Locus 6773

Sequence ID dm3.chr3L
Location 9,689,173 – 9,689,322
Length 149
Max. P 0.966642
window9321 window9322

overview

Window 1

Location 9,689,173 – 9,689,322
Length 149
Sequences 5
Columns 161
Reading direction forward
Mean pairwise identity 90.12
Shannon entropy 0.16671
G+C content 0.39961
Mean single sequence MFE -40.62
Consensus MFE -29.19
Energy contribution -28.59
Covariance contribution -0.60
Combinations/Pair 1.17
Mean z-score -2.55
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.879152
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9689173 149 + 24543557
GAUAAUUGUUGCUCUGCAAAUAUCUCUG-------CUAUGUACUUUGUA----CAUACCAGCAGAAAUGUUUUGUUUUCUAGAUCUCAAAUCC-GAGGUACAGUUCUUGCUUUUUCAUUUCACGGGGGCUCGUCUUUGCUUUUGUUGCCCCCGAGAUGUUU
.................(((((((((((-------((((((((...)))----)))...))))((((((....((...((..(((((......-)))))..)).....)).....))))))..((((((.................))))))))))))))) ( -40.63, z-score =  -2.91, R)
>droEre2.scaffold_4784 9672959 159 + 25762168
GCUAAUUGUUGCUCUGCAAAUAUCUCUAUACAUCUCUAUGUACAUUGUAUGUACAUACGAGCAGGAAUGUUUUGUUUUCUAGAUCUAAAAUCC-AGGGUACAGUUCCUACUUUUUCAUUUCACGGGGGCUCGUCUUUGCUUUUGUUGCCCC-GAGAUGUUU
((........)).....(((((((((.......((((((((((((...))))))))).))).((((((....(((.((((.(((.....))).-)))).)))))))))................(((((.................)))))-))))))))) ( -39.63, z-score =  -2.07, R)
>droYak2.chr3L 21953460 149 - 24197627
GAUAAUUGUUGCUCUGCAAAUAUCUCUG-------CUAUGUACAUUGUA----CAUACGAGCAGGAUUGUUUUGUUUUCUAGAUCUCAAAUCC-GGGGUACAGUUCUUACUUUUUCAUUUCACGGGGGCUCGUCUCUGCUUUGGUAGCCCCCGAGAUGUUU
...((((((.((((((((((.(((.(((-------((((((((...)))----)))...))))))))...)))).......(((.....))))-)))))))))))..........((((((..(((((((.(((........))))))))))))))))... ( -40.60, z-score =  -1.78, R)
>droSec1.super_0 1922742 149 + 21120651
GAUAAUUGUUGCUCUGCAAAUAUCUCUG-------CUAUGUACUUUGUA----CAUACUAGCAGAAAUGUUUUGUUUUCUAGAUCUCAAAUCC-GAGGUACAGUUCUUGCUUCUUUAUUUUACGGGGGCUCGUCUUUGCUUUUGUUGCCCCCGAGAUGUUU
((((.((((......)))).))))((((-------((((((((...)))----))...))))))).................(((((......-((((((.......))))))..........((((((.................))))))))))).... ( -40.83, z-score =  -3.27, R)
>droSim1.chr3L 9066888 150 + 22553184
GAUAAUUGUUGCUCUGCAAAUAUCUCUG-------CUAUGUACAUUGUA----CAUAAUAGCAGAAAUGUUUUGUUUUCUAGAUCUCGAGUCCCGAGGUACAGUUCUUGCUUUUUUAUUUUACGGGGGCUCGACUUUGCUUUUGUUGCCCCCGAGAUGUUU
((((.((((......)))).))))((((-------((((((((...)))----))...)))))))(((((((.((...((..((((((.....))))))..)).....))............(((((((.(((........)))..)))))))))))))). ( -41.40, z-score =  -2.74, R)
>consensus
GAUAAUUGUUGCUCUGCAAAUAUCUCUG_______CUAUGUACAUUGUA____CAUACGAGCAGAAAUGUUUUGUUUUCUAGAUCUCAAAUCC_GAGGUACAGUUCUUGCUUUUUCAUUUCACGGGGGCUCGUCUUUGCUUUUGUUGCCCCCGAGAUGUUU
.................(((((((((.....................................((((((....((...((..(((((.......)))))..)).....)).....))))))..((((((.................))))))))))))))) (-29.19 = -28.59 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,689,173 – 9,689,322
