Locus 11316

Sequence ID dm3.chr3R
Location 20,289,651 – 20,289,781
Length 130
Max. P 0.724545
window15565 window15566 window15567

overview

Window 5

Location 20,289,651 – 20,289,744
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 77.57
Shannon entropy 0.37540
G+C content 0.52724
Mean single sequence MFE -27.12
Consensus MFE -18.54
Energy contribution -19.26
Covariance contribution 0.72
Combinations/Pair 1.16
Mean z-score -1.37
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.643046
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20289651 93 - 27905053
CACUUGAGUUCGUGGCGCUCCCAAAGAGUGGAGAUAUCCUUUCAUAGGAGCGAACAAAGCGAACGGGGAGAAAUCCACACGGCUGCCUUGCUG
.......((((((..((((((....(((.(((....))).)))...))))))......))))))..(((....)))...((((......)))) ( -32.40, z-score =  -2.04, R)
>droSim1.chr3R 20130621 77 - 27517382
CACUUGAGUUCGCUGUGCUCCCAAAGAGUGGAGAUAUCCUUUCAGAGGAGCGAACAAAGCGAACGGCUG-----CCUUGCUG-----------
.......(((((((.((((((....(((.(((....))).)))...)))))).....)))))))(((..-----....))).----------- ( -27.70, z-score =  -2.22, R)
>droSec1.super_0 20626052 77 - 21120651
CACUUGAGUUCGCUGUGCUCCCAAAGAGUGGAGAUAUCCUUUCAGAGGAGCGAACAAAGCGAAUGGCUG-----CCUUACUG-----------
.......(((((((.((((((....(((.(((....))).)))...)))))).....))))))).....-----........----------- ( -22.90, z-score =  -1.24, R)
>droYak2.chr3R 2618802 93 + 28832112
CACUCGAGUUCGCUGUGCUCCAAACGAGUGCAGAUAUCCUUUCAGAGGAGCGAACAAAGCCAACGAGGAGAAAUCCACACUGCAUCCUUGCUG
.......((((((((..(((.....)))..))....(((((...)))))))))))...........(((....))).....(((....))).. ( -28.00, z-score =  -1.82, R)
>droEre2.scaffold_4820 2700341 92 + 10470090
CACUUGAGUUCUCUGUGCUCCAAACGAGUGCAGGUAUCCUUUCAGAGGAGCG-ACAAAGCGACCGGGGAGAAAUCCACACUGCCUCCUUGCUG
............(((..(((.....)))..)))((.(((((...)))))...-))..(((((..(((.((.........)).)))..))))). ( -24.60, z-score =   0.44, R)
>consensus
CACUUGAGUUCGCUGUGCUCCCAAAGAGUGGAGAUAUCCUUUCAGAGGAGCGAACAAAGCGAACGGGGAGAAAUCCACACUGC__CCUUGCUG
.......(((((((.((((((....(((.(((....))).)))...)))))).....)))))))............................. (-18.54 = -19.26 +   0.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,289,687 – 20,289,781
Length 94
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 73.68
Shannon entropy 0.45842
G+C content 0.43817
Mean single sequence MFE -25.13
Consensus MFE -15.93
Energy contribution -15.85
Covariance contribution -0.08
Combinations/Pair 1.46
Mean z-score -1.08
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.603639
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20289687 94 + 27905053
---------UUGUUCGCUCCUAUGAAAGGA--UAUCUCCACUCUUUGGGAGCGCCACGAACUCAAG----UGCGAAGUUGUUCGCCAUUCAGGAUA---AUCCAUAUUUGGG
---------((((.((((((((.((..(((--....)))..))..))))))))..)))).((((((----((((((....)))))......((...---..))..))))))) ( -28.90, z-score =  -2.16, R)
>droSim1.chr3R 20130641 97 + 27517382
---------UUGUUCGCUCCUCUGAAAGGA--UAUCUCCACUCUUUGGGAGCACAGCGAACUCAAG----UGCGAAGUUGUUCGCCAUUCAGGAUAAUAAUCCAUAUUUGGG
---------..(((((((.((((.((((..--(......)..)))).))))...)))))))(((((----((((((....)))))......((((....))))..)))))). ( -28.70, z-score =  -2.08, R)
>droSec1.super_0 20626072 97 + 21120651
---------UUGUUCGCUCCUCUGAAAGGA--UAUCUCCACUCUUUGGGAGCACAGCGAACUCAAG----UGCGAAGUUGUUCGCCAUUCAGGAUAAUAAUCCAUAUUUGGG
---------..(((((((.((((.((((..--(......)..)))).))))...)))))))(((((----((((((....)))))......((((....))))..)))))). ( -28.70, z-score =  -2.08, R)
>droYak2.chr3R 2618838 94 - 28832112
---------UUGUUCGCUCCUCUGAAAGGA--UAUCUGCACUCGUUUGGAGCACAGCGAACUCGAG----UGCGAAGUUGUUCGCCAUUCAGGAUA---AUCCAUAUUUGGG
