Locus 3916

Sequence ID dm3.chr2R
Location 8,945,110 – 8,945,270
Length 160
Max. P 0.861175
window5365 window5366 window5367

overview

Window 5

Location 8,945,110 – 8,945,218
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.53
Shannon entropy 0.41591
G+C content 0.46476
Mean single sequence MFE -29.70
Consensus MFE -19.00
Energy contribution -18.88
Covariance contribution -0.12
Combinations/Pair 1.29
Mean z-score -1.29
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.629326
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8945110 108 - 21146708
AUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCAAUUUUCUGGCCUUAAUGUUGAAUCUUUCCUCGAACAAAUGGC------------CACACUGCGUAUGCGUAAUGCUUUAGACCAAC
.((.((((((((...(((.((((((((((...........(((((......((((........))))......)))------------)))))).)))))))))...)))))))).)).. ( -30.20, z-score =  -1.86, R)
>droSim1.chr2R 7397328 108 - 19596830
AUGCUUUAAGGCCACACGGCGUAUGAUUGAUGCCAUUUUCUGGCCUUAAAGUUCAAUCCCACUUCGAACAUAGUGCAAGUAAGG---CCACACUGCGUAUGCGUGAUGCAC---------
..((((((((((((...(((((.......)))))......))))))))))))...........(((..((((.((((.((....---....))))))))))..))).....--------- ( -29.90, z-score =  -0.87, R)
>droSec1.super_1 6461403 106 - 14215200
AUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCCAUUUUCUGGCCUUAAAGUUCAAUCCCACUUCGAACAUAGUGCAAGUAAGG---CCACACUGCGUAUACGUGAUUC-----------
..((((((((((((...(((((.......)))))......))))))))))))(((....((((........))))...((((.(---(......)).).))).)))...----------- ( -27.50, z-score =  -0.92, R)
>droYak2.chr2R 13121748 109 + 21139217
AUACUUUAAGGCUACACUGCGUAUGAGCAAUGUAGUUUGCUGGCCUUAAAGUUCCAUCUCACUUCGAACAUAGAGCAACUAAGGGCAACACACUGCGUAUGCGUGAUGC-----------
..((((((((((((.(((((((.......)))))))....))))))))))))...........(((..((((..(((......(....)....))).))))..)))...----------- ( -28.60, z-score =  -0.39, R)
>droEre2.scaffold_4845 5716610 107 + 22589142
AUACUUUAGGGCCACACGGCGUAUGAGUGAUGC-ACUGGCUGGCCUUAAAGUUCAAUCUUACUUCGAACACAGUGCCACUAAGG-CCACACUUUUCACCAACGCACUGC-----------
..((((((((((((..(((.((((.....))))-.)))..))))))))))))..................((((((....(((.-.....))).........)))))).----------- ( -32.32, z-score =  -2.42, R)
>consensus
AUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCAAUUUUCUGGCCUUAAAGUUCAAUCUCACUUCGAACAUAGUGCAACUAAGG___ACACACUGCGUAUGCGUGAUGC___________
..((((((((((((...(((((.......)))))......)))))))))))).........................................((((....))))............... (-19.00 = -18.88 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,945,145 – 8,945,258
Length 113
Sequences 5
Columns 121
Reading direction reverse
Mean pairwise identity 78.80
Shannon entropy 0.37959
G+C content 0.44823
Mean single sequence MFE -30.41
Consensus MFE -21.54
Energy contribution -21.30
Covariance contribution -0.24
Combinations/Pair 1.25
Mean z-score -1.30
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.687374
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8945145 113 - 21146708
GCGAUGUGUAUACCAGCUA-GUGCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCAAUUUUCUGGCCUUAAUGUUGAAUCUUUCCUCGAACAAAU-------
.(((((((..(((......-)))..))))........((((.....(((((((((....((((.......)))).......)))))))))..))))........))).......------- ( -25.70, z-score =   0.11, R)
>droSim1.chr2R 7397356 120 - 19596830
GCGAUAUGCAUACCAGCUA-GUCCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAUUGAUGCCAUUUUCUGGCCUUAAAGUUCAAUCCCACUUCGAACAUAGUGCAAGU
(.(((..((......))..-))))((((..(((....(((((.((((((((((((...(((((.......)))))......))))))))))))..........))))).))).)))).... ( -32.20, z-score =  -1.96, R)
>droSec1.super_1 6461429 120 - 14215200
