1. CDS 24mer marks in promoter regions actin-depolymerizing factor 2 gene (AY038062 ) zinc-finger DNA binding protein gene (PETZFDB3) Sense batch1Sense batch2 Antisense batch1Antisense batch2

2. Pi061803d putative pollen thioesterase mRNA (AY577288 ) 24mer marks in 5’ or 3’UTR regions C2H2 zinc finger protein, 4 finger (ZPT4-4) mRNA (AB006606 ) CDS Sense batch1Sense batch2 Antisense batch1Antisense batch2

3. 24mer marks in an intron region CDS Sense batch1Sense batch2 Antisense batch1Antisense batch2 Hf1 gene for flavonoid 3',5'- hydroxylase gene (AB244229)

4. CDS Sense batch1Sense batch2 Antisense batch1Antisense batch2 24mer marks in coding regions chlorophyll a/b binding protein cab 13 gene (X02357) rbcS gene (ssu8) for ribulose 1,5-bisphosphate carboxylase small subunit gene (X03820 ) dTph9 gene for mutator transposase-like polypeptide (AB196431 )

5. 24mer marks in EST sequences Petunia-PP-15-D06 (5' end) cDNA clone (EST887452) CDS Sense batch1Sense batch2 Antisense batch1Antisense batch2

6. CDS Sense batch1Sense batch2 Antisense batch1Antisense batch2 24mer marks in transposon sequences transposon Dad- one (AY745251) Repeat region 1..1100 transposon dTph1-3 in exon 3 of nia gene (PHU27321) Repeat region 172..470 V69 defective transposon dTPH10 (DQ515972 ) Repeat region 1176

7. CDS Sense batch1Sense batch2 Antisense batch1Antisense batch2 24mer marks in retro-transposon sequences Retrotransposon rTph1genes for polypeptide with a gag-like domain, polypeptide with an integrase domain, polypepetide with reverse transcriptase and RNaseH domains (AB196430 ) Direct repeats copia-like retrotransposon reverse transcriptase gene (PETCOPIA)

8. CDS Sense batch1Sense batch2 Antisense batch1Antisense batch2 24mer marks in a viral sequence integrated petunia vein clearing virus, partial sequence (AY333912 )