Table 1. Description of the results of the alignments on PN40024 for the different sequenced clones by 454 methodology and for PN115 available sequences.

		PN386	PN583	PN777	Mean of 3 clones	PN115
% of aligned sequences	Alignment Step 1	48.1	42.5	40.2	43.6	57.7
	Alignment Step 2	0.9	1.1	1.0	1.0	1.3
	Alignment Step 3	12.5	21.7	16.7	16.9	8.0
	Total of aligned reads	61.5	65.3	57.9	61.5	67.0
% of unaligned sequences	Repeat elements	12.5	13.4	13.90	13.2	12.7
	Paralogs	12.0	10.1	13.0	11.7	20.3
	Cytoplasmic DNA	4.2	3.6	3.7	3.8
	Unknown	8.1	6.8	10.4	8.4
	Contamination (other organisms)	0.01	0.01	0.01	0.01
	Low quality reads	1.7	0.8	1.4	1.3
	Total of unaligned reads	38.5	34.8	42.1	38.4	33.0

Proportion of aligned reads in each steps of the alignment process and proportion of unaligned reads on the reference genome. First alignment step: aligned reads with 95% identity on single loci with reference sequence; Second alignment step: reads aligned in this step are composed by a repeat element (between 50–300 b) which was masked and by a unique sequence (greater than 150 b) which allowed alignment; Third alignment step: reads in this step are aligned on reference sequence with a gap parameter fixed at a minimum.