|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.