Locus 3782

Sequence ID dm3.chr2R
Location 7,897,041 – 7,897,148
Length 107
Max. P 0.860269
window5179 window5180

overview

Window 9

Location 7,897,041 – 7,897,148
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 79.61
Shannon entropy 0.27616
G+C content 0.53659
Mean single sequence MFE -30.83
Consensus MFE -20.92
Energy contribution -22.42
Covariance contribution 1.50
Combinations/Pair 1.09
Mean z-score -2.17
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.860269
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7897041 107 + 21146708
GGACUUAUGCAGCCCUUCUGCGCUUCCAUCUAUCCAGUUGUCCAACUGGAAAACUGGACACUGGCCAGUGGCUAGCGGCUAGUGGCCACUCCACUCCAUUUCACUUC
(((....(((((.....)))))..))).....(((((((.(((....))).)))))))...((((((.((((.....)))).))))))................... ( -37.80, z-score =  -3.07, R)
>droSec1.super_1 5447374 95 + 14215200
GGACUUACGCAGCCCUUCU------------AUCCAGUUGUGCAAGUGGAAAACUGGACACUGUCCAGUGGCCAGUGGCUAGUGGCCACUCCACUCCAUUUCACUUC
(((....((((((......------------.....))))))...(((((..(((((((...)))))))(((((.(....).)))))..)))))))).......... ( -32.40, z-score =  -1.79, R)
>droSim1.chr2R 6433464 81 + 19596830
GGACUUACGCAGCCCUUCU------------AUCCAGUUGUGCAACUGGAAAACUGGACACUG--------------GCCAGUGGCCACUCCACUCCAUUUCACUUC
(((................------------.(((((((....)))))))....((((...((--------------(((...))))).)))).))).......... ( -22.30, z-score =  -1.66, R)
>consensus
GGACUUACGCAGCCCUUCU____________AUCCAGUUGUGCAACUGGAAAACUGGACACUG_CCAGUGGC_AG_GGCUAGUGGCCACUCCACUCCAUUUCACUUC
(((........(((..................(((((((....)))))))..(((((...(((((.....)))))...))))))))........))).......... (-20.92 = -22.42 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 7,897,041 – 7,897,148
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 79.61
Shannon entropy 0.27616
G+C content 0.53659
Mean single sequence MFE -34.90
Consensus MFE -21.54
Energy contribution -21.93
Covariance contribution 0.39
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.662473
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7897041 107 - 21146708
GAAGUGAAAUGGAGUGGAGUGGCCACUAGCCGCUAGCCACUGGCCAGUGUCCAGUUUUCCAGUUGGACAACUGGAUAGAUGGAAGCGCAGAAGGGCUGCAUAAGUCC
...(((......(((((((((((.....))))))..)))))..(((.(((((((((.(((....))).)))))))))..)))...)))....(((((.....))))) ( -43.00, z-score =  -3.13, R)
>droSec1.super_1 5447374 95 - 14215200
GAAGUGAAAUGGAGUGGAGUGGCCACUAGCCACUGGCCACUGGACAGUGUCCAGUUUUCCACUUGCACAACUGGAU------------AGAAGGGCUGCGUAAGUCC
...(((.....((((((((.(((((........)))))(((((((...))))))).)))))))).)))........------------....(((((.....))))) ( -34.60, z-score =  -1.55, R)
>droSim1.chr2R 6433464 81 - 19596830
GAAGUGAAAUGGAGUGGAGUGGCCACUGGC--------------CAGUGUCCAGUUUUCCAGUUGCACAACUGGAU------------AGAAGGGCUGCGUAAGUCC
..........(((.(...(..(((((((((--------------....).)))))..(((((((....))))))).------------.....)))..)...).))) ( -27.10, z-score =  -1.60, R)
>consensus
GAAGUGAAAUGGAGUGGAGUGGCCACUAGCC_CU_GCCACUGG_CAGUGUCCAGUUUUCCAGUUGCACAACUGGAU____________AGAAGGGCUGCGUAAGUCC
..........(((.(...(..((((((..(((........)))..)))((((((((...(....)...)))))))).................)))..)...).))) (-21.54 = -21.93 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:16:36 2011