Molecular features of the gene subsets affected by amplification defaults. The EST from Pane1 1 (n = 109) and Panel 2 (n = 45) were compared to the EST of the core array (or 1 K array; n = 987) whenever interesting. The distributions of EST size, Bt. size and EST positions within the referenced transcripts from the Bos taurus Unigene index (or Bt.) were represented by box plots (A-C). Sizes were expressed in base pairs. Positions within the Bt. were expressed as % of the whole Bt. size, starting from the 5' end which is defined here as 0. The GC content in these subsets and in the corresponding Bt. was also represented by box plots (D-E). Boxes from the box-plots extended from the 25th percentile to the 75th percentile with a horizontal bar representing the median. Statistical significance between median EST size, Bt. size, EST positions and GC contents has been estimated with T tests (null hypothesis: no differences). (*) means significant (P < 0.05) and (***) highly significant (P < 0.01).