Locus 11973

Sequence ID dm3.chr3R
Location 24,896,557 – 24,896,673
Length 116
Max. P 0.969023
window16446 window16447

overview

Window 6

Location 24,896,557 – 24,896,673
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 64.82
Shannon entropy 0.67634
G+C content 0.36441
Mean single sequence MFE -26.55
Consensus MFE -10.84
Energy contribution -11.51
Covariance contribution 0.67
Combinations/Pair 1.45
Mean z-score -1.76
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965221
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24896557 116 + 27905053
AGCUCAUGCAUUUCUCCGCAAAGAGCGACGGGGGAAAUGCGGUGUAUCUAAUUUAGUUAUUUGGUUAUUUUCGAGCUAAAACUACUCGAAUUC----UAUAUUCUAAUUUAUAGUUUGGU
(((((..((((((((((((.....))....))))))))))((.(((.((((.........)))).)))..)))))))........(((((..(----((((........)))))))))). ( -27.20, z-score =  -1.35, R)
>droSim1.chr3R 24583502 120 + 27517382
AGCUCAUGCAUUUCUCCGCAAAGAGCGUUGGGGGAAAUGCGGUGUAUCUAAUUUAGUUAUUUGGUUAUUUUCAAGCUAAAAGUAGUCGAAUUCUACAUAUAUUUUAAUUUAUAUUUGGGU
.(((((.((((((((((.(((......)))))))))))))(((((((....((((((...((((......)))))))))).((((.......)))))))))))............))))) ( -29.80, z-score =  -2.63, R)
>droSec1.super_4 3761160 120 + 6179234
AGCUCAUGCAUUUCUCCGCAAAGAGCAUUGGGGGAAAUGCGGUGUAUCUUAUUUAGUUAUUUGGUUAUUUUCAAGCUAAAAGUACUCGAAUUCUACAUAUAUUUUAAUUUAUAUUUGGGU
.((((((((((((((((.(((......))))))))))))))(((((....(((((((..(((((((.......)))))))...))).))))..))))).................))))) ( -29.10, z-score =  -2.61, R)
>droYak2.chr3R 7231349 103 - 28832112
AGCUCAUGCAUUUCUCCGCAAAAAGCGGUGGGGGAAAUGCAGUGUAUCUAAUUUAGUUAUAU--------UCGAGCUAAGAGCAAACGAAUU---------UUCUAAUUUAUAUGUGGGG
(((((.(((((((((((.((........)))))))))))))(((((.(((...))).)))))--------..)))))....(((.(..((((---------....))))..).))).... ( -27.30, z-score =  -2.08, R)
>droEre2.scaffold_4820 7336215 103 - 10470090
AGUUCAGGCAUUUCGCCGCAAAAAGCGGUAUGGGAAAUGCAUUGUAUCUAAUUUAGUUAUUU--------UCGAGCUAAGAGUACACGAAUU---------UUCAAAUUUAUAUUUAGAU
(((((..((((((((((((.....)))))....)))))))..((((.((...((((((....--------...)))))).)))))).)))))---------................... ( -23.60, z-score =  -2.27, R)
>droVir3.scaffold_12855 9228610 105 - 10161210
AGUCCCAGUCCUGUUUCAUACUUAGC-------GAAAUUUUACGCGUC-AGCUCAUUUUUGCA--UAACUCUGAAUAGAAGACAGGCAAGUGUGCUCUGUGACCGCAAGUACAGC-----
.......(.(((((((..((.(((((-------(........)))...-.((........)).--......))).))..))))))))...((((((.(((....)))))))))..----- ( -22.30, z-score =   0.39, R)
>consensus
AGCUCAUGCAUUUCUCCGCAAAGAGCGGUGGGGGAAAUGCGGUGUAUCUAAUUUAGUUAUUUG__UAUUUUCGAGCUAAAAGUACUCGAAUUC____UAUAUUCUAAUUUAUAUUUGGGU
.((...(((((((((((((.....))....)))))))))))..))......(((((((...............)))))))........................................ (-10.84 = -11.51 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 24,896,557 – 24,896,673
