Locus 3480

Sequence ID dm3.chr2R
Location 5,656,648 – 5,656,764
Length 116
Max. P 0.763620
window4776 window4777

overview

Window 6

Location 5,656,648 – 5,656,764
Length 116
Sequences 7
Columns 116
Reading direction forward
Mean pairwise identity 64.73
Shannon entropy 0.69545
G+C content 0.60510
Mean single sequence MFE -38.99
Consensus MFE -15.31
Energy contribution -16.40
Covariance contribution 1.09
Combinations/Pair 1.44
Mean z-score -1.14
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.688344
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5656648 116 + 21146708
GGAAGGGGUGCAGCAGCAGCACCCAUGCCACAGACACCUGCGGCCAUAAAACCGUUAUCGGUCAGAGCGGCUGCCCCUCUGCCGGCUCCGCUGACAAGCAUUGGUGCUCCAGCCGU
((.(((((.(((((.((.........(((.(((....))).)))......((((....))))....)).))))).))))).))(((...(((....)))..(((....)))))).. ( -46.00, z-score =  -0.51, R)
>droWil1.scaffold_180701 3629786 89 + 3904529
---------GCUGGCGGGGCAACAUUGCCACAGACACCUGCGGCUAUAAAACUGUUAUCGGACAUUGUUGUUGUUGCAACGCCCACACUUCCCCCUGU------------------
---------...((((..((((((..(((.(((....))).))).((((...((((....))))...))))))))))..))))...............------------------ ( -27.70, z-score =  -0.99, R)
>droSim1.chr2R_random 1739244 116 + 2996586
GGAAGGGGGGCAGCAGCAGCACCCAUGCCACAGACACCUGCGGCCAUAAAACCGUUAUCGGUCAGAGCGGCUGCCCCUCUGCCUGCUCCGCCGACAAGCAUUGGUGCUCCUGCCGU
((.(((((((((((.((.........(((.(((....))).)))......((((....))))....)).))))))))))).)).((..((((((......)))))).....))... ( -47.80, z-score =  -0.72, R)
>droSec1.super_1 3265714 110 + 14215200
GGAAGGGGGGCAGCAGC------CAUGCCACAGACACCUGCGGCCAUAAAACCGUUAUCGGUCAGAGCGGCUGCCCCUCUGCCCGCUCCACCGACAAGCAUUGGUGCUCCUGCCGU
((.(((((((((((.((------(..(((.(((....))).)))......((((....))))..).)).)))))))))))..))((..((((((......)))))).....))... ( -48.20, z-score =  -1.90, R)
>droYak2.chr2L 18281101 116 + 22324452
GGAAGAGGAGCAUCAUGAGCACCCAUGCCACAGACACCUGCGGCCAUAAAACCGUUAUCGGUCAGAGCGGCUGCCCCUCGGCCUCCUUCCCCAGUAAGCAUUGAUGCUCCUGCCGU
((...((((((((((((.((......(((.(((....))).)))......((((....))))....))(((((.....)))))...............)).)))))))))).)).. ( -40.70, z-score =  -1.98, R)
>droEre2.scaffold_4929 17931097 95 - 26641161
GGAAGGGGAGCAAGAGGAGCAGCCAUGCCACAGACACCUGCGGCCAUAAAACCGUUAUCGGUCAGAGCGGCUGCCACCAUUGGUGCCCCAGCGGU---------------------
....(((((.(((..(..((((((..(((.(((....))).)))......((((....))))......))))))..)..))).).))))......--------------------- ( -37.80, z-score =  -1.60, R)
>droAna3.scaffold_13266 12927202 89 + 19884421
GCAGUUGUUGCUCCGCCUGCUGCAAUGCCACAAAUACCUGCGGCCAUAAAACUGUUAUCGGACAGUGUUGCCGCCGAUGUUGCACCCAG---------------------------
(((((.((......))..)))))..(((.(((.....(.(((((......((((((....))))))...))))).).))).))).....--------------------------- ( -24.70, z-score =  -0.29, R)
>consensus
GGAAGGGGAGCAGCAGCAGCACCCAUGCCACAGACACCUGCGGCCAUAAAACCGUUAUCGGUCAGAGCGGCUGCCCCUCUGCCUGCUCCACCGACAAGCAUUG_UGCUCC_GCCGU
