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Table 1 The distribution of SSRs in different areas of genome

From: A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from next-generation sequence data

Genome regions Overall SSRsa Unique SSRsb Unique SSRs with polymorphismsc Ratei(%)
  Count Intervald (Kbp) Lengthe (bp) GCf (%) Count Intervald (Kbp) Length (bp) GC (%) Rateg(%) Count Intervald(Kbp) Length (bp) GC (%) Rateh (%)  
Promotor 14202 5.51 20.98 31.26 11158 7.01 18.98 36.63 78.57 5297 14.78 13.94 24.94 46.42 37.30
5'UTR 3350 4.13 20.93 53.76 3002 4.61 19.64 62.57 89.61 1175 11.79 15.94 45.45 38.59 35.07
3'UTR 3776 5.38 18.18 30.93 3347 6.07 16.61 38.42 88.64 1930 10.52 12.79 21.02 57.13 51.11
CDS 5737 18.79 22.03 70.77 4933 21.85 20.39 80.12 85.99 890 121.12 17.23 64.89 17.86 15.51
INTRON 19232 7.64 19.11 37.89 15367 9.56 17.89 45.34 79.90 7779 18.90 14.18 31.66 49.52 40.45
INTERGENIC 138796 13.67 20.42 43.19 49635 38.23 19.45 41.91 35.76 19955 95.08 13.85 37.33 37.81 14.38
Totalj 179681 11.46 20.34 42.39 82694 24.90 19.09 43.90 46.02 35046 58.74 13.96 34.38 40.52 19.50
  1. aThe overall SSRs were identified on the whole 10 chromosomes;
  2. bThe unique SSRs were SSRs with unique flanking sequences on the genome;
  3. cUnique SSRs with polymorphisms were SSRs with length information results in ten or more than ten genomes, and PIC Value ≥ 0.5;
  4. dInterval was calculated by number/Kb;
  5. eSSR average length was expressed in base pairs (bp);
  6. fGC content was evaluated by percentages (%);
  7. gThis rate was the percentage of unique SSRs against overall SSRs;
  8. hThis rate was the percentage of unique SSRs with polymorphisms against unique SSRs;
  9. iThis rate was the percentage of unique SSRs with polymorphisms against overall SSRs;
  10. jThere were 179681 SSRs in total, due to the alternative splicing occurring in maize genome, and the same SSRs might be divided into different regions and double counting.