Locus 10066

Sequence ID dm3.chr3R
Location 10,987,297 – 10,987,387
Length 90
Max. P 0.845404
window13837 window13838

overview

Window 7

Location 10,987,297 – 10,987,387
Length 90
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 69.80
Shannon entropy 0.42307
G+C content 0.37123
Mean single sequence MFE -19.07
Consensus MFE -8.94
Energy contribution -9.05
Covariance contribution 0.12
Combinations/Pair 1.20
Mean z-score -2.22
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.89
SVM RNA-class probability 0.845404
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10987297 90 + 27905053
-----------------AAACCUCAAUUAACUUUACCUCUUCGAGCUGCCAAUAGUUGAAAAACAAUUCGAAUCAAUAAGCCACAAUGAAAUAAA-GCAACUGCAAUC---------
-----------------.............(((((..((.....(((........(((((......))))).......)))......))..))))-)...........--------- (  -7.46, z-score =   0.05, R)
>droEre2.scaffold_4770 10513575 117 + 17746568
AAAUCAAUUUAAUUUCAUUAGGACAGCUUACUCUACCUCUCCAAGCUGCCAAUAGUUGGAGAACAAUCCAACUCAAUAAACCACAAUGAAGAGAACGCAACUGCAACCGCAUUAAUC
............(((((((.((.((((((.............))))))))...(((((((......)))))))...........))))))).....((....))............. ( -23.52, z-score =  -3.32, R)
>droYak2.chr3R 13389133 117 - 28832112
AAAUCAAUUUAUUUUCAUAACGGCAGCUUACUUCACCUCUUCAAGCUGCCAAUAGUUGGAAAACAAUCCGACUCAGAAAGCCACAAUGAAAUGAAAGCAACUGCAACCGCAUUUAUC
.......(((((((.(((...((((((((.............))))))))...(((((((......)))))))............))))))))))......(((....)))...... ( -26.22, z-score =  -3.38, R)
>consensus
AAAUCAAUUUA_UUUCAUAACGACAGCUUACUUUACCUCUUCAAGCUGCCAAUAGUUGGAAAACAAUCCGACUCAAUAAGCCACAAUGAAAUGAA_GCAACUGCAACCGCAUU_AUC
.......................((((((.............)))))).....(((((((......))))))).......................((....))............. ( -8.94 =  -9.05 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 10,987,297 – 10,987,387
Length 90
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 69.80
Shannon entropy 0.42307
G+C content 0.37123
Mean single sequence MFE -26.87
Consensus MFE -18.63
Energy contribution -17.43
Covariance contribution -1.20
Combinations/Pair 1.37
Mean z-score -1.10
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.639023
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10987297 90 - 27905053
---------GAUUGCAGUUGC-UUUAUUUCAUUGUGGCUUAUUGAUUCGAAUUGUUUUUCAACUAUUGGCAGCUCGAAGAGGUAAAGUUAAUUGAGGUUU-----------------
---------(((..(((((((-((((((((.(((.((((..(..((..(((......)))....))..).))))))).))))))))).))))))..))).----------------- ( -20.30, z-score =  -1.10, R)
>droEre2.scaffold_4770 10513575 117 - 17746568
GAUUAAUGCGGUUGCAGUUGCGUUCUCUUCAUUGUGGUUUAUUGAGUUGGAUUGUUCUCCAACUAUUGGCAGCUUGGAGAGGUAGAGUAAGCUGUCCUAAUGAAAUUAAAUUGAUUU
(((((((..((((((((((((..((((((((..((.(((.....(((((((......)))))))...))).)).))))))))....)).))))))........))))..))))))). ( -29.70, z-score =  -1.09, R)
>droYak2.chr3R 13389133 117 + 28832112
GAUAAAUGCGGUUGCAGUUGCUUUCAUUUCAUUGUGGCUUUCUGAGUCGGAUUGUUUUCCAACUAUUGGCAGCUUGAAGAGGUGAAGUAAGCUGCCGUUAUGAAAAUAAAUUGAUUU
.......(((((.((..((((((.((((((.....((((.((..(((.(((......))).)))...)).))))....)))))))))))))).)))))(((....)))......... ( -30.60, z-score =  -1.12, R)
>consensus
GAU_AAUGCGGUUGCAGUUGC_UUCAUUUCAUUGUGGCUUAUUGAGUCGGAUUGUUUUCCAACUAUUGGCAGCUUGAAGAGGUAAAGUAAGCUGACGUUAUGAAA_UAAAUUGAUUU
.............((((((((.((((((((.(((.((((..(..(((.(((......))).)))...)..))))))).)))))))))).))))))...................... (-18.63 = -17.43 +  -1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:16:45 2011