| AFLP primer pairs | Total No of bands generated | Total No of G. hirsutum bands
| No of G. hirsutum specific (non specific) bands | No of G. hirsutum specific bands present (absent) in the hexaploid | Total No of G. longicalyx bands | No of G. longicalyx specific (non specific) bands | No of G. longicalyx specific bands present (absent) in the hexaploid | Total No of bands in the hexaploid |
| E-ACC/M-CAG | 52 | 34 | 10 (24) | 10 (0) | 42 | 18 (24) | 16 (2) | 50 |
| E-ACT/M-CTG | 45 | 36 | 21 (15) | 21 (0) | 24 | 9 (15) | 9 (0) | 45 |
| E-ACT/M-CAG | 46 | 31 | 13 (18) | 13 (0) | 33 | 15 (18) | 13 (2) | 44 |
| Total | 143 | 101 | 44 (57) | 44 (0) | 99 | 42 (57) | 38 (4) | 139 |