((.(((((.((...............(((.(((....))).))).......(((....)))...........)).))))).))................................. (-15.31 = -16.40 +   1.09)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 5,656,648 – 5,656,764
Length 116
Sequences 7
Columns 116
Reading direction reverse
Mean pairwise identity 64.73
Shannon entropy 0.69545
G+C content 0.60510
Mean single sequence MFE -44.71
Consensus MFE -16.40
Energy contribution -17.30
Covariance contribution 0.90
Combinations/Pair 1.12
Mean z-score -1.35
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763620
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5656648 116 - 21146708
ACGGCUGGAGCACCAAUGCUUGUCAGCGGAGCCGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUGCUGCUGCACCCCUUCC
.((((.(.((((((.(((((.....(((((((((((((((.((...)).))))).)).....(((((....)))))..))).)))))))))).)))))).).)))).......... ( -50.10, z-score =  -0.20, R)
>droWil1.scaffold_180701 3629786 89 - 3904529
------------------ACAGGGGGAAGUGUGGGCGUUGCAACAACAACAAUGUCCGAUAACAGUUUUAUAGCCGCAGGUGUCUGUGGCAAUGUUGCCCCGCCAGC---------
------------------...(((((..((.(((((((((.........)))))))))...)).((..(((.(((((((....))))))).)))..))))).))...--------- ( -33.60, z-score =  -1.73, R)
>droSim1.chr2R_random 1739244 116 - 2996586
ACGGCAGGAGCACCAAUGCUUGUCGGCGGAGCAGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUGCUGCUGCCCCCCUUCC
.((((((.((((((..((.(((((((((((((.(((.........))))))))).)))))))))........(((((((....)))))))...)))))).)))))).......... ( -58.50, z-score =  -2.10, R)
>droSec1.super_1 3265714 110 - 14215200
ACGGCAGGAGCACCAAUGCUUGUCGGUGGAGCGGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUG------GCUGCUGCCCCCCUUCC
..(((((.((((((.....(((((((((((((((((......))..))))))).)))))))).)))......(((((((....)))))))...------))).)))))........ ( -51.50, z-score =  -1.29, R)
>droYak2.chr2L 18281101 116 - 22324452
ACGGCAGGAGCAUCAAUGCUUACUGGGGAAGGAGGCCGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUCAUGAUGCUCCUCUUCC
..((.((((((((((.......((.((........)).))(((((.(((....(((((....))))).....(((((((....))))))).))).))))).))))))))))))... ( -50.40, z-score =  -1.96, R)
>droEre2.scaffold_4929 17931097 95 + 26641161
---------------------ACCGCUGGGGCACCAAUGGUGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGCUGCUCCUCUUGCUCCCCUUCC
---------------------......((((...(((.((..(((((((....(((((....))))).....(((((((....))))))).)))))))..)).)))..)))).... ( -41.80, z-score =  -2.31, R)
>droAna3.scaffold_13266 12927202 89 - 19884421
---------------------------CUGGGUGCAACAUCGGCGGCAACACUGUCCGAUAACAGUUUUAUGGCCGCAGGUAUUUGUGGCAUUGCAGCAGGCGGAGCAACAACUGC
---------------------------.....(((((.((((((((.....))).)))))............(((((((....))))))).)))))((((..(......)..)))) ( -27.10, z-score =   0.14, R)
>consensus
ACGGC_GGAGCA_CAAUGCUUGUCGGCGGAGCAGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUGCUGCUGCACCCCUUCC
..........................................(((.((.....(((((....))))).....(((((((....)))))))..)).))).................. (-16.40 = -17.30 +   0.90)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:10:59 2011