Locus 8085

Sequence ID dm3.chr3L
Location 20,139,424 – 20,139,520
Length 96
Max. P 0.774251
window11129 window11130

overview

Window 9

Location 20,139,424 – 20,139,520
Length 96
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 62.29
Shannon entropy 0.65297
G+C content 0.64292
Mean single sequence MFE -41.22
Consensus MFE -15.13
Energy contribution -17.01
Covariance contribution 1.88
Combinations/Pair 1.50
Mean z-score -1.53
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.774251
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20139424 96 + 24543557
CACUUGGACACCACAGAGGU----CCCUUCUGCCACCGGAGGGGCAGCCACCCGCCGGGUUAACUGGGUGGUGGCCUGGGUGGUUCGCAAGUGGCAAGGU
((((((((.(((((..((((----((((((.......)))))))).((((((.(((.((....)).)))))))))))..))))))).))))))....... ( -49.00, z-score =  -1.93, R)
>droSim1.chr3L 19427127 75 + 22553184
CACUUGGACACCACAGAGGU----CCCUUCU---------GGGGCAGCCACCCGUCGGGUGAAC------------UGGGUGGUUCGCAAGUGGCAAGGU
((((((((.(((((..((((----(((....---------)))))...(((((...)))))..)------------)..))))))).))))))....... ( -33.70, z-score =  -1.63, R)
>droYak2.chr3L 3766041 88 - 24197627
CACUUGGACACCACAGCGGUGGUGUCCUUCUGCCAAAGGAGGAGCACCCACCCACCAUGUGGCC------------UGGGCGGCUCGCAAGUGGCGAGGU
..((((((((((((....)))))))))....((((...(..((((.((((.((((...))))..------------))))..)))).)...))))))).. ( -40.70, z-score =  -1.46, R)
>droEre2.scaffold_4784 19867074 91 + 25762168
CACUUGGACACCACAGAGGU----GCCUCCUGCCACAGGAGCAGC-UCCACUGGCCGUGUGGUCGGGGUGG----CACGGUGGCACGCAAGUGGCGAGGU
..((((....((((....((----(((.((((((((.((((...)-))).((((((....)))))).))))----)).)).)))))....)))))))).. ( -43.50, z-score =  -1.05, R)
>droAna3.scaffold_13337 6262242 88 + 23293914
CACUUGGCCACCAGCCAGGC-----CACUGAGUCAGGGAGGAGACGGUAUAUGGUAUGGUAUAUCCGGUGG----CCCGGUGGCUC---AGUGCCCAGGU
.((((((.(((.((((((((-----(((((.(((........)))(((((((......)))))))))))))----))...))))).---.))).)))))) ( -39.20, z-score =  -1.60, R)
>consensus
CACUUGGACACCACAGAGGU____CCCUUCUGCCACAGGAGGGGCAGCCACCCGCCGGGUGAAC__GGUGG____CUGGGUGGCUCGCAAGUGGCAAGGU
..((((..(((.............((((((.......))))))(((((((((((......................))))))))).))..))).)))).. (-15.13 = -17.01 +   1.88)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,139,424 – 20,139,520
Length 96
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 62.29
Shannon entropy 0.65297
G+C content 0.64292
Mean single sequence MFE -36.84
Consensus MFE -14.18
Energy contribution -14.30
Covariance contribution 0.12
Combinations/Pair 1.40
Mean z-score -1.42
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.735813
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20139424 96 - 24543557
ACCUUGCCACUUGCGAACCACCCAGGCCACCACCCAGUUAACCCGGCGGGUGGCUGCCCCUCCGGUGGCAGAAGGG----ACCUCUGUGGUGUCCAAGUG
.......((((((.(((((((..(((((.((((((.(((.....)))))))))(((((((...)).)))))...))----.)))..))))).)))))))) ( -42.50, z-score =  -1.64, R)
>droSim1.chr3L 19427127 75 - 22553184
ACCUUGCCACUUGCGAACCACCCA------------GUUCACCCGACGGGUGGCUGCCCC---------AGAAGGG----ACCUCUGUGGUGUCCAAGUG
.......((((((.(((((((.((------------((.(((((...))))))))).(((---------....)))----......))))).)))))))) ( -28.90, z-score =  -1.50, R)
>droYak2.chr3L 3766041 88 + 24197627
ACCUCGCCACUUGCGAGCCGCCCA------------GGCCACAUGGUGGGUGGGUGCUCCUCCUUUGGCAGAAGGACACCACCGCUGUGGUGUCCAAGUG
..(((((.....)))))((((((.------------.(((....))))))))).((((........))))...(((((((((....)))))))))..... ( -39.60, z-score =  -1.43, R)
>droEre2.scaffold_4784 19867074 91 - 25762168
ACCUCGCCACUUGCGUGCCACCGUG----CCACCCCGACCACACGGCCAGUGGA-GCUGCUCCUGUGGCAGGAGGC----ACCUCUGUGGUGUCCAAGUG
.......((((((.(..((((.(((----((...((..(((((.((.(((....-.)))..)))))))..)).)))----))....))))..).)))))) ( -38.30, z-score =  -0.88, R)
>droAna3.scaffold_13337 6262242 88 - 23293914
ACCUGGGCACU---GAGCCACCGGG----CCACCGGAUAUACCAUACCAUAUACCGUCUCCUCCCUGACUCAGUG-----GCCUGGCUGGUGGCCAAGUG
((.(((.((((---.(((((...((----((((.((((((........)))).))(((........)))...)))-----)))))))))))).))).)). ( -34.90, z-score =  -1.66, R)
>consensus
ACCUCGCCACUUGCGAGCCACCCAG____CCACC__GUCCACCCGGCGGGUGGCUGCCCCUCCUGUGGCAGAAGGG____ACCUCUGUGGUGUCCAAGUG
.......((((((...(((((..........................((((....))))..........((.(((......))))))))))...)))))) (-14.18 = -14.30 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:39:12 2011