Locus 8019

Sequence ID dm3.chr3L
Location 19,482,488 – 19,482,632
Length 144
Max. P 0.956775
window11036 window11037

overview

Window 6

Location 19,482,488 – 19,482,632
Length 144
Sequences 5
Columns 144
Reading direction forward
Mean pairwise identity 68.92
Shannon entropy 0.57126
G+C content 0.60718
Mean single sequence MFE -51.98
Consensus MFE -22.21
Energy contribution -23.69
Covariance contribution 1.48
Combinations/Pair 1.33
Mean z-score -2.06
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956775
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19482488 144 + 24543557
AGACGCCCAGGCGGCUACAGGCGAAAAAGUACGUAAGACGUGGGGCGAAGGACCAACCAGCCAGCCUGCAGCAUCCAGGAUACAGGUCCUGAGACCCAGGACGUAGGUCGCAGGACGCAGGACCGAGAAUCUGCGAAUGAGCCG
...(((....)))(((.(((((.......((((.....)))).(((...((.....)).))).))))).))).....((...((.((((((.((((.........)))).))))))(((((........)))))...))..)). ( -51.00, z-score =  -1.37, R)
>droAna3.scaffold_13337 5291826 109 - 23293914
AGACGCCCAAGCAGCUGCAGGCGGCAAGGCAAUCCGGACG---------AGUCC--UUAGCAAGC----------CAGGAUAGAGGUCCUGGGACCCUGAAAACGGCAGACAGGAUCCGGGACUGAGCCC--------------
...((((...((....)).))))....(((.((((((.(.---------.((..--...))..))----------).))))...(((((((((..((((...........)))).)))))))))..))).-------------- ( -36.20, z-score =   0.30, R)
>droYak2.chr3L 3140702 143 - 24197627
AGACGCCCAAGCGGCUGCAGGCGGAAAAGUAUGUAAGACG-GGGGCUAAAGCCCCACCAGCCAGCUUUCAGCUUGCAGCAUCCAGGAUACAGGCUCUGGGACGUAGGAUGAAGGACGCAGGACCGAGAAUCUGCGAAUGAGGCG
...((((((.((((((((((((.((((.((.((.......-(((((....)))))......)))))))).))))))))).((((((........)))))).)))...........((((((........))))))..)).)))) ( -54.72, z-score =  -1.73, R)
>droSec1.super_29 186851 130 + 700605
AGACGCCCAGGCGGCUGCAGGCGGAAAAGUACGUAAGAAGGGGGGUGAAGUACCAACCAGCCAGCCUGCAGCAUCCAGGAUACAGGUCCUGGGACUC--------------AGGACGCAGGACCGAGAAUCUGCGAAUGAGCCG
...(((....)))(((((((((((.......(....)..((..((((...))))..))..)).))))))))).((((((((....)))))))).(((--------------(...((((((........))))))..))))... ( -57.40, z-score =  -3.76, R)
>droSim1.chr3L 18814757 137 + 22553184
AGACGCCCAGGCGGCUGCAGGCGGAAAAGUACGUAAGAAGGGGGGUGAAGUACCAACCAGCCAGCCUGCAGCAUCCAGGAUACAGGUCCUGGGACUCAGGACGC-------AGGACUCAGGACCGAGAAUCUGCGAAUGAGCCG
...(((....)))(((((((((((.......(....)..((..((((...))))..))..)).))))))))).((((((((....)))))))).((((...(((-------(((.(((......)))..))))))..))))... ( -60.60, z-score =  -3.76, R)
>consensus
AGACGCCCAGGCGGCUGCAGGCGGAAAAGUACGUAAGACG_GGGGCGAAGGACCAACCAGCCAGCCUGCAGCAUCCAGGAUACAGGUCCUGGGACCCAGGACGC_G_____AGGACGCAGGACCGAGAAUCUGCGAAUGAGCCG
...(((.((((((((((...((......))............((........))...))))).)))))................(((((((.(.((................)).).)))))))........)))......... (-22.21 = -23.69 +   1.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,482,488 – 19,482,632
