Locus 10678

Sequence ID dm3.chr3R
Location 15,612,726 – 15,612,842
Length 116
Max. P 0.929053
window14678 window14679 window14680 window14681

overview

Window 8

Location 15,612,726 – 15,612,833
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 88.22
Shannon entropy 0.20899
G+C content 0.46042
Mean single sequence MFE -33.32
Consensus MFE -23.16
Energy contribution -24.60
Covariance contribution 1.44
Combinations/Pair 1.12
Mean z-score -2.62
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.34
SVM RNA-class probability 0.929053
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15612726 107 + 27905053
UUCCGAUCGGUGAUCGGUGAUCGGAGAUCGCAGAUCUCAGUUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUU
.((((((((.(....).))))))))((((((((((..(.(((....))).)...))))))))))..........((((((......))))))(((((.....))))) ( -34.60, z-score =  -2.08, R)
>droEre2.scaffold_4770 11696146 107 - 17746568
UUCCGAUCGGCGAUUGGAGAUUGGAGAUCACAGAUCUCAGAUCCAGAAUCGCAAAUCUGCGAUCUAAUCCGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUU
....((((((((..((((((((.((((((...)))))).)))).(((.(((((....))))))))..))))..))))))))...........(((((.....))))) ( -34.70, z-score =  -2.68, R)
>droYak2.chr3R 4374736 93 + 28832112
--------------UUCCGAUCGGAGAUCGCAGAUCUCAGAUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUU
--------------...(((.((((((((((((((....(((.....)))....))))))))))).........((((((......))))))..))))))....... ( -29.00, z-score =  -2.81, R)
>droSec1.super_1 14195114 107 - 14215200
UUCCGAUCGGUGAUCUGAGAUCGCAGAGCUCAGAUCACAGUUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCCGAUUAAUUCAUUAGCAACUGUCGACCAGUU
....(((((((((((((((.((...)).))))))))...((..((((((((((....))))))....)))).)))))))))...........(((((.....))))) ( -33.50, z-score =  -2.70, R)
>droSim1.chr3R 21641473 107 - 27517382
UUCCGAUCGGUGAUCUGAGAUCGCAGAGCUCAGAUCACAGUUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUU
...((((.(((((((((((.((...)).)))))))))).((..((((((((((....))))))....)))).))((((((......))))))..).))))....... ( -34.80, z-score =  -2.82, R)
>consensus
UUCCGAUCGGUGAUCUGAGAUCGGAGAUCGCAGAUCUCAGUUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUU
...........(((((((((((...))))))))))).......((((((((((....))))))....))))...((((((......))))))(((((.....))))) (-23.16 = -24.60 +   1.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,612,726 – 15,612,833
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 88.22
Shannon entropy 0.20899
G+C content 0.46042
Mean single sequence MFE -36.84
Consensus MFE -25.52
Energy contribution -29.44
Covariance contribution 3.92
Combinations/Pair 1.08
Mean z-score -2.58
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.909653
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15612726 107 - 27905053
AACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGAGAUCUGCGAUCUCCGAUCACCGAUCACCGAUCGGAA
...((((((....((((...(((.....)))....))))...(((((((((((((.((.((....)).))))))))))))))).))))))((((((...)))))).. ( -36.40, z-score =  -2.48, R)
>droEre2.scaffold_4770 11696146 107 + 17746568
AACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCGGAUUAGAUCGCAGAUUUGCGAUUCUGGAUCUGAGAUCUGUGAUCUCCAAUCUCCAAUCGCCGAUCGGAA
..(((((((.(....(((.((......)).))).((.((((((((((((((((((..((((...))))..)))))))))))))..))))).))...).))))))).. ( -34.70, z-score =  -1.70, R)
>droYak2.chr3R 4374736 93 - 28832112
AACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAUCUGAGAUCUGCGAUCUCCGAUCGGAA--------------
..(((((((....((((...(((.....)))....))))...(((((((((((((..((((...))))..))))))))))))).)))))))..-------------- ( -33.60, z-score =  -2.64, R)
>droSec1.super_1 14195114 107 + 14215200
AACUGGUCGACAGUUGCUAAUGAAUUAAUCGGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGUGAUCUGAGCUCUGCGAUCUCAGAUCACCGAUCGGAA
..(((((((((((((((..((......))..))...((((....(((((......))))))))).))))))((((((((.((...)).))))))))..))))))).. ( -40.10, z-score =  -3.13, R)
>droSim1.chr3R 21641473 107 + 27517382
AACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGUGAUCUGAGCUCUGCGAUCUCAGAUCACCGAUCGGAA
..((((((((((((((((.((......)).)))...((((....(((((......))))))))).))))))((((((((.((...)).))))))))..))))))).. ( -39.40, z-score =  -2.97, R)
>consensus
AACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGAGAUCUGAGAUCUCCGAUCUCAGAUCACCGAUCGGAA
..(((((((.((((((((.((......)).)))...((((....(((((......))))))))).))))).(((((((((((...)))))))))))..))))))).. (-25.52 = -29.44 +   3.92)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,612,736 – 15,612,842
Length 106
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 82.89
Shannon entropy 0.32393
G+C content 0.43806
Mean single sequence MFE -30.03
Consensus MFE -17.58
Energy contribution -17.50
