Locus 6173

Sequence ID dm3.chr3L
Location 4,343,294 – 4,343,385
Length 91
Max. P 0.701980
window8486 window8487

overview

Window 6

Location 4,343,294 – 4,343,385
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 81.38
Shannon entropy 0.32740
G+C content 0.49991
Mean single sequence MFE -20.24
Consensus MFE -16.38
Energy contribution -16.22
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.21
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.701980
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4343294 91 + 24543557
AGCUCGUGGCGGCACGUCUAUACGUAAGUCUAUUGGUUUCCGCCACGCCCCCUUUUACCGCCUUCAGUUCGAUGGAAUUUUUUUUCUUCUG
....((((((((.....(((.((....))....)))...)))))))).......................((.((((.....)))).)).. ( -18.90, z-score =  -0.54, R)
>droSim1.chr3L 3880629 78 + 22553184
AGCUCGUGGCGGCACGUCUAUACACAUGUCUAUUGGCUUCCGCCACGCCCCCUUUUACCGCCUGCAAUUCGAUGGAAU-------------
....((((((((...(((.(((........))).)))..))))))))..........(((.(........).)))...------------- ( -18.20, z-score =   0.15, R)
>droSec1.super_2 4335604 89 + 7591821
AGCUCGUGGCGGCACGUCUAUACAUAUGUCUAUUGGCUUCCGCCACGCCCCCUUUUACCGCCUGCAAUUUGAUGGACUUUUUUUUCUGU--
....((((((((...(((.(((........))).)))..))))))))..........(((.(........).)))..............-- ( -18.80, z-score =  -0.27, R)
>droYak2.chr3L 4918647 86 + 24197627
AGCUCGUGGCGGCACGUCAAUA----UGUCUAUUGGCUUCCGCCACGCCCCUUUUUACCGCCUUCCAUGCAAUGUUAUUUUUUUUUUUUU-
....((((((((...(((((((----....)))))))..))))))))............((.......))....................- ( -21.70, z-score =  -2.86, R)
>droEre2.scaffold_4784 7052704 85 + 25762168
AGCUCGUGGCGGCACGUCAAUA----UGUCUAUUGGCUUCCGCCACGCCCCUUUUUACCGCCUUCCCUGCAAUGGUAUUUUUUUCUGUU--
....((((((((...(((((((----....)))))))..))))))))........((((((.......))...))))............-- ( -23.60, z-score =  -2.52, R)
>consensus
AGCUCGUGGCGGCACGUCUAUAC__AUGUCUAUUGGCUUCCGCCACGCCCCCUUUUACCGCCUUCAAUUCGAUGGAAUUUUUUUUCUUU__
....((((((((...(((.(((........))).)))..))))))))............................................ (-16.38 = -16.22 +  -0.16)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 4,343,294 – 4,343,385
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 81.38
Shannon entropy 0.32740
G+C content 0.49991
Mean single sequence MFE -23.53
Consensus MFE -18.43
Energy contribution -18.63
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.16
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.571868
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4343294 91 - 24543557
CAGAAGAAAAAAAAUUCCAUCGAACUGAAGGCGGUAAAAGGGGGCGUGGCGGAAACCAAUAGACUUACGUAUAGACGUGCCGCCACGAGCU
..............((((.....((((....)))).....))))((((((((.............(((((....))))))))))))).... ( -22.41, z-score =  -0.82, R)
>droSim1.chr3L 3880629 78 - 22553184
-------------AUUCCAUCGAAUUGCAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAUGUGUAUAGACGUGCCGCCACGAGCU
-------------......(((..((((.....))))..((.(((.((((....))))......((((......))))))).)).)))... ( -23.60, z-score =  -0.26, R)
>droSec1.super_2 4335604 89 - 7591821
--ACAGAAAAAAAAGUCCAUCAAAUUGCAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAUAUGUAUAGACGUGCCGCCACGAGCU
--...........................(((((((.......((.((((....))))(((....))))).......)))))))....... ( -22.64, z-score =  -0.63, R)
>droYak2.chr3L 4918647 86 - 24197627
-AAAAAAAAAAAAAUAACAUUGCAUGGAAGGCGGUAAAAAGGGGCGUGGCGGAAGCCAAUAGACA----UAUUGACGUGCCGCCACGAGCU
-.................(((((.......))))).....((..((((((((..(.(((((....----))))).)...))))))))..)) ( -24.30, z-score =  -2.30, R)
>droEre2.scaffold_4784 7052704 85 - 25762168
--AACAGAAAAAAAUACCAUUGCAGGGAAGGCGGUAAAAAGGGGCGUGGCGGAAGCCAAUAGACA----UAUUGACGUGCCGCCACGAGCU
--............((((...((.......))))))....((..((((((((..(.(((((....----))))).)...))))))))..)) ( -24.70, z-score =  -1.76, R)
>consensus
__AAAAAAAAAAAAUUCCAUCGAAUUGAAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAU__GUAUAGACGUGCCGCCACGAGCU
.............................(((((((..........((((....))))...................)))))))....... (-18.43 = -18.63 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:02:35 2011