Locus 12310

Sequence ID dm3.chr3R
Location 27,290,838 – 27,290,932
Length 94
Max. P 0.997043
window16922 window16923

overview

Window 2

Location 27,290,838 – 27,290,932
Length 94
Sequences 8
Columns 106
Reading direction forward
Mean pairwise identity 65.76
Shannon entropy 0.62451
G+C content 0.52285
Mean single sequence MFE -27.86
Consensus MFE -17.11
Energy contribution -16.68
Covariance contribution -0.44
Combinations/Pair 1.38
Mean z-score -1.87
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.03
SVM RNA-class probability 0.997043
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27290838 94 + 27905053
UUUCCACUUCCACUUGCAUCUCCCAAGUC-CGAUCCGCGAUCUGUGAUCCUCGGCAGCUG-UAGAUGUUGCUGCCGUGGAAAAUCGAUGAAAGAUU----------
............(((.((((((.((..((-((...)).))..)).))(((.(((((((..-........))))))).))).....)))).)))...---------- ( -27.40, z-score =  -2.05, R)
>droSim1.chr3R 26922292 94 + 27517382
UUUCCACUUCCACUUGCAUCUCCCAAGUC-CGAUCCGCGAUCUGUGAUCCUCGGCAGCUG-UAGAUGUUGCUGCCGUGGAAAAUCGAUGAAAGAUU----------
............(((.((((((.((..((-((...)).))..)).))(((.(((((((..-........))))))).))).....)))).)))...---------- ( -27.40, z-score =  -2.05, R)
>droSec1.super_4 6090527 94 + 6179234
UUUCCACUUCCACUUGCAUCCCCCAAGUC-CGAUCCGCGAUCUGUGAUCCUCGGCAGCUG-UAGAUGUUGCUGCCGUGGAAAAUCGAUGAAAGAUU----------
............(((.((((.........-.((((...)))).....(((.(((((((..-........))))))).))).....)))).)))...---------- ( -26.10, z-score =  -1.90, R)
>droYak2.chr3R 28223400 91 + 28832112
---CUACUUCCACUUGCAUCUCCCAAGUC-CGAUUCGCGAUCUGUGAUCCUCGGCAGCCG-UAGAUGUUGCUGCCGUGGAAAAUCGAUGAAAGAUU----------
---.........(((.((((((.((..((-((...)).))..)).))(((.(((((((..-........))))))).))).....)))).)))...---------- ( -26.20, z-score =  -1.80, R)
>droEre2.scaffold_4820 9776488 90 - 10470090
-----ACUUCCAGUUACAUCUCCCAAGUC-CGAUCCGCGAUCUGUGAUCCUCGGCAGCUGGUAGAUUUUGCUGCCGUGGAAAAUCGAUGAAAGAUU----------
-----...........((((((.((..((-((...)).))..)).))(((.(((((((...........))))))).))).....)))).......---------- ( -25.40, z-score =  -1.41, R)
>droAna3.scaffold_13340 16416172 90 + 23697760
------------UUUCCAUUUCC--ACUU-CCACCUUCAGCC-ACGAUCCUCAGCUGCUCCGACUGAGUGCUGCUGUGGUGAAUCGAUGAACGAUUGGCGGUGCUG
------------..........(--(((.-((.......(((-(((.....((((.((((.....)))))))).)))))).(((((.....))))))).))))... ( -24.00, z-score =  -0.48, R)
>dp4.chr2 4516765 90 + 30794189
------------UUUCCAUCUUCAAUCUGGUGGUGCCUACCGUUGGAGCCACUGCCUCUG----CUUCUGCGGCUGUGGUGAAUCGAUGAACGAUUGGCGCUGCCG
------------................((..(((((...((((((.(((((.(((...(----(....))))).)))))...)))))).......)))))..)). ( -33.20, z-score =  -2.64, R)
>droPer1.super_19 215552 90 + 1869541
------------UUUCCAUCUUCAAUCUGGUGGUGCCUACCGUUGGAGCCACUGCCUCUG----CUUCUGCGGCUGUGGUGAAUCGAUGAACGAUUGGCGCUGCCG
------------................((..(((((...((((((.(((((.(((...(----(....))))).)))))...)))))).......)))))..)). ( -33.20, z-score =  -2.64, R)
>consensus
_____ACUUCCACUUGCAUCUCCCAAGUC_CGAUCCGCGAUCUGUGAUCCUCGGCAGCUG_UAGAUGUUGCUGCCGUGGAAAAUCGAUGAAAGAUU__________
................((((...............((.......)).(((.(((((((...........))))))).))).....))))................. (-17.11 = -16.68 +  -0.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 27,290,838 – 27,290,932
