Skip to main content

Table 1 Summary statistics of designed probe sets for several microbial genomes of different sizes

From: Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

Species S. cellulosum'So ce 56' P. gingivalis W83 Candidatus C. ruddii PV
Genome size Large, 13 Mbp Medium, 2.34 Mbp Small, 0.16 Mbp
Probe number (NimbleGen format) 1620 K (12*135 K) 385 K 72 K (4*72 K)
Window size 16 12 5
Min. distance = smallest gap size 4 3 2
Total non-redundant probes 1620000 385000 72000
Total forward strand starts 818857 204991 36069
Total reverse-compl. strand starts 818947 205024 35931
  Gap size Number Gap size Number Gap size Number
Probe distribution 4 123253 3 42959 2 24802
  5 66143 4 22608 3 11222
  6 55731 5 21595 4 20978
  7 54928 6 20832 5 9846
  8 62274 7 21503 6 5152
  9 59254 8 25340   
  10 63218 9 25927   
  11 79015 10 28351   
  12 74532 11 39237   
  13 78092 12 24979   
  14 92854 13 21136   
  15 111273 14 19371   
  16 78459 15 17735   
  17 75716 16 16567   
  18 61562 17 17007   
  19 57317 18 16602   
  20 59414 19 12493   
  21 50445 20 10402   
  22 47169 21 5371   
  23 49842     
  24 42842     
  25 41557     
  26 41786     
  27 32553     
  28 28835     
  29 27753     
  30 21987