Locus 4040

Sequence ID dm3.chr2R
Location 9,893,230 – 9,893,324
Length 94
Max. P 0.996678
window5527 window5528

overview

Window 7

Location 9,893,230 – 9,893,324
Length 94
Sequences 7
Columns 94
Reading direction forward
Mean pairwise identity 72.76
Shannon entropy 0.54566
G+C content 0.58398
Mean single sequence MFE -36.40
Consensus MFE -22.55
Energy contribution -25.04
Covariance contribution 2.50
Combinations/Pair 1.45
Mean z-score -2.20
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.97
SVM RNA-class probability 0.996678
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9893230 94 + 21146708
UUUCCUCGAUUUUUCCCUCAGUCUGCCGCUCGCCUUUGUCCCGGCCGGAUGGCUUGGAUUUUGGCCCGGACAUCCAGGUGGGCGGCACUCCAAA
.......((((........))))((((((((((((.(((((.(((((((..........))))))).)))))...))))))))))))....... ( -42.00, z-score =  -3.20, R)
>droSim1.chr2R 8329766 93 + 19596830
UUUCCUCGAUUUU-CCCUCAGUCUGCCGCUCGCCUUUGUCCCGGCCGGAUGGCUUGGAUUUUGGCCCGGACAUCCAGGUGGGCGGCACUCCGAA
.............-...((.(..((((((((((((.(((((.(((((((..........))))))).)))))...))))))))))))..).)). ( -43.10, z-score =  -3.20, R)
>droSec1.super_1 7418377 93 + 14215200
UUUCCUCGAUUUU-CCCUCAGUCUGCCGCUCGCCUUUGUCCCGGCCGGAUGGCUUGGAUUUUGGCCCGGACAUCCAGGUGGGCGGCACUCCGAA
.............-...((.(..((((((((((((.(((((.(((((((..........))))))).)))))...))))))))))))..).)). ( -43.10, z-score =  -3.20, R)
>droYak2.chr2R 14078698 93 - 21139217
UUUCCUUGAUUUU-CCCUCAGUCUGCCGCUCGCCUUUGUCCCGGCCGGAUGGCUUGGAUUUUGGCCCGGACAUCCAGGGGGGCGGCACUCCGAA
.............-...((.(..((((((((.(((.(((((.(((((((..........))))))).)))))...))).))))))))..).)). ( -40.90, z-score =  -1.89, R)
>droEre2.scaffold_4845 6660634 93 - 22589142
UUUCCUCGAUUUU-CCCUCAGUCAGCCGCUCGCCUUUGUCCCGGCCGGAUGGCUUGGAUUUUGGCCCGGACAUCCAGGGGGGCGGCACUCCGAA
.....((((((..-.....)))).(((((((.(((.(((((.(((((((..........))))))).)))))...))).))))))).....)). ( -39.90, z-score =  -1.39, R)
>droAna3.scaffold_13266 13877511 82 - 19884421
----------UUUUUUCUCAGUCUGCCACUCGUCUUUGGCCCGGCCGGAUGGCUUGGAGACCAAAUUCGAU-UCCUGGUGACUGG-ACUCCGAA
----------.....((.(((((.((((.(((..((((((((((((....))).))).).)))))..))).-...))))))))))-)....... ( -27.20, z-score =  -1.42, R)
>droWil1.scaffold_180745 1099893 73 - 2843958
----------UAUCUCUUCAGUAUGCUGGCCACCUUUGGCCAUGGUGGAUGUGUUUGUCCACUCUCUCCACUUGCCAUCACAU-----------
----------..........((((((((((((....)))))).(((((((......)))))))..........).))).))..----------- ( -18.60, z-score =  -1.12, R)
>consensus
UUUCCUCGAUUUU_CCCUCAGUCUGCCGCUCGCCUUUGUCCCGGCCGGAUGGCUUGGAUUUUGGCCCGGACAUCCAGGUGGGCGGCACUCCGAA