GCGAUAUGUAUACCAGCUA-GUGCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCCAUUUUCUGGCCUUAAAGUUCAAUCCCACUUCGAACAUAGUGCAAGU
(((.(((((......((..-..)).............(((((.((((((((((((...(((((.......)))))......))))))))))))..........)))))))))).))).... ( -33.90, z-score =  -1.82, R)
>droYak2.chr2R 13121777 114 + 21139217
------GCUAUUUCAGUUA-GAGCGCACAAAUGAACAUCGAAUACUUUAAGGCUACACUGCGUAUGAGCAAUGUAGUUUGCUGGCCUUAAAGUUCCAUCUCACUUCGAACAUAGAGCAACU
------(((..((((....-...........))))..(((((.((((((((((((.(((((((.......)))))))....))))))))))))..........)))))......))).... ( -26.06, z-score =  -0.68, R)
>droEre2.scaffold_4845 5716638 105 + 22589142
---------------GCGAUGUGCGCGCAAAUGAACAUCGAAUACUUUAGGGCCACACGGCGUAUGAGUGAUGC-ACUGGCUGGCCUUAAAGUUCAAUCUUACUUCGAACACAGUGCCACU
---------------.....(((.((((...((....(((((.((((((((((((..(((.((((.....))))-.)))..))))))))))))..........))))).))..))))))). ( -34.20, z-score =  -2.13, R)
>consensus
GCGAU_UGUAUACCAGCUA_GUGCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCAAUUUUCUGGCCUUAAAGUUCAAUCUCACUUCGAACAUAGUGCAACU
...............((.......))...........(((((.((((((((((((...(((((.......)))))......))))))))))))..........)))))............. (-21.54 = -21.30 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,945,150 – 8,945,270
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.50
Shannon entropy 0.30900
G+C content 0.45612
Mean single sequence MFE -32.73
Consensus MFE -27.70
Energy contribution -28.70
Covariance contribution 1.00
Combinations/Pair 1.19
Mean z-score -1.42
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.861175
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8945150 120 - 21146708
CACUGCGUAUGAGCGAUGUGUAUACCAGCUAGUGCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCAAUUUUCUGGCCUUAAUGUUGAAUCUUUCCUCGAA
...(((((((.(((...((....))..))).)))))))..........((((..((.(((((((((....((((.......)))).......))))))))).))...........)))). ( -29.52, z-score =   0.20, R)
>droSim1.chr2R 7397368 120 - 19596830
CGCUGCGUAUGAGCGAUAUGCAUACCAGCUAGUCCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAUUGAUGCCAUUUUCUGGCCUUAAAGUUCAAUCCCACUUCGAA
.((((.(((((.........)))))))))...................(((((.((((((((((((...(((((.......)))))......))))))))))))..........))))). ( -35.00, z-score =  -2.18, R)
>droSec1.super_1 6461441 120 - 14215200
CGCUGCGUUUGAGCGAUAUGUAUACCAGCUAGUGCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCCAUUUUCUGGCCUUAAAGUUCAAUCCCACUUCGAA
.(.(((((...(((.............)))...)))))).........(((((.((((((((((((...(((((.......)))))......))))))))))))..........))))). ( -34.92, z-score =  -1.61, R)
>droYak2.chr2R 13121789 114 + 21139217
CACGGCGUAUAAGCUAUUU------CAGUUAGAGCGCACAAAUGAACAUCGAAUACUUUAAGGCUACACUGCGUAUGAGCAAUGUAGUUUGCUGGCCUUAAAGUUCCAUCUCACUUCGAA
....((((.(.((((....------.)))).).))))...........(((((.((((((((((((.(((((((.......)))))))....))))))))))))..........))))). ( -29.60, z-score =  -1.39, R)
>droEre2.scaffold_4845 5716650 105 + 22589142
CAUUGCGUAUGAGCGAU--------------GUGCGCGCAAAUGAACAUCGAAUACUUUAGGGCCACACGGCGUAUGAGUGAUGCA-CUGGCUGGCCUUAAAGUUCAAUCUUACUUCGAA
....((((((.......--------------))))))...........(((((.((((((((((((..(((.((((.....)))).-)))..))))))))))))..........))))). ( -34.60, z-score =  -2.11, R)
>consensus
CACUGCGUAUGAGCGAUAUG_AUACCAGCUAGUGCGCACAAAUGAACAUCGAAUGCUUUAAGGCCACACGGCGUAUGAGUGAUGCAAUUUUCUGGCCUUAAAGUUCAAUCUCACUUCGAA
....((((((.(((.............))).))))))...........(((((.((((((((((((...(((((.......)))))......))))))))))))..........))))). (-27.70 = -28.70 +   1.00)

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 22:19:14 2011