DEFINITIONS FOR COLUMN HEADERS AT THE MAIZE RFLP FLIS PROJECT SITE

Best Sequence Match in B73

The sequence record listed for the B73 best match is the *current* best match found for the probe sequence. The last sequence matching was carried out November 18, 2005.


Exemplar?

Because the genome is to be covered multiple times by sequencing, we are choosing an example or 'exemplar' which can be used as a representative of the sequence for the B73 genome. In instances where a B73 sequence is 100% identical to the probe's FLIS and there are no gaps in the alignment between the probe and B73 sequences, choosing an exemplar is simple.


% ID Between Probe and B73 Match

Listed in this column is the % ID followed by the number of matching base pairs over the length of the match identified. For BLASTing purposes, the entire probe sequence was used as the query and default parameters were used with the following exception: the low complexity filter was not used. Note that gaps were allowed for matching.

What does this mean? If the query sequence (probe sequence) were 710 base pairs in length and the B73 best match were 907 base pairs in length, the match could be reported as 95% (691/723), which conveys that the matching segment is 723 bp in length and includes some gaps (if there were no gaps, the length could not be more than the length of the query sequence). Within the matched segment, 691 of 723 aligned positions are identical.

The sequence record listed for the B73 best match is the *current* best match found for the probe sequence. The sequence record for the probe may have a note for % ID to B73, but these notes can be outdated as new sequences are released. The % ID listed in this table is calculated over the entire length of the match between the query (probe) sequence and the identified B73 sequence. Matching is accomplished via BLASTn without filtering for low complexity.