Locus 11733

Sequence ID dm3.chr3R
Location 23,395,847 – 23,395,937
Length 90
Max. P 0.916095
window16119 window16120

overview

Window 9

Location 23,395,847 – 23,395,937
Length 90
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 87.54
Shannon entropy 0.21581
G+C content 0.49118
Mean single sequence MFE -21.89
Consensus MFE -20.28
Energy contribution -19.80
Covariance contribution -0.48
Combinations/Pair 1.20
Mean z-score -1.54
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.916095
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23395847 90 + 27905053
--CGCAGCCACUUUUUCGCAUUUUCCACCCAUUUUUCACACUGAGUGGCGGUGGUCAGCGCUUUUCAACGCGUUGCCCUGUUUAUAAUUGAA
--....(((((((.............................)))))))((.((.((((((........))))))))))............. ( -21.25, z-score =  -0.94, R)
>droSim1.chr3R 23127098 82 + 27517382
----------CUUUUUCCCAUUUUCCACCCGUUUUCCACGCUGAGUGGCGGUGGUCAGCGCUUUUCAACGCGCUGCCCUGUUUAUAAUUGAA
----------..............(((((......((((.....)))).))))).((((((........))))))................. ( -20.80, z-score =  -1.56, R)
>droSec1.super_22 29585 82 + 1066717
----------CUUUUUCCCAUUUUCCACCCGUUUUCCACGCUGAGUGGCGGUGGUCAGCGCUUUUCAACGCGCUGCCCUGUUUAUAAUUGAA
----------..............(((((......((((.....)))).))))).((((((........))))))................. ( -20.80, z-score =  -1.56, R)
>droYak2.chr3R 5738809 91 - 28832112
CGCAUAGCCACUUUUUC-CAUUUUCCAACCAUUUUCCACGUUGAGUGGCAGUGGCCAGCGCUUUUCAACGCGCUGCCCUGUUUAUAAUUGAA
......(((((((....-........................)))))))((.(((.(((((........))))))))))............. ( -23.69, z-score =  -2.27, R)
>droEre2.scaffold_4820 5827956 89 - 10470090
--CGCAGCCCCUUUUUU-CAUUUUCCACCCAUUUUCCACGCUGAGUGGCGGUGGUCAGCGCUUUUCAACGCGCUGCCCUGAUUAUAAUUGAA
--.(((((.........-......(((((......((((.....)))).)))))...(((........))))))))................ ( -22.90, z-score =  -1.38, R)
>consensus
__C__AGCC_CUUUUUC_CAUUUUCCACCCAUUUUCCACGCUGAGUGGCGGUGGUCAGCGCUUUUCAACGCGCUGCCCUGUUUAUAAUUGAA
...................................((((.....))))(((.((.((((((........)))))))))))............ (-20.28 = -19.80 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,395,847 – 23,395,937
Length 90
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 87.54
Shannon entropy 0.21581
G+C content 0.49118
Mean single sequence MFE -25.99
Consensus MFE -21.40
Energy contribution -22.20
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.808490
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23395847 90 - 27905053
UUCAAUUAUAAACAGGGCAACGCGUUGAAAAGCGCUGACCACCGCCACUCAGUGUGAAAAAUGGGUGGAAAAUGCGAAAAAGUGGCUGCG--
................(((..(((((....)))))...((((..(((((((...(....).))))))).............)))).))).-- ( -23.06, z-score =  -0.49, R)
>droSim1.chr3R 23127098 82 - 27517382
UUCAAUUAUAAACAGGGCAGCGCGUUGAAAAGCGCUGACCACCGCCACUCAGCGUGGAAAACGGGUGGAAAAUGGGAAAAAG----------
(((..............((((((........)))))).(((((.((((.....))))......))))).......)))....---------- ( -24.30, z-score =  -1.90, R)
>droSec1.super_22 29585 82 - 1066717
UUCAAUUAUAAACAGGGCAGCGCGUUGAAAAGCGCUGACCACCGCCACUCAGCGUGGAAAACGGGUGGAAAAUGGGAAAAAG----------
(((..............((((((........)))))).(((((.((((.....))))......))))).......)))....---------- ( -24.30, z-score =  -1.90, R)
>droYak2.chr3R 5738809 91 + 28832112
UUCAAUUAUAAACAGGGCAGCGCGUUGAAAAGCGCUGGCCACUGCCACUCAACGUGGAAAAUGGUUGGAAAAUG-GAAAAAGUGGCUAUGCG
................(((..(((((....)))))((((((((.((((.....))))....(.(((....))).-)....))))))))))). ( -28.50, z-score =  -2.18, R)
>droEre2.scaffold_4820 5827956 89 + 10470090
UUCAAUUAUAAUCAGGGCAGCGCGUUGAAAAGCGCUGACCACCGCCACUCAGCGUGGAAAAUGGGUGGAAAAUG-AAAAAAGGGGCUGCG--
................((((((((((....)))))...(((((.((((.....))))......)))))......-.........))))).-- ( -29.80, z-score =  -2.32, R)
>consensus
UUCAAUUAUAAACAGGGCAGCGCGUUGAAAAGCGCUGACCACCGCCACUCAGCGUGGAAAAUGGGUGGAAAAUG_GAAAAAG_GGCU__G__
..............((.((((((........)))))).))....(((((((...(....).)))))))........................ (-21.40 = -22.20 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:48:31 2011