Locus 10301

Sequence ID dm3.chr3R
Location 12,841,721 – 12,841,827
Length 106
Max. P 0.963849
window14165 window14166

overview

Window 5

Location 12,841,721 – 12,841,827
Length 106
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 74.96
Shannon entropy 0.37718
G+C content 0.42538
Mean single sequence MFE -19.18
Consensus MFE -12.89
Energy contribution -12.20
Covariance contribution -0.69
Combinations/Pair 1.18
Mean z-score -1.76
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.875551
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12841721 106 + 27905053
ACCAUUGCGGGUCUUUCGACAAAGGUUUCCAUUCAACUAAAAUCUAAAAAAAA--AAUUAAAAUCAUUAAAACCAAAAUCGAAAAAACCACAUUGAUCCGGCACCCGC
......((((((.((((((....(((((.........................--..............)))))....))))))...((..........)).)))))) ( -15.03, z-score =  -1.17, R)
>droEre2.scaffold_4770 8957570 82 - 17746568
GCCAUAGCGGGUCUUUCGAAAAAGGUUUCCAGUCGACCAAAAACUGAAAA-----------------------CCAAGCCGAAAA--CCACAUUGAUC-GGCACCCGC
......((((((...........(((((.((((.........)))).)))-----------------------))..(((((...--.........))-))))))))) ( -25.40, z-score =  -3.40, R)
>droYak2.chr3R 17289587 83 - 28832112
UCCAUUGCGGGUCUUUCGACAAAGGUUUCCAGUCGACCAAAAACUGAAAA-----------------------CCAUUCCGAAAAA-CCACAUUGAUC-GGCGCCCGC
......((((((...(((((((.(((((.((((.........)))).)))-----------------------)).....(.....-.)...))).))-)).)))))) ( -20.90, z-score =  -1.42, R)
>droSec1.super_12 808831 106 - 2123299
UCCAUUGCGGGUCUUUCGACAAAGGUUUCCAUUCAACUAAAAACCAAAAAAAUUUAAAAAAAAACAUUAAAACCAAAACCGAAAAA-CCACAUUGAUC-GGCACCCGC
......((((((...(((((((.(((((............))))).......(((((.........)))))...............-.....))).))-)).)))))) ( -15.40, z-score =  -1.06, R)
>consensus
UCCAUUGCGGGUCUUUCGACAAAGGUUUCCAGUCAACCAAAAACUAAAAA_______________________CAAAACCGAAAAA_CCACAUUGAUC_GGCACCCGC
......((((((((.((((....((((.......))))..........................................(.......)...))))...)).)))))) (-12.89 = -12.20 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,841,721 – 12,841,827
Length 106
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 74.96
Shannon entropy 0.37718
G+C content 0.42538
Mean single sequence MFE -30.60
Consensus MFE -15.41
Energy contribution -15.72
Covariance contribution 0.31
Combinations/Pair 1.12
Mean z-score -2.77
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.73
SVM RNA-class probability 0.963849
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12841721 106 - 27905053
GCGGGUGCCGGAUCAAUGUGGUUUUUUCGAUUUUGGUUUUAAUGAUUUUAAUU--UUUUUUUUAGAUUUUAGUUGAAUGGAAACCUUUGUCGAAAGACCCGCAAUGGU
((((((((((.(....).)))).((((((((...((((((..(((((..((((--(.......)))))..)))))....))))))...))))))))))))))...... ( -30.60, z-score =  -3.04, R)
>droEre2.scaffold_4770 8957570 82 + 17746568
GCGGGUGCC-GAUCAAUGUGG--UUUUCGGCUUGG-----------------------UUUUCAGUUUUUGGUCGACUGGAAACCUUUUUCGAAAGACCCGCUAUGGC
(((((((((-((.........--...)))))..((-----------------------(((((((((.......))))))))))).....(....)))))))...... ( -32.50, z-score =  -3.49, R)
>droYak2.chr3R 17289587 83 + 28832112
GCGGGCGCC-GAUCAAUGUGG-UUUUUCGGAAUGG-----------------------UUUUCAGUUUUUGGUCGACUGGAAACCUUUGUCGAAAGACCCGCAAUGGA
.(((...))-).(((.(((((-((((((((...((-----------------------(((((((((.......)))))))))))....)))))))).))))).))). ( -31.90, z-score =  -2.71, R)
>droSec1.super_12 808831 106 + 2123299
GCGGGUGCC-GAUCAAUGUGG-UUUUUCGGUUUUGGUUUUAAUGUUUUUUUUUAAAUUUUUUUGGUUUUUAGUUGAAUGGAAACCUUUGUCGAAAGACCCGCAAUGGA
(((((((((-(.......)))-)(((((((....((((((...((((..((..(((((.....)))))..))..)))).))))))....)))))))))))))...... ( -27.40, z-score =  -1.84, R)
>consensus
GCGGGUGCC_GAUCAAUGUGG_UUUUUCGGUUUGG_______________________UUUUCAGUUUUUAGUCGAAUGGAAACCUUUGUCGAAAGACCCGCAAUGGA
(((((.....................................................(((((((((.......)))))))))......((....)))))))...... (-15.41 = -15.72 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:20 2011