Locus 1917

Sequence ID dm3.chr2L
Location 14,733,247 – 14,733,361
Length 114
Max. P 0.683304
window2643 window2644

overview

Window 3

Location 14,733,247 – 14,733,361
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 65.32
Shannon entropy 0.65101
G+C content 0.56781
Mean single sequence MFE -21.36
Consensus MFE -11.47
Energy contribution -12.25
Covariance contribution 0.78
Combinations/Pair 1.35
Mean z-score -0.57
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.683304
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14733247 114 + 23011544
CACACCGGCACUUGGCCACGCCCCGCACAUCCGGAGCCGCAUCCGUAGUCCCAUCCGUUUCCCCAUCCGUACACCCAACUCCAGGCUGCACAAUAUCAAUUAUCGGGCUUCAAG
......(((.....)))..((((.........(((......)))((((((.................................))))))...............))))...... ( -20.71, z-score =   0.86, R)
>droSim1.chr2L 14483348 114 + 22036055
CACACCGGCACUUUGCCACGCCCCCCACAUCCGGAGACGCAUCCGUAGUCCCAUCCGUUGCCCCAUCCGUACACCCAACUCCAGGCUGCACAAUAUCAAUUAUCGGGCUUCAAG
......(((.....)))..((((.........(((......)))((((((......((((...............))))....))))))...............))))...... ( -23.36, z-score =  -0.72, R)
>droSec1.super_3 1009003 113 + 7220098
CACACCGGCACUUGGCCACGCCCCC-ACAUCCGGAGACGCAUCCGUAGUCCCAUCCGUUGCCCCAUCCGUACACCCAACUCCAGGGUGCACAAUAUCAAUUAUCGGGCUUCAAG
......(((.....)))..((((..-.....(((((((((....)).)))...))))...........((.(((((.......))))).)).............))))...... ( -28.00, z-score =  -1.01, R)
>droYak2.chr2L 14840973 102 + 22324452
CUCACCGGUACUUGGCCACGCCCACCACAUCCGGAGCCACAUCCGUA------------UUUCUAUCCGUACACCCAACUCCGGGCCGCACAAUAUCAAUUAUCGGGCUUCAAG
....((((((.(((((...((((.........(((......)))(((------------(........))))..........)))).)).......))).))))))........ ( -21.31, z-score =  -0.70, R)
>droVir3.scaffold_12963 5025630 103 + 20206255
----CAGACACUGCGUCCGCCCCCUUCUACACCCCCACCCACUGGCAAAC-------GUGCCCCGCUUGCUAGCAGCCCUUUUCCGCUUACAAUAUCAAUUAUCGGGCGUCAAG
----..(((...((((..(((......................)))..))-------))((((.(((....)))(((........)))................)))))))... ( -21.25, z-score =  -1.23, R)
>droMoj3.scaffold_6500 8911723 86 + 32352404
----CAAGUAUAU-GCCCCGCCCCUUACACCC--------ACUCGC------------UAUUCGCUCUGUAAACCCUUUUGCUGU---UACGAUAUCAAUUAUCGGGCGUCAAG
----.........-....(((((.........--------....((------------.....))...(((((....)))))...---...((((.....)))))))))..... ( -13.50, z-score =  -0.62, R)
>consensus
CACACCGGCACUUGGCCACGCCCCCCACAUCCGGAGACGCAUCCGUAGUC_______UUGCCCCAUCCGUACACCCAACUCCAGGCUGCACAAUAUCAAUUAUCGGGCUUCAAG
......(((.....)))..((((........((((......)))).......................((.((.((.......)).)).)).............))))...... (-11.47 = -12.25 +   0.78)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 14,733,247 – 14,733,361
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 65.32
Shannon entropy 0.65101
G+C content 0.56781
Mean single sequence MFE -33.33
Consensus MFE -19.74
Energy contribution -19.33
Covariance contribution -0.41
Combinations/Pair 1.62
Mean z-score -0.34
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.649220
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14733247 114 - 23011544
CUUGAAGCCCGAUAAUUGAUAUUGUGCAGCCUGGAGUUGGGUGUACGGAUGGGGAAACGGAUGGGACUACGGAUGCGGCUCCGGAUGUGCGGGGCGUGGCCAAGUGCCGGUGUG
.......(((.((........(((((((.((.......)).))))))))).)))..(((..(((.(((..((..(((.(((((......))))))))..)).))).))).))). ( -35.30, z-score =   0.64, R)
>droSim1.chr2L 14483348 114 - 22036055
CUUGAAGCCCGAUAAUUGAUAUUGUGCAGCCUGGAGUUGGGUGUACGGAUGGGGCAACGGAUGGGACUACGGAUGCGUCUCCGGAUGUGGGGGGCGUGGCAAAGUGCCGGUGUG
......((((.((........(((((((.((.......)).))))))))).)))).(((..(((.(((...(..((((((((.......))))))))..)..))).))).))). ( -38.80, z-score =  -0.71, R)
>droSec1.super_3 1009003 113 - 7220098
CUUGAAGCCCGAUAAUUGAUAUUGUGCACCCUGGAGUUGGGUGUACGGAUGGGGCAACGGAUGGGACUACGGAUGCGUCUCCGGAUGU-GGGGGCGUGGCCAAGUGCCGGUGUG
......((((.((........((((((((((.......)))))))))))).)))).(((..(((.(((..((..(((((((((....)-))))))))..)).))).))).))). ( -45.90, z-score =  -2.23, R)
>droYak2.chr2L 14840973 102 - 22324452
CUUGAAGCCCGAUAAUUGAUAUUGUGCGGCCCGGAGUUGGGUGUACGGAUAGAAA------------UACGGAUGUGGCUCCGGAUGUGGUGGGCGUGGCCAAGUACCGGUGAG
......((((.(((((....)))))((.(((((((((((.((...((........------------..)).)).)))))))))..)).)))))).(.(((.......))).). ( -29.10, z-score =   0.40, R)
>droVir3.scaffold_12963 5025630 103 - 20206255
CUUGACGCCCGAUAAUUGAUAUUGUAAGCGGAAAAGGGCUGCUAGCAAGCGGGGCAC-------GUUUGCCAGUGGGUGGGGGUGUAGAAGGGGGCGGACGCAGUGUCUG----
.....(((((.....(((...((((.(((((.......))))).)))).))).((((-------.((..((....))..)).))))......)))))(((.....)))..---- ( -34.00, z-score =  -0.90, R)
>droMoj3.scaffold_6500 8911723 86 - 32352404
CUUGACGCCCGAUAAUUGAUAUCGUA---ACAGCAAAAGGGUUUACAGAGCGAAUA------------GCGAGU--------GGGUGUAAGGGGCGGGGC-AUAUACUUG----
......((((((((.....))))...---...((....(.(..(((...((.....------------))..))--------)..).).....)).))))-.........---- ( -16.90, z-score =   0.77, R)
>consensus
CUUGAAGCCCGAUAAUUGAUAUUGUGCAGCCUGGAGUUGGGUGUACGGAUGGGGCAA_______GACUACGGAUGCGUCUCCGGAUGUGGGGGGCGUGGCCAAGUGCCGGUGUG
......((((...........(((((((.((.......)).))))))).....................((((......))))........)))).((((.....))))..... (-19.74 = -19.33 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:41:21 2011