Table I.

Classification of nonredundant exemplar sequences used for probe set design on the Barley1 GeneChip probe array

Section	Content	No. with Unknown Function	No. with Known or Predicted Functiona	Total No. of Sequencesb
1.	Specially sequences (Mla alleles; Rpg1)	0	16	16
2.	Reporter genes (for investigation of transgenics)	0	26	26
Main assembly contigs
3.	Contains 3′ end read (including NCBI nr cDNA or gene)	3,360	10,783	14,143
4.	No 3′-end read but has poly(A+) at terminal end	706	577	1,283
5.	No 3′-end read or poly(A+) terminal but contains GenBank nr sequence	3	76	79
6.	Chloroplast	0	44	44
7.	Mitochondrion	0	44	44
Main assembly singletons
8.	NCBI nr cDNA or gene	2c	93	95
9.	Forward orientation and poly(A+) at terminal end	1,237	279	1,516
10.	Reverse orientation and poly(T) at beginning	2,514	869	3,383
11.	Reverse orientation but no poly(T) at beginning	579	231	810
Additions	Controls (eg., Affymetrix standard spiking controls: BioB, BioC, etc.; barley reliably nonexpressed sequences, housekeeping controls, etc.)	0	48	48
Total of sections 1 to 11		8,401	13,038	21,439

^aDefined by BLASTX cutoff of e-20

^bTotals in each section correspond to non-redundant probe sets. There are 1,524 probe sets that provide multiple representations of the same exemplar

^cThe two unknowns in section 8 are above the e-20 cutoff, but both are putative hordeins