Locus 7517

Sequence ID dm3.chr3L
Location 15,290,633 – 15,290,828
Length 195
Max. P 0.922722
window10354 window10355 window10356

overview

Window 4

Location 15,290,633 – 15,290,742
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 84.86
Shannon entropy 0.24562
G+C content 0.50465
Mean single sequence MFE -37.58
Consensus MFE -31.34
Energy contribution -31.78
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -1.62
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.814689
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15290633 109 - 24543557
GCUAGUUGUCAAUACAUGUCGAGACAGCUCAACGGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAAACUCGAACAAGUUGCGCUAGUUGUCGAUUGCACUUCGA
((((((.(.((((.....(((((.(((((((((.((...(((((......)))))..)).)))))))))...)))))....)))))))))))..((((.......)))) ( -37.90, z-score =  -1.50, R)
>droSim1.chrX 15891148 109 - 17042790
GCUAGUUGUCAAUACAUGUCGAGACAGCUCAACGGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAAACUCGAACAAGUUGCGCUAGUUGUCGAUUGCACUUCGA
((((((.(.((((.....(((((.(((((((((.((...(((((......)))))..)).)))))))))...)))))....)))))))))))..((((.......)))) ( -37.90, z-score =  -1.50, R)
>droSec1.super_232 14022 103 - 21018
ACCGGGUGGCCACAAGU-UCGAAACAGCUCAACAGUGACGAUACACUGGCGUGUCAAACGGUUGGGUUGUGGUUCGAACAAGUAGC-----CGAUUGAGUACAGUUUGA
(((((.((((.((..((-(((((((((((((((.((...(((((......)))))..)).))))))))))..)))))))..)).))-----)).))).))......... ( -36.60, z-score =  -1.98, R)
>droYak2.chr3L_random 2168867 109 - 4797643
GCUAGUUGUCAAUACAUGUCGAGACAGCUCAACGGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAAACUCGAACAAGUUGCGCUAGUUGUCGAUUGCACUUCGA
((((((.(.((((.....(((((.(((((((((.((...(((((......)))))..)).)))))))))...)))))....)))))))))))..((((.......)))) ( -37.90, z-score =  -1.50, R)
>consensus
GCUAGUUGUCAAUACAUGUCGAGACAGCUCAACGGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAAACUCGAACAAGUUGCGCUAGUUGUCGAUUGCACUUCGA
((((((.(.((((.....(((((.(((((((((.((...(((((......)))))..)).)))))))))...)))))....)))))))))))..((((.......)))) (-31.34 = -31.78 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,290,742 – 15,290,828
Length 86
Sequences 5
Columns 87
Reading direction forward
Mean pairwise identity 85.19
Shannon entropy 0.26415
G+C content 0.49893
Mean single sequence MFE -20.62
Consensus MFE -19.32
Energy contribution -18.60
Covariance contribution -0.72
Combinations/Pair 1.27
Mean z-score -1.16
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.849443
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15290742 86 + 24543557
GCAACUUGUUCGAA-CAUCAACCCAACCGCUAGACACGCCAGUGUAUCGUCGCUGUUGAGUUGCCUUCGAAUUUGAAUUAAACCGUC
....(..(((((((-...((((.((((.((...((((....))))......)).)))).))))..)))))))..)............ ( -21.40, z-score =  -2.14, R)
>droSim1.chrX 15891257 86 + 17042790
GCAACUUGUUCGAA-CAUCAACCCAACCGCUAGACACGCCAGUGUAUCGUCGCUGUUGAGUUGCCUUUGAAUUUGAAUUAAACCGUC
....(..(((((((-...((((.((((.((...((((....))))......)).)))).))))..)))))))..)............ ( -19.30, z-score =  -1.45, R)
