R
Location 19,760,077 – 19,760,242
Length 165
Max. P 0.999729
window15458 window15459

overview

Window 8

Location 19,760,077 – 19,760,242
Length 165
Sequences 5
Columns 184
Reading direction forward
Mean pairwise identity 67.30
Shannon entropy 0.56082
G+C content 0.44153
Mean single sequence MFE -48.58
Consensus MFE -20.98
Energy contribution -19.94
Covariance contribution -1.04
Combinations/Pair 1.35
Mean z-score -2.62
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.54
SVM RNA-class probability 0.992475
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19760077 165 + 27905053
CUACAUUAGGGUGGCUCGUUCCACCAGGAUGC-----GGAUCACAACUCCUAUGGA-GAU------CCAAAAUCCGCAAUUAACAUUCUUGUGAAAGGAAAGCGCUAUCGGAUAUAGAAUU---UUCAA----GUACCACCUUGGUAUCGCUGCGCGUAACGAGCCACCCUAAUGCAUUUGUUG
...(((((((((((((((((.(.((....(((-----((((.....((((...)))-)..------.....)))))))....(((....)))....))...((((...((......((...---.))..----(((((.....)))))))..))))).)))))))))))))))))......... ( -59.80, z-score =  -5.04, R)
>droAna3.scaffold_13340 15896564 181 - 23697760
UUCUCGUAGGGUGACUCACUCUUUUUGGAUGCACCUAGGAUGGUGAAAUUAAGAGAUGAUUCUGUUUGGUUUGGGGCUGUGGAAACUGUGAUAACUGAUAACAGAUAUAAGCAAUGUAUUUCGCUUUAACUCUGUUCCAACUGGCGGUUCUGUAUCAUACCGACCCACCCUAAUGCAUAUA---
......(((((((..((((((((..(.....((((......))))..)..))))).))).((.((.((((.((((((((((....).............((((((...((((..........))))....)))))).......))))))))).)))).)).))..))))))).........--- ( -46.40, z-score =  -0.33, R)
>droEre2.scaffold_4820 2172201 159 - 10470090
CUACAUUAGGGUGGCUCGUUCUACCAGGAUGC-----GGAUCACAACGUCUUCGGA-UAUAACCUUCUAUAACCGUCUAU--ACCGUAUAGAAACAGGAAAAGGCUAUCGGAUGUGGAAUU---UCCAA----GUACAAUCUUGCUA-------CCAAAUCGAGCCACCCUAAUGCAGUUG---
((.(((((((((((((((((((((..(((((.-----.(....)..)))))((.((-((...((((......((.(((((--(...))))))....))..)))).)))).)).))))))..---..(((----(......))))...-------......))))))))))))))).))...--- ( -50.40, z-score =  -3.62, R)
>droSec1.super_0 20101805 163 + 21120651
UUACAUUAGGGUGCCUCUUUCCACCAGGAUGC-----GGAUCACAACGCCUAUGGG-GAUU-----CCAUAAUCCGCUAUUAAUCUUCUAGUAGAAAGAAAGAGCUAUCGAAUAUAGAAUU---UUCAA----GUACCACCUUGCUAUCGCUGCCCGUAACGAGCCACCCUAAUGCAUUUG---
...((((((((((.(((..(((....)))(((-----((............(((((-((((-----....))))).))))..........((((...(((((..((((.....))))..))---))).(----(((......))))....)))))))))..))).))))))))))......--- ( -43.50, z-score =  -2.13, R)
>droSim1.chr3R 19584140 162 + 27517382
UUACAUUAGGGUGCCUCUUUCCACCAGGAUGC-----GGAUCACAACGCCUAUGGG-GAU------CCAUAAUCCGCUAUUAAUCUUCUAGUAGAAAGAAAGAGCUAUCGAAUAUAGAAUU---UUCAA----GUACCACCUUGCUAUCGCUGCCCGUAACGAGCCACCCUAAUGCAUUUG---
...((((((((((.(((..(((....)))(((-----((............(((((-(((------.....)))).))))..........((((...(((((..((((.....))))..))---))).(----(((......))))....)))))))))..))).))))))))))......--- ( -42.80, z-score =  -2.00, R)
>consensus
UUACAUUAGGGUGCCUCGUUCCACCAGGAUGC_____GGAUCACAACGCCUAUGGA_GAU______CCAUAAUCCGCUAUUAACCUUCUAGUAAAAGGAAAGAGCUAUCGGAUAUAGAAUU___UUCAA____GUACCACCUUGCUAUCGCUGCCCGUAACGAGCCACCCUAAUGCAUUUG___
...((((((((((.(((..(((....)))........((....................................((((.........))))............((((.....))))...................)).......................))).))))))))))......... (-20.98 = -19.94 +  -1.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,760,077 – 19,760,242
