Locus 10835

Sequence ID dm3.chr3R
Location 16,813,687 – 16,813,788
Length 101
Max. P 0.990379
window14886 window14887

overview

Window 6

Location 16,813,687 – 16,813,788
Length 101
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 73.16
Shannon entropy 0.49171
G+C content 0.35099
Mean single sequence MFE -18.18
Consensus MFE -8.81
Energy contribution -10.56
Covariance contribution 1.75
Combinations/Pair 1.22
Mean z-score -1.62
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.709532
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 16813687 101 + 27905053
GACUUAUUCUUUUUUGUCAAUAUUGGGGAAACA--GACCCCCAAACUGCCAACUUAAUCGCUAAACCAAGUUCUCGUUACUUUAACAAUAUAAGUUGAAUGAC
...............((((...((((((.....--...)))))).....(((((((...(((......)))....((((...))))....)))))))..)))) ( -18.80, z-score =  -1.83, R)
>droSim1.chr3R_random 842746 103 + 1307089
GACUUAUUCUUUUUUGUCAAUAUUGGGGGAACACAGACCCCCAAACUGCCAACUUAAUCGCUAAACCAAGUUCUCGUUACUUUAACAAUAUAAGUUGAAUGAC
...............((((...(((((((........))))))).....(((((((...(((......)))....((((...))))....)))))))..)))) ( -21.70, z-score =  -2.32, R)
>droSec1.super_38 88575 101 - 400794
GACUUAUUCUUUUUUGUCAAUAUUGGGGGAACA--GACCCCCAAACUGCCAACUUAAUCGCUAAACCAAGUUCUCGUUACUUUAACAAUAUAAGUUGAAUGAC
...............((((...(((((((....--..))))))).....(((((((...(((......)))....((((...))))....)))))))..)))) ( -21.90, z-score =  -2.39, R)
>droYak2.chr3R 5605830 85 + 28832112
GACGUUUUCUUUUUUGUCAAUAUUGGGGGAAGA--AACCUCCAAACUGCCAACUUAAUCG----------------UUACUUUAACAAUCUAAGUUGAAUGAC
...............((((...(((((((....--..))))))).....(((((((((.(----------------(((...)))).)).)))))))..)))) ( -18.40, z-score =  -1.88, R)
>droEre2.scaffold_4770 12903494 101 - 17746568
GACUUUUUCUUUUUUGUCAAUAUUGGGGGAACA--GACCUCCAAACUGCCAACUUAAUCGCUAAACCAACUUCUCGUUACUUUAAUAAUCUAAGUUGAAUGAC
...............((((...(((((((....--..))))))).....(((((((.....((((..(((.....)))..))))......)))))))..)))) ( -18.10, z-score =  -1.73, R)
>droVir3.scaffold_12958 748438 82 + 3547706
AGCGCAAAAAUAUAUAAAAAUCUUGGUGCACAA--UAUUUGAAUAUUGUCAAUACGCUUG-------------------CUAUCAGCAUAUAAGUAAAUCCAC
.((((...((.((......)).)).))))((((--(((....)))))))...(((...((-------------------(.....))).....)))....... ( -10.20, z-score =   0.42, R)
>consensus
GACUUAUUCUUUUUUGUCAAUAUUGGGGGAACA__GACCCCCAAACUGCCAACUUAAUCGCUAAACCAAGUUCUCGUUACUUUAACAAUAUAAGUUGAAUGAC
...............((((...(((((((........))))))).....(((((((..................................)))))))..)))) ( -8.81 = -10.56 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,813,687 – 16,813,788
Length 101
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 73.16
Shannon entropy 0.49171
G+C content 0.35099
Mean single sequence MFE -25.39
Consensus MFE -10.79
Energy contribution -14.33
Covariance contribution 3.55
Combinations/Pair 1.23
Mean z-score -2.95
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.42
SVM RNA-class probability 0.990379
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 16813687 101 - 27905053
GUCAUUCAACUUAUAUUGUUAAAGUAACGAGAACUUGGUUUAGCGAUUAAGUUGGCAGUUUGGGGGUC--UGUUUCCCCAAUAUUGACAAAAAAGAAUAAGUC
((((.((((((((.(((((((((.(((.......))).)))))))))))))))))....(((((((..--....)))))))...))))............... ( -29.40, z-score =  -3.72, R)
>droSim1.chr3R_random 842746 103 - 1307089
GUCAUUCAACUUAUAUUGUUAAAGUAACGAGAACUUGGUUUAGCGAUUAAGUUGGCAGUUUGGGGGUCUGUGUUCCCCCAAUAUUGACAAAAAAGAAUAAGUC
((((.((((((((.(((((((((.(((.......))).)))))))))))))))))....(((((((........)))))))...))))............... ( -31.40, z-score =  -3.93, R)
>droSec1.super_38 88575 101 + 400794
GUCAUUCAACUUAUAUUGUUAAAGUAACGAGAACUUGGUUUAGCGAUUAAGUUGGCAGUUUGGGGGUC--UGUUCCCCCAAUAUUGACAAAAAAGAAUAAGUC
((((.((((((((.(((((((((.(((.......))).)))))))))))))))))....(((((((..--....)))))))...))))............... ( -31.60, z-score =  -4.25, R)
>droYak2.chr3R 5605830 85 - 28832112
GUCAUUCAACUUAGAUUGUUAAAGUAA----------------CGAUUAAGUUGGCAGUUUGGAGGUU--UCUUCCCCCAAUAUUGACAAAAAAGAAAACGUC
((((.(((((((.((((((((...)))----------------))))))))))))....((((.((..--....)).))))...))))............... ( -20.20, z-score =  -2.50, R)
>droEre2.scaffold_4770 12903494 101 + 17746568
GUCAUUCAACUUAGAUUAUUAAAGUAACGAGAAGUUGGUUUAGCGAUUAAGUUGGCAGUUUGGAGGUC--UGUUCCCCCAAUAUUGACAAAAAAGAAAAAGUC
((((.(((((((.(((..(((((.((((.....)))).)))))..))))))))))....((((.((..--....)).))))...))))............... ( -24.40, z-score =  -2.68, R)
>droVir3.scaffold_12958 748438 82 - 3547706
GUGGAUUUACUUAUAUGCUGAUAG-------------------CAAGCGUAUUGACAAUAUUCAAAUA--UUGUGCACCAAGAUUUUUAUAUAUUUUUGCGCU
.(((((......(((((((.....-------------------..))))))).......)))))....--..(((((..(((((........)))))))))). ( -15.32, z-score =  -0.60, R)
>consensus
GUCAUUCAACUUAUAUUGUUAAAGUAACGAGAACUUGGUUUAGCGAUUAAGUUGGCAGUUUGGAGGUC__UGUUCCCCCAAUAUUGACAAAAAAGAAUAAGUC
((((.((((((((.(((((((((.(((.......))).)))))))))))))))))....((((.((........)).))))...))))............... (-10.79 = -14.33 +   3.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:31:20 2011