Locus 6431

Sequence ID dm3.chr3L
Location 6,666,964 – 6,667,041
Length 77
Max. P 0.962886
window8856 window8857

overview

Window 6

Location 6,666,964 – 6,667,041
Length 77
Sequences 5
Columns 79
Reading direction forward
Mean pairwise identity 87.63
Shannon entropy 0.21563
G+C content 0.38872
Mean single sequence MFE -15.68
Consensus MFE -13.68
Energy contribution -13.88
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.71
SVM RNA-class probability 0.962886
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 6666964 77 + 24543557
AUUGUGGCCCAAAACUUUGGCCACUCCAAUCCAAAGGAUUUUCCUUCUUGGCAUACCUGCCUCUAAUUUUUUUUUUU--
...((((((.........)))))).........((((.....))))...((((....))))................-- ( -17.30, z-score =  -2.29, R)
>droEre2.scaffold_4784 21063226 79 - 25762168
AUUGUGGCUCAAAACUUUGGCCACUCCAAUCCAAAGGAUUUUCCGCUUUGGCAUACCCACAUACCUCUCUUUUUUUGUU
...(((((.(((....))))))))......(((((((......).))))))............................ ( -14.80, z-score =  -1.29, R)
>droYak2.chr3L 7246779 77 + 24197627
AUUGUGGCUCAAAACUUUGGCCACUCCAAUCCAAAGGAUUUUCCUUUUUGGCAUGCCUACCUCUCUUAUUUUUCUUU--
...(((((.(((....)))))))).((((...(((((.....)))))))))..........................-- ( -15.70, z-score =  -2.07, R)
>droSec1.super_2 6603878 75 + 7591821
AUUGUGGCUCAAAACUUUGGCCACUCCAAUCCAAAGGAUUUUCCUCUUUGGCAUACCCACUUCUAUUUUUUUUUU----
...(((((.(((....))))))))......(((((((.......)))))))........................---- ( -15.30, z-score =  -2.33, R)
>droSim1.chr3L 6149926 75 + 22553184
AUUGUGGCUCAAAACUUUGGCCACUCCAAUCCAAAGGAUUUUCCUCUUUGGCAUACCUACUUCUCUUUUUUUUUU----
...(((((.(((....))))))))......(((((((.......)))))))........................---- ( -15.30, z-score =  -2.65, R)
>consensus
AUUGUGGCUCAAAACUUUGGCCACUCCAAUCCAAAGGAUUUUCCUCUUUGGCAUACCUACCUCUCUUUUUUUUUUU___
...(((((.(((....))))))))......(((((((.....)))..))))............................ (-13.68 = -13.88 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,666,964 – 6,667,041
Length 77
Sequences 5
Columns 79
Reading direction reverse
Mean pairwise identity 87.63
Shannon entropy 0.21563
G+C content 0.38872
Mean single sequence MFE -18.74
Consensus MFE -16.86
Energy contribution -16.66
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.951761
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 6666964 77 - 24543557
--AAAAAAAAAAAUUAGAGGCAGGUAUGCCAAGAAGGAAAAUCCUUUGGAUUGGAGUGGCCAAAGUUUUGGGCCACAAU
--................((((....))))..(((((.....)))))........((((((.........))))))... ( -22.00, z-score =  -2.51, R)
>droEre2.scaffold_4784 21063226 79 + 25762168
AACAAAAAAAGAGAGGUAUGUGGGUAUGCCAAAGCGGAAAAUCCUUUGGAUUGGAGUGGCCAAAGUUUUGAGCCACAAU
..(((..((((.((....(((.((....))...))).....))))))...)))..((((((((....))).)))))... ( -18.60, z-score =  -1.05, R)
>droYak2.chr3L 7246779 77 - 24197627
--AAAGAAAAAUAAGAGAGGUAGGCAUGCCAAAAAGGAAAAUCCUUUGGAUUGGAGUGGCCAAAGUUUUGAGCCACAAU
--................((((....))))..(((((.....)))))........((((((((....))).)))))... ( -18.50, z-score =  -1.96, R)
>droSec1.super_2 6603878 75 - 7591821
----AAAAAAAAAAUAGAAGUGGGUAUGCCAAAGAGGAAAAUCCUUUGGAUUGGAGUGGCCAAAGUUUUGAGCCACAAU
----........................(((((((((.....)))))...)))).((((((((....))).)))))... ( -17.30, z-score =  -1.72, R)
>droSim1.chr3L 6149926 75 - 22553184
----AAAAAAAAAAGAGAAGUAGGUAUGCCAAAGAGGAAAAUCCUUUGGAUUGGAGUGGCCAAAGUUUUGAGCCACAAU
----........................(((((((((.....)))))...)))).((((((((....))).)))))... ( -17.30, z-score =  -2.24, R)
>consensus
___AAAAAAAAAAAGAGAAGUAGGUAUGCCAAAGAGGAAAAUCCUUUGGAUUGGAGUGGCCAAAGUUUUGAGCCACAAU
............................(((((((((.....)))))...)))).((((((((....))).)))))... (-16.86 = -16.66 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:07:41 2011