Length 165
Sequences 5
Columns 184
Reading direction reverse
Mean pairwise identity 67.30
Shannon entropy 0.56082
G+C content 0.44153
Mean single sequence MFE -57.11
Consensus MFE -24.59
Energy contribution -27.19
Covariance contribution 2.60
Combinations/Pair 1.41
Mean z-score -3.88
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.27
SVM RNA-class probability 0.999729
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19760077 165 - 27905053
CAACAAAUGCAUUAGGGUGGCUCGUUACGCGCAGCGAUACCAAGGUGGUAC----UUGAA---AAUUCUAUAUCCGAUAGCGCUUUCCUUUCACAAGAAUGUUAAUUGCGGAUUUUGG------AUC-UCCAUAGGAGUUGUGAUCC-----GCAUCCUGGUGGAACGAGCCACCCUAAUGUAG
.......(((((((((((((((((((.(((.(((.(((......((((...----..(((---(...((((.....))))...))))...)))).............(((((((....------..(-(((...))))....)))))-----))))))))))).))))))))))))))))))). ( -64.70, z-score =  -5.41, R)
>droAna3.scaffold_13340 15896564 181 + 23697760
---UAUAUGCAUUAGGGUGGGUCGGUAUGAUACAGAACCGCCAGUUGGAACAGAGUUAAAGCGAAAUACAUUGCUUAUAUCUGUUAUCAGUUAUCACAGUUUCCACAGCCCCAAACCAAACAGAAUCAUCUCUUAAUUUCACCAUCCUAGGUGCAUCCAAAAAGAGUGAGUCACCCUACGAGAA
---.........(((((((((.((((..........))))))..((((((((((....((((((......))))))...))))))....((....))..................))))......(((.(((((.....((((......))))........))))))))..)))))))...... ( -40.82, z-score =  -0.89, R)
>droEre2.scaffold_4820 2172201 159 + 10470090
---CAACUGCAUUAGGGUGGCUCGAUUUGG-------UAGCAAGAUUGUAC----UUGGA---AAUUCCACAUCCGAUAGCCUUUUCCUGUUUCUAUACGGU--AUAGACGGUUAUAGAAGGUUAUA-UCCGAAGACGUUGUGAUCC-----GCAUCCUGGUAGAACGAGCCACCCUAAUGUAG
---...((((((((((((((((((.((((.-------(((((((......)----)))..---.....((((..((((((((((((.((((((.(((...))--).))))))....)))))))))).-((....)))).))))....-----.....))).)))).)))))))))))))))))) ( -57.30, z-score =  -4.42, R)
>droSec1.super_0 20101805 163 - 21120651
---CAAAUGCAUUAGGGUGGCUCGUUACGGGCAGCGAUAGCAAGGUGGUAC----UUGAA---AAUUCUAUAUUCGAUAGCUCUUUCUUUCUACUAGAAGAUUAAUAGCGGAUUAUGG-----AAUC-CCCAUAGGCGUUGUGAUCC-----GCAUCCUGGUGGAAAGAGGCACCCUAAUGUAA
---....((((((((((((.(((.....((((..(((...((((......)----)))..---..........)))...))))....((((((((((..(((.....((((((((..(-----...(-(.....))..)..))))))-----)))))))))))))))))).)))))))))))). ( -61.26, z-score =  -4.33, R)
>droSim1.chr3R 19584140 162 - 27517382
---CAAAUGCAUUAGGGUGGCUCGUUACGGGCAGCGAUAGCAAGGUGGUAC----UUGAA---AAUUCUAUAUUCGAUAGCUCUUUCUUUCUACUAGAAGAUUAAUAGCGGAUUAUGG------AUC-CCCAUAGGCGUUGUGAUCC-----GCAUCCUGGUGGAAAGAGGCACCCUAAUGUAA
---....((((((((((((.(((.....((((..(((...((((......)----)))..---..........)))...))))....((((((((((..(((.....((((((((..(------..(-(.....))..)..))))))-----)))))))))))))))))).)))))))))))). ( -61.46, z-score =  -4.35, R)
>consensus
___CAAAUGCAUUAGGGUGGCUCGUUACGGGCAGCGAUAGCAAGGUGGUAC____UUGAA___AAUUCUAUAUCCGAUAGCUCUUUCCUUUUACUAGAAGAUUAAUAGCGGAUUAUGG______AUC_UCCAUAGGCGUUGUGAUCC_____GCAUCCUGGUGGAAAGAGCCACCCUAAUGUAA
.......(((((((((((((((((((.............................................(((((.........(((((......))))).......)))))................(((((((...(((..........))).))).))))))))))))))))))))))). (-24.59 = -27.19 +   2.60)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:39:16 2011