Locus 5945

Sequence ID dm3.chr3L
Location 2,700,194 – 2,700,344
Length 150
Max. P 0.951680
window8172 window8173 window8174

overview

Window 2

Location 2,700,194 – 2,700,314
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.33
Shannon entropy 0.27328
G+C content 0.37567
Mean single sequence MFE -29.30
Consensus MFE -20.16
Energy contribution -19.88
Covariance contribution -0.28
Combinations/Pair 1.19
Mean z-score -1.95
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.751170
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2700194 120 - 24543557
UUACAGUAACAUUUGAAAAAUGUCCUUGCUAAUUGGCAGCAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACGAAGCAGAUAUGUUUCUAAAUUCAUAAAUUGUACCAUACAAUU
.((((((......((((...((.(.(((((...((((((((((.(((.....))).))))))))))))))).).)).((((((....))))))....))))...)))))).......... ( -33.80, z-score =  -3.51, R)
>droEre2.scaffold_4784 2724645 119 - 25762168
-UACAACAAGAUUUGGUUGAUUUCCUUGCAAAUUGGCAGCACAUGUUUGCUCGACCAGUGCUGCCAAGCUCAGCUACAAAGCAGAAUUGCUGCCUAAUUCAUAAAUUGUACCAUAAAAUC
-(((((.......(((((((.......((...((((((((((.((.((....)).)))))))))))))))))))))....((((.....))))............))))).......... ( -29.81, z-score =  -1.32, R)
>droYak2.chr3L 14965016 120 + 24197627
CUUUAGCAAGAUUUGAUUGAUUUCCUUGCAAAUUGGCAUCACUUGUUUGCCCGACCAGUGCUGCCAAGCUAGGCUACAAAGCAGAUCUGUUUCCUAACUCAAAAUUUUAACCAUAAAAUU
....((((.((((((........(((.((...((((((.((((.(((.....))).)))).)))))))).)))........))))))))))...........(((((((....))))))) ( -27.39, z-score =  -1.65, R)
>droSec1.super_2 2726005 120 - 7591821
CUACAGUAACAUUUGAAAAAUGUCCUUGCUAAUUGGCAGGAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACAAAGCAGAUCUGUUUCUAAAUUCAUAAAUUGUACCAUACAAUU
..((((....(((((.....((.(.(((((...((((((.(((.(((.....))).))).))))))))))).).)).....))))))))).............(((((((...))))))) ( -26.10, z-score =  -0.95, R)
>droSim1.chr3L 2256334 120 - 22553184
CUACAGUAACAUUUGAAUAAAGUCCUUGCUAAUUGGCAGCAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACAAAGCAGAUCUGAUUCUAAAUUCAUAAAUUGUACCAUACAAUU
.((((((......(((((...(.(.(((((...((((((((((.(((.....))).))))))))))))))).).).......(((......)))..)))))...)))))).......... ( -29.40, z-score =  -2.34, R)
>consensus
CUACAGUAACAUUUGAAUAAUGUCCUUGCUAAUUGGCAGCAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACAAAGCAGAUCUGUUUCUAAAUUCAUAAAUUGUACCAUACAAUU
.((((((.(((((.....)))))..((((...(((((((((((.(((.....))).)))))))))))((...))......))))....................)))))).......... (-20.16 = -19.88 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,700,224 – 2,700,344
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.75
Shannon entropy 0.51725
G+C content 0.41406
Mean single sequence MFE -29.86
Consensus MFE -18.00
Energy contribution -19.84
Covariance contribution 1.84
Combinations/Pair 1.21
Mean z-score -1.38
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.908913
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2700224 120 + 24543557
ACAUAUCUGCUUCGUGACAUUGCUUGGCAGCACUGGUCGAGCAAACAAAUGCUGCCAAUUAGCAAGGACAUUUUUCAAAUGUUACUGUAAAAGAAAGAAAAUUUCUGUACAACAGAAGAC
.........(((((((((((((((((((((((...((.......))...))))))))...)))..(((.....))).))))))))((((..(((((.....))))).))))...)))).. ( -32.50, z-score =  -2.44, R)
>droEre2.scaffold_4784 2724675 91 + 25762168
GCAAUUCUGCUUUGUAGCUGAGCUUGGCAGCACUGGUCGAGCAAACAUGUGCUGCCAAUUUGCAAGGAAAUCAACCAAAUCUUGUUGUAGC-----------------------------
(((((((.(((....))).))).((((((((((((..........)).)))))))))).))))........((((........))))....----------------------------- ( -26.60, z-score =  -0.36, R)
>droYak2.chr3L 14965046 111 - 24197627
