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Table 5 Detection of long ncRNAs using scanning windows.

From: Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

  percent identity of entire alignment total number of scanning windows number of scanning windows with P> 0.5 number of scanning windows with P> 0.9 number of scanning windows with P> 0.99
16S rRNA
Borrelia burgdorferi and Bacillus subtilis 74.5% 30 17 12 6
Homo sapiens (mitochondrial) and Thermotoga maritima 39.3% 30 1 1 0
Archaeoglobus fulgidus and Borrelia burgdorferi 61.8% 30 22 17 14
23S rRNA
Escherichia coli and Thermoplasma acidophilum 59.4% 57 49 41 37
Bacillus subtilis and Bos taurus 37.1% 57 35 26 21
Bacillus subtilis and Thermoproteus tenax 60.1% 61 3 2 1
  1. The Dynalign/LIBSVM classifier is used to compute P values for sets of 150-nucleotide scanning windows iterating (in steps of 75 nucleotides) through global alignments of three 16S and three 23S rRNA pairs randomly selected from a database [48]. The quantity of windows above three P value cutoffs is listed, indicating that long ncRNAs can be detected with short scanning windows.