Locus 1463

Sequence ID dm3.chr2L
Location 11,398,733 – 11,398,880
Length 147
Max. P 0.543310
window1995 window1996

overview

Window 5

Location 11,398,733 – 11,398,840
Length 107
Sequences 8
Columns 126
Reading direction reverse
Mean pairwise identity 56.61
Shannon entropy 0.78245
G+C content 0.45345
Mean single sequence MFE -18.95
Consensus MFE -5.57
Energy contribution -4.83
Covariance contribution -0.75
Combinations/Pair 1.50
Mean z-score -1.31
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.543310
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11398733 107 - 23011544
---------------UGUGCAACACAGAGCACUAGAC--GAUUCCC--UUCAUUUAGGCCCCCCCUUCCAACGAGAGACACAGCCAAAAAUCGAAAAUGAAAAUAUUUAUUUCUGAUACUCAGUAG
---------------((((.........((.(((((.--((.....--.)).)))))))............(....).)))).......((((.(((((((....))))))).))))......... ( -13.90, z-score =  -0.36, R)
>droPer1.super_1 8297032 115 - 10282868
UGUACACCAGAGCUCUAGGCAGCGGUGUGCCUCGUAAGUAACCACCUCCCGCCUCCCACCAC-----------AGAAUUGUAGUCAAAAAUCGAAAACUAAAAUGCUUAUCCCCGGCGUAGGGUAG
.(((((((...((.....))...))))))).............((((..((((........(-----------(.....((..((.......))..)).....)).........))))..)))).. ( -24.33, z-score =   0.19, R)
>dp4.chr4_group3 6849139 115 - 11692001
UGUACACCAGAGCUCUAGGCAGCGGUGUGCCUCGUAAGUAACCUCCUCCCGCCUCCCACCAC-----------AGAAUUGUAGUCAAAAAUCGAAAACUAAAAUGGUUAUCCCCGGCGUAGGGUAG
.(((((((...((.....))...)))))))............(((((..((((....((.((-----------......)).))........((.((((.....)))).))...))))..))).)) ( -25.20, z-score =   0.23, R)
>droAna3.scaffold_12916 12107411 98 + 16180835
---------------UGUGCAGCACCCAGCACUAGACCAGAUCCCCGAACUUCCCCCAAAGCU----------GGCGAAAAAGUCAAAAAUCUAAUUUGAAAAUUUUU-UUACCGC--CUCAAUAG
---------------.((((........))))...............................----------(((((((((.(((((.......)))))...)))))-....)))--)....... ( -13.40, z-score =  -0.77, R)
>droEre2.scaffold_4929 12600231 91 + 26641161
---------------UGUGCAACACACGGCACUAGAC--GAUUCCC---CCGAUCCGGAGAG---------------UCGGAGUCAAAAAUCGAAAAUUAAAAUUUCCAUCUGUGCUACCCAGCAG
---------------.(((.....)))(((((.(((.--(((((.(---(......)).)))---------------))((((.....................)))).))))))))......... ( -19.70, z-score =  -1.17, R)
>droYak2.chr2L 7796913 93 - 22324452
---------------UGUGCAACACACAGCACUAGAC--GAUUCCCACUCCGCUACGAAAGU----------------CAGAGUCAAAAAUCGAAAAUUAAAAUUUUUAACUCUGCUACUCAGUAG
---------------.((((........)))).....--.............((((...(((----------------((((((.((((((...........)))))).))))))..)))..)))) ( -17.20, z-score =  -2.08, R)
>droSec1.super_3 6792942 106 - 7220098
---------------UGUGCAACACACAGCACUAGAC--GAUUCCC---CCGAUCCGAACCCCUUUCCCUACUAGAGCCAGAGUCAAAAAUCGAAAAUGAAAAUUUUUAUCUCUGAUACUCAGUAG
---------------.((((........))))....(--(..((..---..))..))...........(((((.(((.(((((..((((((...........))))))..)))))...)))))))) ( -19.80, z-score =  -2.90, R)
>droSim1.chr2L 11207156 82 - 22036055
---------------UGUGCAACACACUGCACUAGAC--GAUUCCC---CCGAUCCGAACCC------------------------AGAGUCAAAAAUGAAAAUUUUUAUCUCUGAUACUCAGUAG
---------------.(((((......)))))....(--(..((..---..))..))....(------------------------((((..((((((....))))))..)))))........... ( -18.10, z-score =  -3.59, R)
>consensus
_______________UGUGCAACACACAGCACUAGAC__GAUUCCC___CCGCUCCGAACAC___________AGA_UCAGAGUCAAAAAUCGAAAAUGAAAAUUUUUAUCUCUGAUACUCAGUAG
................((((........)))).............................................................................................. ( -5.57 =  -4.83 +  -0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 11,398,773 – 11,398,880
