Following data is an example of BLAST result using an amino acid sequence of rice as query.
Line of Sbjct: is amino acid sequence from the flanking sequence of Tos17. In this case, alignment begins at 3 bp from 5'end of the flanking sequence. This result indicates that Tos17 was inserted at the position 387 amino acids of the query sequence.
Because the flanking sequence is genomic sequence of rice which includes both exon and intron regions, gaps in the result are intron regions of the flanking sequence.
If Sbjct does not begin within several base from the 5'-end of flanking sequence, Tos17 may be inserted in intron region. In such case, the inserted Tos17 will be spliced out and no phenotype will appear.
In the case of nucleotide sequence as query, it is same situation as amino acid sequence as query. If the match is not began within several base from the 5'-end of flanking sequence, it is a hopeless.
Score = 173 bits (435), Expect(2) = 5e-71 Identities = 91/121 (75%), Positives = 91/121 (75%), Gaps = 28/121 (23%) Frame = +3 Query: 388 IINTFPSCTVFKGTLSSGVEISVVSTAILSLKEWPKSSETCFRKQ--------------- 432 IINTFPSCTVFKGTLSSGVEISVVSTAILSLKEWPKSSETCFRKQ Sbjct: 3 IINTFPSCTVFKGTLSSGVEISVVSTAILSLKEWPKSSETCFRKQVHGFLHVLVGAVNPS 182 Query: 433 -------------IDTLSRVNHKNFINLLGYCLENQPFMRMMVFEYAPNGTLSEHLHLKE 479 IDTLSRVNHKNFINLLGYCLENQPFMRMMVFEYAPNGTLSEHLH K Sbjct: 183 MLDLR*SPDLLV*IDTLSRVNHKNFINLLGYCLENQPFMRMMVFEYAPNGTLSEHLHRKL 362 Query: 480 F 480 F Sbjct: 363 F 365 Score = 111 bits (274), Expect(2) = 5e-71 Identities = 50/52 (96%), Positives = 51/52 (97%) Frame = +2 Query: 477 LKEFEHLDWAARMRIIMGVAYCLQYMHHDLNPPVAITDMRSDTIFMTDDYAA 528 +KEFEHLDWAARMRIIMGVAYCLQYMHHDLNPPVA TDMRSDTIFMTDDYAA Sbjct: 431 VKEFEHLDWAARMRIIMGVAYCLQYMHHDLNPPVAXTDMRSDTIFMTDDYAA 586