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Table 2.

Distribution of Hammerhead and Hammerhead-like Motifs in the Different Sections of the GenBank: Mutants of the Single Stranded Regions

	pri	rod	mam	vrt	inv	pln	bct	rna	vrl	phg	syn	una	est	pat	sts	gss	htg	Total	Total over expected	Expected (A = C = G = T)
HH-I	51	21	0	14	176	119	130	0	37	3	5	0	186	45	4	17	108	916	0.56	1635
HH-I-3	182	72	12	45	997	560	553	2	159	16	6	0	702	125	10	119	486	4046	0.57	7081
HH-I-4	270	29	0	32	365	228	226	10	69	3	8	1	358	55	4	33	272	1963	0.55	3576
HH-I-5	310	70	14	97	506	400	309	2	77	10	7	1	641	60	13	92	382	2991	0.46	6488
HH-I-6	197	60	17	37	516	312	399	3	107	5	8	1	700	93	11	67	288	2821	0.49	6973
HH-I-8	171	44	11	22	790	407	455	10	138	11	5	0	521	86	10	61	420	3162	0.46	6883
HH-I-9	247	56	12	29	508	260	454	0	107	9	7	3	536	99	9	65	344	2745	0.38	7314
HH-I-12	946	224	41	103	754	613	454	0	180	13	8	2	1856	137	48	263	794	6436	0.94	6865
HH-I-13	209	76	16	41	428	308	462	5	93	10	11	0	739	143	12	66	226	2845	0.42	6775
HH-I-14	317	94	30	36	404	377	487	7	104	5	30	5	737	102	8	77	327	3147	0.50	6362
HH-I-17	65	25	0	18	201	144	162	0	50	4	11	0	225	53	4	19	122	1103	0.l54	2031
HH-II	83	33	1	5	175	126	141	1	80	1	1	3	435	30	4	8	91	1218	0.54	2246
HH-II-3	180	78	8	29	994	645	715	3	204	14	25	23	1022	102	11	82	502	4637	0.66	7063
HH-II-4	133	56	7	11	387	261	278	1	100	1	2	5	658	43	7	39	188	2177	0.51	4277
HH-II-5	244	82	16	37	573	477	372	7	141	10	4	4	910	70	12	71	362	3392	0.39	8788
HH-II-6	234	81	23	17	522	348	977	38	153	7	7	9	856	74	8	59	311	3724	0.49	7674
HH-II-8	209	64	11	22	921	385	519	16	130	3	10	4	1265	53	7	65	452	4136	0.54	7710
HH-II-9	255	58	8	24	457	319	540	6	140	9	11	5	884	82	10	51	281	3140	0.39	7979
HH-II-12	1290	253	61	60	879	716	534	1	209	14	18	3	2491	125	56	273	1027	8010	0.97	8285
HH-II-13	214	91	45	26	421	326	534	7	162	8	23	3	1031	71	7	53	228	3250	0.44	7404
HH-II-14	281	81	15	37	414	524	493	6	142	7	2	4	1038	87	9	67	256	3463	0.43	8069
HH-II-17	100	35	1	7	220	152	173	1	97	1	1	4	504	36	7	16	108	1463	0.53	2786
HH-III	42	6	0	2	93	67	65	0	21	1	2	0	96	57	3	8	64	527	0.55	952
HH-III-3	96	32	8	18	625	305	245	0	74	6	3	0	310	72	5	74	291	2164	0.64	3397
HH-III-4	295	12	1	21	192	128	98	0	36	3	5	0	204	63	3	23	229	1313	0.76	1725
HH-III-5	144	38	16	35	301	205	231	0	34	2	2	0	388	76	11	32	219	1734	0.48	3612
HH-III-6	134	29	5	18	290	183	197	9	58	2	3	0	426	66	10	33	180	1643	0.46	3540
HH-III-8	92	26	4	6	528	203	260	0	722	1	2	0	294	154	4	29	255	2580	0.68	3774
HH-III-9	109	22	0	12	239	143	196	0	87	3	4	0	462	63	7	38	164	1549	0.49	3918
HH-III-12	658	97	40	32	369	318	217	0	98	3	6	0	1071	135	20	121	477	3662	1.03	3540
HH-III-13	119	29	8	14	226	176	246	3	53	6	2	0	345	70	6	28	142	1473	0.41	3576
HH-III-14	133	33	10	11	242	184	195	1	65	2	21	0	408	86	5	39	146	1581	0.45	3504
HH-III-17	49	6	0	3	123	81	86	0	23	2	2	0	154	67	4	11	74	685	0.49	1402
GenBank relative size	0.14	0.03	0.01	0.01	0.07	0.07	0.07	<0.01	0.03	<0.01	<0.01	<0.01	0.37	0.02	0.01	0.06	0.10	1.00

[i] The motifs are named as explained in Methods and in Figure 1. The “expected” number of occurrences was obtained by searching the different motifs in a database of 1000 random sequences of 100,000 nucleotides (equal representations of A, C, G, and T) and correcting the frequency to the relative size of the GenBank. The “total over expected” shows the ratio of occurrences obtained in the GenBank versus the expected ones according to the search performed in a random database with the size of the GenBank.

[ii] (pri) Primate sequence entries (from the two GenBank files); (rod) rodent sequence entries; (mam) other mammalian sequence entries; (vrt) other vertebrate sequence entries; (inv) invertebrate sequence entries; (pln) plant sequence entries (including fungi and algae); (bct) bacterial sequence entries; (rna) structural RNA sequence entries; (vrl) viral sequence entries; (phg) phage sequence entries; (syn) synthetic and chimeric sequence entries; (una) unannotated sequence entries; (est) EST (expressed sequence tag) (from 23 GenBank files); (pat) patent sequence entries; (sts) STS (sequence tagged site) sequence entries; (gss) GSS (genome survery sequence) sequence entries; (htg) HTGS (high throughput genomic sequencing) sequence entries.