Length 149
Sequences 5
Columns 161
Reading direction reverse
Mean pairwise identity 90.12
Shannon entropy 0.16671
G+C content 0.39961
Mean single sequence MFE -39.11
Consensus MFE -23.26
Energy contribution -23.34
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -3.49
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.77
SVM RNA-class probability 0.966642
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9689173 149 - 24543557
AAACAUCUCGGGGGCAACAAAAGCAAAGACGAGCCCCCGUGAAAUGAAAAAGCAAGAACUGUACCUC-GGAUUUGAGAUCUAGAAAACAAAACAUUUCUGCUGGUAUG----UACAAAGUACAUAG-------CAGAGAUAUUUGCAGAGCAACAAUUAUC
.....((.(((((((.................))))))).)).........(((((..(((...(((-(....))))...)))..........((((((((((((((.----......)))).)))-------))))))).)))))............... ( -38.63, z-score =  -3.10, R)
>droEre2.scaffold_4784 9672959 159 - 25762168
AAACAUCUC-GGGGCAACAAAAGCAAAGACGAGCCCCCGUGAAAUGAAAAAGUAGGAACUGUACCCU-GGAUUUUAGAUCUAGAAAACAAAACAUUCCUGCUCGUAUGUACAUACAAUGUACAUAGAGAUGUAUAGAGAUAUUUGCAGAGCAACAAUUAGC
..(((((((-(((((.................))))).............((((((((.(((...((-(((((...)))))))...))).....))))))))..(((((((((...))))))))))))))))..........((((...))))........ ( -41.33, z-score =  -3.66, R)
>droYak2.chr3L 21953460 149 + 24197627
AAACAUCUCGGGGGCUACCAAAGCAGAGACGAGCCCCCGUGAAAUGAAAAAGUAAGAACUGUACCCC-GGAUUUGAGAUCUAGAAAACAAAACAAUCCUGCUCGUAUG----UACAAUGUACAUAG-------CAGAGAUAUUUGCAGAGCAACAAUUAUC
.....((.((((((((..(........)...)))))))).)).................(((.....-(((((....................)))))(((((.((((----(((...)))))))(-------((((....))))).))))))))...... ( -38.55, z-score =  -3.12, R)
>droSec1.super_0 1922742 149 - 21120651
AAACAUCUCGGGGGCAACAAAAGCAAAGACGAGCCCCCGUAAAAUAAAGAAGCAAGAACUGUACCUC-GGAUUUGAGAUCUAGAAAACAAAACAUUUCUGCUAGUAUG----UACAAAGUACAUAG-------CAGAGAUAUUUGCAGAGCAACAAUUAUC
......(((((((((.................)))))).............(((((..(((...(((-(....))))...)))..........((((((((((((((.----......)))).)))-------))))))).))))).)))........... ( -37.53, z-score =  -3.65, R)
>droSim1.chr3L 9066888 150 - 22553184
AAACAUCUCGGGGGCAACAAAAGCAAAGUCGAGCCCCCGUAAAAUAAAAAAGCAAGAACUGUACCUCGGGACUCGAGAUCUAGAAAACAAAACAUUUCUGCUAUUAUG----UACAAUGUACAUAG-------CAGAGAUAUUUGCAGAGCAACAAUUAUC
......(((((((((.................)))))).............(((((..(((...((((.....))))...)))..........((((((((((...((----(((...))))))))-------))))))).))))).)))........... ( -39.53, z-score =  -3.92, R)
>consensus
AAACAUCUCGGGGGCAACAAAAGCAAAGACGAGCCCCCGUGAAAUGAAAAAGCAAGAACUGUACCUC_GGAUUUGAGAUCUAGAAAACAAAACAUUUCUGCUAGUAUG____UACAAUGUACAUAG_______CAGAGAUAUUUGCAGAGCAACAAUUAUC
....(((((((((((.................))))))(((..(((....((((.(((.(((......(((((...)))))..........))).)))))))..))).....)))....................)))))..((((...))))........ (-23.26 = -23.34 +   0.08)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:14:12 2011