ACAGAUCUGCUUUGUAGCCUAGCUUGGCAGCACUGGUCGGGCAAACAAGUGAUGCCAAUUUGCAAGGAAAUCAAUCAAAUCUUGCUAAAGGACAUAAACACAAGAGUGGGC---------
.....((..((((...(((..(((.(......).)))..)))......((((((((.....((((((............))))))....)).)))...))).))))..)).--------- ( -25.80, z-score =   0.64, R)
>droSec1.super_2 2726035 120 + 7591821
ACAGAUCUGCUUUGUGACAUUGCUUGGCAGCACUGGUCGAGCAAACAAAUCCUGCCAAUUAGCAAGGACAUUUUUCAAAUGUUACUGUAGAAGAAAGAACUUUUCUGUACAGCAGAAAAC
.....(((((...(((((((((((((((.......))))))).......((((((......)).)))).........)))))))).))))).........(((((((.....))))))). ( -34.80, z-score =  -2.41, R)
>droSim1.chr3L 2256364 104 + 22553184
UCAGAUCUGCUUUGUGACAUUGCUUGGCAGCACUGGUCGAGCAAACAAAUGCUGCCAAUUAGCAAGGACUUUAUUCAAAUGUUACUGUAGAAUAAAGAAAUUUU----------------
.....(((((...(((((((((((((((((((...((.......))...))))))))...)))..(((.....))).)))))))).))))).............---------------- ( -29.60, z-score =  -2.31, R)
>consensus
ACAGAUCUGCUUUGUGACAUUGCUUGGCAGCACUGGUCGAGCAAACAAAUGCUGCCAAUUAGCAAGGACAUUAUUCAAAUGUUACUGUAGAAGAAAGAAAUUUU________________
.....(((((...(((((((((((((((((((...((.......))...)))))))))...))..(((.....))).)))))))).)))))............................. (-18.00 = -19.84 +   1.84)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,700,224 – 2,700,344
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.75
Shannon entropy 0.51725
G+C content 0.41406
Mean single sequence MFE -28.86
Consensus MFE -19.23
Energy contribution -20.19
Covariance contribution 0.96
Combinations/Pair 1.11
Mean z-score -1.37
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.951680
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2700224 120 - 24543557
GUCUUCUGUUGUACAGAAAUUUUCUUUCUUUUACAGUAACAUUUGAAAAAUGUCCUUGCUAAUUGGCAGCAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACGAAGCAGAUAUGU
....(((((((((.(((((.....)))))..)))................((.(.(((((...((((((((((.(((.....))).))))))))))))))).).))...))))))..... ( -32.10, z-score =  -2.04, R)
>droEre2.scaffold_4784 2724675 91 - 25762168
-----------------------------GCUACAACAAGAUUUGGUUGAUUUCCUUGCAAAUUGGCAGCACAUGUUUGCUCGACCAGUGCUGCCAAGCUCAGCUACAAAGCAGAAUUGC
-----------------------------....((((........))))........((((.((((((((((.((.((....)).)))))))))))).....(((....)))....)))) ( -25.70, z-score =  -0.62, R)
>droYak2.chr3L 14965046 111 + 24197627
---------GCCCACUCUUGUGUUUAUGUCCUUUAGCAAGAUUUGAUUGAUUUCCUUGCAAAUUGGCAUCACUUGUUUGCCCGACCAGUGCUGCCAAGCUAGGCUACAAAGCAGAUCUGU
---------...(((....))).............(((.((((((........(((.((...((((((.((((.(((.....))).)))).)))))))).)))........))))))))) ( -27.89, z-score =  -0.76, R)
>droSec1.super_2 2726035 120 - 7591821
GUUUUCUGCUGUACAGAAAAGUUCUUUCUUCUACAGUAACAUUUGAAAAAUGUCCUUGCUAAUUGGCAGGAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACAAAGCAGAUCUGU
......(((((((.(((((.....)))))..)))))))..(((((.....((.(.(((((...((((((.(((.(((.....))).))).))))))))))).).)).....))))).... ( -31.20, z-score =  -1.20, R)
>droSim1.chr3L 2256364 104 - 22553184
----------------AAAAUUUCUUUAUUCUACAGUAACAUUUGAAUAAAGUCCUUGCUAAUUGGCAGCAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACAAAGCAGAUCUGA
----------------.......((((((((.............))))))))...(((((...((((((((((.(((.....))).)))))))))))))))................... ( -27.42, z-score =  -2.20, R)
>consensus
________________AAAAUUUCUUUCUUCUACAGUAACAUUUGAAUAAUGUCCUUGCUAAUUGGCAGCAUUUGUUUGCUCGACCAGUGCUGCCAAGCAAUGUCACAAAGCAGAUCUGU
.................................(((....(((((........(.((((...(((((((((((.(((.....))).))))))))))))))).)........)))))))). (-19.23 = -20.19 +   0.96)

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 22:58:14 2011