Locus 7164

Sequence ID dm3.chr3L
Location 12,628,114 – 12,628,212
Length 98
Max. P 0.982608
window9861 window9862

overview

Window 1

Location 12,628,114 – 12,628,212
Length 98
Sequences 7
Columns 103
Reading direction forward
Mean pairwise identity 83.41
Shannon entropy 0.33018
G+C content 0.36671
Mean single sequence MFE -23.86
Consensus MFE -15.07
Energy contribution -16.64
Covariance contribution 1.57
Combinations/Pair 1.11
Mean z-score -2.75
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.11
SVM RNA-class probability 0.982608
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12628114 98 + 24543557
GAACUCAUUUAUUCGCAUUUUUU--CCCCAUGCUUUUUU---GCUGCUCUUUUGGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGA
..(((((....(((((((((...--......((......---)).(((.....))))))))))))(((((..((((((....))))))..))))).))))).. ( -26.70, z-score =  -3.31, R)
>droSim1.chr3L 12013619 98 + 22553184
GAACUCAUUUAUUCGCAUUUUUU--CCCCCGGCUUUUUU---GCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGA
..(((((....(((((((((...--.....(((......---)))((.......)))))))))))(((((..((((((....))))))..))))).))))).. ( -27.70, z-score =  -3.81, R)
>droSec1.super_0 4814230 98 + 21120651
GAACUCAUUUAUUCGCAUUUUUU--CCCCCGGCUUUUUU---GCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGA
..(((((....(((((((((...--.....(((......---)))((.......)))))))))))(((((..((((((....))))))..))))).))))).. ( -27.70, z-score =  -3.81, R)
>droYak2.chr3L 12694114 103 + 24197627
GAACUCAUUUAUUCGCAUUUUUUUGGCCCCUGCUUUUUUUUUGCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGA
..(((((....(((((((((....(((....)))...........((.......)))))))))))(((((..((((((....))))))..))))).))))).. ( -25.60, z-score =  -2.81, R)
>droEre2.scaffold_4784 12632586 95 + 25762168
GAACUCAUUUAUUCGCAUUUUUU--GCCC-UGCUUUCU----GCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUU-CCGCCAUCAUUUUGAGUGA
..(((((....(((((((((...--....-.((.....----)).((.......)))))))))))(((((..(((((.....)-))))..))))).))))).. ( -25.20, z-score =  -3.21, R)
>droAna3.scaffold_13337 19896049 86 - 23293914
GAACUCAUUUAUUCGCAUUUUUU--CUUCUCGUUUUUU------------UUUUGU---UGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGA
..(((((....((((((......--.............------------......---))))))(((((..((((((....))))))..))))).))))).. ( -19.31, z-score =  -2.55, R)
>droGri2.scaffold_15110 7681540 97 - 24565398
-UAGUCCCAUUUUCGAACUCAUUU-AUUCGCAUUUUUUU---GUUUGUGUUUGUGUAU-UGCGAAAACGAAUGUGAAAAGUUUUCUGCCAUCAUUUUGAGUGA
-...............(((((...-.(((((((((((((---((..(((......)))-.))))))..)))))))))..((.....))........))))).. ( -14.80, z-score =   0.29, R)
>consensus
GAACUCAUUUAUUCGCAUUUUUU__CCCCCUGCUUUUUU___GCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGA
..(((((....(((((((((...........((.........))............)))))))))(((((..((((((....))))))..))))).))))).. (-15.07 = -16.64 +   1.57)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,628,114 – 12,628,212
Length 98
Sequences 7
Columns 103
Reading direction reverse
Mean pairwise identity 83.41
Shannon entropy 0.33018
G+C content 0.36671
Mean single sequence MFE -20.57
Consensus MFE -13.74
Energy contribution -14.82
Covariance contribution 1.08
Combinations/Pair 1.12
Mean z-score -1.61
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.632134
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12628114 98 - 24543557
UCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCCAAAAGAGCAGC---AAAAAAGCAUGGGG--AAAAAAUGCGAAUAAAUGAGUUC
..(((((((((((((..((((....)))).)).))))))((((((((.((......((...---......))....))--...)))))))).....))))).. ( -24.00, z-score =  -2.03, R)
>droSim1.chr3L 12013619 98 - 22553184
UCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGC---AAAAAAGCCGGGGG--AAAAAAUGCGAAUAAAUGAGUUC
..(((((((((((((..((((....)))).)).))))))((((((((((.......)).((---......))......--...)))))))).....))))).. ( -22.90, z-score =  -1.61, R)
>droSec1.super_0 4814230 98 - 21120651
UCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGC---AAAAAAGCCGGGGG--AAAAAAUGCGAAUAAAUGAGUUC
..(((((((((((((..((((....)))).)).))))))((((((((((.......)).((---......))......--...)))))))).....))))).. ( -22.90, z-score =  -1.61, R)
>droYak2.chr3L 12694114 103 - 24197627
UCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGCAAAAAAAAAGCAGGGGCCAAAAAAAUGCGAAUAAAUGAGUUC
..(((((((((((((..((((....)))).)).))))))((((((((((.......)).((.........))...........)))))))).....))))).. ( -22.80, z-score =  -1.77, R)
>droEre2.scaffold_4784 12632586 95 - 25762168
UCACUCAAAAUGAUGGCGG-AAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGC----AGAAAGCA-GGGC--AAAAAAUGCGAAUAAAUGAGUUC
..(((((((((((((..((-(.....))).)).))))))((((((((((.......)).((----.....)).-....--...)))))))).....))))).. ( -22.70, z-score =  -1.80, R)
>droAna3.scaffold_13337 19896049 86 + 23293914
UCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCA---ACAAAA------------AAAAAACGAGAAG--AAAAAAUGCGAAUAAAUGAGUUC
..(((((((((((((..((((....)))).)).))))))(((((---......------------.............--......))))).....))))).. ( -15.71, z-score =  -1.89, R)
>droGri2.scaffold_15110 7681540 97 + 24565398
UCACUCAAAAUGAUGGCAGAAAACUUUUCACAUUCGUUUUCGCA-AUACACAAACACAAAC---AAAAAAAUGCGAAU-AAAUGAGUUCGAAAAUGGGACUA-
...((((...((....))......(((((..(((((((((((((-................---.......)))))..-))))))))..)))))))))....- ( -13.00, z-score =  -0.55, R)
>consensus
UCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGC___AAAAAAGCAGGGGG__AAAAAAUGCGAAUAAAUGAGUUC
..(((((((((((..(.((((....)))).)..))))))((((((((....................................)))))))).....))))).. (-13.74 = -14.82 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:21:40 2011