Locus 10015

Sequence ID dm3.chr3R
Location 10,569,533 – 10,569,593
Length 60
Max. P 0.999294
window13764 window13765

overview

Window 4

Location 10,569,533 – 10,569,593
Length 60
Sequences 6
Columns 60
Reading direction forward
Mean pairwise identity 77.33
Shannon entropy 0.44416
G+C content 0.42350
Mean single sequence MFE -12.92
Consensus MFE -11.13
Energy contribution -10.72
Covariance contribution -0.41
Combinations/Pair 1.50
Mean z-score -2.92
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.44
SVM RNA-class probability 0.998666
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 10569533 60 + 27905053
UUGUUUGCCAGUAUUUUUUGCCCAGCUUCGGUUUUUCCCGAAGCUACACACAUUUUCAUG
.(((.((...(((.....)))..((((((((......)))))))).)).)))........ ( -14.00, z-score =  -3.81, R)
>droEre2.scaffold_4770 10103584 60 + 17746568
AUGUUUGCCAGUACUUUUUGCCCAGCUUCGGGUUUUCCCGAAGCUACACACAUUUUUAUG
((((.((.(((......)))...(((((((((....))))))))).)).))))....... ( -17.10, z-score =  -4.07, R)
>droYak2.chr3R 12970658 59 - 28832112
AUGUUUGCCAGUA-UUUUUGCCCAGCUUCGGUUUUUCCCGAUGCUACACACAUUUUUACG
((((.((...(((-....)))..(((.((((......)))).))).)).))))....... ( -10.30, z-score =  -2.13, R)
>droSec1.super_0 9756545 60 - 21120651
AUGUUUGCCAGUAUUUUUUGCCCAGCUUCGGAUUUUCCCGAAGCUACACACAUUUUCAUG
((((.((...(((.....)))..((((((((......)))))))).)).))))....... ( -14.90, z-score =  -4.07, R)
>droSim1.chr3R 16625827 60 - 27517382
AUGUUUGCCAGUAUUUUUUGCCCAGCUUCGGAUUUUCCCGAAGCUACACACAUUUUCAUG
((((.((...(((.....)))..((((((((......)))))))).)).))))....... ( -14.90, z-score =  -4.07, R)
>droGri2.scaffold_14624 1721388 53 + 4233967
CAUUUUGUGCGUACUCUCAG---AGAGCCAGUCUCUUCUCCUUUUAAGCUCAGUUU----
....(((.((........((---((((.....))).)))........)).)))...---- (  -6.29, z-score =   0.66, R)
>consensus
AUGUUUGCCAGUAUUUUUUGCCCAGCUUCGGUUUUUCCCGAAGCUACACACAUUUUCAUG
.......................((((((((......))))))))............... (-11.13 = -10.72 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,569,533 – 10,569,593
Length 60
Sequences 6
Columns 60
Reading direction reverse
Mean pairwise identity 77.33
Shannon entropy 0.44416
G+C content 0.42350
Mean single sequence MFE -17.68
Consensus MFE -15.40
Energy contribution -15.73
Covariance contribution 0.34
Combinations/Pair 1.25
Mean z-score -3.55
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.77
SVM RNA-class probability 0.999294
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 10569533 60 - 27905053
CAUGAAAAUGUGUGUAGCUUCGGGAAAAACCGAAGCUGGGCAAAAAAUACUGGCAAACAA
(((....)))(((.(((((((((......))))))))).))).................. ( -21.20, z-score =  -5.20, R)
>droEre2.scaffold_4770 10103584 60 - 17746568
CAUAAAAAUGUGUGUAGCUUCGGGAAAACCCGAAGCUGGGCAAAAAGUACUGGCAAACAU
..........(((.((((((((((....)))))))))).))).................. ( -21.90, z-score =  -4.65, R)
>droYak2.chr3R 12970658 59 + 28832112
CGUAAAAAUGUGUGUAGCAUCGGGAAAAACCGAAGCUGGGCAAAAA-UACUGGCAAACAU
.((.......(((.((((.((((......)))).)))).)))....-.....))...... ( -16.79, z-score =  -3.39, R)
>droSec1.super_0 9756545 60 + 21120651
CAUGAAAAUGUGUGUAGCUUCGGGAAAAUCCGAAGCUGGGCAAAAAAUACUGGCAAACAU
(((....)))(((.(((((((((......))))))))).))).................. ( -20.00, z-score =  -4.55, R)
>droSim1.chr3R 16625827 60 + 27517382
CAUGAAAAUGUGUGUAGCUUCGGGAAAAUCCGAAGCUGGGCAAAAAAUACUGGCAAACAU
(((....)))(((.(((((((((......))))))))).))).................. ( -20.00, z-score =  -4.55, R)
>droGri2.scaffold_14624 1721388 53 - 4233967
----AAACUGAGCUUAAAAGGAGAAGAGACUGGCUCU---CUGAGAGUACGCACAAAAUG
----.....(.((((....(((((..........)))---))..)))).).......... (  -6.20, z-score =   1.05, R)
>consensus
CAUGAAAAUGUGUGUAGCUUCGGGAAAAACCGAAGCUGGGCAAAAAAUACUGGCAAACAU
..........(((.(((((((((......))))))))).))).................. (-15.40 = -15.73 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:46 2011