Locus 5656

Sequence ID dm3.chr3L
Location 312,086 – 312,221
Length 135
Max. P 0.848597
window7769 window7770 window7771

overview

Window 9

Location 312,086 – 312,189
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.59
Shannon entropy 0.26579
G+C content 0.48911
Mean single sequence MFE -37.58
Consensus MFE -26.57
Energy contribution -27.01
Covariance contribution 0.44
Combinations/Pair 1.19
Mean z-score -2.08
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.848597
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 312086 103 + 24543557
AACUGCCAAUGGGUCAUCCCGUAUAGC-----------------UGCUGCUGAAAAGCGGAACACUCCCUUUAUGUGGCCAUCCCGGAAAUAAAAUUUGAAUACGGGUCAGCCAACGUGA
....((..(((((....)))))...))-----------------..(((((....)))))..........(((((((((...((((.................))))...))).)))))) ( -29.53, z-score =  -1.13, R)
>droYak2.chr3L 291350 119 + 24197627
AACUGCCAACGGGUCGUUCCGUAUGAAAACCGAAAGG-CUUUUCCGCUUCUGAAAAGCGGAGCACUCCCAUUGUGCGGCCAUCCCGGAAAUGAUAUUUGAAUACGGGACAGCCCAUGGGA
.....(((..((((.(((((((((..((((((...((-((..(((((((.....)))))))((((.......))))))))....)))........)))..))))))))).)))).))).. ( -45.50, z-score =  -3.02, R)
>droSec1.super_2 343745 120 + 7591821
AACUGUCUAUGGGUCAUCCCGUAUAGCAACCGAAAGGGCUUAUCUGCUGCUGAAAAGCGGAACACUCCCUUUAUGUGGCCAUCCCGGAAAUAAUAUUUGAAUACGGGACAGCCAACGUGA
...(((.((((((....))))))..)))....((((((........(((((....)))))......))))))(((((((..(((((.................)))))..))).)))).. ( -37.67, z-score =  -2.12, R)
>droSim1.chr2R 8537746 120 + 19596830
AACUGCCUAUGGGUCAUCCCGUAUAGCAACCGAAAGGGCUUAUCUGUUGCUGAAAAGCGGAACACUCCCUUUAUGUGGCCAUCCCGGAAAUAAUAUUUGAAUACGGGACAGCCAACGUGA
..((((.((((((....))))))(((((.((....))((......)))))))....))))..........(((((((((..(((((.................)))))..))).)))))) ( -37.63, z-score =  -2.04, R)
>consensus
AACUGCCAAUGGGUCAUCCCGUAUAGCAACCGAAAGG_CUUAUCUGCUGCUGAAAAGCGGAACACUCCCUUUAUGUGGCCAUCCCGGAAAUAAUAUUUGAAUACGGGACAGCCAACGUGA
........(((((....))))).......((....)).....((((((.......)))))).........(((((((((..(((((.................)))))..))).)))))) (-26.57 = -27.01 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 312,086 – 312,189
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.59
Shannon entropy 0.26579
G+C content 0.48911
Mean single sequence MFE -35.91
Consensus MFE -30.19
Energy contribution -30.76
Covariance contribution 0.56
Combinations/Pair 1.18
Mean z-score -1.26
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.650454
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 312086 103 - 24543557
UCACGUUGGCUGACCCGUAUUCAAAUUUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAGCA-----------------GCUAUACGGGAUGACCCAUUGGCAGUU
....((.(((((.((((.................)))).))))))).....(((..(((((((......(((....-----------------)))...))))))).))).......... ( -25.33, z-score =   0.57, R)
>droYak2.chr3L 291350 119 - 24197627
UCCCAUGGGCUGUCCCGUAUUCAAAUAUCAUUUCCGGGAUGGCCGCACAAUGGGAGUGCUCCGCUUUUCAGAAGCGGAAAAG-CCUUUCGGUUUUCAUACGGAACGACCCGUUGGCAGUU
.......((((((((((.................))))))))))((.(((((((.....((((((((...))))))))((((-((....))))))............))))))))).... ( -45.13, z-score =  -2.62, R)
>droSec1.super_2 343745 120 - 7591821
