Locus 9827

Sequence ID dm3.chr3R
Location 9,329,435 – 9,329,553
Length 118
Max. P 0.967676
window13489 window13490

overview

Window 9

Location 9,329,435 – 9,329,553
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 77.13
Shannon entropy 0.41241
G+C content 0.53312
Mean single sequence MFE -41.49
Consensus MFE -25.81
Energy contribution -26.13
Covariance contribution 0.31
Combinations/Pair 1.39
Mean z-score -2.17
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.967676
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9329435 118 + 27905053
ACGGUGGUGUUCGGUGGUUUUUUGGGUGGUUUUCGGGUGAUUUUCUGGAGGUGGUACUGGCGGACUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAA
.((.(((..((((((((((.((((((.....)))))).((((..((((.((.(((...(..((((....))))..)..))))).))))..))))))))))))))...))).))..... ( -40.60, z-score =  -0.69, R)
>droSim1.chr3R 15415540 104 - 27517382
----------ACGGUGGUGUUC--GGUGGUUUUUGGGUGAUUUUCUGGAGGUGGUA--AGCGGACUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAA
----------.((.(((..(((--(((((((.......((((..((((.((.((..--((.((((....))).).))..)))).))))..))))))))))))))...))).))..... ( -41.51, z-score =  -2.55, R)
>droSec1.super_0 8444325 104 - 21120651
----------ACGGUGGUGUUC--GGUGGUUUUUGGGUGAUUUUUUGGAGGUGGUA--AGCGGACUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAA
----------.((.(((..(((--(((((((.......((((((((((.((.((..--((.((((....))).).))..)))).))))))))))))))))))))...))).))..... ( -38.81, z-score =  -2.01, R)
>droYak2.chr3R 13638049 115 + 28832112
ACGGUGGUGUUCGGUGGUUUUU-GGGUGGCUUUUGGGUGAUUUUCUGGUGGUGGUA--AGCGGACUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAA
..........(((.((..((((-.(((((((.......((((..(((((((.((..--((.((((....))).).))..)))))))))..))))))))))).))))..)).))).... ( -48.11, z-score =  -3.36, R)
>droEre2.scaffold_4770 5435372 113 - 17746568
--GGUGGUGCUCGGUGGUUUUU-GGGUGGCUUUCGGGUGAUUUUCUGGUGGUGGCA--AGCGGCCUGGUGUCUCGCUCGCCCCAUCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAA
--((((((((((((.((((...-....)))).))))))((((..(((((((.(((.--(((((.(....).).)))).))))))))))..)))).))))))................. ( -48.00, z-score =  -2.83, R)
>droAna3.scaffold_13340 1886315 92 + 23697760
------------------------GGAGGUGUGCGGGUGGCGAGGGGUUGGCGGUA--AGCGGUGAACGGUGGAGUUGACCUCUCCUGGGAGUUGGCCACCAAAAAUUCAAUGAUUAA
------------------------.(((.......(((((((((((((..((....--.((.(....).))...))..)))))))(........))))))).....)))......... ( -31.90, z-score =  -1.55, R)
>consensus
__________UCGGUGGUUUUU__GGUGGUUUUCGGGUGAUUUUCUGGAGGUGGUA__AGCGGACUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAA
........................(((((((.......((((((((((.((.(((...((.((((....))).).)).))))).)))))))))))))))))................. (-25.81 = -26.13 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 9,329,435 – 9,329,553
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 77.13
Shannon entropy 0.41241
G+C content 0.53312
Mean single sequence MFE -30.10
Consensus MFE -15.45
Energy contribution -16.84
Covariance contribution 1.39
Combinations/Pair 1.14
Mean z-score -2.57
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.77
SVM RNA-class probability 0.966701
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9329435 118 - 27905053
UUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAGUCCGCCAGUACCACCUCCAGAAAAUCACCCGAAAACCACCCAAAAAACCACCGAACACCACCGU
..............((((((((..........(((((..(..(((.(((....))))))..)..))))).........((....))...............))))))))......... ( -29.70, z-score =  -1.47, R)
>droSim1.chr3R 15415540 104 + 27517382
UUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAGUCCGCU--UACCACCUCCAGAAAAUCACCCAAAAACCACC--GAACACCACCGU----------
..............((((((((........((((.((((..((((.(((....)))))))--..)).)).))))...............)))))--))).........---------- ( -31.20, z-score =  -2.63, R)
>droSec1.super_0 8444325 104 + 21120651
UUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAGUCCGCU--UACCACCUCCAAAAAAUCACCCAAAAACCACC--GAACACCACCGU----------
..............(((((((((((......))).((((..((((.(((....)))))))--..)).))....................)))))--))).........---------- ( -28.60, z-score =  -2.07, R)
>droYak2.chr3R 13638049 115 - 28832112
UUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAGUCCGCU--UACCACCACCAGAAAAUCACCCAAAAGCCACCC-AAAAACCACCGAACACCACCGU
..............((((((((........(((((((((..((((.(((....)))))))--..)).)))))))..............(.....)-.....))))))))......... ( -36.30, z-score =  -4.05, R)
>droEre2.scaffold_4770 5435372 113 + 17746568
UUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGAUGGGGCGAGCGAGACACCAGGCCGCU--UGCCACCACCAGAAAAUCACCCGAAAGCCACCC-AAAAACCACCGAGCACCACC--
..............((((((((........(((.(((((((((((.(........)))))--)))).))).))).........(....)......-.....)))))))).......-- ( -35.00, z-score =  -3.70, R)
>droAna3.scaffold_13340 1886315 92 - 23697760
UUAAUCAUUGAAUUUUUGGUGGCCAACUCCCAGGAGAGGUCAACUCCACCGUUCACCGCU--UACCGCCAACCCCUCGCCACCCGCACACCUCC------------------------
.................((((((...(((....))).(((.(((......))).)))...--...............))))))...........------------------------ ( -19.80, z-score =  -1.49, R)
>consensus
UUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAGUCCGCU__UACCACCACCAGAAAAUCACCCAAAAACCACC__AAAAACCACCGA__________
............((((.(((((..........(((((....((((.(((....)))))))....))))).........))))).)))).............................. (-15.45 = -16.84 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:11:59 2011