Locus 12859

Sequence ID dm3.chrX
Location 2,702,228 – 2,702,345
Length 117
Max. P 0.916207
window17679 window17680

overview

Window 9

Location 2,702,228 – 2,702,345
Length 117
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 70.23
Shannon entropy 0.49551
G+C content 0.51884
Mean single sequence MFE -25.70
Consensus MFE -13.20
Energy contribution -13.20
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.916207
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2702228 117 + 22422827
GCCUCCUUCGCAGCUUCUCCACCGCCUUUUGCCUAUGGUACAUACAUACAUACGUACGUACUACGUACUACCCAUGACACUACUCAUGGGC-GCAAACUUUGUGCACAGCCUGUCAAC
.........((((((....(((.....(((((...((((((.(((........))).)))))).......(((((((......))))))).-)))))....)))...)).)))).... ( -26.80, z-score =  -1.81, R)
>droSec1.super_10 2461625 96 + 3036183
---GCCUCCGCAGCUUCUCCUCCG------------------UACAUAUAUACGUACGUACUACGUACUACCCAUGACACUACUCAUGGGC-GCAAACUUUCUGCACAGCCUGUCAAC
---......((((...........------------------...........(((((.....)))))..(((((((......))))))).-.........))))............. ( -21.40, z-score =  -2.43, R)
>droYak2.chrX 16127478 96 - 21770863
---GCCACAGGAGCACUUCCUUCGCCUUUUACCCACGG--UAUGUA-----------------CGUACUACCCAUGACACUACUCAUGGGCUGCAAACUUUCUGCACAGCCUGUCAAC
---...(((((.(((........((...........((--(((...-----------------.))))).(((((((......)))))))..))........)))....))))).... ( -21.89, z-score =  -1.20, R)
>droEre2.scaffold_4690 136682 113 + 18748788
---GCCACCGGAGCACCUCCCUCGCCUUUCACCCAUGGG-UAUGUAGUACGUACGUAUAGCUACGUACUACCCAUGACACUACUCAUGGGC-GCAAACUUUCUGCACAGCCUGUCAAC
---.....(((.((.................((((((((-(((((.(((.(((((((....)))))))))).....))).)))))))))).-(((.......)))...)))))..... ( -32.70, z-score =  -2.01, R)
>consensus
___GCCACCGCAGCACCUCCUCCGCCUUUUACCCAUGG__UAUACAUA_AUACGUACGUACUACGUACUACCCAUGACACUACUCAUGGGC_GCAAACUUUCUGCACAGCCUGUCAAC
............((........................................................(((((((......)))))))..(((.......)))...))........ (-13.20 = -13.20 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,702,228 – 2,702,345
Length 117
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 70.23
Shannon entropy 0.49551
G+C content 0.51884
Mean single sequence MFE -35.17
Consensus MFE -16.38
Energy contribution -16.38
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.632505
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2702228 117 - 22422827
GUUGACAGGCUGUGCACAAAGUUUGC-GCCCAUGAGUAGUGUCAUGGGUAGUACGUAGUACGUACGUAUGUAUGUAUGUACCAUAGGCAAAAGGCGGUGGAGAAGCUGCGAAGGAGGC
.(((...((((.(.(((....(((((-((((((((......))))))))........((((((((((....)))))))))).....))))).....))).)..)))).)))....... ( -38.40, z-score =  -1.65, R)
>droSec1.super_10 2461625 96 - 3036183
GUUGACAGGCUGUGCAGAAAGUUUGC-GCCCAUGAGUAGUGUCAUGGGUAGUACGUAGUACGUACGUAUAUAUGUA------------------CGGAGGAGAAGCUGCGGAGGC---
.......(.((.(((((....(((.(-((((((((......)))))))).(((((((((((....)))).))))))------------------)...).)))..))))).)).)--- ( -34.40, z-score =  -3.09, R)
>droYak2.chrX 16127478 96 + 21770863
GUUGACAGGCUGUGCAGAAAGUUUGCAGCCCAUGAGUAGUGUCAUGGGUAGUACG-----------------UACAUA--CCGUGGGUAAAAGGCGAAGGAAGUGCUCCUGUGGC---
....(((((..(..(......(((((.((((((((......))))))))..(((.-----------------(((...--..))).)))....)))))....)..).)))))...--- ( -29.80, z-score =  -0.94, R)
>droEre2.scaffold_4690 136682 113 - 18748788
GUUGACAGGCUGUGCAGAAAGUUUGC-GCCCAUGAGUAGUGUCAUGGGUAGUACGUAGCUAUACGUACGUACUACAUA-CCCAUGGGUGAAAGGCGAGGGAGGUGCUCCGGUGGC---
.....((((((........))))))(-(((((((.(((.(((....(((((((((((....))))))).)))))))))-).))))))))...(.((..((((...))))..)).)--- ( -38.10, z-score =  -0.54, R)
>consensus
GUUGACAGGCUGUGCAGAAAGUUUGC_GCCCAUGAGUAGUGUCAUGGGUAGUACGUAGUACGUACGUAU_UAUACAUA__CCAUGGGUAAAAGGCGAAGGAGAAGCUCCGGAGGC___
.....((((((........))))))..((((((((......))))))))..................................................................... (-16.38 = -16.38 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:10:09 2011