Locus 3488

Sequence ID dm3.chr2R
Location 5,715,311 – 5,715,409
Length 98
Max. P 0.963071
window4785 window4786

overview

Window 5

Location 5,715,311 – 5,715,409
Length 98
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 63.17
Shannon entropy 0.57396
G+C content 0.43827
Mean single sequence MFE -27.73
Consensus MFE -12.75
Energy contribution -14.50
Covariance contribution 1.75
Combinations/Pair 1.32
Mean z-score -1.89
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.62
SVM RNA-class probability 0.955661
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5715311 98 + 21146708
AAUUCCCCAUGAAUCAAAGGCUGACUUCGGCGGGCAAAGCCCUGGAGAUCUAGAGAUCUAGAUUUCCAUAUAGCGAUA----------------CGCAACUCAAUGCGCCAUUU
..................(((........((((((...))))(((((((((((....)))))))))))....))....----------------.(((......)))))).... ( -31.50, z-score =  -2.78, R)
>droSim1.chr2R_random 1755133 114 + 2996586
AAUACCCCAUGAAUCAACGGCUGACUUCGGCGGGCAAAGCCCUGGAGAUCCAGAGAUCUAGAUUUCCAUAUAGCGAUAGGAUACGAUACAAUAGCGCAACUCAAUGCGCCAUUU
.........((.(((....((((....))))((((...))))((((((((.((....)).))))))))................))).))...(((((......)))))..... ( -31.10, z-score =  -1.75, R)
>droSec1.super_1 3324210 113 + 14215200
AAUACCCCAUGAAUCAAAGGCUGACUUCGGCGGGCAAAGCC-UGGAGAUCCAGAGAUCUAGAUUUCCAUAUAGCAAUACGAUACGAUACAAUAGCGCAACUCAAUGCGCCAUUU
.........((.(((....((((....))))((((...)))-)(((((((.((....)).))))))).................))).))...(((((......)))))..... ( -28.30, z-score =  -1.67, R)
>droGri2.scaffold_15112 955221 92 + 5172618
----ACUUUUGUGCCAAAAUGUAGACUUGGCAGAAAAUGGACCUGCU-UCUGUAUGAUUGAAUUUUCAGGAAUGAAU-----------------UUCAAGCUAAUCCAACUUUG
----..((((.((((((.........)))))).))))((((...((.-((.....))(((((..((((....)))).-----------------)))))))...))))...... ( -20.00, z-score =  -1.38, R)
>consensus
AAUACCCCAUGAAUCAAAGGCUGACUUCGGCGGGCAAAGCCCUGGAGAUCCAGAGAUCUAGAUUUCCAUAUAGCAAUA________________CGCAACUCAAUGCGCCAUUU
....(((..(((((((.....))).))))..)))....((..(((((((((((....)))))))))))....))...................(((((......)))))..... (-12.75 = -14.50 +   1.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,715,311 – 5,715,409
Length 98
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 63.17
Shannon entropy 0.57396
G+C content 0.43827
Mean single sequence MFE -32.70
Consensus MFE -14.46
Energy contribution -19.27
Covariance contribution 4.81
Combinations/Pair 1.24
Mean z-score -2.04
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.72
SVM RNA-class probability 0.963071
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5715311 98 - 21146708
AAAUGGCGCAUUGAGUUGCG----------------UAUCGCUAUAUGGAAAUCUAGAUCUCUAGAUCUCCAGGGCUUUGCCCGCCGAAGUCAGCCUUUGAUUCAUGGGGAAUU
.....(((((......))))----------------).((.((((.((((.((((((....)))))).))))((((...))))..(((((.....)))))....)))).))... ( -32.00, z-score =  -1.52, R)
>droSim1.chr2R_random 1755133 114 - 2996586
AAAUGGCGCAUUGAGUUGCGCUAUUGUAUCGUAUCCUAUCGCUAUAUGGAAAUCUAGAUCUCUGGAUCUCCAGGGCUUUGCCCGCCGAAGUCAGCCGUUGAUUCAUGGGGUAUU
.(((((((((......))))))))).....(((((((((.((....((((.((((((....)))))).))))((((...)))))).(((.((((...)))))))))))))))). ( -41.90, z-score =  -2.92, R)
>droSec1.super_1 3324210 113 - 14215200
AAAUGGCGCAUUGAGUUGCGCUAUUGUAUCGUAUCGUAUUGCUAUAUGGAAAUCUAGAUCUCUGGAUCUCCA-GGCUUUGCCCGCCGAAGUCAGCCUUUGAUUCAUGGGGUAUU
.(((((((((......)))))))))((((.(((......))).))))(((.((((((....)))))).))).-(((((((.....))))))).(((((........)))))... ( -36.60, z-score =  -1.96, R)
>droGri2.scaffold_15112 955221 92 - 5172618
CAAAGUUGGAUUAGCUUGAA-----------------AUUCAUUCCUGAAAAUUCAAUCAUACAGA-AGCAGGUCCAUUUUCUGCCAAGUCUACAUUUUGGCACAAAAGU----
......(((((..(((((((-----------------.((((....))))..)))).((.....))-)))..)))))((((.(((((((.......))))))).))))..---- ( -20.30, z-score =  -1.74, R)
>consensus
AAAUGGCGCAUUGAGUUGCG________________UAUCGCUAUAUGGAAAUCUAGAUCUCUAGAUCUCCAGGGCUUUGCCCGCCGAAGUCAGCCUUUGAUUCAUGGGGUAUU
.(((((((((......)))))))))...............(((...((((.((((((....)))))).)))).)))..(((((...(((.(((.....))))))...))))).. (-14.46 = -19.27 +   4.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:11:07 2011