---------..(((((((.(((..((.(..--(......)..).))..)))...)))))))..(((----((((((....)))).)))))......---..(((....))). ( -25.50, z-score =  -0.50, R)
>droEre2.scaffold_4820 2700377 93 - 10470090
---------UUGU-CGCUCCUCUGAAAGGA--UACCUGCACUCGUUUGGAGCACAGAGAACUCAAG----UGCGAAGUUGUUCGCCAUUCAGGAUA---AUCCAUAUUUGGG
---------((((-.(((((..(((.(((.--..)))....)))...)))))))))....((((((----((((((....)))))......((...---..))..))))))) ( -23.40, z-score =  -0.25, R)
>droWil1.scaffold_181108 297265 106 - 4707319
CCUCAGAUGGUAUCUGUAGAUUUGACAGGAAUUUACUUUAUUACUUAUUAUUGUAAAAUAUCGAAAAGUAUGUGAAGUCUGAAACUAUCCCGUAGA------CAAAUUUUGA
.....((((((.((...((((((.((.....(((((..((........))..)))))((((......)))))).)))))))).)))))).......------.......... ( -15.60, z-score =   0.58, R)
>consensus
_________UUGUUCGCUCCUCUGAAAGGA__UAUCUCCACUCUUUGGGAGCACAGCGAACUCAAG____UGCGAAGUUGUUCGCCAUUCAGGAUA___AUCCAUAUUUGGG
...............((((((..((..(((......)))..))...))))))........((((((.....(((((....)))))......((((....))))...)))))) (-15.93 = -15.85 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,289,687 – 20,289,781
Length 94
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 73.68
Shannon entropy 0.45842
G+C content 0.43817
Mean single sequence MFE -24.08
Consensus MFE -14.64
Energy contribution -15.37
Covariance contribution 0.73
Combinations/Pair 1.30
Mean z-score -1.29
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.724545
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20289687 94 - 27905053
CCCAAAUAUGGAU---UAUCCUGAAUGGCGAACAACUUCGCA----CUUGAGUUCGUGGCGCUCCCAAAGAGUGGAGAUA--UCCUUUCAUAGGAGCGAACAA---------
.(((....)))..---...(((((((.(((((....))))).----.....))))).))((((((....(((.(((....--))).)))...)))))).....--------- ( -25.50, z-score =  -1.30, R)
>droSim1.chr3R 20130641 97 - 27517382
CCCAAAUAUGGAUUAUUAUCCUGAAUGGCGAACAACUUCGCA----CUUGAGUUCGCUGUGCUCCCAAAGAGUGGAGAUA--UCCUUUCAGAGGAGCGAACAA---------
..(((....((((....))))......(((((....))))).----.))).((((((....(((((.....).))))...--(((((...)))))))))))..--------- ( -26.80, z-score =  -1.76, R)
>droSec1.super_0 20626072 97 - 21120651
CCCAAAUAUGGAUUAUUAUCCUGAAUGGCGAACAACUUCGCA----CUUGAGUUCGCUGUGCUCCCAAAGAGUGGAGAUA--UCCUUUCAGAGGAGCGAACAA---------
..(((....((((....))))......(((((....))))).----.))).((((((....(((((.....).))))...--(((((...)))))))))))..--------- ( -26.80, z-score =  -1.76, R)
>droYak2.chr3R 2618838 94 + 28832112
CCCAAAUAUGGAU---UAUCCUGAAUGGCGAACAACUUCGCA----CUCGAGUUCGCUGUGCUCCAAACGAGUGCAGAUA--UCCUUUCAGAGGAGCGAACAA---------
.(((....)))..---.....(((...(((((....))))).----.))).((((((((..(((.....)))..))....--(((((...)))))))))))..--------- ( -28.20, z-score =  -2.36, R)
>droEre2.scaffold_4820 2700377 93 + 10470090
CCCAAAUAUGGAU---UAUCCUGAAUGGCGAACAACUUCGCA----CUUGAGUUCUCUGUGCUCCAAACGAGUGCAGGUA--UCCUUUCAGAGGAGCG-ACAA---------
.(((....)))..---..((((.....(((((....))))).----.(((((...((((..(((.....)))..))))..--....)))))))))...-....--------- ( -23.20, z-score =  -0.58, R)
>droWil1.scaffold_181108 297265 106 + 4707319
UCAAAAUUUG------UCUACGGGAUAGUUUCAGACUUCACAUACUUUUCGAUAUUUUACAAUAAUAAGUAAUAAAGUAAAUUCCUGUCAAAUCUACAGAUACCAUCUGAGG
.....(((((------...((((((.((((...)))).....((((((....(((((.........)))))..))))))...)))))))))))((.(((((...))))))). ( -14.00, z-score =   0.03, R)
>consensus
CCCAAAUAUGGAU___UAUCCUGAAUGGCGAACAACUUCGCA____CUUGAGUUCGCUGUGCUCCCAAAGAGUGGAGAUA__UCCUUUCAGAGGAGCGAACAA_________
.........((((....))))......(((((....)))))..........((((((...((((.....)))).........((((.....))))))))))........... (-14.64 = -15.37 +   0.73)

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 00:40:45 2011