Locus 6317

Sequence ID dm3.chr3L
Location 5,501,957 – 5,502,090
Length 133
Max. P 0.995964
window8685 window8686 window8687

overview

Window 5

Location 5,501,957 – 5,502,051
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 68.46
Shannon entropy 0.60170
G+C content 0.57516
Mean single sequence MFE -33.05
Consensus MFE -24.16
Energy contribution -24.50
Covariance contribution 0.34
Combinations/Pair 1.24
Mean z-score -1.66
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.87
SVM RNA-class probability 0.995964
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5501957 94 + 24543557
UGCAAGUCAGCACACAAAAUGCAGCAGAACGAGCGGUGGCAGAUGGAA---UUGGUCCUGGAAACAGGACGCUGUGGCGGGA---AUCCUGCAGUGCCAC
.........((((.......(((((.......((....))........---...((((((....))))))))))).(((((.---..))))).))))... ( -35.00, z-score =  -2.07, R)
>dp4.chrXR_group6 5161415 99 - 13314419
UCAAAGUCAGCAACACUCAACAUCCACCAGAUGCAGAUGCGGAUGCGGAUGCGGAUGC-AGAAGGAGCGCCUGCUGGCGGGAUGGGAACUGCAGUGCGAC
.....(((.(((.((.....(((((.((...((((..((((........))))..)))-)...))..((((....))))))))).....))...)))))) ( -31.70, z-score =  -0.19, R)
>droSim1.chr3L 5017633 94 + 22553184
UGCAAGUCAGCACACAGAAUGCAGCAGAAUGAGCGGUGGCAGAUGGAA---GCGGUCCUGGAAACAGGACGCUGAGGCGGGA---AUCCUGCAGUGCCAC
.(((..(((((...((...(((.((.......))....)))..))...---...((((((....))))))))))).(((((.---..)))))..)))... ( -35.70, z-score =  -2.30, R)
>droSec1.super_2 5438357 94 + 7591821
UGCAAGUCAGCACACAGAAUGCAGCAGAAUGAGCGGUGGCAGAUGGAA---GCGGUCCUGGAAACAGGACGCUGAGGCGGGA---AUCCUGCAGUACCAC
(((...(((((...((...(((.((.......))....)))..))...---...((((((....))))))))))).(((((.---..))))).))).... ( -34.30, z-score =  -2.41, R)
>droYak2.chr3L 6064384 97 + 24197627
UCCAAGUCAGCACAACAAAUGCAGCAGGAUGAGCGGUGGCAGAUGCGGUGGCAGGUCCUUGCAACAGGACGAUGAGGCGGGA---AUCCUGCAGUGCCAC
.........((((......((((..(((((..((.((.((....)).)).))..))))))))).............(((((.---..))))).))))... ( -28.10, z-score =   1.02, R)
>droEre2.scaffold_4784 8186773 74 + 25762168
-------------------UCCAA-AAUGCAUAUGGUGGCAUAUGGAG---CAGGUCCUGGAAACAGGACGCUGAGGCGGGA---AUCCUGCAGUGCCAC
-------------------.....-..........(((((((......---(((((((((....)))))).)))..(((((.---..))))).))))))) ( -33.50, z-score =  -4.03, R)
>consensus
UGCAAGUCAGCACACAAAAUGCAGCAGAAUGAGCGGUGGCAGAUGGAA___CAGGUCCUGGAAACAGGACGCUGAGGCGGGA___AUCCUGCAGUGCCAC
...................................((((((.............((((((....))))))......(((((......)))))..)))))) (-24.16 = -24.50 +   0.34)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,501,957 – 5,502,051
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 68.46
Shannon entropy 0.60170
G+C content 0.57516
Mean single sequence MFE -27.88
Consensus MFE -15.95
Energy contribution -16.57
Covariance contribution 0.61
Combinations/Pair 1.20
Mean z-score -0.75
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.744921
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5501957 94 - 24543557
GUGGCACUGCAGGAU---UCCCGCCACAGCGUCCUGUUUCCAGGACCAA---UUCCAUCUGCCACCGCUCGUUCUGCUGCAUUUUGUGUGCUGACUUGCA
((((((..((((((.---...(((....))))))))).....(((....---.)))...)))))).((..(((..((.((((...)))))).)))..)). ( -28.00, z-score =  -0.84, R)
>dp4.chrXR_group6 5161415 99 + 13314419
GUCGCACUGCAGUUCCCAUCCCGCCAGCAGGCGCUCCUUCU-GCAUCCGCAUCCGCAUCCGCAUCUGCAUCUGGUGGAUGUUGAGUGUUGCUGACUUUGA
((.(((((((((.........((((....))))......))-)))((.((((((((....((....)).....)))))))).)))))).))......... ( -31.76, z-score =  -0.46, R)
>droSim1.chr3L 5017633 94 - 22553184
GUGGCACUGCAGGAU---UCCCGCCUCAGCGUCCUGUUUCCAGGACCGC---UUCCAUCUGCCACCGCUCAUUCUGCUGCAUUCUGUGUGCUGACUUGCA
((((((..((.((..---..))))...(((((((((....))))).)))---)......)))))).((....((.((.((((...)))))).))...)). ( -28.40, z-score =  -0.86, R)
>droSec1.super_2 5438357 94 - 7591821
GUGGUACUGCAGGAU---UCCCGCCUCAGCGUCCUGUUUCCAGGACCGC---UUCCAUCUGCCACCGCUCAUUCUGCUGCAUUCUGUGUGCUGACUUGCA
