Table 3. BLAST results of ten randomly selected polymorphic methylated fragments and their location on rice genome.
| MSAPfragment | Methylation status under stress | Tissuetype | Genotype | Gene | TIGR Locus ID | E value | Position |
| P1 | Methylated | shoot | IR29 | Peptidyl-prolyl cis-transisomerase, FKBP-type | Os02g52290 | 8.3e-24 | 3′ UTR |
| P2 | Methylated | shoot | Geumgangbyeo | Calcineurin B | Os01g39770 | 2.9e-41 | 3′ UTR |
| P3 | Demethylated | shoot | IR29 | Cystathionine gamma-synthase | Os03g25940 | 1.8e-07 | Exon |
| P4 | Methylated | shoot | IR29 | Rho guanine nucleotideexchange factor | Os02g44330 | 2.1e-19 | Exon |
| P5 | Demethylated | shoot | IR29 | DUF1230 domain containing protein | Os03g32490 | 7.3e-60 | Exon |
| P6 | Demethylated | shoot | IR29 | Methyl-CpG domain containing protein | Os04g19684 | 2.3e-29 | Exon |
| P7 | Methylated | shoot | IR29 | Histone-lysineN-methyltransferase | Os01g70220 | 8.9e-56 | 5′ UTR |
| P8 | Demethylated | shoot | Nipponbare | Retrotransposon protein | Os11g23900 | 3.7e-56 | Exon |
| P9 | Demethylated | shoot | IR29 | Retrotransposon protein,Ty1-copia subclass | Os01g60309 | 2.5e-40 | Exon |
| P10 | Demethylated | shoot | IR29 | Pentatricopeptide repeatdomain containing protein | Os11g37330 | 8.9e-48 | Exon |