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

The SSR motifs represent variants of both strands of the DNA sequence (e.g., AAT/ATA/TAA includes the reverse complements ATT, TTA and TAT).

Yang et al.

Yang et al. BMC Genomics 2012 13:653   doi:10.1186/1471-2164-13-653

Open Data