........................(((((((.(((.(((((.(((((((..........))))))).)))))...))).)))))))........ (-22.55 = -25.04 +   2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 9,893,230 – 9,893,324
Length 94
Sequences 7
Columns 94
Reading direction reverse
Mean pairwise identity 72.76
Shannon entropy 0.54566
G+C content 0.58398
Mean single sequence MFE -33.49
Consensus MFE -19.71
Energy contribution -23.15
Covariance contribution 3.43
Combinations/Pair 1.29
Mean z-score -1.38
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.936796
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9893230 94 - 21146708
UUUGGAGUGCCGCCCACCUGGAUGUCCGGGCCAAAAUCCAAGCCAUCCGGCCGGGACAAAGGCGAGCGGCAGACUGAGGGAAAAAUCGAGGAAA
((..(..((((((.(.(((...(((((.((((................)))).))))).))).).))))))..)..))................ ( -35.99, z-score =  -1.21, R)
>droSim1.chr2R 8329766 93 - 19596830
UUCGGAGUGCCGCCCACCUGGAUGUCCGGGCCAAAAUCCAAGCCAUCCGGCCGGGACAAAGGCGAGCGGCAGACUGAGGG-AAAAUCGAGGAAA
(((((..((((((.(.(((...(((((.((((................)))).))))).))).).))))))..)))))..-............. ( -38.39, z-score =  -1.74, R)
>droSec1.super_1 7418377 93 - 14215200
UUCGGAGUGCCGCCCACCUGGAUGUCCGGGCCAAAAUCCAAGCCAUCCGGCCGGGACAAAGGCGAGCGGCAGACUGAGGG-AAAAUCGAGGAAA
(((((..((((((.(.(((...(((((.((((................)))).))))).))).).))))))..)))))..-............. ( -38.39, z-score =  -1.74, R)
>droYak2.chr2R 14078698 93 + 21139217
UUCGGAGUGCCGCCCCCCUGGAUGUCCGGGCCAAAAUCCAAGCCAUCCGGCCGGGACAAAGGCGAGCGGCAGACUGAGGG-AAAAUCAAGGAAA
(((((..((((((.(.(((...(((((.((((................)))).))))).))).).))))))..)))))..-............. ( -37.49, z-score =  -1.24, R)
>droEre2.scaffold_4845 6660634 93 + 22589142
UUCGGAGUGCCGCCCCCCUGGAUGUCCGGGCCAAAAUCCAAGCCAUCCGGCCGGGACAAAGGCGAGCGGCUGACUGAGGG-AAAAUCGAGGAAA
(((((...(((((.(.(((...(((((.((((................)))).))))).))).).)))))...)))))..-............. ( -35.49, z-score =  -0.30, R)
>droAna3.scaffold_13266 13877511 82 + 19884421
UUCGGAGU-CCAGUCACCAGGA-AUCGAAUUUGGUCUCCAAGCCAUCCGGCCGGGCCAAAGACGAGUGGCAGACUGAGAAAAAA----------
(((..(((-(..(((((.....-.(((..((((((((....(((....))).))))))))..)))))))).))))..)))....---------- ( -27.00, z-score =  -1.60, R)
>droWil1.scaffold_180745 1099893 73 + 2843958
-----------AUGUGAUGGCAAGUGGAGAGAGUGGACAAACACAUCCACCAUGGCCAAAGGUGGCCAGCAUACUGAAGAGAUA----------
-----------..(((...((..(((((....(((......))).)))))..((((((....)))))))).)))..........---------- ( -21.70, z-score =  -1.83, R)
>consensus
UUCGGAGUGCCGCCCACCUGGAUGUCCGGGCCAAAAUCCAAGCCAUCCGGCCGGGACAAAGGCGAGCGGCAGACUGAGGG_AAAAUCGAGGAAA
(((((..((((((.(.(((...(((((.((((................)))).))))).))).).))))))..)))))................ (-19.71 = -23.15 +   3.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:21:30 2011