Locus 14885

Sequence ID dm3.chrX
Location 16,061,815 – 16,061,994
Length 179
Max. P 0.989410
window20501 window20502 window20503

overview

Window 1

Location 16,061,815 – 16,061,928
Length 113
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 79.34
Shannon entropy 0.32313
G+C content 0.37604
Mean single sequence MFE -30.35
Consensus MFE -21.21
Energy contribution -20.53
Covariance contribution -0.69
Combinations/Pair 1.20
Mean z-score -2.73
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989410
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16061815 113 + 22422827
UGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAAAAAAAACCCAGACACAUAUGA--GUAUAUGAAUAUAUAUGUAUAUACACAUAUGCGCACAUAGGUGGAC
((((((((((.((.((((......)))).)).))))))))))................(((.((((.--(((((((..(((((....)))))..)))))))...)))).)))... ( -29.70, z-score =  -2.83, R)
>droSim1.chrX 12402699 101 + 17042790
UGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAAAAAC--CCCAGACACAUAUGA--GUAUAUGAAUAUAUAUACAUAUGCACAUAGGUGGAC----------
((((((((((.((.((((......)))).)).))))))))))........--......(((.((((.--(((((((.((....)).))))))).)))).)))...---------- ( -28.00, z-score =  -2.83, R)
>droSec1.super_47 119360 99 + 216421
UGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAAAACC--CCCAGACACAUAUGA--GUAUAUGAAUAUAU--ACAUAUGCACAUAGGUGGAC----------
((((((((((.((.((((......)))).)).))))))))))........--......(((.((((.--(((((((.......--.))))))).)))).)))...---------- ( -28.60, z-score =  -2.78, R)
>droEre2.scaffold_4690 7730316 110 - 18748788
UGGGUGUUACCUUCUGGCAGUAAAGUCAGAAAGUGGCAUCUAAAAAG-----CCCAGACACAUAUGACUAUAUAUGUACGCACAUAUGUGUAUAUACACAUGUACAUUGGUGGAC
((((((((((.(((((((......))))))).)))))))))).....-----......(((..(((((....((((((((((....)))))))))).....)).)))..)))... ( -35.10, z-score =  -2.49, R)
>consensus
UGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAAAAAC__CCCAGACACAUAUGA__GUAUAUGAAUAUAUAUACAUAUACACAUAGGUGGAC__________
((((((((((.((.((((......)))).)).))))))))))................(((.((((...(((((((..........))))))).)))).)))............. (-21.21 = -20.53 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,061,815 – 16,061,928
Length 113
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 79.34
Shannon entropy 0.32313
G+C content 0.37604
Mean single sequence MFE -26.80
Consensus MFE -18.36
Energy contribution -17.30
Covariance contribution -1.06
Combinations/Pair 1.21
Mean z-score -1.77
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.784425
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16061815 113 - 22422827
GUCCACCUAUGUGCGCAUAUGUGUAUAUACAUAUAUAUUCAUAUAC--UCAUAUGUGUCUGGGUUUUUUUUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAACACCCA
....(((((.(.(((((((((.((((((............))))))--.))))))))))))))).................((((((((.(......).))))))))........ ( -26.00, z-score =  -1.91, R)
>droSim1.chrX 12402699 101 - 17042790
----------GUCCACCUAUGUGCAUAUGUAUAUAUAUUCAUAUAC--UCAUAUGUGUCUGGG--GUUUUUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAACACCCA
----------.....((((.(..((((((..(((((....))))).--.))))))..).))))--................((((((((.(......).))))))))........ ( -22.80, z-score =  -1.20, R)
>droSec1.super_47 119360 99 - 216421
----------GUCCACCUAUGUGCAUAUGU--AUAUAUUCAUAUAC--UCAUAUGUGUCUGGG--GGUUUUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAACACCCA
----------((..((((....(((((((.--.((((....)))).--.))))))).(((((.--(((....(((((........)))))....))).))))))))).))..... ( -24.70, z-score =  -1.36, R)
>droEre2.scaffold_4690 7730316 110 + 18748788
GUCCACCAAUGUACAUGUGUAUAUACACAUAUGUGCGUACAUAUAUAGUCAUAUGUGUCUGGG-----CUUUUUAGAUGCCACUUUCUGACUUUACUGCCAGAAGGUAACACCCA
(((((...((((((((((((......))))))))))))((((((((....)))))))).))))-----)............((((((((.(......).))))))))........ ( -33.70, z-score =  -2.62, R)
>consensus
__________GUCCACCUAUGUGCAUAUAUAUAUAUAUUCAUAUAC__UCAUAUGUGUCUGGG__GUUUUUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAACACCCA
.................((((((.(((((....))))).)))))).........(((((((((........))))))))).((((((((.(......).))))))))........ (-18.36 = -17.30 +  -1.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,061,895 – 16,061,994
Length 99
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 83.84
Shannon entropy 0.24912
G+C content 0.44068
Mean single sequence MFE -19.70
Consensus MFE -16.15
Energy contribution -16.65
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.25
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.517923
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16061895 99 + 22422827
UAUGUAUAUACACAUAUGCGCACAUAGGUGGACACAGUUUUUA----AGCGCUUUUCUCUGGCUCUUCCAUCUCGCCAUCAUCGUCCAAUCUGUGGGCCUUUU
...((((((....))))))((.(((((((((((...(((....----))).........((((...........)))).....)))).))))))).))..... ( -24.10, z-score =  -2.02, R)
>droSim1.chrX 12402777 89 + 17042790
----------UAUACAUAUGCACAUAGGUGGACACAGUUUUUA----AGCGCUUUUCUCUGGCUCUACCAUCUCCCCAUCAUCGUCCAAUCUGUGGGCCUUUU
----------.........((.(((((((((((...(((....----)))(((.......)))....................)))).))))))).))..... ( -18.50, z-score =  -1.05, R)
>droSec1.super_47 119436 89 + 216421
----------UAUACAUAUGCACAUAGGUGGACACAGUUUUUA----AGCGCUUUUCUCUGGCUCCUCCAUCUCCCCAUCAUCGUCCAAUCUGUGGGCCUUUU
----------.........((.(((((((((((...(((....----)))(((.......)))....................)))).))))))).))..... ( -18.50, z-score =  -1.05, R)
>droEre2.scaffold_4690 7730397 98 - 18748788
----UGUGUAUAUACACAUGUACAUUGGUGGACACAGUUUUUAUUUAAGCGCUUUUCUCUGGCUCUUUCAUCUCCCCAUCAUCGUCCAAUCUGUGGCCUUUU-
----(((((....))))).(..(((.(((((((...((((......))))(((.......)))....................)))).))).)))..)....- ( -17.70, z-score =  -0.87, R)
>consensus
__________UAUACAUAUGCACAUAGGUGGACACAGUUUUUA____AGCGCUUUUCUCUGGCUCUUCCAUCUCCCCAUCAUCGUCCAAUCUGUGGGCCUUUU
...................((.(((((((((((...(((........)))(((.......)))....................)))).))))))).))..... (-16.15 = -16.65 +   0.50)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:48:46 2011