Table 2.

Analysis of Stagonospora nodorum repeat families for evidence of RIP ranked by CpA↔TpA dominance.

Repeat Family	$\frac{TpA}{ApT}$	$\frac{CpA+TpG}{ApC+GpT}$	CpA↔TpA Dominance	Alignment Length	Description/Homology
R8	1.70 ± 0.03	0.74 ± 0.02	2.96	9548	Ubiquitin conjugating enzyme
X0	1.75 ± 0.02	0.49 ± 0.02	2.13	4103	Non LTR transposon
R10	1.76 ± 0.06	0.56 ± 0.05	1.91	1360	Unknown
R9	1.99 ± 0.03	0.48 ± 0.02	1.88	4483	Non LTR transposon
X48	1.35 ± 0.11	1.26 ± 0.13	1.82	275	Sub-telomeric repeat
rDNA Non-tandem	2.68 ± 0.18	0.69 ± 0.04	1.50	9938	Non-array rDNA repeats ≥ 1 kb
X35	1.76 ± 0.07	0.58 ± 0.07	1.50	1185	Sub-telomeric repeat
MOLLY	1.90 ± 0.06	0.40 ± 0.04	1.21	1946	Mariner-like transposon
R22	1.73 ± 0.08	0.27 ± 0.04	1.20	710	Sub-telomeric repeat
X26	1.70 ± 0.03	0.52 ± 0.02	1.16	5034	Sub-telomeric repeat/Transposon remnant
R31	1.65 ± 0.04	0.44 ± 0.04	0.99	3119	Unknown
X36	1.97 ± 0.18	0.44 ± 0.10	0.89	516	Unknown
X96	1.87 ± 0.19	0.56 ± 0.18	0.87	319	Unknown
ELSA	1.67 ± 0.04	0.46 ± 0.05	0.86	5273	Copia-like transposon
X11	2.04 ± 0.03	0.38 ± 0.02	0.83	7570	Gypsy-like transposon
X28	2.22 ± 0.13	0.39 ± 0.03	0.83	1975	Unknown
PIXIE	1.84 ± 0.07	0.36 ± 0.03	0.77	1918	Mariner-like transposon
X12	2.06 ± 0.07	0.33 ± 0.04	0.67	2059	Gypsy-like transposon
X3	1.91 ± 0.03	0.74 ± 0.01	0.63	10673	Helicase
X15	1.87 ± 0.04	0.33 ± 0.02	0.61	6437	Sub-telomeric repeat/Gypsy-like transposon
R39	1.92 ± 0.08	0.30 ± 0.03	0.59	2102	Unknown
rDNA Tandem	2.08 ± 0.09	0.94 ± 0.02	0.53	9938	rDNA repeats in tandem array
R37	1.85 ± 0.03	0.28 ± 0.02	0.49	2264	Mariner-like transposon
R51	1.93 ± 0.07	0.27 ± 0.03	0.47	870	Unknown
X23	1.85 ± 0.09	0.31 ± 0.03	0.45	613	Unknown
rDNA Short	3.55 ± 0.39	0.25 ± 0.03	0.26	280*	Non-array rDNA repeats < 1 kb
R25	2.16 ± 0.15	0.31 ± 0.03	0.25	3407	Transposon remnant
R38	2.10 ± 0.18	0.24 ± 0.05	0.20	391	Unknown
Non-Repetitive Control	0.83 ± 0.01	1.25 ± 0.00	N/A	N/A	Genomic regions not corresponding to repeat matches

Two RIP index scores are given within a 95% confidence interval. The alignment-based comparison of CpA↔TpA RIP-mutation is used to give dominance score. CpA↔TpA dominance is a numerical indicator of frequency of that mutation over other CpN↔TpN mutations as described in the methods. Values for the rDNA repeat are sub-classified according to physical location and length. The length of the alignment is also given. (*rDNA short alignments are a subset of the full-length rDNA alignment.)