Covariance contribution -0.08
Combinations/Pair 1.14
Mean z-score -2.37
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.899027
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15612736 106 + 27905053
UGAUCGGUGAUCGGAGAUCGCAGAUCUCAGUUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUUUGUCAGUUA
(((((((((..((((((((((((((..(.(((....))).)...))))))))))...))))..)))))))))..........(((((.(((.....))).))))). ( -32.80, z-score =  -2.10, R)
>droEre2.scaffold_4770 11696156 106 - 17746568
CGAUUGGAGAUUGGAGAUCACAGAUCUCAGAUCCAGAAUCGCAAAUCUGCGAUCUAAUCCGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUUUGUCAGUUA
.(((((((((((.((((((...)))))).)))).....(((((....)))))))))))).....((((((......))))))(((((.(((.....))).))))). ( -33.40, z-score =  -2.86, R)
>droYak2.chr3R 4374744 94 + 28832112
------------GGAGAUCGCAGAUCUCAGAUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUUUGUCAGUUA
------------..(((((((((((....(((.....)))....))))))))))).........((((((......))))))(((((.(((.....))).))))). ( -29.70, z-score =  -2.98, R)
>droAna3.scaffold_13340 2194980 80 + 23697760
--------------------------ACAGAUCUGCGAUCGCGAAUCUGCGAUCUAAUCUCCGUGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUUUGUCAGUUA
--------------------------..((((.((.(((((((....)))))))))))))....((((((......))))))(((((.(((.....))).))))). ( -21.00, z-score =  -1.59, R)
>droSec1.super_1 14195124 106 - 14215200
UGAUCUGAGAUCGCAGAGCUCAGAUCACAGUUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCCGAUUAAUUCAUUAGCAACUGUCGACCAGUUUGUCAGUUA
(((((((((.((...)).)))))))))..((..((((((((((....))))))....)))).))((..((......))..))(((((.(((.....))).))))). ( -29.90, z-score =  -1.98, R)
>droSim1.chr3R 21641483 106 - 27517382
UGAUCUGAGAUCGCAGAGCUCAGAUCACAGUUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUUUGUCAGUUA
(((((((((.((...)).)))))))))..((..((((((((((....))))))....)))).))((((((......))))))(((((.(((.....))).))))). ( -33.40, z-score =  -2.69, R)
>consensus
UGAUC_GAGAUCGGAGAUCGCAGAUCACAGAUCCAGAAUCGCAAAUCUGCGAUCUAAUCUGCACGCUGAUUAAUUCAUUAGCAACUGUCGACCAGUUUGUCAGUUA
..................................(((.(((((....)))))))).........((((((......))))))(((((.(((.....))).))))). (-17.58 = -17.50 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,612,736 – 15,612,842
Length 106
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 82.89
Shannon entropy 0.32393
G+C content 0.43806
Mean single sequence MFE -30.08
Consensus MFE -16.83
Energy contribution -16.92
Covariance contribution 0.08
Combinations/Pair 1.14
Mean z-score -1.91
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.00
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr3R 15612736 106 - 27905053
UAACUGACAAACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGAGAUCUGCGAUCUCCGAUCACCGAUCA
...(((((.(((((.....)))))(((.((......)).))))).)))...(((((((((((((.((.((....)).)))))))))))))))..((((...)))). ( -31.40, z-score =  -1.89, R)
>droEre2.scaffold_4770 11696156 106 + 17746568
UAACUGACAAACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCGGAUUAGAUCGCAGAUUUGCGAUUCUGGAUCUGAGAUCUGUGAUCUCCAAUCUCCAAUCG
.........(((((.....)))))(((.((......)).))).((.((((((((((((((((((..((((...))))..)))))))))))))..))))).)).... ( -29.50, z-score =  -1.40, R)
>droYak2.chr3R 4374744 94 - 28832112
UAACUGACAAACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAUCUGAGAUCUGCGAUCUCC------------
...(((((.(((((.....)))))(((.((......)).))))).)))...(((((((((((((..((((...))))..)))))))))))))..------------ ( -31.00, z-score =  -2.83, R)
>droAna3.scaffold_13340 2194980 80 - 23697760
UAACUGACAAACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCACGGAGAUUAGAUCGCAGAUUCGCGAUCGCAGAUCUGU--------------------------
...(((...(((((.....)))))(((.((......)).))).)))(((((.((((((......))))))...)))))..-------------------------- ( -22.30, z-score =  -1.71, R)
>droSec1.super_1 14195124 106 + 14215200
UAACUGACAAACUGGUCGACAGUUGCUAAUGAAUUAAUCGGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGUGAUCUGAGCUCUGCGAUCUCAGAUCA
...((((..(((((.....)))))((..((......))..)).(((((((((((((((((.(((........))).)))))))))))..))))))...)))).... ( -33.50, z-score =  -1.93, R)
>droSim1.chr3R 21641483 106 + 27517382
UAACUGACAAACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGUGAUCUGAGCUCUGCGAUCUCAGAUCA
...((((..(((((.....)))))(((.((......)).))).(((((((((((((((((.(((........))).)))))))))))..))))))...)))).... ( -32.80, z-score =  -1.71, R)
>consensus
UAACUGACAAACUGGUCGACAGUUGCUAAUGAAUUAAUCAGCGUGCAGAUUAGAUCGCAGAUUUGCGAUUCUGGAACUGAGAUCUGAGAUCUCCGAUCUC_GAUCA
...(((((.(((((.....)))))(((.((......)).))))).)))....((((((......)))))).................................... (-16.83 = -16.92 +   0.08)

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 00:28:28 2011