Locus 8324

Sequence ID dm3.chr3L
Location 22,006,153 – 22,006,256
Length 103
Max. P 0.666015
window11435 window11436

overview

Window 5

Location 22,006,153 – 22,006,256
Length 103
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 87.65
Shannon entropy 0.22486
G+C content 0.36146
Mean single sequence MFE -28.20
Consensus MFE -21.32
Energy contribution -21.18
Covariance contribution -0.13
Combinations/Pair 1.23
Mean z-score -1.70
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.605109
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22006153 103 + 24543557
-------AUGCACGAAG---AUGUGCAUAUUUAUGUUUAAAUAGACAGUUGUAUGCGGAUGAAUUAAUCUCGCAAAUUGAUGUCAGACAGCAUUUGCAAUGAGAUUGUGAGAA
-------...(((....---((.(((((((...(((((....)))))...))))))).)).....((((((((((((...((.....))..))))))...))))))))).... ( -25.30, z-score =  -1.00, R)
>droSim1.chr3L_random 933358 103 + 1049610
-------GUGCACGAAG---AUGUGCAUAUUUAUGUUUAAAUAGACAGAUGUAUGCGGAUGAAUUAAUCUCGCAAAUUGAUGUCAGACAGCAUUUGCAAUGAGAUUGUGCUAA
-------..((((....---((.(((((((...(((((....)))))...))))))).)).....((((((((((((...((.....))..))))))...))))))))))... ( -28.60, z-score =  -1.75, R)
>droSec1.super_11 1932603 103 + 2888827
-------GUGCACGAAG---AUGUGCAUAUUUAUGUUUAAAUAGACAGAUGUAUGCGGAUGAAUUAAUCUCGCAAAUUGAUGUCAGACAGCAUUUGCAAUGAGAUUGUGCUAA
-------..((((....---((.(((((((...(((((....)))))...))))))).)).....((((((((((((...((.....))..))))))...))))))))))... ( -28.60, z-score =  -1.75, R)
>droYak2.chr3L 22342732 103 + 24197627
-------AGGCACGAAG---AUGUGCAUAUUUAUGUUUAAAUAGACAGAUGUAUGCGGAUAAAUUAAUCUCACAAAUUGAUGUCAGACAGCAUUUGCAAUGAGAUUGUGCUAA
-------.(((((....---((.(((((((...(((((....)))))...))))))).)).....(((((((......(((((......))))).....)))))))))))).. ( -29.10, z-score =  -2.82, R)
>droEre2.scaffold_4784 21680650 103 + 25762168
-------AUGCACGAAG---AUGUGCAUGUUUAUGUUUAAAUAGACAGAUGUAUGUGGAUGAAUUAAUCUCGCAAAUUGAUGUCACACAGCAUUUGCAAUGAGAUUGUGCUAG
-------..((((((..---...(((((((((((......)))))))(((((.(((((((..((((((.......))))))))).)))))))))))))......))))))... ( -26.00, z-score =  -0.61, R)
>droAna3.scaffold_13337 21142544 112 + 23293914
CCGGAAGACACAUGCAGUUCGUGCGAGUGUCUCCGAUUAUAUAGACA-AUAUAUGCAGAUGAAUUAAUCUCACAAAUUGAUGUCAGACAGCAUUUGCAAUGAGAUUGUGCCAA
.((((.(((((.((((.....)))).))))))))).........(((-((...((((((((......(((.(((......))).)))...)))))))).....)))))..... ( -31.60, z-score =  -2.25, R)
>consensus
_______AUGCACGAAG___AUGUGCAUAUUUAUGUUUAAAUAGACAGAUGUAUGCGGAUGAAUUAAUCUCGCAAAUUGAUGUCAGACAGCAUUUGCAAUGAGAUUGUGCUAA
.........((((.......((.(((((((...(((((....)))))...))))))).)).....(((((((......(((((......))))).....)))))))))))... (-21.32 = -21.18 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,006,153 – 22,006,256
Length 103
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 87.65
Shannon entropy 0.22486
G+C content 0.36146
Mean single sequence MFE -22.03
Consensus MFE -15.87
Energy contribution -16.73
Covariance contribution 0.86
Combinations/Pair 1.12
Mean z-score -1.94
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.666015
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22006153 103 - 24543557
UUCUCACAAUCUCAUUGCAAAUGCUGUCUGACAUCAAUUUGCGAGAUUAAUUCAUCCGCAUACAACUGUCUAUUUAAACAUAAAUAUGCACAU---CUUCGUGCAU-------
....(((((((((...((((((..((.....))...)))))))))))).........(((((....(((........)))....)))))....---....)))...------- ( -17.70, z-score =  -1.53, R)
>droSim1.chr3L_random 933358 103 - 1049610
UUAGCACAAUCUCAUUGCAAAUGCUGUCUGACAUCAAUUUGCGAGAUUAAUUCAUCCGCAUACAUCUGUCUAUUUAAACAUAAAUAUGCACAU---CUUCGUGCAC-------
...((((((((((...((((((..((.....))...)))))))))))).........(((((....(((........)))....)))))....---....))))..------- ( -22.50, z-score =  -2.53, R)
>droSec1.super_11 1932603 103 - 2888827
UUAGCACAAUCUCAUUGCAAAUGCUGUCUGACAUCAAUUUGCGAGAUUAAUUCAUCCGCAUACAUCUGUCUAUUUAAACAUAAAUAUGCACAU---CUUCGUGCAC-------
...((((((((((...((((((..((.....))...)))))))))))).........(((((....(((........)))....)))))....---....))))..------- ( -22.50, z-score =  -2.53, R)
>droYak2.chr3L 22342732 103 - 24197627
UUAGCACAAUCUCAUUGCAAAUGCUGUCUGACAUCAAUUUGUGAGAUUAAUUUAUCCGCAUACAUCUGUCUAUUUAAACAUAAAUAUGCACAU---CUUCGUGCCU-------
...((((((((((...((((((..((.....))...)))))))))))).........(((((....(((........)))....)))))....---....))))..------- ( -20.20, z-score =  -1.92, R)
>droEre2.scaffold_4784 21680650 103 - 25762168
CUAGCACAAUCUCAUUGCAAAUGCUGUGUGACAUCAAUUUGCGAGAUUAAUUCAUCCACAUACAUCUGUCUAUUUAAACAUAAACAUGCACAU---CUUCGUGCAU-------
...((((((((((...((((((..((.....))...))))))))))))..................(((.(((......))).))).......---....))))..------- ( -17.30, z-score =  -0.30, R)
>droAna3.scaffold_13337 21142544 112 - 23293914
UUGGCACAAUCUCAUUGCAAAUGCUGUCUGACAUCAAUUUGUGAGAUUAAUUCAUCUGCAUAUAU-UGUCUAUAUAAUCGGAGACACUCGCACGAACUGCAUGUGUCUUCCGG
.(((.(((((.....((((.(((..((((.(((......))).)))).....))).))))...))-))))))......(((((((((..(((.....)))..))))).)))). ( -32.00, z-score =  -2.85, R)
>consensus
UUAGCACAAUCUCAUUGCAAAUGCUGUCUGACAUCAAUUUGCGAGAUUAAUUCAUCCGCAUACAUCUGUCUAUUUAAACAUAAAUAUGCACAU___CUUCGUGCAU_______
...((((((((((...((((((..((.....))...)))))))))))).........(((((....(((........)))....)))))...........))))......... (-15.87 = -16.73 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:43:31 2011