Locus 9427

Sequence ID dm3.chr3R
Location 6,583,002 – 6,583,145
Length 143
Max. P 0.983047
window12926 window12927 window12928 window12929

overview

Window 6

Location 6,583,002 – 6,583,111
Length 109
Sequences 3
Columns 109
Reading direction forward
Mean pairwise identity 84.66
Shannon entropy 0.20219
G+C content 0.49281
Mean single sequence MFE -28.90
Consensus MFE -21.70
Energy contribution -22.37
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.788163
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6583002 109 + 27905053
GUGUUCAGAGAUAGCCACGUCACGAUCACGAUGACGAGGCGUUAAGUGAGAUUGCAGAUAAGCCCAAUCUACAGAUCCAGACCAUAACUAGAUCUGCUAUCUCCAAGCA
.((((..(((((((((.(((((((....)).))))).)))........((((((..........)))))).((((((.((.......)).)))))).))))))..)))) ( -32.30, z-score =  -3.18, R)
>droSim1.chr3R 12739222 95 - 27517382
GUGUGCAGAGAUAGCCACGUCACGAUCACGAUGACGAGGCGUUAAGUGAGCUGCCAGAUAAGCGCAAUCUGAAGAUCCAGACCAGAUCUAGAUCA--------------
.....((((....(((.(((((((....)).))))).)))......((.(((........))).)).))))..((((.(((.....))).)))).-------------- ( -27.20, z-score =  -1.52, R)
>droSec1.super_0 5761749 95 - 21120651
GUGUGCAGAGAUAGCCACGUCACGAUCACGAUGACGAGGCGUUAAGUGAGCUGCCAGAUAAGCGCAAUCUGAAGAUCCAGACCAGAUCUAGAUCA--------------
.....((((....(((.(((((((....)).))))).)))......((.(((........))).)).))))..((((.(((.....))).)))).-------------- ( -27.20, z-score =  -1.52, R)
>consensus
GUGUGCAGAGAUAGCCACGUCACGAUCACGAUGACGAGGCGUUAAGUGAGCUGCCAGAUAAGCGCAAUCUGAAGAUCCAGACCAGAUCUAGAUCA______________
.....((((....(((.(((((((....)).))))).)))......((.(((........))).)).))))..((((.((.......)).))))............... (-21.70 = -22.37 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,583,002 – 6,583,111
Length 109
Sequences 3
Columns 109
Reading direction reverse
Mean pairwise identity 84.66
Shannon entropy 0.20219
G+C content 0.49281
Mean single sequence MFE -34.40
Consensus MFE -28.33
Energy contribution -27.56
Covariance contribution -0.77
Combinations/Pair 1.12
Mean z-score -2.68
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.12
SVM RNA-class probability 0.983047
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6583002 109 - 27905053
UGCUUGGAGAUAGCAGAUCUAGUUAUGGUCUGGAUCUGUAGAUUGGGCUUAUCUGCAAUCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGAACAC
((.(..((((((((((((((((.......))))))))))((((((.(......).))))))........(((.(((((.((....))))))).)))))))))..).)). ( -41.60, z-score =  -3.92, R)
>droSim1.chr3R 12739222 95 + 27517382
--------------UGAUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGCACAC
--------------.(((((((((...)))))))))..((((..(((((.....))).)).........(((.(((((.((....))))))).)))....))))..... ( -30.80, z-score =  -2.06, R)
>droSec1.super_0 5761749 95 + 21120651
--------------UGAUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGCACAC
--------------.(((((((((...)))))))))..((((..(((((.....))).)).........(((.(((((.((....))))))).)))....))))..... ( -30.80, z-score =  -2.06, R)
>consensus
______________UGAUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGCACAC
...............((((((((.....)))))))).((((((.......))))))..((.........(((.(((((.((....))))))).))).......)).... (-28.33 = -27.56 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,583,025 – 6,583,145
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 66.52
Shannon entropy 0.51389
G+C content 0.43057
Mean single sequence MFE -29.14
Consensus MFE -8.44
Energy contribution -12.00
Covariance contribution 3.56
Combinations/Pair 1.12
Mean z-score -2.31
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.519833
