Table 1.

Alu family members differ in Z-DNA and editing potential

Repeat	Canonical sequence	Z-score canonical	Total annotated	Number canonical	Number edited	Fraction edited	Z-score <250	Z-score >250	Ratio (Z/Non-Z)	Mean Z-score	SE(Mean)
AluSc	gcgcgcgcctgt	5976.64	33,903	127	27,893	0.82	19,702	8191	0.42	785.07	31.31
AluSc5	gcgcgTgcctgt	1352.02	6775	145	4927	0.73	3607	1320	0.37	450.97	18.21
AluSx4	gcgcgcgcctgt	5976.64	5670	16	5164	0.91	3787	1377	0.36	748.13	53.24
AluSc8	gcAcgcgcctgt	1349.93	21,507	412	17,194	0.80	12,674	4520	0.36	747.01	37.16
AluSg	gcgcgcgcctgt	5976.64	40,784	101	36,345	0.89	26,985	9360	0.35	802.28	32.27
AluSx3	gcgcgcgcctgt	5976.64	29,020	43	24,892	0.86	19,373	5519	0.28	761.09	33.02
AluSx	gcgcgcgcctgt	5976.64	141,949	141	106,512	0.75	83,741	22,771	0.27	485.89	9.29
AluSz	gcgcgcgcctgt	5976.64	97,073	70	94,472	0.97	74,353	20,119	0.27	473.83	8.84
AluSz6	gcgcgcgcctgt	5976.64	45,181	13	41,524	0.92	34,094	7430	0.22	461.63	10.80
AluSp	gcgcATgcctgt	342.70	49,103	0	38,146	0.78	32,359	5787	0.18	433.95	12.07
AluJb	gcgcgcgcctgt	5976.64	142,591	21	117,452	0.82	101,831	15,621	0.15	480.80	8.10
AluJo	gcgcgcgcctgt	5976.64	71,274	7	53,397	0.75	47,380	6017	0.13	462.01	9.06
AluSq	gcgGgcgcctgt	257.42	21,499	1	15,103	0.70	13,403	1700	0.13	695.93	38.39
AluSq2	gcgGgcgcctgt	257.42	54,418	3	38,215	0.70	34,086	4129	0.12	448.86	12.54
AluJr	gcgcgcgcctgt	5976.64	76,315	10	59,166	0.78	52,801	6365	0.12	458.69	9.06
AluJr4	gcgcgcgcctgt	5976.64	17,432	0	14,743	0.85	13,479	1264	0.09	472.08	16.62
AluY	gcgGgcgcctgt	257.42	118,506	73	46,885	0.40	44,732	2153	0.05	469.60	15.21
AluSx1	gcgGgcgcctgt	257.42	109,158	13	73,920	0.68	72,578	1342	0.02	411.67	12.44

The results derived from a genome-wide survey of Alu elements are presented. The Z-score for each Alu RepeatMasker consensus sequence was determined using the ZHUNT3 program¹⁰. Differences in base sequence are capitalized. The count for each consensus sequence in hg19 (February 2009) is given along with the number of elements that actually have the consensus sequence. The number of Alu’s with edits in each family is derived from the RADAR database V2. The mean Z-score based on the actual genomic sequences for each family is calculated using sequences with a Z-Score >250. The ratio of edited Alu’s that have Z-scores >250 to those with Z-Scores <250 is given. The Pearson correlation between this ratio and the Z-score, weighted by the count of actual elements with a Z-score’s >250, is 0.69 when calculated using the wCor package