Locus 9824

Sequence ID dm3.chr3R
Location 9,321,114 – 9,321,212
Length 98
Max. P 0.996627
window13485 window13486

overview

Window 5

Location 9,321,114 – 9,321,212
Length 98
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.14
Shannon entropy 0.35885
G+C content 0.52046
Mean single sequence MFE -33.40
Consensus MFE -21.94
Energy contribution -24.67
Covariance contribution 2.72
Combinations/Pair 1.16
Mean z-score -2.41
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976400
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9321114 98 + 27905053
ACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA-CAUCUCUGUCUCCGACUCCGACUCAGAGUCGCAGUUGCAUUCGCCGUG------------
((.(((((....))))).))((((((.((((((....(((...((((((.-...)))))).)))(((((.......)))))))))))...))))))...------------ ( -36.00, z-score =  -3.20, R)
>droSim1.chr3R 15407237 98 - 27517382
ACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUGCAGAGA-CAUCUCUGUCUCCGACUCCGACUCAGAGUCGCAGUUGCAUUCGCCGUG------------
((.(((((....))))).))((((((.((((((....(((...((((((.-...)))))).)))(((((.......)))))))))))...))))))...------------ ( -36.30, z-score =  -2.88, R)
>droSec1.super_0 8436205 98 - 21120651
ACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUGCAGAGA-CAUCUCUGUCUCCGACUCCGACUCAGAGUCGCAGUUGCAUUCGCCGUG------------
((.(((((....))))).))((((((.((((((....(((...((((((.-...)))))).)))(((((.......)))))))))))...))))))...------------ ( -36.30, z-score =  -2.88, R)
>droYak2.chr3R 13629712 82 + 28832112
ACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA-CAUCUCUGUCUCCGACUCAGAGUCGCAGUCGC----------------------------
((.(((((....))))).)).......((((((....(((...((((((.-...)))))).)))(((.....)))))))))..---------------------------- ( -24.40, z-score =  -1.27, R)
>droEre2.scaffold_4770 5427261 94 - 17746568
ACAAGUGUGCAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA-CAUCUCUGUCUCCGACUCCGACUCCGACUCAGAGUCGCAGUUGC----------------
((.(((((....))))).))((.((.(((.(((((((.......))).))-))..))).)).))((((.((((((.......)))))).))))..---------------- ( -31.20, z-score =  -1.69, R)
>droAna3.scaffold_13340 1878124 109 + 23697760
ACGAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGACAUCUUCUCUGUUUCUGUCUCAGUCUCCA--UCGCCGCCACCGCCGCCGCAGCAGUCGCAGUC
((((((((....))))))))(((((.((((((.....(((((((.(((.....))).)))))))....))))))...--)))))((.((.((.......)).)).)).... ( -36.20, z-score =  -2.55, R)
>consensus
ACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA_CAUCUCUGUCUCCGACUCCGACUCAGAGUCGCAGUUGCAUUCGCCGUG____________
((.(((((....))))).))(((((..((((((....(((...((((((.....)))))).)))(((((.......)))))))))))....)))))............... (-21.94 = -24.67 +   2.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,321,114 – 9,321,212
Length 98
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.14
Shannon entropy 0.35885
G+C content 0.52046
Mean single sequence MFE -38.47
Consensus MFE -25.45
Energy contribution -27.45
Covariance contribution 2.00
Combinations/Pair 1.17
Mean z-score -3.09
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.96
SVM RNA-class probability 0.996627
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9321114 98 - 27905053
------------CACGGCGAAUGCAACUGCGACUCUGAGUCGGAGUCGGAGACAGAGAUG-UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGU
------------...((((((.....((.((((((((...)))))))).))((((((...-.)))))).................))))))((((((((....)))))))) ( -40.60, z-score =  -3.78, R)
>droSim1.chr3R 15407237 98 + 27517382
------------CACGGCGAAUGCAACUGCGACUCUGAGUCGGAGUCGGAGACAGAGAUG-UCUCUGCAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGU
------------...((((((((((....((((((((...))))))))((((((....))-))))))))..((....))......))))))((((((((....)))))))) ( -41.00, z-score =  -3.72, R)
>droSec1.super_0 8436205 98 + 21120651
------------CACGGCGAAUGCAACUGCGACUCUGAGUCGGAGUCGGAGACAGAGAUG-UCUCUGCAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGU
------------...((((((((((....((((((((...))))))))((((((....))-))))))))..((....))......))))))((((((((....)))))))) ( -41.00, z-score =  -3.72, R)
>droYak2.chr3R 13629712 82 - 28832112
----------------------------GCGACUGCGACUCUGAGUCGGAGACAGAGAUG-UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGU
----------------------------((((((.((((.....)))).))...((((((-((.(((.......)))))).))))))))).((((((((....)))))))) ( -29.40, z-score =  -2.48, R)
>droEre2.scaffold_4770 5427261 94 + 17746568
----------------GCAACUGCGACUCUGAGUCGGAGUCGGAGUCGGAGACAGAGAUG-UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGCACACUUGU
----------------...(((.((((((((...)))))))).))).((.((.(((..((-((.(((.......))))))).))).)).))((((((((....)))))))) ( -35.90, z-score =  -2.22, R)
>droAna3.scaffold_13340 1878124 109 - 23697760
GACUGCGACUGCUGCGGCGGCGGUGGCGGCGA--UGGAGACUGAGACAGAAACAGAGAAGAUGUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUCGU
....((.(((((((...))))))).))(((((--.(((..(((.((..((.(((((.......))))).)))).))).....))).)))))((((((((....)))))))) ( -42.90, z-score =  -2.63, R)
>consensus
____________CACGGCGAAUGCAACUGCGACUCUGAGUCGGAGUCGGAGACAGAGAUG_UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGU
...............(((((..........(((((((...)))))))((((((((((.....)))))..)))))............)))))((((((((....)))))))) (-25.45 = -27.45 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:11:56 2011