Length 94
Sequences 8
Columns 106
Reading direction reverse
Mean pairwise identity 65.76
Shannon entropy 0.62451
G+C content 0.52285
Mean single sequence MFE -27.39
Consensus MFE -13.90
Energy contribution -13.70
Covariance contribution -0.20
Combinations/Pair 1.38
Mean z-score -1.12
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.876626
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27290838 94 - 27905053
----------AAUCUUUCAUCGAUUUUCCACGGCAGCAACAUCUA-CAGCUGCCGAGGAUCACAGAUCGCGGAUCG-GACUUGGGAGAUGCAAGUGGAAGUGGAAA
----------...(((((((.((((((((.(((((((........-..))))))).)))....)))))(((..((.-.......))..)))..)))))))...... ( -30.00, z-score =  -1.75, R)
>droSim1.chr3R 26922292 94 - 27517382
----------AAUCUUUCAUCGAUUUUCCACGGCAGCAACAUCUA-CAGCUGCCGAGGAUCACAGAUCGCGGAUCG-GACUUGGGAGAUGCAAGUGGAAGUGGAAA
----------...(((((((.((((((((.(((((((........-..))))))).)))....)))))(((..((.-.......))..)))..)))))))...... ( -30.00, z-score =  -1.75, R)
>droSec1.super_4 6090527 94 - 6179234
----------AAUCUUUCAUCGAUUUUCCACGGCAGCAACAUCUA-CAGCUGCCGAGGAUCACAGAUCGCGGAUCG-GACUUGGGGGAUGCAAGUGGAAGUGGAAA
----------...(((((((.((((((((.(((((((........-..))))))).)))....)))))(((..((.-.......))..)))..)))))))...... ( -29.10, z-score =  -1.37, R)
>droYak2.chr3R 28223400 91 - 28832112
----------AAUCUUUCAUCGAUUUUCCACGGCAGCAACAUCUA-CGGCUGCCGAGGAUCACAGAUCGCGAAUCG-GACUUGGGAGAUGCAAGUGGAAGUAG---
----------...(((((((.((((((((.(((((((........-..))))))).)))....)))))(((..((.-.......))..)))..)))))))...--- ( -28.70, z-score =  -1.95, R)
>droEre2.scaffold_4820 9776488 90 + 10470090
----------AAUCUUUCAUCGAUUUUCCACGGCAGCAAAAUCUACCAGCUGCCGAGGAUCACAGAUCGCGGAUCG-GACUUGGGAGAUGUAACUGGAAGU-----
----------.((((..((((((...(((.(((((((...........)))))))..((((...))))..))))))-)...))..))))............----- ( -27.80, z-score =  -1.73, R)
>droAna3.scaffold_13340 16416172 90 - 23697760
CAGCACCGCCAAUCGUUCAUCGAUUCACCACAGCAGCACUCAGUCGGAGCAGCUGAGGAUCGU-GGCUGAAGGUGG-AAGU--GGAAAUGGAAA------------
((...((((...(((.....)))((((((.((((.((.((((((.......))))))....))-.))))..)))))-).))--))...))....------------ ( -27.50, z-score =  -0.53, R)
>dp4.chr2 4516765 90 - 30794189
CGGCAGCGCCAAUCGUUCAUCGAUUCACCACAGCCGCAGAAG----CAGAGGCAGUGGCUCCAACGGUAGGCACCACCAGAUUGAAGAUGGAAA------------
.(((...))).....((((((...(((((((.(((((....)----)...))).)))).......(((.(....))))....))).))))))..------------ ( -23.00, z-score =   0.07, R)
>droPer1.super_19 215552 90 - 1869541
CGGCAGCGCCAAUCGUUCAUCGAUUCACCACAGCCGCAGAAG----CAGAGGCAGUGGCUCCAACGGUAGGCACCACCAGAUUGAAGAUGGAAA------------
.(((...))).....((((((...(((((((.(((((....)----)...))).)))).......(((.(....))))....))).))))))..------------ ( -23.00, z-score =   0.07, R)
>consensus
__________AAUCUUUCAUCGAUUUUCCACGGCAGCAACAUCUA_CAGCUGCCGAGGAUCACAGAUCGCGGAUCG_GACUUGGGAGAUGCAAGUGGAAGU_____
.................(((((((((((...((((((...........)))))))))))))......(.(((........))).).))))................ (-13.90 = -13.70 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:59:43 2011