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Table 1 Composition and length distribution of major SSR types in the apple genome

From: Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

Repeat unit Repeat type Repeat length (bp) Total Frequency (%)
   <30 30-40 40-50 >50   
Dimer AC/CA 1883 357 106 73 2419 8.48
  AG/GA 5115 2090 953 595 8753 30.67
  AT/TA 6035 1968 854 495 9352 32.77
  CG 1 0 0 0 1 0.00
  Total 13033 4415 1913 1163 20524 71.92
Trimer AAT/ATA/TAA 591 97 41 44 773 2.71
  AAC/ACA/CAA 1342 44 7 3 1396 4.89
  AAG/AGA/GAA 643 66 20 44 773 2.71
  Others 520 31 4 6 561 1.97
  Total 3096 238 72 97 3503 12.27
Tetramer AAAT/TAAA/ATAA/AATA 631 10 0 1 642 2.25
  AATT/ATTA/TTAA/TAAT 93 0 0 0 93 0.33
  AAAG/AAGA/AGAA/GAAA 109 10 2 2 123 0.43
  TACA/ACAT/CATA/ATAC 404 76 15 8 503 1.76
  GTTT/TGTT/TTGT/TTTG 90 1 1 0 92 0.32
  AGGG/GAGG/GGAG/GGGA 91 4 0 0 95 0.33
  Others 222 17 5 1 245 0.86
  Total 1640 118 23 12 1793 6.28
Pentamer AAAAT/AAATA/AATAA/ATAAA/TAAAA 494 2 0 0 496 1.74
  GTTTT/TGTTT/TTGTT/TTTGT/TTTTG 154 1 0 0 155 0.54
  AATTT/ATTTA/TTTAA/TTAAT/TAATT 94 1 0 0 95 0.33
  AAAAG/AAAGA/AAGAA/AGAAA/GAAAA 115 0 0 0 115 0.40
  AAGCC/AGCCA/GCCAA/CCAAG/CAAGC 170 0 0 0 170 0.60
  CCCTG/CCTGC/CTGCC/TGCCC/GCCCT 121 7 0 1 129 0.45
  Others 747 15 1 1 764 2.68
  Total 1895 26 1 2 1924 6.74
Hexamer AAAAAT/AAAATA/AAATAA/AATAAA/ATAAAA/TAAAAA 106 2 2 0 110 0.39
  AAAAAG/AAAAGA/AAAGAA/AAGAAA/AGAAAA/GAAAAA 38 1 0 0 39 0.14
  AAAAAC/AAAACA/AAACAA/AACAAA/ACAAAA/CAAAAA 34 0 0 0 34 0.12
  CCCTCT/CCTCTC/CTCTCC/TCTCCC/CTCCCT/TCCCTC 33 2 2 0 37 0.13
  ATACAT/TACATA/ACATAT/CATATA/ATATAC/TATACA 40 6 0 1 47 0.16
  AGAGTG/GAGTGA/AGTGAG/GTGAGA/TGAGAG/GAGAGT 21 1 0 0 22 0.08
  CCTCTC/CTCTCC/TCTCCC/CTCCCT/TCCCTC/CCCTCT 35 3 1 0 39 0.14
  Others 434 23 7 1 465 1.63
  Total 741 38 12 2 793 2.78
  1. SSRs with at least 20 bp in length and more than 3 repeats were recorded. SSR motifs represent variants of both strands of the DNA sequence (e.g., AC/CA includes the reverse complements GT and TG).