Locus 15644

Sequence ID dm3.chrX
Location 20,190,256 – 20,190,382
Length 126
Max. P 0.942239
window21565 window21566

overview

Window 5

Location 20,190,256 – 20,190,348
Length 92
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 66.61
Shannon entropy 0.50688
G+C content 0.36924
Mean single sequence MFE -22.88
Consensus MFE -6.68
Energy contribution -9.37
Covariance contribution 2.69
Combinations/Pair 1.17
Mean z-score -2.34
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.519152
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20190256 92 + 22422827
----ACAGAAUGCCACAGAAGUGCAUGU--GGUAUUGAAAUCACAAGAACC-UAAAAGUAUGCAGUGAAAAUACAAUUUAAAAUGUAACGCA-GCAUACU--------
----....(((((((((........)))--))))))...............-....(((((((.(((....((((........)))).))).-)))))))-------- ( -22.40, z-score =  -3.04, R)
>droSec1.super_8 2375838 94 + 3762037
----ACAGAAUGCCACAGAAGUGCAUGUGUGGUGUUGAAAUCACAAGAACC-UGAAAGUAUGCAAUGAAAAUACAUUCUAAAAUGUAGCGCA-GCAUACU--------
----.(((.((((.((....)))))).((((((......)))))).....)-))..(((((((..((....((((((....)))))).))..-)))))))-------- ( -23.90, z-score =  -1.88, R)
>droSim1.chrX 15471324 94 + 17042790
----ACAGAAUGCCACAGAAGUGCAUGUGUGGUGUUGAAAUCACAAGAACC-UGAAAGUAUGCAAUGAAAAUACAUUCUAAAAUGUAACGCA-GCAUACU--------
----.(((.((((.((....)))))).((((((......)))))).....)-))..(((((((..((....((((((....))))))...))-)))))))-------- ( -22.60, z-score =  -1.81, R)
>droVir3.scaffold_13042 4532434 107 - 5191987
AGCUAACAAACGCAAAACAUAUGCAGAUG-GAUAUUCAAUUGAUGCAACCCACAAACAUCCUUUUUGCCCUUUCACUGACUAAUUUAGUGGAAGGACACGCAUUAAAU
.((........((((((...(((....((-(....((....))......)))....)))...))))))(((((((((((.....)))))))))))....))....... ( -22.60, z-score =  -2.64, R)
>consensus
____ACAGAAUGCCACAGAAGUGCAUGUG_GGUAUUGAAAUCACAAGAACC_UAAAAGUAUGCAAUGAAAAUACAUUCUAAAAUGUAACGCA_GCAUACU________
........(((((((((.(......).)))))))))....................(((((((........((((((....))))))......)))))))........ ( -6.68 =  -9.37 +   2.69)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,190,292 – 20,190,382
Length 90
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 61.95
Shannon entropy 0.57047
G+C content 0.33565
Mean single sequence MFE -20.91
Consensus MFE -4.94
Energy contribution -6.38
Covariance contribution 1.44
Combinations/Pair 1.31
Mean z-score -3.13
Structure conservation index 0.24
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.942239
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20190292 90 + 22422827
ACAAGAACCUAAAAGUAUGCAGU--GAAAAUACAAUUUAAAAUGUAACGCAGCAUACUUUUACACACCUUUAUACAUACAU---GUGUGCUAUAU-------------
.........(((((((((((.((--(....((((........)))).))).)))))))))))(((((..............---)))))......------------- ( -18.84, z-score =  -2.58, R)
>droSec1.super_8 2375876 86 + 3762037
ACAAGAACCUGAAAGUAUGCAAU--GAAAAUACAUUCUAAAAUGUAGCGCAGCAUACUUUUACACACCCUUAUACAU-------GUGUGAUAUGU-------------
.........(((((((((((..(--(....((((((....)))))).))..)))))))))))(((((..........-------)))))......------------- ( -20.90, z-score =  -3.29, R)
>droSim1.chrX 15471362 90 + 17042790
ACAAGAACCUGAAAGUAUGCAAU--GAAAAUACAUUCUAAAAUGUAACGCAGCAUACUUUUACACACCCUUAUACAUACAU---GUGUGAUAUGU-------------
.........(((((((((((..(--(....((((((....))))))...)))))))))))))(((((..............---)))))......------------- ( -19.24, z-score =  -2.85, R)
>droVir3.scaffold_13042 4532474 107 - 5191987
GAUGCAACCCACAAACAUCCUUUUUGCCCUUUCACUGACUAAUUUAGUGGAA-GGACACGCAUUAAAUUUAACACAUUCAAUUGAUGCGAUUUGCUGACCUAUUUCGU
...((((.................((.(((((((((((.....)))))))))-)).))((((((((...............))))))))..))))............. ( -24.66, z-score =  -3.81, R)
>consensus
ACAAGAACCUAAAAGUAUGCAAU__GAAAAUACAUUCUAAAAUGUAACGCAGCAUACUUUUACACACCCUUAUACAUACAU___GUGUGAUAUGU_____________
.........(((((((((((...............................)))))))))))..........(((((.......)))))................... ( -4.94 =  -6.38 +   1.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:03:17 2011