Locus 11871

Sequence ID dm3.chr3R
Location 24,288,450 – 24,288,588
Length 138
Max. P 0.937390
window16316 window16317 window16318

overview

Window 6

Location 24,288,450 – 24,288,548
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 89.46
Shannon entropy 0.14736
G+C content 0.35034
Mean single sequence MFE -23.52
Consensus MFE -16.81
Energy contribution -15.93
Covariance contribution -0.87
Combinations/Pair 1.26
Mean z-score -2.72
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.894022
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24288450 98 + 27905053
GUCAGGAUAAGAAGACAAUGAAUAUUAAAACAUUUUAAUAUAUUUUCAUUCGCUCUGAGCCGGCACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUUG
.(((((....(((((.(((..((((((((....))))))))))).)).)))..)))))((((((((((....)))))).))))............... ( -21.70, z-score =  -2.49, R)
>droYak2.chr3R 6622269 98 - 28832112
GGCAGGAUAAGAAGGCCAUGAAUAUUAAAAUAUUUCAAUAUAUUUCCAUUUGCCCCGAACCGGCACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUAG
((((((....((((....((((...........)))).....))))..)))))).(((((((((((((....)))))).)))))))............ ( -25.40, z-score =  -2.97, R)
>droEre2.scaffold_4820 6719799 98 - 10470090
GGCAGGAUAAGAAGCGAAUGAAUAUUAAAAUAUUUCAAUAUAUUUCCGUUCGCCCUGUACCGACACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUUG
.(((((.......((((((((((((..............)))))..))))))))))))((((((((((....))))).)))))............... ( -23.45, z-score =  -2.71, R)
>consensus
GGCAGGAUAAGAAGACAAUGAAUAUUAAAAUAUUUCAAUAUAUUUCCAUUCGCCCUGAACCGGCACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUUG
(((.((((..(((.....((((...........)))).....)))..))))))).(((((((((((((....))))).))))))))............ (-16.81 = -15.93 +  -0.87)

alignment

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secondary structure

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dotplot

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Window 7

Location 24,288,450 – 24,288,548
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 89.46
Shannon entropy 0.14736
G+C content 0.35034
Mean single sequence MFE -22.67
Consensus MFE -17.57
Energy contribution -17.47
Covariance contribution -0.10
Combinations/Pair 1.20
Mean z-score -2.17
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.789253
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24288450 98 - 27905053
CAAUUUGUUAAUCAAACCGAGCACUUGAUUAAGUGCCGGCUCAGAGCGAAUGAAAAUAUAUUAAAAUGUUUUAAUAUUCAUUGUCUUCUUAUCCUGAC
..(((((((.......(((.((((((....))))))))).....)))))))((....((((((((....))))))))......))............. ( -18.20, z-score =  -1.45, R)
>droYak2.chr3R 6622269 98 + 28832112
CUAUUUGUUAAUCAAACCGAGCACUUGAUUAAGUGCCGGUUCGGGGCAAAUGGAAAUAUAUUGAAAUAUUUUAAUAUUCAUGGCCUUCUUAUCCUGCC
((((((((...((.(((((.((((((....))))))))))).)).))))))))....((((((((....))))))))....(((...........))) ( -25.70, z-score =  -2.37, R)
>droEre2.scaffold_4820 6719799 98 + 10470090
CAAUUUGUUAAUCAAACCGAGCACUUGAUUAAGUGUCGGUACAGGGCGAACGGAAAUAUAUUGAAAUAUUUUAAUAUUCAUUCGCUUCUUAUCCUGCC
...............(((((.(((((....)))))))))).(((((.(((((((...((((((((....))))))))...)))).)))...))))).. ( -24.10, z-score =  -2.69, R)
>consensus
CAAUUUGUUAAUCAAACCGAGCACUUGAUUAAGUGCCGGUUCAGGGCGAAUGGAAAUAUAUUGAAAUAUUUUAAUAUUCAUUGCCUUCUUAUCCUGCC
..(((((((.....(((((.((((((....)))))))))))...))))))).(((((((......))))))).......................... (-17.57 = -17.47 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,288,480 – 24,288,588
Length 108
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 85.80
Shannon entropy 0.19556
G+C content 0.39506
Mean single sequence MFE -26.93
Consensus MFE -21.85
Energy contribution -21.20
Covariance contribution -0.65
Combinations/Pair 1.22
Mean z-score -2.27
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.937390
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24288480 108 + 27905053
CAUUUUAAUAUAUUUUCAUUCGCUCUGAGCCGGCACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUUGUGUUUCCCGCGAUCUCGAAAUAUACAUUUAGGUCCGAACU
........((((((((...((((...((((((((((((....)))))).))))))((...((.....))...))..))))....))))))))................ ( -25.30, z-score =  -2.35, R)
>droYak2.chr3R 6622299 108 - 28832112
UAUUUCAAUAUAUUUCCAUUUGCCCCGAACCGGCACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUAGGGCUGCCCGCGGUCAGGAAAUAUUCAUUUAAGACCGAAAU
.(((((...(((((((((((((...(((((((((((((....)))))).))))))).....)))))..(((((....))))).))))))))((......))..))))) ( -33.80, z-score =  -3.83, R)
>droEre2.scaffold_4820 6719829 108 - 10470090
UAUUUCAAUAUAUUUCCGUUCGCCCUGUACCGACACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUUGGGUUGCCCGCGGUCACGAAAUAUUUAUUCAAGUCCGAAAU
.........(((((((...((((.....((((((((((....))))).)))))..............(((...)))))))....)))))))................. ( -21.70, z-score =  -0.62, R)
>consensus
UAUUUCAAUAUAUUUCCAUUCGCCCUGAACCGGCACUUAAUCAAGUGCUCGGUUUGAUUAACAAAUUGGGUUGCCCGCGGUCACGAAAUAUUCAUUUAAGUCCGAAAU
.........(((((((...((((..(((((((((((((....))))).))))))))...........(((...)))))))....)))))))................. (-21.85 = -21.20 +  -0.65)

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 Wed Apr 20 00:51:17 2011