Locus 7907

Sequence ID dm3.chr3L
Location 18,399,044 – 18,399,138
Length 94
Max. P 0.887619
window10883 window10884

overview

Window 3

Location 18,399,044 – 18,399,138
Length 94
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 79.10
Shannon entropy 0.33233
G+C content 0.49117
Mean single sequence MFE -30.66
Consensus MFE -16.72
Energy contribution -17.12
Covariance contribution 0.40
Combinations/Pair 1.10
Mean z-score -2.09
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.667199
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18399044 94 + 24543557
GACUCACGAGAGUUGUCAGCUUUUGUUUUGCUCGCCAUGUGC--GCGAGCAAGUGAUAUAUUUUGAUACCCCGUGAUGGUAGGGUAUAUCCCUACA-----------------
...(((((.(.(.((((((..(.(((((((((((((....).--))))))))..)))).)..)))))).)))))))..((((((.....)))))).----------------- ( -33.90, z-score =  -3.89, R)
>droSim1.chr3L 17733956 91 + 22553184
GACUCACCAGAGUUGUCAGCUUUUG-----CUCGCCAUGUGCGUGCGAGCAAGUAAGAUUUUUUGAUACCCUGUGAUGGGAGGGUAUGUCCGUUUU-----------------
(((....(((((..(((....((((-----((((((......).)))))))))...))).)))))(((((((........))))))))))......----------------- ( -28.30, z-score =  -1.67, R)
>droSec1.super_19 394479 90 + 1257711
GACUCGCCAGAGUUGUCAGCUUUUG-----CUCGCCAUGUGCGUGCGAGCAAGUGAGAUUUUU-GAUACCCCGUGAUGGGAGGGUAUAUCCCUUUU-----------------
..(((((..((((.....))))(((-----((((((......).)))))))))))))......-....(((......)))((((.....))))...----------------- ( -28.20, z-score =  -1.54, R)
>droYak2.chr3L 8554199 91 - 24197627
GCCUCACGAGAGUUGUCAGCUUUUCCA--UGUCGCCAUGUGC--GCGAGCAAGUGGGAUUUUU-GAUACCCUGUUAUGGGAGGGUAUAUCCAUUUU-----------------
.......((((((.....)))))).((--.(((.((((.(((--....))).)))))))...)-)(((((((.(....).))))))).........----------------- ( -25.80, z-score =  -0.67, R)
>droEre2.scaffold_4784 10270644 104 - 25762168
GACUCACGAGAGUUGUCAGCUUU------GGUCGCCAUGUGC--GCGAGCAAGUGGGAUUUUU-GAUACCCCGUGAUGGCCGGGUAUAUCCCUUUUCCACUAACUGAAGCAUA
(((..((....)).))).((((.------.((.......(((--....)))(((((((.....-.((((((.((....)).)))))).......))))))).))..))))... ( -37.12, z-score =  -2.66, R)
>consensus
GACUCACGAGAGUUGUCAGCUUUUG_____CUCGCCAUGUGC__GCGAGCAAGUGAGAUUUUU_GAUACCCCGUGAUGGGAGGGUAUAUCCCUUUU_________________
..(((((.(((((.....))))).......(((((.........)))))...)))))........((((((..........)))))).......................... (-16.72 = -17.12 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,399,044 – 18,399,138
Length 94
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 79.10
Shannon entropy 0.33233
G+C content 0.49117
Mean single sequence MFE -27.35
Consensus MFE -15.57
Energy contribution -16.21
Covariance contribution 0.64
Combinations/Pair 1.14
Mean z-score -2.37
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.887619
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18399044 94 - 24543557
-----------------UGUAGGGAUAUACCCUACCAUCACGGGGUAUCAAAAUAUAUCACUUGCUCGC--GCACAUGGCGAGCAAAACAAAAGCUGACAACUCUCGUGAGUC
-----------------.((((((.....))))))..(((((((((.(((...........((((((((--.......)))))))).........)))..)).)))))))... ( -31.15, z-score =  -4.12, R)
>droSim1.chr3L 17733956 91 - 22553184
-----------------AAAACGGACAUACCCUCCCAUCACAGGGUAUCAAAAAAUCUUACUUGCUCGCACGCACAUGGCGAG-----CAAAAGCUGACAACUCUGGUGAGUC
-----------------....(((.((((((((........))))))).............((((((((.((....)))))))-----)))..))))...((((....)))). ( -25.20, z-score =  -2.62, R)
>droSec1.super_19 394479 90 - 1257711
-----------------AAAAGGGAUAUACCCUCCCAUCACGGGGUAUC-AAAAAUCUCACUUGCUCGCACGCACAUGGCGAG-----CAAAAGCUGACAACUCUGGCGAGUC
-----------------....((((((((((((........))))))).-....)))))..((((((((.((....)))))))-----))).........((((....)))). ( -26.70, z-score =  -2.39, R)
>droYak2.chr3L 8554199 91 + 24197627
-----------------AAAAUGGAUAUACCCUCCCAUAACAGGGUAUC-AAAAAUCCCACUUGCUCGC--GCACAUGGCGACA--UGGAAAAGCUGACAACUCUCGUGAGGC
-----------------.....(((((((((((........))))))).-....))))......(((((--(..((((....))--))........((....)).)))))).. ( -22.20, z-score =  -1.14, R)
>droEre2.scaffold_4784 10270644 104 + 25762168
UAUGCUUCAGUUAGUGGAAAAGGGAUAUACCCGGCCAUCACGGGGUAUC-AAAAAUCCCACUUGCUCGC--GCACAUGGCGACC------AAAGCUGACAACUCUCGUGAGUC
......((((((..(((....(((((((((((.(......).)))))).-....)))))......((((--.......))))))------).))))))..((((....)))). ( -31.50, z-score =  -1.58, R)
>consensus
_________________AAAAGGGAUAUACCCUCCCAUCACGGGGUAUC_AAAAAUCUCACUUGCUCGC__GCACAUGGCGAG_____CAAAAGCUGACAACUCUCGUGAGUC
.....................((((((((((((........)))))))......)))))....((((((........(((.............)))..........)))))). (-15.57 = -16.21 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:35:45 2011