Locus 5435

Sequence ID	dm3.chr2R
Location	20,273,906 – 20,274,016
Length	110
Max. P	0.821619

overview

Window 8

Location	20,273,906 – 20,274,007
Length	101
Sequences	7
Columns	113
Reading direction	forward
Mean pairwise identity	79.17
Shannon entropy	0.38934
G+C content	0.48889
Mean single sequence MFE	-29.94
Consensus MFE	-21.96
Energy contribution	-22.31
Covariance contribution	0.35
Combinations/Pair	1.29
Mean z-score	-1.37
Structure conservation index	0.73
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.76
SVM RNA-class probability	0.808982
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20273906 101 + 21146708
GCCACCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGUGCGCC---------
(((((...((((........))))..)))))..........(((((((((((((.....))......((((((((....---.)))))))).)))))))).)))--------- ( -32.20, z-score =  -1.65, R)
>droSim1.chr2R 18725102 101 + 19596830
GCCACCUGAUUGAUAGGCCACGAUACGUGGCGGAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGUGCGCC---------
.((..(((.....)))((((((...))))))))........(((((((((((((.....))......((((((((....---.)))))))).)))))))).)))--------- ( -32.40, z-score =  -1.31, R)
>droSec1.super_23 144358 101 + 989336
GCCACCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGUGCGCC---------
(((((...((((........))))..)))))..........(((((((((((((.....))......((((((((....---.)))))))).)))))))).)))--------- ( -32.20, z-score =  -1.65, R)
>droEre2.scaffold_4845 21632150 101 + 22589142
GCCACCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGUGAAGUUAUUGUGCGCC---------
(((((...((((........))))..)))))..........(((((((((((.((((((((((.((.....)).)).))---))))....)))))))))).)))--------- ( -30.30, z-score =  -1.22, R)
>droYak2.chr2R 20234926 101 + 21139217
GCCAGCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGUGCGCC---------
(((((((.((((....((((((...))))))....((.......)))))).)))))..((..((...((((((((....---.))))))))...))..)).)).--------- ( -34.00, z-score =  -1.92, R)
>droAna3.scaffold_13266 5737365 94 - 19884421
GCCACCUGAUUGAUAGGCCGAGAUACG------AGUGGACA-----CAAUGAAAUGCCCAUGAUUGAUUCGCAUUCAAUAC-GAAUGUGACGGUAUUGUUGGCUCU-------
...............(((((((((((.------.((((.((-----........)).)))).......((((((((.....-))))))))..))))).))))))..------- ( -23.60, z-score =  -0.86, R)
>dp4.chr3 1378378 100 - 19779522
GCCACCUGAUUGAUAGACACUGAUACG-----AUAUGAAUAG--------GCGUGUCCCAUGAUUGACUGGCAUUCAGUACUAGAUGCCAGCUUAUUUCCUGUAUUGUGUGCU
................((((.((((((-----....((((((--------((..(((........)))(((((((........)))))))))))))))..))))))))))... ( -24.90, z-score =  -0.99, R)
>consensus
GCCACCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU___GGAUGCGAAGUUAUUGUGCGCC_________
...............((((((((((.(((((...........)))))....................(((((((((......)))))))))..))))))).)))......... (-21.96 = -22.31 +   0.35)

alignment

secondary structure

dotplot

Window 9

Location	20,273,910 – 20,274,016
Length	106
Sequences	7
Columns	118
Reading direction	forward
Mean pairwise identity	78.09
Shannon entropy	0.41266
G+C content	0.48921
Mean single sequence MFE	-33.47
Consensus MFE	-19.27
Energy contribution	-19.04
Covariance contribution	-0.23
Combinations/Pair	1.42
Mean z-score	-1.78
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.80
SVM RNA-class probability	0.821619
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20273910 106 + 21146708
CCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGU--GCGCCGCGCCAUUG-------
((((.((.((..((((((...))))))...)).))))))...(((((.((.((.((..((...((((((((....---.))))))))...))..)--).)).))..)))))------- ( -37.00, z-score =  -2.21, R)
>droSim1.chr2R 18725106 106 + 19596830
CCUGAUUGAUAGGCCACGAUACGUGGCGGAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGU--GCGCCGCGCCAUUG-------
((((.((.((..((((((...))))))...)).))))))...(((((.((.((.((..((...((((((((....---.))))))))...))..)--).)).))..)))))------- ( -37.00, z-score =  -1.83, R)
>droSec1.super_23 144362 106 + 989336
CCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGU--GCGCCGCGCCAUUG-------
((((.((.((..((((((...))))))...)).))))))...(((((.((.((.((..((...((((((((....---.))))))))...))..)--).)).))..)))))------- ( -37.00, z-score =  -2.21, R)
>droEre2.scaffold_4845 21632154 106 + 22589142
CCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGUGAAGUUAUUGU--GCGCCGAGCCAUUG-------
((((.((.((..((((((...))))))...)).))))))...(((((.(((((.((..((...((((((((....---.))))))))...))..)--).))..))))))))------- ( -34.40, z-score =  -2.14, R)
>droYak2.chr2R 20234930 106 + 21139217
GCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU---GGAUGCGAAGUUAUUGU--GCGCCGCGCCAUUG-------
(((..((.((..((((((...))))))...)).))..)))..(((((.((.((.((..((...((((((((....---.))))))))...))..)--).)).))..)))))------- ( -35.50, z-score =  -1.40, R)
>droAna3.scaffold_13266 5737369 99 - 19884421
CCUGAUUGAUAGGCCGAGAUACG------AGUGGA-----CACAAUGAAAUGCCCAUGAUUGAUUCGCAUUCAAUAC-GAAUGUGACGGUAUUGUUGGCUCUUCUCCAUUG-------
.......((..(((((((((((.------.((((.-----((........)).)))).......((((((((.....-))))))))..))))).))))))..)).......------- ( -26.10, z-score =  -1.26, R)
>dp4.chr3 1378382 104 - 19779522
CCUGAUUGAUAGACACUGAUACG-----AUAUGAAU--------AGGCGUGUCCCAUGAUUGACUGGCAUUCAGUACUAGAUGCCAGCUUAUUUCCUGUAUUGUGU-GCUGCCUGUAG
........((((.((...(((((-----((((((((--------((((..(((........)))(((((((........)))))))))))))))...)))))))))-..)).)))).. ( -27.30, z-score =  -1.42, R)
>consensus
CCUGAUUGAUAGGCCACGAUACGUGGCGAAAUGAACAGGCCACAAUGAGCUGUCCGUGAUUGAUUCGCAUUCAAU___GGAUGCGAAGUUAUUGU__GCGCCGCGCCAUUG_______
...........(((........(((((...........))))).....((.((..(..((...(((((((((......)))))))))...))..)..))))...)))........... (-19.27 = -19.04 +  -0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:17 2011