Length 107
Sequences 8
Columns 117
Reading direction reverse
Mean pairwise identity 60.15
Shannon entropy 0.77498
G+C content 0.58372
Mean single sequence MFE -27.12
Consensus MFE -12.66
Energy contribution -13.10
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -0.27
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.522273
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11398773 107 - 23011544
CUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACAGAGCACUAGACGAUUCC--CUUCAUUUAGGCCCCCCCUUCCAACGAGAGACACAGCCA--------
.((((((((((......))))).))).))((((((.......(((........)))(((((.((....--..)).))))))))...........(....).....))).-------- ( -27.70, z-score =  -0.06, R)
>droPer1.super_1 8297072 110 - 10282868
-----CCCUCCCCCCAAGUCGGCGCCACAGGCGGCAAUAAUGUACACCA--GAGCUCUAGGCAGCGGUGUGCCUCGUAAGUAACCACCUCCCGCCUCCCACCACAGAAUUGUAGUCA
-----............((.((.(....((((((.......(((((((.--..((.....))...)))))))..(....)..........))))))..).))))............. ( -24.00, z-score =   0.99, R)
>dp4.chr4_group3 6849179 110 - 11692001
-----CCCUCCCCCCAAGUCGGCGCCACAGGCGGCAAUAAUGUACACCA--GAGCUCUAGGCAGCGGUGUGCCUCGUAAGUAACCUCCUCCCGCCUCCCACCACAGAAUUGUAGUCA
-----............((.((.(....((((((.......(((((((.--..((.....))...)))))))..(....)..........))))))..).))))............. ( -24.00, z-score =   0.96, R)
>droAna3.scaffold_12916 12107448 101 + 16180835
CUGGGCCCGGCAUUCGAGUCGGCGCCACAGACGGCAAUAAUGUGCAGCACCCAGCACUAGACCAGAUC--CCCGAACUU--CCCCCAAAGCUGGCGAAAAAGUCA------------
(((((((((((......))))).))).)))..(((......((((........))))..(.((((...--.........--.........)))))......))).------------ ( -27.90, z-score =  -0.09, R)
>droEre2.scaffold_4929 12600271 91 + 26641161
CUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACGGCACUAGACGAUUCC--CCCGAUCCGGAGAGUCGGAGUCA------------------------
(((((((((((......))))).))).)))..(((......((((........))))....((((((.--((......)).))))))..))).------------------------ ( -31.50, z-score =  -0.90, R)
>droYak2.chr2L 7796953 93 - 22324452
CUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACAGCACUAGACGAUUCCCACUCCGCUACGAAAGUCAGAGUCA------------------------
...((((((((......((((.((((...)))).)......((((........))))..)))(.....).....)))((....))..))))).------------------------ ( -26.50, z-score =  -0.82, R)
>droSec1.super_3 6792982 106 - 7220098
CUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACAGCACUAGACGAUUCC--CCCGAUCCGAA-CCCCUUUCCCUACUAGAGCCAGAGUCA--------
...((((((((.((((.((((.((((...)))).)......((((........))))..)))((((..--...))))....-.............))))))).))))).-------- ( -29.30, z-score =  -0.82, R)
>droSim1.chr2L 11207196 82 - 22036055
CUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACUGCACUAGACGAUUCC--CCCGAUCCGAACCC---------------------------------
.((((.((((.......((((.((((...)))).)......(((((......)))))..)))......--.)))))))).....--------------------------------- ( -26.04, z-score =  -1.41, R)
>consensus
CUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACAGCACUAGACGAUUCC__CCCGAUCAAGAAACCCCCUCCCA_C______CACA____________
.................((((.((((...)))).)......((((........))))..)))....................................................... (-12.66 = -13.10 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:32:25 2011