Example:
| Probename | SNP01_10 | SNP11_20 | seq01_10 | seq11_20 | seg_seq | SNPpos | basepaire | rmbase |
| 10000_at--100--121 | 0 | 0 | tacttacggaAGAACGTGCAGTAGATACTGCTGAAgaattcgaag@tacttacggaAGAACGTGCAGTAGATACTGCTGAAgaattcgaag | gaactaactcAGAACGTGCAGTAGATACTGCTGAAatgatgattg@gaactaactcAGAACGTGCAGTAGATACTGCTGAAatgatgattg | TTGAAGAACTAACTCTACTTACGGAAGAACGTGCAGTAGATACTGCTGAAGAATTCGAAGATGATGATTGCACGA@TTGAAGAACTAACTCTACTTACGGAAGAACGTGCAGTAGATACTGCTGAAGAATTCGAAGATGATGATTGCACGA | 0 | 0 | |
| 10000_at--101--121 | 0 | 0 | cggaagaacgTGCAGTAGATACTGCTGAAGAATTCgaagatgatg@cggaagaacgTGCAGTAGATACTGCTGAAGAATTCgaagatgatg | actctacttaTGCAGTAGATACTGCTGAAGAATTCattgcacgaa@actctacttaTGCAGTAGATACTGCTGAAGAATTCattgcacgaa | AACTAACTCTACTTACGGAAGAACGTGCAGTAGATACTGCTGAAGAATTCGAAGATGATGATTGCACGAAAAATT@AACTAACTCTACTTACGGAAGAACGTGCAGTAGATACTGCTGAAGAATTCGAAGATGATGATTGCACGAAAAATT | 0 | 0 | |
| 10000_at--89--121 | 1 | 0 | cagaggaagaGCTGCTGGTGCTTGAATCTGATGAGaaactgaatg@cagatgaagaGCTGCTGGTGCTTGAATCTGATGAGaaactgaatg | tctgaagaagGCTGCTGGTGCTTGAATCTGATGAGatgtgaacga@tctgaagaagGCTGCTGGTGCTTGAATCTGATGAGatgtgaacga | AAGAATCTGAAGAAGCAGAGGAAGAGCTGCTGGTGCTTGAATCTGATGAGAAACTGAATGATGTGAACGATATGG@AAGAATCTGAAGAAGCAGATGAAGAGCTGCTGGTGCTTGAATCTGATGAGAAACTGAATGATGTGAACGATATGG | -18mGT| | GT | T |
Definition:
| Probe_name | Probe name in the Affymetrix Rice GeneChip microarray, the two numbers are coordinates in the chip |
| SNP01_10 | SNPs in probe flanking 1-10 bases region. '0': non-SNP, '1': SNP. |
| SNP11_20 | SNPs in probe flanking 11-20 bases region. '0': non-SNP, '1': SNP. |
| seq01_10 | Sequences information in probe flanking 1-10 bases region. "cagaggaagaGCTGCTGGTGCTTGAATCTGATGAGaaactgaatg@cagatgaagaGCTGCTGGTGCTTGAATCTGATGAGaaactgaatg": (left flanking 10-1 bases of BY, lowercase)(probe region,25 bases, uppercase)(right flanking 1-10 bases of BY, lowercase)@(left flanking 10-1 bases of RM, lowercase)(probe region,25 bases, uppercase)(right flanking 1-10 bases of RM, lowercase) |
| seq11_20 | Sequences information in probe flanking 11-20 bases region. "tctgaagaagGCTGCTGGTGCTTGAATCTGATGAGatgtgaacga@tctgaagaagGCTGCTGGTGCTTGAATCTGATGAGatgtgaacga": (left flanking 20-11 bases of BY, lowercase)(probe region,25 bases, uppercase)(right flanking 11-20 bases of BY, lowercase)@(left flanking 20-11 bases of RM, lowercase)(probe region,25 bases, uppercase)(right flanking 11-20 bases of RM, lowercase) |
| seg_seq | 75-bp DNA sequences that flank the center of the probe. (BY sequence)@(RM sequence). When calculating the minimum free energies (DG) of cRNA, we need change it to reverse complement cRNA sequence |
| SNPpos | Base position refer to probe. The positon of the center base of probe is defined as 0. For a probe is a 25 bases DNA oligonucleotide, the first base of a probe is defined as 'SNPpos=-12'. For example, 'SNPpos=-18mGT|' means the 6th base adjacent the left side of the probe is a mismatch (m) between BY and RM and the base is 'G' in BY and 'T' in RM. |