UCACGUUGGCUGUCCCGUAUUCAAAUAUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAGCAGAUAAGCCCUUUCGGUUGCUAUACGGGAUGACCCAUAGACAGUU
....(((((((((((((.................)))))))))).......(((..(((((((......((((((.((.........)).))))))...))))))).)))...))).... ( -36.83, z-score =  -1.66, R)
>droSim1.chr2R 8537746 120 - 19596830
UCACGUUGGCUGUCCCGUAUUCAAAUAUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAACAGAUAAGCCCUUUCGGUUGCUAUACGGGAUGACCCAUAGGCAGUU
....(((((((((((((.................)))))))))).......(((..(((((((......((((((.((.........)).))))))...))))))).)))...))).... ( -36.33, z-score =  -1.34, R)
>consensus
UCACGUUGGCUGUCCCGUAUUCAAAUAUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAGCAGAUAAG_CCUUUCGGUUGCUAUACGGGAUGACCCAUAGGCAGUU
.......((((((((((.................)))))))))).......(((..(((((((......((((((.((.........)).))))))...))))))).))).......... (-30.19 = -30.76 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 312,112 – 312,221
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.33
Shannon entropy 0.28468
G+C content 0.50765
Mean single sequence MFE -37.66
Consensus MFE -25.25
Energy contribution -26.41
Covariance contribution 1.16
Combinations/Pair 1.12
Mean z-score -1.70
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.516503
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 312112 109 - 24543557
-----GCGCAAAUGAUGGUAGGACACCAGCCAGA---UGAUCACGUUGGCUGACCCGUAUUCAAAUUUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAGCAG---
-----..((...(((.((..((((((((((((.(---((....)))))))))...................((((...(((....)))...))))))))))..))..)))...))..--- ( -31.20, z-score =  -0.85, R)
>droEre2.scaffold_4784 304596 112 - 25762168
-----GCGCGGAUGUUGGUAGGACAGCAGCCAGA---AGAUCCCACUGGCUGUCCCGUAUGUAAAUAUCAUUUCCGGGAUGGCCACAUAGUGGGAGUGUUCCGCGUUUCGGGAGCGGAAG
-----((((((((((((......)))))......---...(((((((((((((((((.(((.......)))...))))))))))....)))))))....)))))))((((....)))).. ( -48.90, z-score =  -3.70, R)
>droYak2.chr3L 291389 120 - 24197627
ACCGAGCGCGAAUGUUGGUAGGACACCAUGAUGACGUUGAUCCCAUGGGCUGUCCCGUAUUCAAAUAUCAUUUCCGGGAUGGCCGCACAAUGGGAGUGCUCCGCUUUUCAGAAGCGGAAA
.((((((((.(((((((((.....)))).....)))))..((((((.((((((((((.................)))))))))).....)))))))))))).(((((...)))))))... ( -44.23, z-score =  -1.88, R)
>droSec1.super_2 343785 112 - 7591821
-----GCGCAAAUGAUAGUAGCACGCCAGCCAGA---UGAUCACGUUGGCUGUCCCGUAUUCAAAUAUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAGCAGAUA
-----..((...(((.((((((((.((.....((---((....))))((((((((((.................))))))))))........)).)))))..)))..)))...))..... ( -31.33, z-score =  -0.84, R)
>droSim1.chr2R 8537786 112 - 19596830
-----GCGCAAAUGAUGGUAGGACACCAGCCAGA---UGAUCACGUUGGCUGUCCCGUAUUCAAAUAUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAACAGAUA
-----..((...(((.((..((((((...((.((---((....))))((((((((((.................))))))))))........)).))))))..))..)))))........ ( -32.63, z-score =  -1.21, R)
>consensus
_____GCGCAAAUGAUGGUAGGACACCAGCCAGA___UGAUCACGUUGGCUGUCCCGUAUUCAAAUAUUAUUUCCGGGAUGGCCACAUAAAGGGAGUGUUCCGCUUUUCAGCAGCAGAAA
.......((...((..((..((((((...((.((......)).....((((((((((.................))))))))))........)).))))))..))...))...))..... (-25.25 = -26.41 +   1.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:52:37 2011