Table 3.

Output loci from the TAS gene prediction algorithm (P < 0.005) using rdr2 MPSS small RNA data

Locus*	Name*	Coordinate†	Strand†	n‡	k‡	P value‡	Ref.§
At1g50055	TAS1b	18,553,151	W	46	13	2.04 × 10−9	2, 8
At2g39681	TAS2	16,547,078	C	73	15	6.58 × 10−9	2
At1g63150	PPR	23,423,856	C	23	9	7.12 × 10−8	16, 17
At1g63080	PPR	23,393,654	W	27	9	3.70 × 10−7	16, 17
At2g27400	TAS1a	11,729,168	C	56	12	4.18 × 10−7	2, 3, 8a
At1g63130	PPR	23,417,098	W	36	10	4.56 × 10−7	16, 17
At1g62910	PPR	23,303,391	C	10	6	7.87 × 10−7	16, 17
At1g63070	PPR	23,390,043	W	24	7	3.00 × 10−5	16
At1g12820	AFB3	4,368,842	W	6	4	4.55 × 10−5	16, 17
At2g39675	TAS1c	16,544,896	W	37	8	7.66 × 10−5	2, 8
At1g15400/At1g15410	IGR	5,297,945	W	51	9	1.30 × 10−4	16
At1g48410	AGO1	17,895,163	C	10	4	5.64 × 10−4	17a
At5g39370	SLG	15,774,916	W	37	7	6.17 × 10−4	16
At1g62930	PPR	23,311,213	C	40	7	1.03 × 10−3	16, 17
At3g17185	TAS3	5,862,213	W	42	7	1.40 × 10−3	2
At1g63400	PPR	23,511,931	C	31	6	1.50 × 10−3	16, 17
At3g06433/At3g06435	IGR	1,966,491	W	175	15	1.54 × 10−3
At2g16586	Unknown	7,198,532	W	14	4	2.38 × 10−3	16
At3g23690	MYM9.3	8,530,582	C	7	3	2.55 × 10−3	17

*Loci mapped to intergenic regions (IGR) were indicated between two AGI loci. An rRNA locus with P value of 3.29 × 10⁻³was excluded from the list.

^†The strand and the coordinate for the start site of the small RNA were used to determine the phased positions in calculating the corresponding P value. W, Watson; C, Crick.

^‡n, k, and P value abbreviations are described in Results.

^§Literature with TAS or potential TAS loci initially described.