Locus 10338

Sequence ID dm3.chr3R
Location 13,163,957 – 13,164,059
Length 102
Max. P 0.711346
window14216 window14217

overview

Window 6

Location 13,163,957 – 13,164,059
Length 102
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 81.66
Shannon entropy 0.32901
G+C content 0.46446
Mean single sequence MFE -29.53
Consensus MFE -18.41
Energy contribution -17.72
Covariance contribution -0.69
Combinations/Pair 1.19
Mean z-score -1.89
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.711346
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13163957 102 + 27905053
UAUUCUCCGCUUCGCACAGAAGCGCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGG-CUUGGUGCGCGAAACUGGAGACGGGC--UGG--
...((((((.(((((......(((((((((........(.....).....(((..((.....))..)))...)-)))))))))))))..)))))).....--...-- ( -31.90, z-score =  -2.21, R)
>droSec1.super_12 1140196 106 - 2123299
UAUCCUCCGCUUCGCACAGAAGCGCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAUUAUUGUGCAGACGG-CUUGGUGCGCGAAACUGGAGACGGGUGAUGGUA
...((..((((((((......(((((((((........(.....).....(((..((.....))..)))...)-))))))))))))).(((....))))))..)).. ( -33.50, z-score =  -2.13, R)
>droSim1.chr3R 19209211 106 - 27517382
UAUCCUCCGCUUCGCACAGAAGCGCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGG-CUUGGUGCGCGAAACUGGAGACGGUCGAUGGUC
((((..((((((((.......(((((((((........(.....).....(((..((.....))..)))...)-)))))))).......))))).)))..))))... ( -33.14, z-score =  -2.17, R)
>droAna3.scaffold_13340 10377377 83 + 23697760
UAUUCUCCGCUUUGCACAGAAGCGCUAAGCAAAUAAAACAAAAAGGAUAACUGGGCAAAUAUUGUGCAGACGGGCGGGAUGAG------------------------
(((((((((.(((((((((..((.....)).............((.....)).........))))))))))))..))))))..------------------------ ( -19.80, z-score =  -1.35, R)
>droYak2.chr3R 17255210 97 + 28832112
UAUCCUCCGCUUUGCACAGAAGCGCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGG-CUUGGUGUGCUGGUGUGAUGGUGU---------
.......(((((..(((....(((((((((........(.....).....(((..((.....))..)))...)-))))))))....)))..).)))).--------- ( -29.30, z-score =  -1.60, R)
>consensus
UAUCCUCCGCUUCGCACAGAAGCGCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGG_CUUGGUGCGCGAAACUGGAGACGG____UGG__
((((((..(((((.....)))))((...)).............)))))).(((..((.....))..)))...................(((....)))......... (-18.41 = -17.72 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,163,957 – 13,164,059
Length 102
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 81.66
Shannon entropy 0.32901
G+C content 0.46446
Mean single sequence MFE -25.32
Consensus MFE -15.32
Energy contribution -16.16
Covariance contribution 0.84
Combinations/Pair 1.19
Mean z-score -1.78
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.581345
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13163957 102 - 27905053
--CCA--GCCCGUCUCCAGUUUCGCGCACCAAG-CCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCGAAGCGGAGAAUA
--...--.....(((((.((((((((((..(((-(.((..(((.((((...(((.((.......)).)))..)))))))...)))))).)))))))))))))))... ( -31.00, z-score =  -3.14, R)
>droSec1.super_12 1140196 106 + 2123299
UACCAUCACCCGUCUCCAGUUUCGCGCACCAAG-CCGUCUGCACAAUAAUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCGAAGCGGAGGAUA
............(((((.((((((((((..(((-(.((..(((.(((((..(((.((.......)).))).))))))))...)))))).)))))))))))))))... ( -30.60, z-score =  -2.88, R)
>droSim1.chr3R 19209211 106 + 27517382
GACCAUCGACCGUCUCCAGUUUCGCGCACCAAG-CCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCGAAGCGGAGGAUA
............(((((.((((((((((..(((-(.((..(((.((((...(((.((.......)).)))..)))))))...)))))).)))))))))))))))... ( -30.10, z-score =  -2.05, R)
>droAna3.scaffold_13340 10377377 83 - 23697760
------------------------CUCAUCCCGCCCGUCUGCACAAUAUUUGCCCAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCAAAGCGGAGAAUA
------------------------....((((((.....((((((.....(((..(((...................)))..)))....))))))..)))).))... ( -15.91, z-score =  -0.76, R)
>droYak2.chr3R 17255210 97 - 28832112
---------ACACCAUCACACCAGCACACCAAG-CCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCAAAGCGGAGGAUA
---------.....(((.(.((.(((.((....-..)).)))......(((((((((.....((....((.......))..)).....)))))))))..)).)))). ( -19.00, z-score =  -0.07, R)
>consensus
__CCA____CCGUCUCCAGUUUCGCGCACCAAG_CCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCGAAGCGGAGGAUA
............(((((.......................(((.......)))........................((((.((((....)))).)))))))))... (-15.32 = -16.16 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:22:03 2011