((((((..((.((..---..))))...(((((((((....))))).)))---)......)))))).((....((.((.((((...)))))).))...)). ( -26.40, z-score =  -0.53, R)
>droYak2.chr3L 6064384 97 - 24197627
GUGGCACUGCAGGAU---UCCCGCCUCAUCGUCCUGUUGCAAGGACCUGCCACCGCAUCUGCCACCGCUCAUCCUGCUGCAUUUGUUGUGCUGACUUGGA
((((((.(((.((..---..))........(((((......)))))........)))..))))))......(((..(.((((.....)))).)....))) ( -27.60, z-score =   0.31, R)
>droEre2.scaffold_4784 8186773 74 - 25762168
GUGGCACUGCAGGAU---UCCCGCCUCAGCGUCCUGUUUCCAGGACCUG---CUCCAUAUGCCACCAUAUGCAUU-UUGGA-------------------
((((((..(((((..---...(((....)))(((((....)))))))))---)......))))))..........-.....------------------- ( -25.10, z-score =  -2.11, R)
>consensus
GUGGCACUGCAGGAU___UCCCGCCUCAGCGUCCUGUUUCCAGGACCGG___CUCCAUCUGCCACCGCUCAUUCUGCUGCAUUCUGUGUGCUGACUUGCA
(((((...((.((......)).))......((((((....))))))..............)))))................................... (-15.95 = -16.57 +   0.61)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,501,984 – 5,502,090
Length 106
Sequences 7
Columns 110
Reading direction forward
Mean pairwise identity 70.16
Shannon entropy 0.60086
G+C content 0.52619
Mean single sequence MFE -33.02
Consensus MFE -17.30
Energy contribution -19.10
Covariance contribution 1.80
Combinations/Pair 1.29
Mean z-score -1.20
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.882718
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5501984 106 + 24543557
AACGAGCGGUGGCAGAUGGA---AUUGGUCCUGGAAACAGGACGCUGUGGCGGGAAUCCUGCAGUGCCACGCGUGCAUUGAACAUCGACAACAAAGCAAUUUCAGCUUA-
...((((.((((((......---....((((((....))))))......(((((...)))))..))))))...(((.(((...........))).)))......)))).- ( -37.50, z-score =  -1.70, R)
>droWil1.scaffold_180698 7311012 82 - 11422946
------------------------AACAUGCGACUGACUACUCACUACACCAUGG---CCGCCG-ACAGAGCGUGCAUUGAACAUUGACAACAAAGCAAUUUUAGUUUUA
------------------------..((((....(((....)))......))))(---(((((.-...).))).))((((((.((((.(......))))))))))).... ( -10.50, z-score =   0.95, R)
>dp4.chrXR_group6 5161454 100 - 13314419
------CGGAUGCGGAUGCGGAUGCAGAAG--GAGCGCCUGCUGGCGGGAUGGGAA--CUGCAGUGCGACGCGUGCAUCGAACAUCGACAACAAAGCAAUUUUAGUUUUA
------.(.(((((..((((..(((((...--.....((((....)))).......--))))).)))).))))).).(((.....)))....(((((.......))))). ( -27.26, z-score =   0.79, R)
>droSim1.chr3L 5017660 106 + 22553184
AAUGAGCGGUGGCAGAUGGA---AGCGGUCCUGGAAACAGGACGCUGAGGCGGGAAUCCUGCAGUGCCACGCGUGCAUUGAACAUCGACAACAAAGCAAUUUCAGCUUA-
((((.(((((((((......---((((.(((((....)))))))))...(((((...)))))..)))))).))).))))..............((((.......)))).- ( -41.80, z-score =  -2.99, R)
>droSec1.super_2 5438384 107 + 7591821
AAUGAGCGGUGGCAGAUGGA---AGCGGUCCUGGAAACAGGACGCUGAGGCGGGAAUCCUGCAGUACCACGCGUGCAUUGAACAUCGACAACAAAGCAAUUUCAGCUGAA
.....((((((...((((.(---.(((((((((....))))))(.((..(((((...)))))..)).).))).).))))...))))).).....(((.......)))... ( -37.60, z-score =  -2.10, R)
>droYak2.chr3L 6064411 108 + 24197627
GAUGAGCGGUGGCAGAUGCGGUGGCAGGUCCUUGCAACAGGACGAUGAGGCGGGAAUCCUGCAGUGCCACGCGUGCAUUGAACAUCGACAACAAAGCAAUUUCAGCUA--
.....((((((...((((((((((((.(((((......)))))......(((((...)))))..))))))...))))))...))))).).....(((.......))).-- ( -37.20, z-score =  -0.76, R)
>droEre2.scaffold_4784 8186785 100 + 25762168
-----AUGGUGGCAUAUGGA---GCAGGUCCUGGAAACAGGACGCUGAGGCGGGAAUCCUGCAGUGCCACGCGUGCAUUGAACAUCGGCAACAAAGCAAUUUCAGCUA--
-----((((((((((.....---.(((((((((....)))))).)))..(((((...))))).))))))).)))((..((((.....((......))...))))))..-- ( -39.30, z-score =  -2.61, R)
>consensus
_A_GAGCGGUGGCAGAUGGA___ACAGGUCCUGGAAACAGGACGCUGAGGCGGGAAUCCUGCAGUGCCACGCGUGCAUUGAACAUCGACAACAAAGCAAUUUCAGCUUA_
........((((((.............((((((....))))))......((((.....))))..))))))((.(((.(((...........))).)))......)).... (-17.30 = -19.10 +   1.80)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:05:21 2011