Locus 11189

Sequence ID dm3.chr3R
Location 19,284,755 – 19,284,862
Length 107
Max. P 0.775121
window15372 window15373

overview

Window 2

Location 19,284,755 – 19,284,862
Length 107
Sequences 8
Columns 130
Reading direction forward
Mean pairwise identity 60.59
Shannon entropy 0.70093
G+C content 0.39540
Mean single sequence MFE -22.05
Consensus MFE -9.40
Energy contribution -9.40
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.01
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.775121
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19284755 107 + 27905053
AAUAUAUUGCAUCUCUCACACCACAAGAUGCACUCGAAAAGAGGUGAACUGCAA---------------------GAUAAAAGCC--AAAAAUUCGUGUGGUAAUCUAAAUUGACUGGGAUUAAGCGAGG
......((((...(((((.((((((.(((((((((.....)))(....))))).---------------------(........)--......)).))))))..((......)).)))))....)))).. ( -19.00, z-score =   0.15, R)
>dp4.chr2 2768224 105 + 30794189
AAAAUAUGGCAUCUCUCACACUCAGAGAUGGCGUCUAAAGAUGGAAAAUUAAAGCGAAAUAUUG------CAUAUGAAAAAUGCGGUUUGGUUGGGUUUU-AAUCGCAGAUU------------------
.......(.(((((((.......))))))).)((((...(((..(((((..((.(((...((((------(((.......)))))))))).))..)))))-.)))..)))).------------------ ( -24.00, z-score =  -1.52, R)
>droPer1.super_7 2861441 105 - 4445127
AAAAUAUGGCAUCUCUCACACUCAGAGAUGGCGUCUAAAGAUGGAAAAUUAAAGCGAAAUAUUG------CAUAUGAAAAAUGCGGUUUGGCUGGGUUUU-AAUCGCAGAUU------------------
.......(.(((((((.......))))))).)((((...(((..(((((...(((.((((...(------(((.......)))).)))).)))..)))))-.)))..)))).------------------ ( -25.80, z-score =  -1.92, R)
>droAna3.scaffold_13340 3428462 90 - 23697760
--AAUAUUGCAUCUCUCACACCACGAGAUGCACUCAAAAAUGGAUAAAGCCAGA---------------------GAUAAAAGCAC-GAAGCUGUGUUUCGAAAUUAAAAUUGC----------------
--.....((((((((.........)))))))).((.....(((......)))((---------------------((((..(((..-...))).))))))))............---------------- ( -19.70, z-score =  -2.07, R)
>droEre2.scaffold_4820 1705384 107 - 10470090
GAUAUAUUGCAUCUCUCACACCACGAGAUGCACUCGAAAAGAGGUGAACUGCGC---------------------GAUAAAAGCC--GAAAAUUCAUGUGGAAAUUGAAGUUGACUGAGAUUAACAGAGG
.......((((((((.........))))))))(((.......(((.((((...(---------------------(((.....((--(..........)))..)))).)))).)))..........))). ( -21.73, z-score =  -0.51, R)
>droYak2.chr3R 20168000 130 + 28832112
AAUAUAUUGCAUCUCUCACACCACGAGAUGCACUCGAAAAGAGGUGAACUGCAAACUGCAAACUGCGAACUGCGAGAUAAAAGCCCCAAAAAUUCGUGUGGAAAUUGAAGUUGACUGAGAUUAACAGAGG
.......((((((((.........))))))))(((.......(((.((((.(((..(((.....)))..(..((.((................)).))..)...))).)))).)))..........))). ( -26.02, z-score =  -0.41, R)
>droSec1.super_0 19647894 86 + 21120651
AAUAUAUUGCAUCUCUCACACCACGAGAUGCACUCGAAAAGAGGUGAACUGCGA---------------------GAUAAAAACC--GAAAAUUCGUGUGGUAACUUAA---------------------
.......((((((((.........))))))))(((.....)))((..((..((.---------------------((........--......)).))..)).))....--------------------- ( -18.14, z-score =  -1.47, R)
>droSim1.chr3R 19104714 107 + 27517382
AAUAUAUUGCAUCUCUCACACCACGAGAUGCACUCGAAAAGAGGUGAACUGCGA---------------------GAUAAAAGCC--GAAAAUUCGUGUGGUAACUUAAAUUGACUGGGAUUAAGCGAGG
.......((((((((.........))))))))((((......((....)).)))---------------------).........--.....(((((.((((..(...........)..)))).))))). ( -22.00, z-score =  -0.34, R)
>consensus
AAUAUAUUGCAUCUCUCACACCACGAGAUGCACUCGAAAAGAGGUGAACUGCAA_____________________GAUAAAAGCC__GAAAAUUCGUGUGGAAACUUAAAUUGA________________
.......((((((((.........)))))))).................................................................................................. ( -9.40 =  -9.40 +   0.00)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 19,284,755 – 19,284,862
