Locus 7005

Sequence ID dm3.chr3L
Location 11,421,581 – 11,421,764
Length 183
Max. P 0.981687
window9640 window9641

overview

Window 0

Location 11,421,581 – 11,421,764
Length 183
Sequences 4
Columns 184
Reading direction forward
Mean pairwise identity 83.15
Shannon entropy 0.27378
G+C content 0.35859
Mean single sequence MFE -46.36
Consensus MFE -34.75
Energy contribution -34.94
Covariance contribution 0.19
Combinations/Pair 1.18
Mean z-score -2.61
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.08
SVM RNA-class probability 0.981687
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11421581 183 + 24543557
UUUAAAAAUAAUCACAAAUUUCAUCACAAUCACAUAGACAUAGUUCUCGAGCGCUGAGAACUAAGAGAUCAGCUUUCUCUUGAGUGAUCGCGGCAAGCUCAAGAGUGUCAAAAAAUUGAAAAAAAAGAGAGCAACAAUUUCCACUCAAUUGCUCUUAAAU-UGGCGUGAAGAUCGCUCAAGAGC
.................(((((.......((.....))..(((((((((.....))))))))).))))).......((((((((((((((((.((((((....))).((((....)))).......((((((((..............))))))))...)-)).)))...))))))))))))). ( -47.14, z-score =  -2.11, R)
>droSim1.chr3L 10815828 182 + 22553184
UUUAAAAAUAAUGACAAAUUUAAUCACAACCACAUAGACAUAGUUCUUGAGCGCUGAGAACUAAGAGAUCGGCUUUCUCUUGAGUGAUCGCGGCAAACUCAAGAGAGUCAAAAAAUUGUAAAAAA-GAGAGCAACAAAUUCCACUCAAUUGCUCUUAAAU-UGGCGUGAAGAUCACUCAAGAGC
........................................((((((((.......)))))))).............((((((((((((((((.(((((((....)))).................-((((((((..............))))))))...)-)).)))...))))))))))))). ( -45.34, z-score =  -2.38, R)
>droSec1.super_0 3630556 182 + 21120651
UUUAAAAAUAAUGAAAAAUUUAAUCACAACCACAUAGACAUAGUUCUUGAGCGCUGAGAACUAAGAGAUCGGCUUUCUCUUGAGUGAUCGCCGCUAACUCAAAAGAGUCAAAAAAUUUAAAAAAA-GAGAGCAACAAUUUUCACUCAAUUGCUCUUAAAU-UGGCGUGAAGAUCACUCAAGAGC
........................................((((((((.......)))))))).............(((((((((((((..(((((((((....)))).................-((((((((..............))))))))....-)))))....))))))))))))). ( -45.94, z-score =  -3.11, R)
>droYak2.chr3L 11460716 172 + 24197627
UGUACCAAUAAU-----AUUUAAACAAGAUUUGGCA--CAUAGUUCUUGAGUUCUGAGAAAUAAGAGUUCAGCUUUCUCUUGAGUGAUCGCG----UUUUAAGAGAGUCAAAAAACCGAGUUAAA-GAGAUUCAAUUUUCUCACUCAAUUGCUCUUAAACAUAGCGUGAAGAUCACUCAAGAGA
(((.((((....-----.............)))).)--))......((((..(((........)))..))))...(((((((((((((((((----(((((((((.((......)).((((....-((((........)))))))).....))))))))....))))...)))))))))))))) ( -47.03, z-score =  -2.85, R)
>consensus
UUUAAAAAUAAUGACAAAUUUAAUCACAACCACAUAGACAUAGUUCUUGAGCGCUGAGAACUAAGAGAUCAGCUUUCUCUUGAGUGAUCGCGGCAAACUCAAGAGAGUCAAAAAAUUGAAAAAAA_GAGAGCAACAAUUUCCACUCAAUUGCUCUUAAAU_UGGCGUGAAGAUCACUCAAGAGC
........................................(((((((((.....))))))))).............(((((((((((((.......((((....))))..................((((((((..............))))))))..............))))))))))))). (-34.75 = -34.94 +   0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,421,581 – 11,421,764
