Locus 7927

Sequence ID dm3.chr3L
Location 18,641,734 – 18,641,893
Length 159
Max. P 0.625801
window10911 window10912

overview

Window 1

Location 18,641,734 – 18,641,854
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.65
Shannon entropy 0.16415
G+C content 0.40774
Mean single sequence MFE -27.65
Consensus MFE -20.47
Energy contribution -20.99
Covariance contribution 0.52
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.625801
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18641734 120 + 24543557
UCAUUACAAAUGUAUUGUGUGUAAGCAUCGUAAGCACACCUCGCAUUUCGCACAUCAGGUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGU
...((((((((((...((((((..((...))..))))))...)))))).((((((..(((.(((((......))))).)))))))))...................)))).......... ( -28.90, z-score =  -2.27, R)
>droEre2.scaffold_4784 10486905 118 - 25762168
UCGUUACAAAUUUAUUCUGUGUAUGCGUCGUAA--GCACCUCGCAUUUUGCACACCAGAUUUUUGCAUAUCGGCAAUUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGU
.......(((((((((.((((((((((..((..--..))..)))))...)))))........((((((((.(((....)))))))))))................)))))))))...... ( -27.00, z-score =  -2.04, R)
>droYak2.chr3L 8779641 118 - 24197627
UUACUACAAAGGUAUUGUGUGUAUGCAUCAUAA--ACACCUCGCAUUUCGCACAUCAAAUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUCCUUUCAAGGUGAAUUUCCCAGU
(((((..(((((...((((((.((((.......--.......))))..))))))........((((((((.(((....)))))))))))........)))))...))))).......... ( -29.44, z-score =  -2.40, R)
>droSec1.super_19 621872 120 + 1257711
UCAUUAAAAACUUAUUGUGUGUAAGCAUAGCAAACACACCUCGCAUUUUGCACAUCAGGUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCUCAGU
.........((((...((((((..((...))..))))))........((((((((..(((.(((((......))))).)))))))))))...............))))............ ( -26.50, z-score =  -1.65, R)
>droSim1.chr3L 17952031 120 + 22553184
UCAUUACAAACUUAUUGUGUGUAAGCAUCGCAAACACACCUCGCAUUUCGCACAUCAGGUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGU
...((((.........((((((..((...))..))))))..........((((((..(((.(((((......))))).)))))))))...................)))).......... ( -26.40, z-score =  -1.93, R)
>consensus
UCAUUACAAACUUAUUGUGUGUAAGCAUCGUAA_CACACCUCGCAUUUCGCACAUCAGGUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGU
...((((((((((..((((((...((................))....))))))..))))))((((((((.(((....))))))))))).................)))).......... (-20.47 = -20.99 +   0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,641,774 – 18,641,893
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.23
Shannon entropy 0.35956
G+C content 0.38207
Mean single sequence MFE -25.12
Consensus MFE -14.42
Energy contribution -15.23
Covariance contribution 0.81
Combinations/Pair 1.33
Mean z-score -1.72
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.522979
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18641774 119 + 24543557
UCGCAUUUCGCACAUCAGGUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGUUCAAAGGAAU-GAAAUUUUCGGUACAAAAACUGCAACAAC
..(((....((((((..(((.(((((......))))).)))))))))......(((((((((...((........)).....))))))))-)...................)))...... ( -27.20, z-score =  -1.83, R)
>droAna3.scaffold_13337 4517240 105 - 23293914
-----AUUCUCUCUGCAGAAAUAU-----UUACCAACUUAAGCAUAUAUCCCACAUUUCUUUCAAGGUGAAUUUUCCUGUUUAAAGGAAAAGAAAUAUUUGG--CAGGCACCAUGAG---
-----......(((((..((((((-----((......................(((((......)))))..(((((((......))))))).)))))))).)--)))).........--- ( -18.80, z-score =  -0.63, R)
>droEre2.scaffold_4784 10486943 119 - 25762168
UCGCAUUUUGCACACCAGAUUUUUGCAUAUCGGCAAUUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGUUCAAAGGAAU-GAGAUUUUCGGUACGAUAAUUACAACAAC
..((.....))..(((......((((((((.(((....)))))))))))....(((((((((...((........)).....))))))))-)........)))................. ( -25.20, z-score =  -1.50, R)
>droYak2.chr3L 8779679 119 - 24197627
UCGCAUUUCGCACAUCAAAUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUCCUUUCAAGGUGAAUUUCCCAGUUCAAAGGAAU-GAAAUUUUUGGUACGAAAAUUACAACAAC
.....(((((.((...((((((((((((((.(((....)))))))))))....((((((((......(((((......))))))))))))-)))))))...)).)))))........... ( -30.90, z-score =  -3.06, R)
>droSec1.super_19 621912 119 + 1257711
UCGCAUUUUGCACAUCAGGUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCUCAGUUCAAAGGAAU-GAAAUUUUCGGUAUAAAAACUACAACAAC
..((...((((((((..(((.(((((......))))).)))))))))))....(((((((((..(((......)))......))))))))-).........))................. ( -24.00, z-score =  -1.54, R)
>droSim1.chr3L 17952071 119 + 22553184
UCGCAUUUCGCACAUCAGGUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGUUCAAAGGAAU-GAAAUUUUCGGUACAAAAACUACAACAAC
..((.....))......(((((((((((((.(((....)))))))))......(((((((((...((........)).....))))))))-).............)))))))........ ( -24.60, z-score =  -1.73, R)
>consensus
UCGCAUUUCGCACAUCAGAUUUUUGCAUAUCGGCAAAUGCCAUGUGCAGCCCACAUUUCUUUCAAGGUAAAUUUCCCAGUUCAAAGGAAU_GAAAUUUUCGGUACAAAAACUACAACAAC
.................(((((((((((((.(((....))))))))).(((......(((....))).(((((((...((((....)))).)))))))..)))..)))))))........ (-14.42 = -15.23 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:36:09 2011