Table 1 Distributions of the major SSR motifs identified from the genome of Nelumbo nucifera ‘Chinese Antique’
Motif | Number | Frequency (%) | Range (bp) | Primers designed | Proportion (%) |
|---|---|---|---|---|---|
Dinucleotide | 52282 | 60.73 | 16-110 | 44824 | 61.20 |
AG/GA | 26753 | 31.08 | 16-98 | 23084 | 31.52 |
AT/TA | 23158 | 26.90 | 16-110 | 19656 | 26.84 |
AC/CA | 2367 | 2.75 | 16-72 | 2081 | 2.84 |
CG/GC | 4 | 0.00 | 16-20 | 3 | 0.00 |
Trinucleotide | 27258 | 31.66 | 15-141 | 22745 | 31.05 |
AAG/AGA/GAA | 10146 | 11.79 | 15-141 | 8668 | 11.83 |
AAT/ATA/TAA | 9212 | 10.70 | 15-102 | 7049 | 9.62 |
ATG/GAT/TGA | 3485 | 4.05 | 15-84 | 3158 | 4.31 |
AAC/ACA/CAA | 1160 | 1.35 | 15-90 | 962 | 1.31 |
AGG/GAG/GGA | 1099 | 1.28 | 15-48 | 958 | 1.31 |
other | 2156 | 2.50 | 15-138 | 1950 | 2.66 |
Tetranucleotide | 4964 | 5.77 | 20-184 | 4276 | 5.84 |
AAAT/TAAA/ATAA/AATA | 1314 | 1.53 | 20-164 | 1190 | 1.62 |
ATAC/TACA/ACAT/CATA | 1257 | 1.46 | 20-184 | 1071 | 1.46 |
TATC/ATCT/TCTA/CTAT | 858 | 1.00 | 20-84 | 741 | 1.01 |
TTTC/TTCT/TCTT/CTTT | 740 | 0.86 | 20-60 | 596 | 0.81 |
TTAA/TAAT/AATT/ATTA | 179 | 0.21 | 20-36 | 164 | 0.22 |
Other | 616 | 0.72 | 20-144 | 514 | 0.70 |
Pentanucleotide | 1045 | 1.21 | 25-145 | 964 | 1.32 |
AGAAG/GAAGA/AAGAG/AGAGA/GAGAA | 253 | 0.29 | 25-80 | 211 | 0.29 |
AAAAG/AAAGA/AAGAA/AGAAA/GAAAA | 109 | 0.13 | 25-45 | 106 | 0.14 |
TTTCC/TTCCT/TCCTT/CCTTT/CTTTC | 104 | 0.12 | 25-145 | 102 | 0.14 |
AAAGG/AAGGA/AGGAA/GGAAA/GAAAG | 98 | 0.11 | 25-70 | 90 | 0.12 |
ATATA/TATAA/ATAAT/TAATA/AATAT | 95 | 0.11 | 25-95 | 90 | 0.12 |
Other | 386 | 0.45 | 25-80 | 365 | 0.50 |