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6583025 120 + 27905053
GAUCACGAUGACGAGGCGUUAAGUGAGAUUGCAGAUAAGCCCAAUCUACAGAUCCAGACCAUAACUAGAUCUGCUAUCUCCAAGCAUUAUCUGCAGAUCAAAACCAGAUCUAGAUCUGCU
..((((..(((((...))))).))))((((((((((((((........((((((.((.......)).))))))..........)).))))))))).))).....(((((....))))).. ( -32.47, z-score =  -2.46, R)
>droSim1.chr3R 12739245 106 - 27517382
GAUCACGAUGACGAGGCGUUAAGUGAGCUGCCAGAUAAGCGCAAUCUGAAGAUCCAGACCAGAUCUAGAUC--------------AUUAUCUACAGAUCAAAACCAGAUCUAGAUCUGCU
..((((..(((((...))))).))))(((........)))....((((......)))).((((((((((((--------------.....................)))))))))))).. ( -29.30, z-score =  -2.03, R)
>droSec1.super_0 5761772 106 - 21120651
GAUCACGAUGACGAGGCGUUAAGUGAGCUGCCAGAUAAGCGCAAUCUGAAGAUCCAGACCAGAUCUAGAUC--------------AUUAUCUACAGAUCAAAACCAGAUCUAGAUCUGCU
..((((..(((((...))))).))))(((........)))....((((......)))).((((((((((((--------------.....................)))))))))))).. ( -29.30, z-score =  -2.03, R)
>droAna3.scaffold_13340 1229188 92 + 23697760
AAUAAGGAUGAUGAAGCACUAAACUGGCUGGCUGAUAACACUUAUCUGUAGAGCUGUGCUUCAUCCCUCUU----------------CAUCC-UACUUCAG---UAUAUCUU--------
....(((((((((((((((......((((.((.((((.....)))).))..)))))))))))).......)----------------)))))-).......---........-------- ( -25.51, z-score =  -2.73, R)
>consensus
GAUCACGAUGACGAGGCGUUAAGUGAGCUGCCAGAUAAGCCCAAUCUGAAGAUCCAGACCAGAUCUAGAUC______________AUUAUCUACAGAUCAAAACCAGAUCUAGAUCUGCU
..((((..(((((...))))).)))).....(((((.......)))))...........((((((((((((...................................)))))))))))).. ( -8.44 = -12.00 +   3.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,583,025 – 6,583,145
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 66.52
Shannon entropy 0.51389
G+C content 0.43057
Mean single sequence MFE -31.87
Consensus MFE -14.52
Energy contribution -14.40
Covariance contribution -0.12
Combinations/Pair 1.30
Mean z-score -1.43
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.551831
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6583025 120 - 27905053
AGCAGAUCUAGAUCUGGUUUUGAUCUGCAGAUAAUGCUUGGAGAUAGCAGAUCUAGUUAUGGUCUGGAUCUGUAGAUUGGGCUUAUCUGCAAUCUCACUUAACGCCUCGUCAUCGUGAUC
..(((((....))))).....(((.(((((((((.(((..(.....((((((((((.......))))))))))...)..)))))))))))))))((((...(((...)))....)))).. ( -39.80, z-score =  -1.99, R)
>droSim1.chr3R 12739245 106 + 27517382
AGCAGAUCUAGAUCUGGUUUUGAUCUGUAGAUAAU--------------GAUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAUC
.(.(((((((((((.(((((.((((..........--------------)))).))))).))))))))))).).(((..((.......(((............))).......))..))) ( -33.34, z-score =  -1.59, R)
>droSec1.super_0 5761772 106 + 21120651
AGCAGAUCUAGAUCUGGUUUUGAUCUGUAGAUAAU--------------GAUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAUC
.(.(((((((((((.(((((.((((..........--------------)))).))))).))))))))))).).(((..((.......(((............))).......))..))) ( -33.34, z-score =  -1.59, R)
>droAna3.scaffold_13340 1229188 92 - 23697760
--------AAGAUAUA---CUGAAGUA-GGAUG----------------AAGAGGGAUGAAGCACAGCUCUACAGAUAAGUGUUAUCAGCCAGCCAGUUUAGUGCUUCAUCAUCCUUAUU
--------........---.......(-(((((----------------(.((((.((.((((...(((.....((((.....))))....)))..)))).)).)))).))))))).... ( -21.00, z-score =  -0.56, R)
>consensus
AGCAGAUCUAGAUCUGGUUUUGAUCUGUAGAUAAU______________GAUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGCCAGCUCACUUAACGCCUCGUCAUCGUGAUC
..........(((..(((.((((..........................(((((((.......))))))).((((((.......))))))........)))).)))..)))......... (-14.52 = -14.40 +  -0.12)

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 00:04:13 2011