Locus 889

Sequence ID dm3.chr2L
Location 6,480,967 – 6,481,084
Length 117
Max. P 0.998390
window1201 window1202 window1203 window1204

overview

Window 1

Location 6,480,967 – 6,481,065
Length 98
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 93.37
Shannon entropy 0.11589
G+C content 0.45918
Mean single sequence MFE -29.10
Consensus MFE -22.90
Energy contribution -22.50
Covariance contribution -0.40
Combinations/Pair 1.07
Mean z-score -2.53
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.904632
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6480967 98 + 23011544
CAGUGCACUCUGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACCCGGUC
..........(((((.((((........((((((((((....)))))))))).((((((((...))))).))).......)))))))))......... ( -26.50, z-score =  -1.37, R)
>droEre2.scaffold_4929 15389837 98 + 26641161
CAGUGCAUUCAGUAGGCGAGCGUAAUAAAUAUGUGGGAGAAUUCCCACAUAUAUAUAGUAUUCAGUGCCAGUGCCGAGAACUCGGACCGAAAACGGAC
..............((((((..(.(((.(((((((((......))))))))).))).)..)))...)))....((((....)))).(((....))).. ( -28.30, z-score =  -2.70, R)
>droYak2.chr2L 15888557 98 - 22324452
UAGUGCAUUCAGUAGGCGAGCGUAAUAAAUAUGUGGGAGAAUUCCCACAUAUAUAUAGUAUUCAGUGCCAGUGCCGAGAACUCGGAUCGAACACGGAC
..(((..(((....((((((..(.(((.(((((((((......))))))))).))).)..)))...)))....((((....))))...)))))).... ( -29.10, z-score =  -2.76, R)
>droSec1.super_5 4530271 98 + 5866729
CAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACGCGGAC
...(((.(((.((((.((((........((((((((((....)))))))))).((((((((...))))).))).......))))))))))).)))... ( -30.80, z-score =  -2.91, R)
>droSim1.chr2L 6272120 98 + 22036055
CAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACGCGGAC
...(((.(((.((((.((((........((((((((((....)))))))))).((((((((...))))).))).......))))))))))).)))... ( -30.80, z-score =  -2.91, R)
>consensus
CAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACACGGAC
....(((((.....((((...(((.((.((((((((((....)))))))))).))...)))....)))))))))(((....))).............. (-22.90 = -22.50 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,480,967 – 6,481,065
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 93.37
Shannon entropy 0.11589
G+C content 0.45918
Mean single sequence MFE -32.64
Consensus MFE -28.82
Energy contribution -29.86
Covariance contribution 1.04
Combinations/Pair 1.09
Mean z-score -4.08
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.34
SVM RNA-class probability 0.998390
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6480967 98 - 23011544
GACCGGGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACAGAGUGCACUG
....(.(((((((((((((((...((....))...)).....(((.((((((((((....))))))))))....)))))))).)))).)))).).... ( -30.30, z-score =  -2.53, R)
>droEre2.scaffold_4929 15389837 98 - 26641161
GUCCGUUUUCGGUCCGAGUUCUCGGCACUGGCACUGAAUACUAUAUAUAUGUGGGAAUUCUCCCACAUAUUUAUUACGCUCGCCUACUGAAUGCACUG
....((.((((((((((....))))....(((...((.....(((.((((((((((....)))))))))).))).....))))).)))))).)).... ( -29.80, z-score =  -3.61, R)
>droYak2.chr2L 15888557 98 + 22324452
GUCCGUGUUCGAUCCGAGUUCUCGGCACUGGCACUGAAUACUAUAUAUAUGUGGGAAUUCUCCCACAUAUUUAUUACGCUCGCCUACUGAAUGCACUA
....(((((((..((((....))))....(((...((.....(((.((((((((((....)))))))))).))).....)))))...))))))).... ( -28.90, z-score =  -3.22, R)
>droSec1.super_5 4530271 98 - 5866729
GUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUG
....(((((((((((((((((...((....))...)).....(((.((((((((((....))))))))))....)))))))).)))).)))))).... ( -37.10, z-score =  -5.51, R)
>droSim1.chr2L 6272120 98 - 22036055
GUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUG
....(((((((((((((((((...((....))...)).....(((.((((((((((....))))))))))....)))))))).)))).)))))).... ( -37.10, z-score =  -5.51, R)
>consensus
GUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUG
....(((((((((((((((((...((....))...)).....(((.((((((((((....)))))))))).)))...))))).)))).)))))).... (-28.82 = -29.86 +   1.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,480,988 – 6,481,084
