Table 2. Venn Diagram analysis of 26–28 nt small RNA alignment to macronuclear/micronuclear sequence pairs - evidence for a macronuclear origin for the mating-specific small RNAs.

Gene	Micro Length	Macro Length	MDSs	Scrambled?	Micro Count	Macro Count	Union Count	Xsect Count	Xsect Pct	Only Micro Count	Only Micro Pct	Only Macro Count	Only Macro Pct
Actin	2115	1503	10	Yes	718	1056	1078	696	64.56%	22	2.04%	360	33.40%
Zinc Finger	2128	1994	4	No	641	681	681	641	94.13%	0	0.00%	40	5.87%
DNAPolAlpha	7165	4645	47	Yes	1326	1771	1826	1271	69.61%	55	3.01%	500	27.38%
L29Cyclo	1811	1596	3	No	500	503	503	500	99.40%	0	0.00%	3	0.60%
TEBPAlpha	2787	2127	17	Yes	744	992	996	740	74.30%	4	0.40%	252	25.30%
TEBPBeta	1753	1250	7	No	612	651	651	612	94.01%	0	0.00%	39	5.99%

Macronuclear sequences and the micronuclear sequences from which they were derived were used as targets for Bowtie mapping. Micro and macronuclear sequence pairs were trimmed so that all macronuclear sequence was contained within the micronuclear clone and regions of the micronuclear clone outside of the macronuclear gene were trimmed. The result of this is that sequence length differences between the micronuclear and macronuclear versions of the gene are due to IESs and repeated pointers in the micronuclear sequence. The gene name, length of the micronuclear and macronuclear sequences used in the filter, the number of MDSs, and whether the order of the MDSs is scrambled in the micronucleus are indicated. The number of distinct 26–28 nt small RNA sequences from each of the mating-derived small RNA libraries that aligned to each sequence in the pair were determined and then added together (“MicroCount” and “MacroCount”). “UnionCount” is the sum of the distinct sequences in each library found in the union of MicroCount and MacroCount. “XsectCount” is the number of distinct 26–28 nt sequences that aligned to both the macronuclear and micronuclear targets for that gene, and “XsectPct” is the percentage of UnionCount found in XsectCount. “OnlyMicroCount” is the number of distinct sequences in the seven libraries that only align to the micronuclear gene sequence and “OnlyMicroPct” is the percentage of sequences in UnionCount that are found in OnlyMicroCount. “OnlyMacroCount” is the number of distinct sequences in the seven libraries that only align to the macronuclear gene sequence and “OnlyMacroPct” is the percentage of sequences in UnionCount that are found in OnlyMacroCount.