Length 107
Sequences 8
Columns 130
Reading direction reverse
Mean pairwise identity 60.59
Shannon entropy 0.70093
G+C content 0.39540
Mean single sequence MFE -19.35
Consensus MFE -10.70
Energy contribution -10.46
Covariance contribution -0.23
Combinations/Pair 1.25
Mean z-score -0.39
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734371
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19284755 107 - 27905053
CCUCGCUUAAUCCCAGUCAAUUUAGAUUACCACACGAAUUUUU--GGCUUUUAUC---------------------UUGCAGUUCACCUCUUUUCGAGUGCAUCUUGUGGUGUGAGAGAUGCAAUAUAUU
.(((((........((((......))))((((((.((......--.((.......---------------------..)).((....(((.....))).)).)).))))))))))).............. ( -19.10, z-score =   0.12, R)
>dp4.chr2 2768224 105 - 30794189
------------------AAUCUGCGAUU-AAAACCCAACCAAACCGCAUUUUUCAUAUG------CAAUAUUUCGCUUUAAUUUUCCAUCUUUAGACGCCAUCUCUGAGUGUGAGAGAUGCCAUAUUUU
------------------...........-................((((((((((((((------(........))...............(((((.......))))))))))))))))))........ ( -17.80, z-score =  -1.76, R)
>droPer1.super_7 2861441 105 + 4445127
------------------AAUCUGCGAUU-AAAACCCAGCCAAACCGCAUUUUUCAUAUG------CAAUAUUUCGCUUUAAUUUUCCAUCUUUAGACGCCAUCUCUGAGUGUGAGAGAUGCCAUAUUUU
------------------...(((.(...-.....)))).......((((((((((((((------(........))...............(((((.......))))))))))))))))))........ ( -17.90, z-score =  -1.31, R)
>droAna3.scaffold_13340 3428462 90 + 23697760
----------------GCAAUUUUAAUUUCGAAACACAGCUUC-GUGCUUUUAUC---------------------UCUGGCUUUAUCCAUUUUUGAGUGCAUCUCGUGGUGUGAGAGAUGCAAUAUU--
----------------((............(((((((......-))).))))(((---------------------(((.((.....((((....(((.....))))))).)).))))))))......-- ( -18.50, z-score =  -0.28, R)
>droEre2.scaffold_4820 1705384 107 + 10470090
CCUCUGUUAAUCUCAGUCAACUUCAAUUUCCACAUGAAUUUUC--GGCUUUUAUC---------------------GCGCAGUUCACCUCUUUUCGAGUGCAUCUCGUGGUGUGAGAGAUGCAAUAUAUC
....(((...((((((((...((((.........)))).....--)))...((((---------------------(((.((..(((.((.....)))))...))))))))))))))...)))....... ( -19.40, z-score =   0.10, R)
>droYak2.chr3R 20168000 130 - 28832112
CCUCUGUUAAUCUCAGUCAACUUCAAUUUCCACACGAAUUUUUGGGGCUUUUAUCUCGCAGUUCGCAGUUUGCAGUUUGCAGUUCACCUCUUUUCGAGUGCAUCUCGUGGUGUGAGAGAUGCAAUAUAUU
....(((...(((((((.((((.(((........((((((..(((((......))))).))))))....))).)))).))....((((......((((.....)))).)))))))))...)))....... ( -26.40, z-score =   0.41, R)
>droSec1.super_0 19647894 86 - 21120651
---------------------UUAAGUUACCACACGAAUUUUC--GGUUUUUAUC---------------------UCGCAGUUCACCUCUUUUCGAGUGCAUCUCGUGGUGUGAGAGAUGCAAUAUAUU
---------------------.............(((....))--).....((((---------------------((.((...((((......((((.....)))).)))))).))))))......... ( -16.10, z-score =  -0.13, R)
>droSim1.chr3R 19104714 107 - 27517382
CCUCGCUUAAUCCCAGUCAAUUUAAGUUACCACACGAAUUUUC--GGCUUUUAUC---------------------UCGCAGUUCACCUCUUUUCGAGUGCAUCUCGUGGUGUGAGAGAUGCAAUAUAUU
.(((((((((...........))))))........(((((..(--((........---------------------))).)))))..........)))((((((((.........))))))))....... ( -19.60, z-score =  -0.29, R)
>consensus
________________UCAAUUUAAAUUUCCACACGAAUUUUC__GGCUUUUAUC_____________________UCGCAGUUCACCUCUUUUCGAGUGCAUCUCGUGGUGUGAGAGAUGCAAUAUAUU
..................................................................................................((((((((.........))))))))....... (-10.70 = -10.46 +  -0.23)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:38:04 2011