Locus 9024

Sequence ID dm3.chr3R
Location 3,522,800 – 3,522,871
Length 71
Max. P 0.796715
window12388 window12389

overview

Window 8

Location 3,522,800 – 3,522,871
Length 71
Sequences 3
Columns 87
Reading direction forward
Mean pairwise identity 66.28
Shannon entropy 0.46920
G+C content 0.55993
Mean single sequence MFE -29.00
Consensus MFE -12.86
Energy contribution -13.33
Covariance contribution 0.47
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.796715
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3522800 71 + 27905053
CAAUUCAAGAUCUGGCC-----------GGCCAGGUCGCGGCCAU-ACAGAUUGCCCCUGCCCGG----GCAGAAGCUCCCCCAAUC
..........((((.((-----------((.((((..(((..(..-...)..))).)))).))))----.))))............. ( -23.80, z-score =  -0.80, R)
>dp4.Unknown_group_92 4842 87 - 26366
CACUGCAAAAUCAGGCCUCGUGGUUUGAGUCCAGGUUACUGUAAUUACAAGCCGCGAUUGCUCAGUUGAGCACAAGCACGCCUGCCA
...........(((((.(((((((((((((.(((....)))..))).)))))))))).(((((....))))).......)))))... ( -30.90, z-score =  -2.40, R)
>droPer1.super_143 21433 87 + 108547
CACUGCAAAAUCAGGCCUCGCGGUUUGAGACCAGGUUACUGUAAUUACAAGCCGCGAUUGCUCAGUUGAGCACAAGCACGCCUGCCA
...........(((((.((((((((((.((.(((....)))...)).)))))))))).(((((....))))).......)))))... ( -32.30, z-score =  -2.91, R)
>consensus
CACUGCAAAAUCAGGCCUCG_GGUUUGAGACCAGGUUACUGUAAUUACAAGCCGCGAUUGCUCAGUUGAGCACAAGCACGCCUGCCA
........((((.((.((((.....)))).)).))))................((...(((((....)))))...)).......... (-12.86 = -13.33 +   0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 3,522,800 – 3,522,871
Length 71
Sequences 3
Columns 87
Reading direction reverse
Mean pairwise identity 66.28
Shannon entropy 0.46920
G+C content 0.55993
Mean single sequence MFE -29.10
Consensus MFE -17.83
Energy contribution -18.90
Covariance contribution 1.07
Combinations/Pair 1.29
Mean z-score -0.99
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr3R 3522800 71 - 27905053
GAUUGGGGGAGCUUCUGC----CCGGGCAGGGGCAAUCUGU-AUGGCCGCGACCUGGCC-----------GGCCAGAUCUUGAAUUG
((((.((((.((((((((----....))))))))..((((.-.((((((.....)))))-----------)..)))))))).)))). ( -32.00, z-score =  -1.69, R)
>dp4.Unknown_group_92 4842 87 + 26366
UGGCAGGCGUGCUUGUGCUCAACUGAGCAAUCGCGGCUUGUAAUUACAGUAACCUGGACUCAAACCACGAGGCCUGAUUUUGCAGUG
..((((((.(((...(((((....)))))...))))))))).......((((...((.(((.......))).)).....)))).... ( -25.00, z-score =  -0.01, R)
>droPer1.super_143 21433 87 - 108547
UGGCAGGCGUGCUUGUGCUCAACUGAGCAAUCGCGGCUUGUAAUUACAGUAACCUGGUCUCAAACCGCGAGGCCUGAUUUUGCAGUG
...(((((.......(((((....))))).((((((.(((......(((....)))....))).)))))).)))))........... ( -30.30, z-score =  -1.27, R)
>consensus
UGGCAGGCGUGCUUGUGCUCAACUGAGCAAUCGCGGCUUGUAAUUACAGUAACCUGGACUCAAACC_CGAGGCCUGAUUUUGCAGUG
..((((((.(((...(((((....)))))...))))))))).......((((...((((((.......)))))).....)))).... (-17.83 = -18.90 +   1.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:56:41 2011