Locus 3579

Sequence ID dm3.chr2R
Location 6,517,465 – 6,517,588
Length 123
Max. P 0.940439
window4910 window4911

overview

Window 0

Location 6,517,465 – 6,517,588
Length 123
Sequences 3
Columns 149
Reading direction forward
Mean pairwise identity 56.85
Shannon entropy 0.59722
G+C content 0.49879
Mean single sequence MFE -43.17
Consensus MFE -21.41
Energy contribution -19.53
Covariance contribution -1.88
Combinations/Pair 1.37
Mean z-score -1.50
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.44
SVM RNA-class probability 0.940439
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6517465 123 + 21146708
CUUUAGGGGUCGCACUCGACUCCCAUUGGUUAUCGAGUAUGAACUU-CAUACAUACAUAUUGCAGAAUUUGCUAGUGUCAGCACUUGGCUGUCACAAGAGAUCUGCCUGUAGACC-ACACUAAGA------------------------
.....(((((((....)))).)))..(((((.....(((((.....-))))).((((....(((((.(((.((.(((.((((.....)))).))).)))))))))).))))))))-)........------------------------ ( -39.40, z-score =  -2.80, R)
>droSec1.super_104 52315 140 - 95517
----AGCACCUCUCCUCCAGCACCGUCGCUCGGCGACAAUAUAUAU----AUGUAGGAAACGCA-UAUAAGCGUCGCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUCGACUUAGGCUAAGAAACCAUUGUAUGUAGAUCGCCAAG
----..............(((......))).(((((...(((((((----(((.((((.((((.-.....)))).((.(((((((.(((...))).))))))).)))))))).....((........))..))))))))..)))))... ( -47.40, z-score =  -1.39, R)
>droSim1.chrU 5095458 148 + 15797150
CUAUAGCACCCCUCCUCCAGCACCGUCGCUCGGCGACAAUAUAUAUGUAUAUGUAGGAAACGCA-AAUAAGCGUCGCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUCGACUUAGGCUAAGAAACCAUUGUAUUUAGAUCGCCAAA
..................(((......))).((((((...(((((......((.((((.((((.-.....)))).((.(((((((.(((...))).))))))).)))))))).....((........))..)))))...).)))))... ( -42.70, z-score =  -0.31, R)
>consensus
CU_UAGCACCCCUCCUCCAGCACCGUCGCUCGGCGACAAUAUAUAU__AUAUGUAGGAAACGCA_AAUAAGCGUCGCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUCGACUUAGGCUAAGAAACCAUUGUAU_UAGAUCGCCAA_
....(((..........((((...(((((...)))))......................((((.......)))).)))).(((((.(((...))).))))))))...(((......))).............................. (-21.41 = -19.53 +  -1.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,517,465 – 6,517,588
Length 123
Sequences 3
Columns 149
Reading direction reverse
Mean pairwise identity 56.85
Shannon entropy 0.59722
G+C content 0.49879
Mean single sequence MFE -47.20
Consensus MFE -23.74
Energy contribution -27.53
Covariance contribution 3.79
Combinations/Pair 1.26
Mean z-score -1.33
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.892627
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6517465 123 - 21146708
------------------------UCUUAGUGU-GGUCUACAGGCAGAUCUCUUGUGACAGCCAAGUGCUGACACUAGCAAAUUCUGCAAUAUGUAUGUAUG-AAGUUCAUACUCGAUAACCAAUGGGAGUCGAGUGCGACCCCUAAAG
------------------------..((((.(.-((((((((.(((((...((.(((.((((.....)))).))).)).....)))))....))))......-.......((((((((..((...))..)))))))).))))))))).. ( -38.20, z-score =  -2.31, R)
>droSec1.super_104 52315 140 + 95517
CUUGGCGAUCUACAUACAAUGGUUUCUUAGCCUAAGUCGAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGCGACGCUUAUA-UGCGUUUCCUACAU----AUAUAUAUUGUCGCCGAGCGACGGUGCUGGAGGAGAGGUGCU----
(((((((((...........((((....)))).......((((((.(((((((.(((...))).))))))).))(((((.....-.)))))))))....----.........)))))))))....((..((........))..))---- ( -51.90, z-score =  -0.91, R)
>droSim1.chrU 5095458 148 - 15797150
UUUGGCGAUCUAAAUACAAUGGUUUCUUAGCCUAAGUCGAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGCGACGCUUAUU-UGCGUUUCCUACAUAUACAUAUAUAUUGUCGCCGAGCGACGGUGCUGGAGGAGGGGUGCUAUAG
..................(((((..(((..(((.(((..((((((.(((((((.(((...))).))))))).))(((((.....-.)))))))))..............((((((((...)))))))))))..)))..))).))))).. ( -51.50, z-score =  -0.76, R)
>consensus
_UUGGCGAUCUA_AUACAAUGGUUUCUUAGCCUAAGUCGAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGCGACGCUUAUU_UGCGUUUCCUACAUAU__AUAUAUAUUGUCGCCGAGCGACGGUGCUGGAGGAGGGGUGCUA_AG
(((((((((...........(((......))).......((((((.(((((((.(((...))).))))))).))(((((.......))))))))).................)))))))))....((((((........)))))).... (-23.74 = -27.53 +   3.79)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:12:51 2011