Length 183
Sequences 4
Columns 184
Reading direction reverse
Mean pairwise identity 83.15
Shannon entropy 0.27378
G+C content 0.35859
Mean single sequence MFE -49.22
Consensus MFE -31.83
Energy contribution -33.45
Covariance contribution 1.62
Combinations/Pair 1.16
Mean z-score -2.52
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932193
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11421581 183 - 24543557
GCUCUUGAGCGAUCUUCACGCCA-AUUUAAGAGCAAUUGAGUGGAAAUUGUUGCUCUCUUUUUUUUCAAUUUUUUGACACUCUUGAGCUUGCCGCGAUCACUCAAGAGAAAGCUGAUCUCUUAGUUCUCAGCGCUCGAGAACUAUGUCUAUGUGAUUGUGAUGAAAUUUGUGAUUAUUUUUAAA
((((..(((.(............-.....((((((((..(((....)))))))))))........((((....))))).)))..))))....(((((((((..((((((.......))))))(((((((.......)))))))........)))))))))........................ ( -47.60, z-score =  -0.96, R)
>droSim1.chr3L 10815828 182 - 22553184
GCUCUUGAGUGAUCUUCACGCCA-AUUUAAGAGCAAUUGAGUGGAAUUUGUUGCUCUC-UUUUUUACAAUUUUUUGACUCUCUUGAGUUUGCCGCGAUCACUCAAGAGAAAGCCGAUCUCUUAGUUCUCAGCGCUCAAGAACUAUGUCUAUGUGGUUGUGAUUAAAUUUGUCAUUAUUUUUAAA
.(((((((((((((.....((.(-(((((((((.....(((..(......)..)))..-.......(((....)))...)))))))))).))...)))))))))))))..(((((......(((((((.........)))))))........)))))(((((.......))))).......... ( -49.44, z-score =  -2.37, R)
>droSec1.super_0 3630556 182 - 21120651
GCUCUUGAGUGAUCUUCACGCCA-AUUUAAGAGCAAUUGAGUGAAAAUUGUUGCUCUC-UUUUUUUAAAUUUUUUGACUCUUUUGAGUUAGCGGCGAUCACUCAAGAGAAAGCCGAUCUCUUAGUUCUCAGCGCUCAAGAACUAUGUCUAUGUGGUUGUGAUUAAAUUUUUCAUUAUUUUUAAA
.(((((((((((((.....(((.-.....((((((((..(((....))))))))))).-..............(((((((....))))))).))))))))))))))))..(((((......(((((((.........)))))))........)))))((((.........)))).......... ( -51.74, z-score =  -3.12, R)
>droYak2.chr3L 11460716 172 - 24197627
UCUCUUGAGUGAUCUUCACGCUAUGUUUAAGAGCAAUUGAGUGAGAAAAUUGAAUCUC-UUUAACUCGGUUUUUUGACUCUCUUAAAA----CGCGAUCACUCAAGAGAAAGCUGAACUCUUAUUUCUCAGAACUCAAGAACUAUG--UGCCAAAUCUUGUUUAAAU-----AUUAUUGGUACA
((((((((((((((.....((....(((((((......((((.((((((((((.....-......)))))))))).))))))))))).----.))))))))))))))))...((((...........)))).............((--((((((....(((....))-----)...)))))))) ( -48.10, z-score =  -3.62, R)
>consensus
GCUCUUGAGUGAUCUUCACGCCA_AUUUAAGAGCAAUUGAGUGAAAAUUGUUGCUCUC_UUUUUUUCAAUUUUUUGACUCUCUUGAGUUUGCCGCGAUCACUCAAGAGAAAGCCGAUCUCUUAGUUCUCAGCGCUCAAGAACUAUGUCUAUGUGAUUGUGAUUAAAUUUGUCAUUAUUUUUAAA
.(((((((((((((....((.((.(((((((((.....((((((......)))))).........((((....))))..))))))))).)).)).))))))))))))).............(((((((.........)))))))........................................ (-31.83 = -33.45 +   1.62)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:18:37 2011