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 64.82
Shannon entropy 0.67634
G+C content 0.36441
Mean single sequence MFE -20.97
Consensus MFE -7.81
Energy contribution -9.20
Covariance contribution 1.39
Combinations/Pair 1.33
Mean z-score -2.02
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.969023
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24896557 116 - 27905053
ACCAAACUAUAAAUUAGAAUAUA----GAAUUCGAGUAGUUUUAGCUCGAAAAUAACCAAAUAACUAAAUUAGAUACACCGCAUUUCCCCCGUCGCUCUUUGCGGAGAAAUGCAUGAGCU
......(((((........))))----)..(((((((.......))))))).............................(((((((..((((........)))).)))))))....... ( -23.70, z-score =  -2.73, R)
>droSim1.chr3R 24583502 120 - 27517382
ACCCAAAUAUAAAUUAAAAUAUAUGUAGAAUUCGACUACUUUUAGCUUGAAAAUAACCAAAUAACUAAAUUAGAUACACCGCAUUUCCCCCAACGCUCUUUGCGGAGAAAUGCAUGAGCU
........................((((.......))))....(((((................(((...))).......(((((((.(((((......))).)).)))))))..))))) ( -18.30, z-score =  -2.32, R)
>droSec1.super_4 3761160 120 - 6179234
ACCCAAAUAUAAAUUAAAAUAUAUGUAGAAUUCGAGUACUUUUAGCUUGAAAAUAACCAAAUAACUAAAUAAGAUACACCGCAUUUCCCCCAAUGCUCUUUGCGGAGAAAUGCAUGAGCU
.......................((((...(((((((.......))))))).............((.....)).))))..(((((((.(((((......))).)).)))))))....... ( -20.30, z-score =  -2.49, R)
>droYak2.chr3R 7231349 103 + 28832112
CCCCACAUAUAAAUUAGAA---------AAUUCGUUUGCUCUUAGCUCGA--------AUAUAACUAAAUUAGAUACACUGCAUUUCCCCCACCGCUUUUUGCGGAGAAAUGCAUGAGCU
.........(((.((((..---------.(((((...((.....)).)))--------))....)))).)))....((.((((((((.....((((.....)))).)))))))))).... ( -22.40, z-score =  -3.22, R)
>droEre2.scaffold_4820 7336215 103 + 10470090
AUCUAAAUAUAAAUUUGAA---------AAUUCGUGUACUCUUAGCUCGA--------AAAUAACUAAAUUAGAUACAAUGCAUUUCCCAUACCGCUUUUUGCGGCGAAAUGCCUGAACU
((((((.........(...---------.)((((.((.......)).)))--------)..........)))))).....(((((((.....((((.....)))).)))))))....... ( -18.40, z-score =  -2.24, R)
>droVir3.scaffold_12855 9228610 105 + 10161210
-----GCUGUACUUGCGGUCACAGAGCACACUUGCCUGUCUUCUAUUCAGAGUUA--UGCAAAAAUGAGCU-GACGCGUAAAAUUUC-------GCUAAGUAUGAAACAGGACUGGGACU
-----.......((.(((((((((.(((....)))))))......((((..((((--.((........)))-)))(((........)-------))......))))....))))).)).. ( -22.70, z-score =   0.89, R)
>consensus
ACCCAAAUAUAAAUUAGAAUAUA____GAAUUCGAGUACUUUUAGCUCGAAAAUA__CAAAUAACUAAAUUAGAUACACCGCAUUUCCCCCAACGCUCUUUGCGGAGAAAUGCAUGAGCU
...........................................(((((................((.....)).......(((((((((.((........)).)).)))))))..))))) ( -7.81 =  -9.20 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:08 2011