Locus 13181

Sequence ID dm3.chrX
Location 4,818,957 – 4,819,108
Length 151
Max. P 0.999570
window18123 window18124 window18125 window18126

overview

Window 3

Location 4,818,957 – 4,819,068
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.17
Shannon entropy 0.41040
G+C content 0.58621
Mean single sequence MFE -43.00
Consensus MFE -28.32
Energy contribution -29.67
Covariance contribution 1.35
Combinations/Pair 1.21
Mean z-score -2.35
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.28
SVM RNA-class probability 0.987379
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818957 111 + 22422827
--------GGGCCCCCCAGUAUCCUGUAGUUGGACUCAAACAAGUCCCUCC-UUCCGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGC
--------((((....(((....))).....(((((......)))))....-....)))).......(((((((((((..((((..((((((...))))))..))))..))))))))))) ( -39.50, z-score =  -2.72, R)
>droSim1.chrX 13316169 120 - 17042790
GUUGAAUGAGGCGCCCUGGUAGCCUGUAGUUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGC
((((..(((((((....((.(((....((((((.......)))))).)))))...))))))).))))((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))) ( -47.40, z-score =  -2.50, R)
>droSec1.super_4 4252947 110 - 6179234
----------GGGCCCCAGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGC
----------.(((....(.(((..((((..(((((......))))).......))))..))))...)))((((..((..(((((.((((((...)))))).)))))..))..))))... ( -42.10, z-score =  -1.83, R)
>consensus
_________GGCGCCCCAGUAUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCCGCUCGACCGACGCUGGAGAAUCAAAGCCGGCGGAAGUAACUUCCGGCGGUUAAGAUACUCCAGC
........((((....(((....))).....(((((......))))).........)))).......((((((((.((..(((((.((((((...)))))).)))))..)).)))))))) (-28.32 = -29.67 +   1.35)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,818,957 – 4,819,068
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.17
Shannon entropy 0.41040
G+C content 0.58621
Mean single sequence MFE -46.27
Consensus MFE -32.11
Energy contribution -32.90
Covariance contribution 0.79
Combinations/Pair 1.17
Mean z-score -1.81
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946241
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818957 111 - 22422827
GCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCGGAA-GGAGGGACUUGUUUGAGUCCAACUACAGGAUACUGGGGGGCCC--------
(((((((((((..(.(((.((((((...)))))).))).)..))))))))))).((((.....)))).-((..((((((....))))))..(..(((....)))..)..)).-------- ( -45.30, z-score =  -2.50, R)
>droSim1.chrX 13316169 120 + 17042790
GCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCCUCAUUCAAC
...((((..((..(((((.((((((...)))))).)))))..))..)))).((((((((...((.......)).(((((((.(........).))))))))))..))))).......... ( -48.00, z-score =  -1.69, R)
>droSec1.super_4 4252947 110 + 6179234
GCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACUGGGGCCC----------
(((.((((..(((..(((.((((((...)))))).)))((((..(((((.(((....)))))))))))).)))..)))).(..(.((((.......)))).)..))))..---------- ( -45.50, z-score =  -1.24, R)
>consensus
GCUGGAGAAUCUUAACCGCCGGAAGUAACUUCCGCCGGCUUAGAUACUCCAGCGUCGGUCGAGCGGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGAUACUGGGGCGCC_________
((((((((.((....(((.((((((...)))))).)))....)).))))))))....................((((((....))))))..((.(((....))).))............. (-32.11 = -32.90 +   0.79)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,818,989 – 4,819,108
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.22
Shannon entropy 0.38954
G+C content 0.58487
Mean single sequence MFE -56.67
Consensus MFE -50.14
Energy contribution -50.27
Covariance contribution 0.13
Combinations/Pair 1.24
Mean z-score -4.15
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.83
SVM RNA-class probability 0.999369
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818989 119 + 22422827
CAAGUCCCUCC-UUCCGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCGGGAGCGAACUUGUUGGAGUCAAACU
(((((.(((((-(..((((..((((.((((((((((((..((((..((((((...))))))..))))..)))))))))))).))))..))))..))))).).)))))............. ( -56.80, z-score =  -5.32, R)
>droSim1.chrX 13316209 120 - 17042790
CAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACU
.((((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).))).)))(((((...))))). ( -58.80, z-score =  -3.77, R)
>droSec1.super_4 4252977 120 - 6179234
CAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACU
..(((((((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).).)))).............. ( -54.40, z-score =  -3.37, R)
>consensus
CAAGUCCCUCCCUUCCGCUCGACCGACGCUGGAGAAUCAAAGCCGGCGGAAGUAACUUCCGGCGGUUAAGAUACUCCAGCGCCGGUGAAGCGGAAGGAGCGAACUUGUUGGAGUCAAACU
((((((.((((.(((((((..((((..((((((((.((..(((((.((((((...)))))).)))))..)).))))))))..))))..))))))))))).)).))))............. (-50.14 = -50.27 +   0.13)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,818,989 – 4,819,108
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.22
Shannon entropy 0.38954
G+C content 0.58487
Mean single sequence MFE -59.47
Consensus MFE -48.57
Energy contribution -50.80
Covariance contribution 2.23
Combinations/Pair 1.19
Mean z-score -5.06
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.03
SVM RNA-class probability 0.999570
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818989 119 - 22422827
AGUUUGACUCCAACAAGUUCGCUCCCGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCGGAA-GGAGGGACUUG
.............(((((((.((((...(((((.(((((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))))).)))))...-))))))))))) ( -63.30, z-score =  -6.86, R)
>droSim1.chrX 13316209 120 + 17042790
AGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUG
.(((((...)))))(((..(((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).)..))). ( -60.20, z-score =  -4.39, R)
>droSec1.super_4 4252977 120 + 6179234
AGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUG
.............(((((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).)))).))) ( -54.90, z-score =  -3.92, R)
>consensus
AGUUUGACUCCAACAAGUUCGCUCCUUCCGCUUCACCGGCGCUGGAGAAUCUUAACCGCCGGAAGUAACUUCCGCCGGCUUAGAUACUCCAGCGUCGGUCGAGCGGAAGGGAGGGACUUG
.............(((((((.((((((((((((.(((((.((((((((.((....(((.((((((...)))))).)))....)).)))))))).))))).)))))))))).))))))))) (-48.57 = -50.80 +   2.23)

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 01:16:16 2011