Length 144
Sequences 5
Columns 144
Reading direction reverse
Mean pairwise identity 68.92
Shannon entropy 0.57126
G+C content 0.60718
Mean single sequence MFE -50.07
Consensus MFE -21.18
Energy contribution -24.98
Covariance contribution 3.80
Combinations/Pair 1.17
Mean z-score -1.47
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.659743
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19482488 144 - 24543557
CGGCUCAUUCGCAGAUUCUCGGUCCUGCGUCCUGCGACCUACGUCCUGGGUCUCAGGACCUGUAUCCUGGAUGCUGCAGGCUGGCUGGUUGGUCCUUCGCCCCACGUCUUACGUACUUUUUCGCCUGUAGCCGCCUGGGCGUCU
..(((((...((((..(....)..))))((((((.((((((.....)))))).)))))).........((..(((((((((.(((.((.....))...)))..(((.....)))........)))))))))..))))))).... ( -56.20, z-score =  -1.88, R)
>droAna3.scaffold_13337 5291826 109 + 23293914
--------------GGGCUCAGUCCCGGAUCCUGUCUGCCGUUUUCAGGGUCCCAGGACCUCUAUCCUG----------GCUUGCUAA--GGACU---------CGUCCGGAUUGCCUUGCCGCCUGCAGCUGCUUGGGCGUCU
--------------((((..(((((.((((((((...........))))))))(((((......)))))----------.........--)))))---------.))))((((.((((.((.((.....)).))..)))))))) ( -42.90, z-score =  -0.78, R)
>droYak2.chr3L 3140702 143 + 24197627
CGCCUCAUUCGCAGAUUCUCGGUCCUGCGUCCUUCAUCCUACGUCCCAGAGCCUGUAUCCUGGAUGCUGCAAGCUGAAAGCUGGCUGGUGGGGCUUUAGCCCC-CGUCUUACAUACUUUUCCGCCUGCAGCCGCUUGGGCGUCU
((((.((..(((((..(((.((....((((..........)))))).)))..)))).........((((((.((.(((((.((...((.(((((....)))))-...))....)).))))).)).)))))).)..))))))... ( -45.00, z-score =   0.30, R)
>droSec1.super_29 186851 130 - 700605
CGGCUCAUUCGCAGAUUCUCGGUCCUGCGUCCU--------------GAGUCCCAGGACCUGUAUCCUGGAUGCUGCAGGCUGGCUGGUUGGUACUUCACCCCCCUUCUUACGUACUUUUCCGCCUGCAGCCGCCUGGGCGUCU
.((((((..(((((..(....)..)))))...)--------------)))))((((((......))))))..(((((((((.((......(((((.................)))))...)))))))))))(((....)))... ( -50.93, z-score =  -2.29, R)
>droSim1.chr3L 18814757 137 - 22553184
CGGCUCAUUCGCAGAUUCUCGGUCCUGAGUCCU-------GCGUCCUGAGUCCCAGGACCUGUAUCCUGGAUGCUGCAGGCUGGCUGGUUGGUACUUCACCCCCCUUCUUACGUACUUUUCCGCCUGCAGCCGCCUGGGCGUCU
.((((((..(((((...((((....))))..))-------)))...))))))((((((......))))))..(((((((((.((......(((((.................)))))...)))))))))))(((....)))... ( -55.33, z-score =  -2.71, R)
>consensus
CGGCUCAUUCGCAGAUUCUCGGUCCUGCGUCCU_____C_ACGUCCUGGGUCCCAGGACCUGUAUCCUGGAUGCUGCAGGCUGGCUGGUUGGUCCUUCACCCC_CGUCUUACGUACUUUUCCGCCUGCAGCCGCCUGGGCGUCU
....................(((((((.(.(((..............))).).)))))))........(((((((.(((((.(((((...((...............................))..))))))))))))))))) (-21.18 = -24.98 +   3.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:37:52 2011