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 94.06
Shannon entropy 0.10326
G+C content 0.45000
Mean single sequence MFE -29.10
Consensus MFE -23.46
Energy contribution -23.30
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.38
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873600
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6480988 96 + 23011544
GUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACCCGGUCGCGUCGUUCACAUAUGUGU
.......((((((((((....))))))))))(((((.......(.((....)))..((((.(((..((....))...)))..)))).....))))) ( -26.30, z-score =  -2.05, R)
>droEre2.scaffold_4929 15389858 96 + 26641161
GUAAUAAAUAUGUGGGAGAAUUCCCACAUAUAUAUAGUAUUCAGUGCCAGUGCCGAGAACUCGGACCGAAAACGGACGCGUCGUGCACAUAUGCGU
...(((.(((((((((......))))))))).))).((((...(((((.(((((((....)))).(((....))).)))...).))))..)))).. ( -32.20, z-score =  -3.29, R)
>droYak2.chr2L 15888578 96 - 22324452
GUAAUAAAUAUGUGGGAGAAUUCCCACAUAUAUAUAGUAUUCAGUGCCAGUGCCGAGAACUCGGAUCGAACACGGACGCGUCGUGCACAUAUGCGU
((((((.(((((((((......))))))))).))).((((...(((((.(((((((....))))......))))).)))...)))).....))).. ( -29.80, z-score =  -2.16, R)
>droSec1.super_5 4530292 96 + 5866729
GUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACGCGGACGCGUCGUUCACAUAUGCGU
.......((((((((((....)))))))))).....((((...(((.....((.((....))))(((((.(((....)))))))))))..)))).. ( -28.60, z-score =  -2.21, R)
>droSim1.chr2L 6272141 96 + 22036055
GUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACGCGGACGCGUCGUUCACAUAUGCGU
.......((((((((((....)))))))))).....((((...(((.....((.((....))))(((((.(((....)))))))))))..)))).. ( -28.60, z-score =  -2.21, R)
>consensus
GUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACACGGACGCGUCGUUCACAUAUGCGU
.......((((((((((....)))))))))).....((((...(((...((((((.....(((...)))...))).)))......)))..)))).. (-23.46 = -23.30 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,480,988 – 6,481,084
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 94.06
Shannon entropy 0.10326
G+C content 0.45000
Mean single sequence MFE -30.38
Consensus MFE -24.82
Energy contribution -24.66
Covariance contribution -0.16
Combinations/Pair 1.10
Mean z-score -2.80
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.74
SVM RNA-class probability 0.964473
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6480988 96 - 23011544
ACACAUAUGUGAACGACGCGACCGGGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUAC
.(((....))).....((((((.......))))))(((..((((........))))..)))(((.((((((((((....)))))))))).)))... ( -28.50, z-score =  -2.54, R)
>droEre2.scaffold_4929 15389858 96 - 26641161
ACGCAUAUGUGCACGACGCGUCCGUUUUCGGUCCGAGUUCUCGGCACUGGCACUGAAUACUAUAUAUAUGUGGGAAUUCUCCCACAUAUUUAUUAC
........((((..((((....))))..((((((((....)))).))))))))........(((.((((((((((....)))))))))).)))... ( -30.80, z-score =  -3.07, R)
>droYak2.chr2L 15888578 96 + 22324452
ACGCAUAUGUGCACGACGCGUCCGUGUUCGAUCCGAGUUCUCGGCACUGGCACUGAAUACUAUAUAUAUGUGGGAAUUCUCCCACAUAUUUAUUAC
..((....((((.((((((....))).)))...(((....)))))))..))..........(((.((((((((((....)))))))))).)))... ( -30.60, z-score =  -2.77, R)
>droSec1.super_5 4530292 96 - 5866729
ACGCAUAUGUGAACGACGCGUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUAC
.((((....((((((.((....)))))))).))))(((..((((........))))..)))(((.((((((((((....)))))))))).)))... ( -31.00, z-score =  -2.80, R)
>droSim1.chr2L 6272141 96 - 22036055
ACGCAUAUGUGAACGACGCGUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUAC
.((((....((((((.((....)))))))).))))(((..((((........))))..)))(((.((((((((((....)))))))))).)))... ( -31.00, z-score =  -2.80, R)
>consensus
ACGCAUAUGUGAACGACGCGUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUAC
.(((....)))..((((((....))).))).....(((..((((........))))..)))(((.((((((((((....)))))))))).)))... (-24.82 = -24.66 +  -0.16)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:21:27 2011