Locus 5542

Sequence ID dm3.chr3LHet
Location 439,842 – 439,945
Length 103
Max. P 0.997904
window7609 window7610

overview

Window 9

Location 439,842 – 439,945
Length 103
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 69.91
Shannon entropy 0.52170
G+C content 0.49593
Mean single sequence MFE -28.54
Consensus MFE -15.64
Energy contribution -16.48
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -2.71
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.21
SVM RNA-class probability 0.997904
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 439842 103 + 2555491
ACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUAAAACUUCAGCUCCGC-GCGCAACAAGCUUACGGCAU---------
............(((............(((((((((((((....)))))))))...(((((...........)))))))))..-((.......))....)))..--------- ( -28.60, z-score =  -2.60, R)
>droAna3.scaffold_13250 842529 109 - 3535662
AUAUGUGGCAACCCUAAG-CGUUUACCAUAAUACAAUCGAACUCGAUAUCGUAUGAGAGUAU-CGAUAUCGCUUUUUCUGCGCCUCACGACA--UCGACAGCCUCAUCCGCAG
..(((.(((........(-..((......))..)..((((..((((((((((((....))).-)))))))((.......)).......))..--))))..))).)))...... ( -23.20, z-score =  -0.88, R)
>droSim1.chr2h_random 683859 104 + 3178526
ACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUUAAACUUCAGCUCCGCCGCGCAACAAGCUUACGGCAU---------
..((((.((.......)))))).....(((((((((((((....)))))))))...(((((...........)))))))))((((.((.....))...))))..--------- ( -31.80, z-score =  -3.55, R)
>droSec1.super_0 589422 98 + 21120651
------ACAAGUACCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUGGAACUUCAGCUCUGCCGCGCAACAAGCUAACGGCAU---------
------...................(((((((((((((((....)))))))))...(..(.....)..)..))))))...(((((.((.....))...))))).--------- ( -29.70, z-score =  -2.77, R)
>droYak2.chrU 11905997 97 - 28119190
------ACUAACGCCAAGACCUUUCCUGGAUGACGAUAUCUUCUGAUAUCGUCAGACUGGCCACUCU-GGACUUCAACCCCGCCGCGCAACAAGCUUACGGCAU---------
------......((((...((......)).((((((((((....))))))))))...))))......-((.........))((((.((.....))...))))..--------- ( -29.40, z-score =  -3.75, R)
>consensus
A_A_GUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUAAAACUUCAGCUCCGCCGCGCAACAAGCUUACGGCAU_________
.......................(((.....(((((((((....))))))))).....)))....................((((.((.....))...))))........... (-15.64 = -16.48 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 439,842 – 439,945
Length 103
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 69.91
Shannon entropy 0.52170
G+C content 0.49593
Mean single sequence MFE -32.99
Consensus MFE -19.74
Energy contribution -20.14
Covariance contribution 0.40
Combinations/Pair 1.27
Mean z-score -1.70
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.84
SVM RNA-class probability 0.970617
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 439842 103 - 2555491
---------AUGCCGUAAGCUUGUUGCGC-GCGGAGCUGAAGUUUUAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGU
---------((((((..(.(((....(((-(((((((....))))).)))))(((.....(((((((((....))))))))).....)))))).)..)))))).......... ( -31.30, z-score =  -1.28, R)
>droAna3.scaffold_13250 842529 109 + 3535662
CUGCGGAUGAGGCUGUCGA--UGUCGUGAGGCGCAGAAAAAGCGAUAUCG-AUACUCUCAUACGAUAUCGAGUUCGAUUGUAUUAUGGUAAACG-CUUAGGGUUGCCACAUAU
...((.(((((..((((((--((((((..............)))))))))-)))..))))).))..((((....)))).......((((((.(.-....)..))))))..... ( -32.24, z-score =  -1.03, R)
>droSim1.chr2h_random 683859 104 - 3178526
---------AUGCCGUAAGCUUGUUGCGCGGCGGAGCUGAAGUUUAAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGU
---------..(((((..((.....)))))))((.(((((.(((.(((....(((.....(((((((((....))))))))).....))).....)))))).))))).))... ( -35.10, z-score =  -2.19, R)
>droSec1.super_0 589422 98 - 21120651
---------AUGCCGUUAGCUUGUUGCGCGGCAGAGCUGAAGUUCCAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGUACUUGU------
---------.((((((..((.....))))))))((((....)))).((((..........(((((((((....)))))))))..((((((....))))))))))...------ ( -32.20, z-score =  -1.96, R)
>droYak2.chrU 11905997 97 + 28119190
---------AUGCCGUAAGCUUGUUGCGCGGCGGGGUUGAAGUCC-AGAGUGGCCAGUCUGACGAUAUCAGAAGAUAUCGUCAUCCAGGAAAGGUCUUGGCGUUAGU------
---------.((((((..((.....))))))))...((((.(((.-(((.(..((.(..((((((((((....))))))))))..).))...).))).))).)))).------ ( -34.10, z-score =  -2.03, R)
>consensus
_________AUGCCGUAAGCUUGUUGCGCGGCGGAGCUGAAGUUCUAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUAC_U_U
...........(((((..((.....)))))))............................(((((((((....)))))))))..((((((....))))))............. (-19.74 = -20.14 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:50:26 2011