Table 1.

Explanation of parameters contained in the Global Match File.

Parameter	Description	Intended use and comments
TOMATO_AFFY_ID	Tomato Probeset #ID	Tomato Affymetrix probeset identification
POTATO_EST	ID of aligning potato TA/EST	Potato TA/EST identification
DESCRIPTION	TIGR TA annotation	Updated TIGR annotation of potato TA/EST
%_ALIGN/TARG	Ratio between aligned portion of potato TA/EST against the total length of the tomato target (ALIGN_LENGTH/LENGTH_TOM)*100	Rough alignment evaluation between the tomato target and potato TA/EST. Scores higher than 100% reveal gaps in the alignment.
%_PERF_ALIGN	Corrected ratio between aligned portion of potato EST against the tomato target (%_ALIGN/TARG*%_IDENTITY)/100	This improvement of %_ALIGN/TARG parameter is needed to get the percentage of the net alignment, thus hiding the effects of non-contiguous alignment regions. Scores of 100% mean that the entire length of the tomato target sequence is aligned.
%_STOP_DIST	Ratio between the position of the last nucleotide aligned in the tomato target against the total length of the tomato target (LAST_POS_TOM/LENGTH_TOM)*100.	- Similar, lower than 100% values of %_PERF_ALIGN and %_STOP_DIST suggest alignment interruption due to an intervening 3' UTR (outside coding sequence) -Very different values of %_PERF_ALIGN and %_STOP_DIST suggest alignment interruption within coding sequence.

Various indexes were developed in the Global Match File in order to characterize alignment quality between tomato target and matching potato counterparts. The most relevant parameters are listed above along with their intended use in terms of assessing alignment quality.