how to predict Transcription factor binding site for any crop when we have gene sequence, genome sequence, promoter sequence. And also how to find the distribution of that particular transcription factor over all genome using above information??
You could run FIMO on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you binding sites: genomic intervals where those TFs bind. Here's a post where I wrote up step-by-step instructions:
Once you have TF binding sites, you can intersect them with gene promoters or other annotations easily with BEDOPS