Locus 13661

Sequence ID dm3.chrX
Location 8,189,458 – 8,189,600
Length 142
Max. P 0.976835
window18800 window18801

overview

Window 0

Location 8,189,458 – 8,189,600
Length 142
Sequences 4
Columns 143
Reading direction forward
Mean pairwise identity 61.42
Shannon entropy 0.55889
G+C content 0.38610
Mean single sequence MFE -25.40
Consensus MFE -13.41
Energy contribution -16.10
Covariance contribution 2.69
Combinations/Pair 1.23
Mean z-score -1.25
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.832256
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8189458 142 + 22422827
CGCAAACUUAUACCCUCAGUUGU-CAAAGUUAGCAUUAAAACUUUUAUCAAUACCAGCCAGUAGCGCAGCAGCUGAAAGAGUGUUUUCCCUAGCAGGUAAUAUAAUAACAGAAAAGCGAAAUAGAUUAUGCCCAAAAUCUGUA
(((............((((((((-.((((((........))))))...........((.....))...))))))))....(((((..((......)).)))))............)))..(((((((........))))))). ( -23.10, z-score =   0.02, R)
>droSim1.chr4 577828 111 + 949497
------------CCAAAACUUAUAUGAAGCCAGUUGCAAAAUUGUU-UGCAUACCAGCAACUAGCGCUGCGUCUGAAAGAGCAUUUUCAGACGCUCGAAAUUUAAUAUCAGACAAAUGUUCUGC-------------------
------------.((.(((.....(((.((.((((((.....((..-..)).....)))))).))...(((((((((((....))))))))))).............))).......))).)).------------------- ( -28.00, z-score =  -1.96, R)
>droSec1.super_30 461112 111 + 664411
------------CCAAAACUUAUAUGAAGCCAGUUGCAAAAUUGUU-UGCAUACCAGCAACUAGCGCUGCGUCUGAAACAGCAUUUUCAGACGCUCGAAAUUUAAUAACAGACAAACGUUCUGC-------------------
------------............(((.((.((((((.....((..-..)).....)))))).))...((((((((((......)))))))))))))...........((((.......)))).------------------- ( -27.90, z-score =  -2.30, R)
>droEre2.scaffold_4845 20863497 111 - 22589142
------------UCCCGAAUUAUAUAAAGCUAGCUGCACCAUUUUU-UGAAUUCUUCCGAGCAGCUCAGCAUCUGAAAGAGCAUUUUCAUACGCAAGAAAUUUAAUUUCGGAAAAAAGGUGCAU-------------------
------------..((............(((((((((..((.....-))...((....)))))))).))).(((((((......((((........)))).....))))))).....)).....------------------- ( -22.60, z-score =  -0.75, R)
>consensus
____________CCAAAACUUAUAUAAAGCCAGCUGCAAAAUUGUU_UGAAUACCAGCAACUAGCGCAGCAUCUGAAAGAGCAUUUUCAGACGCACGAAAUUUAAUAACAGAAAAACGUUCUAC___________________
............................(((((((((.....((.....)).....)))))))))...(((((((((((....)))))))))))................................................. (-13.41 = -16.10 +   2.69)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,189,458 – 8,189,600
Length 142
Sequences 4
Columns 143
Reading direction reverse
Mean pairwise identity 61.42
Shannon entropy 0.55889
G+C content 0.38610
Mean single sequence MFE -31.77
Consensus MFE -17.66
Energy contribution -17.98
Covariance contribution 0.31
Combinations/Pair 1.42
Mean z-score -1.72
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976835
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8189458 142 - 22422827
UACAGAUUUUGGGCAUAAUCUAUUUCGCUUUUCUGUUAUUAUAUUACCUGCUAGGGAAAACACUCUUUCAGCUGCUGCGCUACUGGCUGGUAUUGAUAAAAGUUUUAAUGCUAACUUUG-ACAACUGAGGGUAUAAGUUUGCG
.(((((....((((............)))).)))))(((((...((((.(((((.((((......))))(((......))).))))).)))).)))))...........((.(((((..-((........))..))))).)). ( -29.20, z-score =   0.19, R)
>droSim1.chr4 577828 111 - 949497
-------------------GCAGAACAUUUGUCUGAUAUUAAAUUUCGAGCGUCUGAAAAUGCUCUUUCAGACGCAGCGCUAGUUGCUGGUAUGCA-AACAAUUUUGCAACUGGCUUCAUAUAAGUUUUGG------------
-------------------.((((((..((((.(((.............((((((((((......))))))))))...(((((((((.....((..-..)).....))))))))).))).)))))))))).------------ ( -36.70, z-score =  -3.63, R)
>droSec1.super_30 461112 111 - 664411
-------------------GCAGAACGUUUGUCUGUUAUUAAAUUUCGAGCGUCUGAAAAUGCUGUUUCAGACGCAGCGCUAGUUGCUGGUAUGCA-AACAAUUUUGCAACUGGCUUCAUAUAAGUUUUGG------------
-------------------.((((((.......................((((((((((......))))))))))...(((((((((.....((..-..)).....))))))))).........)))))).------------ ( -35.30, z-score =  -2.66, R)
>droEre2.scaffold_4845 20863497 111 + 22589142
-------------------AUGCACCUUUUUUCCGAAAUUAAAUUUCUUGCGUAUGAAAAUGCUCUUUCAGAUGCUGAGCUGCUCGGAAGAAUUCA-AAAAAUGGUGCAGCUAGCUUUAUAUAAUUCGGGA------------
-------------------...........(((((((............((((.(((((......))))).))))..((((((((....))..(((-.....))).))))))............)))))))------------ ( -25.90, z-score =  -0.77, R)
>consensus
___________________GCAGAACGUUUGUCUGAUAUUAAAUUUCGAGCGUCUGAAAAUGCUCUUUCAGACGCAGCGCUACUUGCUGGUAUGCA_AAAAAUUUUGCAACUAGCUUCAUAUAAGUUUGGG____________
..............................................(((((((((((((......))))))))))...(((((((((.....((.....)).....)))))))))............)))............. (-17.66 = -17.98 +   0.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:25:30 2011