Locus 12097

Sequence ID dm3.chr3R
Location 25,644,210 – 25,644,332
Length 122
Max. P 0.990554
window16631 window16632 window16633

overview

Window 1

Location 25,644,210 – 25,644,321
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 89.26
Shannon entropy 0.16700
G+C content 0.51838
Mean single sequence MFE -33.45
Consensus MFE -29.50
Energy contribution -29.62
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -1.58
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.778762
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25644210 111 + 27905053
GUUAUGGUGGAUUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGACACCUGCGUACGUACCUUUCUCACUCCCAACUCCCAACUC
....(((..(.((((((((((.....)))))))))).((((((.....(((((.((...(....)(((((.....))))).)))))))......)))))).)..))).... ( -37.40, z-score =  -2.54, R)
>droYak2.chr3R 8007734 100 - 28832112
GUUAUGGUGGAUUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUAUUGUACAUACACCUG-----------
.....((((..((((((((((.....))))))))))............(((((....(((......)))..)))))..((((.....))))...))))..----------- ( -31.70, z-score =  -1.81, R)
>droSec1.super_4 4494747 100 + 6179234
GUUAUGGUGGAUUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUACCUUCCUCACUCCCA-----------
...........((((((((((.....)))))))))).((((((.....(((((.((...(....)((((((...)))))).)))))))......))))))----------- ( -33.50, z-score =  -1.30, R)
>droSim1.chr3R 25316795 100 + 27517382
GUUAUGGUGGAUUUGGCCUAAGCCGAUUAGGCUACAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUACCUUCCUCACUCCCA-----------
.............((((((((.....))))))))...((((((.....(((((.((...(....)((((((...)))))).)))))))......))))))----------- ( -31.20, z-score =  -0.70, R)
>consensus
GUUAUGGUGGAUUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUACCUUCCUCACUCCCA___________
...........((((((((((.....)))))))))).((((((.....(((((....(((......)))..)))))((....))..........))))))........... (-29.50 = -29.62 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,644,221 – 25,644,332
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 83.17
Shannon entropy 0.25980
G+C content 0.52508
Mean single sequence MFE -32.09
Consensus MFE -29.60
Energy contribution -29.72
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -2.33
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.43
SVM RNA-class probability 0.990554
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25644221 111 + 27905053
UUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGACACCUGCGUACGUACCUUUCUCACUCCCAACUCCCAACUCCACACUCCUCA
((((((((((.....)))))))))).((((((.....((((((.(((.......(((((.....)))))........)))))))))....))))))............... ( -33.76, z-score =  -2.63, R)
>droYak2.chr3R 8007745 89 - 28832112
UUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUAUUGUACAUACACCUG----------------------
((((((((((.....))))))))))..(((.......(((((....(((......)))..)))))..((((.....)))).....))).---------------------- ( -28.60, z-score =  -2.13, R)
>droSec1.super_4 4494758 97 + 6179234
UUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUACCUUCCUCACUCCCAACUCCUCA--------------
((((((((((.....)))))))))).((((((.....(((((.((...(....)((((((...)))))).)))))))......))))))........-------------- ( -34.00, z-score =  -2.43, R)
>droSim1.chr3R 25316806 97 + 27517382
UUUGGCCUAAGCCGAUUAGGCUACAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUACCUUCCUCACUCCCAACUCCUCA--------------
..((((((((.....))))))))...((((((.....(((((.((...(....)((((((...)))))).)))))))......))))))........-------------- ( -32.00, z-score =  -2.13, R)
>consensus
UUUGGCCUAAGCCGAUUAGGCUAGAAUGGGAGAAAAUGGGUGACGAGCGAUUUCACGCGGCACCUGCGUACGUACCUUCCUCACUCCCAACUCCUCA______________
((((((((((.....)))))))))).((((((.....(((((....(((......)))..)))))((....))..........))))))...................... (-29.60 = -29.72 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 25,644,221 – 25,644,332
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 83.17
Shannon entropy 0.25980
G+C content 0.52508
Mean single sequence MFE -33.92
Consensus MFE -22.86
Energy contribution -23.67
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.95
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.640889
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25644221 111 - 27905053
UGAGGAGUGUGGAGUUGGGAGUUGGGAGUGAGAAAGGUACGUACGCAGGUGUCGCGUGAAAUCGCUCGUCACCCAUUUUCUCCCAUUCUAGCCUAAUCGGCUUAGGCCAAA
.((..((..((((((.(((((.((((.(((((...(((...(((((.......)))))..))).)))).).))))....)))))))))))..))..))(((....)))... ( -41.40, z-score =  -2.37, R)
>droYak2.chr3R 8007745 89 + 28832112
----------------------CAGGUGUAUGUACAAUACGUACGCAGGUGCCGCGUGAAAUCGCUCGUCACCCAUUUUCUCCCAUUCUAGCCUAAUCGGCUUAGGCCAAA
----------------------...(((((((((...))))))))).((((.((.(((....))).)).)))).................((((((.....)))))).... ( -26.90, z-score =  -2.61, R)
>droSec1.super_4 4494758 97 - 6179234
--------------UGAGGAGUUGGGAGUGAGGAAGGUACGUACGCAGGUGCCGCGUGAAAUCGCUCGUCACCCAUUUUCUCCCAUUCUAGCCUAAUCGGCUUAGGCCAAA
--------------((.((((...((.((((.((.(((((........)))))(((......))))).)))))).....)))))).....((((((.....)))))).... ( -33.70, z-score =  -1.42, R)
>droSim1.chr3R 25316806 97 - 27517382
--------------UGAGGAGUUGGGAGUGAGGAAGGUACGUACGCAGGUGCCGCGUGAAAUCGCUCGUCACCCAUUUUCUCCCAUUGUAGCCUAAUCGGCUUAGGCCAAA
--------------((.((((...((.((((.((.(((((........)))))(((......))))).)))))).....)))))).....((((((.....)))))).... ( -33.70, z-score =  -1.41, R)
>consensus
______________UGAGGAGUUGGGAGUGAGGAAGGUACGUACGCAGGUGCCGCGUGAAAUCGCUCGUCACCCAUUUUCUCCCAUUCUAGCCUAAUCGGCUUAGGCCAAA
......................((((((.(((........(....).((((.((.(((....))).)).))))..))).)))))).....((((((.....)))))).... (-22.86 = -23.67 +   0.81)

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 00:55:41 2011