Locus 4553

Sequence ID dm3.chr2R
Location 13,971,868 – 13,971,963
Length 95
Max. P 0.848090
window6240 window6241

overview

Window 0

Location 13,971,868 – 13,971,963
Length 95
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 55.99
Shannon entropy 0.67848
G+C content 0.43577
Mean single sequence MFE -25.75
Consensus MFE -5.43
Energy contribution -9.05
Covariance contribution 3.62
Combinations/Pair 1.33
Mean z-score -2.58
Structure conservation index 0.21
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.848090
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13971868 95 + 21146708
--AAAUUAAGAUGCGCGGCUUAUGUACG--GUUGGUCACUGACACCGUGUAUAUAAGAAGACAAAUACCUGCUCUGCAACGGCAGAAAAGGGAAAUGAA
--........((((((((....(((.((--((.....)))))))))))))))...............(((..(((((....)))))..)))........ ( -25.20, z-score =  -1.96, R)
>droYak2.chrU 7648380 96 + 28119190
AAAAAAAACAAUGGGCGAGGUAUAUAUG--GUCGGCCACUGACACCGUGUAUAUAACA-GACAAAUAACUGUUCUGCAACUGCACAAAAGGGAAACGAA
...........((.((.(((((((((((--((.(........))))))))))))..((-((((......)).))))...)))).))....(....)... ( -19.40, z-score =  -0.96, R)
>dp4.Unknown_group_140 12030 95 + 24112
--AACACAAAUUAUGCUGCCAAUGCACACAACCAAACGCCGCCAAAUUAUGCACAAUUUGGCG--CAACGAUAGCGUUAUCGAAGUAAAGGCAGCACCA
--...........(((((((..(((............((.((((((((......)))))))))--)..(((((....)))))..)))..)))))))... ( -30.00, z-score =  -4.09, R)
>droPer1.super_158 13903 95 - 72041
--AACACAAAUUAUGCUGCCAAUGCACACAACCAAAUGCCGCCAAAUUAUGCACAAUUUGGCG--CAACGAUAGCGUUACCGAAGUAAAGGCAGCACCA
--...........(((((((..(((............((.((((((((......)))))))))--)((((....))))......)))..)))))))... ( -28.40, z-score =  -3.31, R)
>consensus
__AAAACAAAAUAUGCGGCCAAUGCACA__ACCAAACACCGACAAAGUAUACACAAUAUGACA__CAACGAUACCGCAACCGAAGAAAAGGCAAAACAA
.............(((((((...................(((((((((......))))))))).....(((((....))))).......)))))))... ( -5.43 =  -9.05 +   3.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,971,868 – 13,971,963
Length 95
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 55.99
Shannon entropy 0.67848
G+C content 0.43577
Mean single sequence MFE -26.55
Consensus MFE -8.20
Energy contribution -9.70
Covariance contribution 1.50
Combinations/Pair 1.48
Mean z-score -1.71
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.711141
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13971868 95 - 21146708
UUCAUUUCCCUUUUCUGCCGUUGCAGAGCAGGUAUUUGUCUUCUUAUAUACACGGUGUCAGUGACCAAC--CGUACAUAAGCCGCGCAUCUUAAUUU--
........(((.((((((....)))))).)))....(((...(((((....((((((((...)))..))--)))..)))))....))).........-- ( -18.60, z-score =  -1.03, R)
>droYak2.chrU 7648380 96 - 28119190
UUCGUUUCCCUUUUGUGCAGUUGCAGAACAGUUAUUUGUC-UGUUAUAUACACGGUGUCAGUGGCCGAC--CAUAUAUACCUCGCCCAUUGUUUUUUUU
............(((((.....(((((.(((....)))))-)))......)))))...((((((.(((.--..........))).))))))........ ( -17.30, z-score =  -0.75, R)
>dp4.Unknown_group_140 12030 95 - 24112
UGGUGCUGCCUUUACUUCGAUAACGCUAUCGUUG--CGCCAAAUUGUGCAUAAUUUGGCGGCGUUUGGUUGUGUGCAUUGGCAGCAUAAUUUGUGUU--
..((((((((..(((..(((((((((........--((((((((((....)))))))))))))))..)))).)))....))))))))..........-- ( -32.60, z-score =  -1.73, R)
>droPer1.super_158 13903 95 + 72041
UGGUGCUGCCUUUACUUCGGUAACGCUAUCGUUG--CGCCAAAUUGUGCAUAAUUUGGCGGCAUUUGGUUGUGUGCAUUGGCAGCAUAAUUUGUGUU--
..((((((((..(((....)))((((.((((.((--((((((((((....))))))))).)))..)))).)))).....))))))))..........-- ( -37.70, z-score =  -3.34, R)
>consensus
UGCUGCUCCCUUUACUGCGGUAACACAACAGUUA__CGCCAAAUUAUACACAAGGUGGCAGCGUCCGAC__CGUACAUAGGCAGCACAAUUUGUGUU__
...(((((((.......(((((....))))).....(((((((((......)))))))))((((........))))...)))))))............. ( -8.20 =  -9.70 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:31:23 2011