>droSec1.super_232 14130 86 + 21018
GCAAUCUGCUCGAACCAUCGACCCAACCGUUUGACACGCCAGUGUAUCGUCACUGUUGAGUUGC-UUCGAACAUAUGCUCGACCGGC
(((...((.(((((....((((.((((.((...((((....))))......)).)))).)))).-))))).))..)))......... ( -18.60, z-score =   0.35, R)
>droYak2.chr3L_random 2168976 86 + 4797643
GCAACUUGUUCGAA-CAUCAACCCAACCGCUAGACACGCCAGUGUAUCGUCGCUGUUGAGUUGCCUUCGAAUUUGAAUUAAACCGUC
....(..(((((((-...((((.((((.((...((((....))))......)).)))).))))..)))))))..)............ ( -21.40, z-score =  -2.14, R)
>droEre2.scaffold_4929 2234929 85 - 26641161
GCAACUUGUUCGA--CAUCAGCCCAACAGCUAGACACGCCAGUGGAUCGUCGCUAUUGAGCUGUACUCGAACUCGAACUUGGCCGUC
.......((((((--...((((.(((.(((..(((((....)))..))...))).))).))))...))))))............... ( -22.40, z-score =  -0.43, R)
>consensus
GCAACUUGUUCGAA_CAUCAACCCAACCGCUAGACACGCCAGUGUAUCGUCGCUGUUGAGUUGCCUUCGAAUUUGAAUUAAACCGUC
....(..(((((((....((((.((((.((...((((....))))......)).)))).))))..)))))))..)............ (-19.32 = -18.60 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,290,742 – 15,290,828
Length 86
Sequences 5
Columns 87
Reading direction reverse
Mean pairwise identity 85.19
Shannon entropy 0.26415
G+C content 0.49893
Mean single sequence MFE -27.52
Consensus MFE -23.38
Energy contribution -23.22
Covariance contribution -0.16
Combinations/Pair 1.18
Mean z-score -1.78
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.922722
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15290742 86 - 24543557
GACGGUUUAAUUCAAAUUCGAAGGCAACUCAACAGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAUG-UUCGAACAAGUUGC
(((((......))...((((((.((((((((((.((...(((((......)))))..)).))))))))).).-))))))...))).. ( -27.50, z-score =  -2.40, R)
>droSim1.chrX 15891257 86 - 17042790
GACGGUUUAAUUCAAAUUCAAAGGCAACUCAACAGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAUG-UUCGAACAAGUUGC
(((((......))...(((.((.((((((((((.((...(((((......)))))..)).))))))))).).-)).)))...))).. ( -21.60, z-score =  -0.68, R)
>droSec1.super_232 14130 86 - 21018
GCCGGUCGAGCAUAUGUUCGAA-GCAACUCAACAGUGACGAUACACUGGCGUGUCAAACGGUUGGGUCGAUGGUUCGAGCAGAUUGC
.........(((..((((((((-.(((((((((.((...(((((......)))))..)).)))))))...)).))))))))...))) ( -30.00, z-score =  -1.67, R)
>droYak2.chr3L_random 2168976 86 - 4797643
GACGGUUUAAUUCAAAUUCGAAGGCAACUCAACAGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAUG-UUCGAACAAGUUGC
(((((......))...((((((.((((((((((.((...(((((......)))))..)).))))))))).).-))))))...))).. ( -27.50, z-score =  -2.40, R)
>droEre2.scaffold_4929 2234929 85 + 26641161
GACGGCCAAGUUCGAGUUCGAGUACAGCUCAAUAGCGACGAUCCACUGGCGUGUCUAGCUGUUGGGCUGAUG--UCGAACAAGUUGC
..(((......))).((((((...((((((((((((((((..((...))..))))..))))))))))))...--))))))....... ( -31.00, z-score =  -1.78, R)
>consensus
GACGGUUUAAUUCAAAUUCGAAGGCAACUCAACAGCGACGAUACACUGGCGUGUCUAGCGGUUGGGUUGAUG_UUCGAACAAGUUGC
................((((((..(((((((((.((...(((((......)))))..)).)))))))))....))))))........ (-23.38 = -23.22 +  -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 23:28:29 2011