Locus 3523

Sequence ID dm3.chr2R
Location 5,988,388 – 5,988,478
Length 90
Max. P 0.998408
window4830 window4831

overview

Window 0

Location 5,988,388 – 5,988,478
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 94.67
Shannon entropy 0.09626
G+C content 0.62939
Mean single sequence MFE -36.49
Consensus MFE -33.04
Energy contribution -33.28
Covariance contribution 0.24
Combinations/Pair 1.17
Mean z-score -4.05
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.35
SVM RNA-class probability 0.998408
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5988388 90 + 21146708
ACUUGUCGCACUUUCUCGCUCUCGCCUGAGCCAGCCCCAUAUGCUCCCUCUCAUUCUGCGGCGGCGCAUGUGCCCCUGCUAGAGUGUGCG
......(((((...(((((((......))))(((...(((((((.((.((.(.....).)).)).)))))))...)))...))).))))) ( -30.20, z-score =  -2.08, R)
>droSim1.chr2R_random 1778586 90 + 2996586
ACUUGUCGCACUUUCUCGCUCUCGCCUGCGCCAGCCCCAUAUGCUCCCUCUCAUUCUGCGGCGGCGCAUGUGCCCCUGUGAGAGUGUGCG
......(((((.(((((((...(((.((((((.(((.((.(((........)))..)).))))))))).))).....))))))).))))) ( -37.10, z-score =  -4.33, R)
>droSec1.super_1 3603963 90 + 14215200
ACUUGUCGCACUUUCUCGCUCUCGCCUGCGCCAGCCCCAUAUGCUCCCUCUCAUUCUGCGGCGGCGCAUGUGCCCCUGCGAGAGUGUGCG
......(((((.(((((((...(((.((((((.(((.((.(((........)))..)).))))))))).))).....))))))).))))) ( -39.00, z-score =  -4.68, R)
>droYak2.chr2L 18621293 88 + 22324452
ACUUGUCGCGCUUUCUCGCUCUCACAUGCGCCAAUCC-GUAUGCUCCCUCUCAUUCUGCGGCGGCGCAUGUGCCC-UGCGAGAGUGUGCG
......(((((.(((((((...((((((((((...((-(((...............))))).))))))))))...-.))))))).))))) ( -41.96, z-score =  -5.73, R)
>droEre2.scaffold_4929 18258372 90 - 26641161
ACUUGUCGCACUUUCUCACUCUCGCCUGCGCCAGCCCCAUAUGCUCCCUCUCAUUCUGCGGCGGCGCAUGUGCCCCUGCGAGAGUGUGCG
....(.(((((((((.((....(((.((((((.(((.((.(((........)))..)).))))))))).)))....)).)))))))))). ( -34.20, z-score =  -3.45, R)
>consensus
ACUUGUCGCACUUUCUCGCUCUCGCCUGCGCCAGCCCCAUAUGCUCCCUCUCAUUCUGCGGCGGCGCAUGUGCCCCUGCGAGAGUGUGCG
......(((((.(((((((...(((.((((((.(((.((.(((........)))..)).))))))))).))).....))))))).))))) (-33.04 = -33.28 +   0.24)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 5,988,388 – 5,988,478
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 94.67
Shannon entropy 0.09626
G+C content 0.62939
Mean single sequence MFE -37.72
Consensus MFE -32.64
Energy contribution -33.60
Covariance contribution 0.96
Combinations/Pair 1.11
Mean z-score -3.01
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.31
SVM RNA-class probability 0.988258
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5988388 90 - 21146708
CGCACACUCUAGCAGGGGCACAUGCGCCGCCGCAGAAUGAGAGGGAGCAUAUGGGGCUGGCUCAGGCGAGAGCGAGAAAGUGCGACAAGU
(((((.(((.(((.((.((....)).))(((.((..(((........))).)).)))..)))...((....)))))...)))))...... ( -30.90, z-score =  -0.80, R)
>droSim1.chr2R_random 1778586 90 - 2996586
CGCACACUCUCACAGGGGCACAUGCGCCGCCGCAGAAUGAGAGGGAGCAUAUGGGGCUGGCGCAGGCGAGAGCGAGAAAGUGCGACAAGU
(((((..((((...........(((((((((.((..(((........))).)).))).)))))).((....))))))..)))))...... ( -38.00, z-score =  -3.27, R)
>droSec1.super_1 3603963 90 - 14215200
CGCACACUCUCGCAGGGGCACAUGCGCCGCCGCAGAAUGAGAGGGAGCAUAUGGGGCUGGCGCAGGCGAGAGCGAGAAAGUGCGACAAGU
(((((..((((((....((...(((((((((.((..(((........))).)).))).)))))).))....))))))..)))))...... ( -42.00, z-score =  -4.04, R)
>droYak2.chr2L 18621293 88 - 22324452
CGCACACUCUCGCA-GGGCACAUGCGCCGCCGCAGAAUGAGAGGGAGCAUAC-GGAUUGGCGCAUGUGAGAGCGAGAAAGCGCGACAAGU
(((.(..((((((.-...((((((((((.(((....(((........))).)-))...))))))))))...))))))..).)))...... ( -37.60, z-score =  -3.41, R)
>droEre2.scaffold_4929 18258372 90 + 26641161
CGCACACUCUCGCAGGGGCACAUGCGCCGCCGCAGAAUGAGAGGGAGCAUAUGGGGCUGGCGCAGGCGAGAGUGAGAAAGUGCGACAAGU
(((((..((((((....((...(((((((((.((..(((........))).)).))).)))))).))....))))))..)))))...... ( -40.10, z-score =  -3.55, R)
>consensus
CGCACACUCUCGCAGGGGCACAUGCGCCGCCGCAGAAUGAGAGGGAGCAUAUGGGGCUGGCGCAGGCGAGAGCGAGAAAGUGCGACAAGU
(((((..((((((....((...(((((((((.((..(((........))).)).))).)))))).))....))))))..)))))...... (-32.64 = -33.60 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:11:44 2011