oyster.v9_M.fa.s19.2.7.7.80.10.50.500.3.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.04

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: scaffold3
Parameters: 2 7 7 80 10 50 500
Length:  1336734

Tables:   1   2   3   4   

This is table  3  of  4  ( 390 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
865407--865493	23	3.6	25	68	22	87	27	22	13	35	1.92
865362--865493	71	1.9	71	91	0	219	25	25	13	34	1.93
865422--865517	46	2.1	46	94	0	165	23	22	13	39	1.90
866168--866894	161	4.5	161	87	3	1027	35	19	14	30	1.91
875889--875937	17	3.0	17	82	8	66	18	28	16	36	1.92
878880--878916	17	2.2	17	100	0	74	24	29	18	27	1.98
881528--881576	20	2.5	19	78	12	55	67	2	14	16	1.33
881664--881699	16	2.2	16	90	0	54	36	11	30	22	1.89
889376--889410	18	1.9	18	100	0	70	54	17	5	22	1.64
890228--890290	30	2.1	30	90	0	99	47	20	7	23	1.76
890543--890606	32	2.0	31	82	8	76	37	18	10	32	1.86
890432--891033	77	7.8	77	89	2	870	38	18	11	31	1.87
890924--890997	32	2.3	32	80	0	94	39	17	9	33	1.82
890893--891267	139	2.7	139	93	1	633	37	18	13	30	1.89
891313--891391	32	2.5	32	80	12	90	41	20	10	27	1.84
895253--895333	8	11.1	7	71	20	51	30	17	43	8	1.79
895253--895333	22	3.7	22	85	1	92	30	17	43	8	1.79
896336--896390	22	2.5	22	90	0	92	29	14	43	12	1.82
896336--896397	22	2.8	22	83	9	81	29	14	45	11	1.80
896417--896538	8	16.4	8	65	19	50	10	44	14	30	1.79
896413--896527	22	5.2	22	74	12	101	9	44	15	30	1.79
896448--896528	30	2.7	30	87	11	105	9	44	16	29	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
896428--896494	14	4.6	15	75	15	61	8	43	16	31	1.79
896486--896534	16	3.2	16	80	16	59	12	42	14	30	1.82
910234--910276	21	2.0	21	95	0	77	37	13	13	34	1.85
911669--911721	26	2.0	26	92	0	88	33	9	35	20	1.85
912796--912847	27	1.9	27	84	0	68	51	5	5	36	1.50
916779--916815	18	2.0	18	89	5	56	32	32	29	5	1.80
916966--917373	184	2.2	183	83	3	525	36	14	13	34	1.86
919792--919816	2	12.5	2	100	0	50	0	52	0	48	1.00
921842--922285	185	2.4	183	81	4	500	35	14	14	35	1.88
924727--924756	11	2.7	11	94	0	51	26	13	20	40	1.89
927185--927281	21	4.6	21	98	0	185	38	37	9	15	1.80
927185--927279	10	9.0	11	88	9	153	37	36	9	15	1.80
929891--930063	11	16.5	11	82	10	211	18	8	35	37	1.82
929891--930062	21	8.2	21	86	3	208	18	8	35	37	1.81
933666--933704	21	1.9	21	84	5	53	56	12	7	23	1.62
937583--937666	4	21.0	4	100	0	168	25	25	0	50	1.50
937907--937936	15	2.1	15	93	6	53	46	6	0	46	1.29
951950--951975	4	6.5	4	100	0	52	0	23	26	50	1.50
963332--963364	17	1.9	17	88	11	50	48	9	12	30	1.71
974295--974382	43	2.0	43	91	0	140	37	15	22	23	1.93
978930--978960	16	1.9	16	100	0	62	32	22	19	25	1.97
987231--988206	436	2.2	435	82	4	1144	34	14	17	33	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
997000--997160	53	2.9	55	77	9	159	17	20	18	44	1.87
997024--997164	56	2.6	56	80	9	141	16	21	16	46	1.84
1009365--1009404	2	20.0	2	100	0	80	50	0	50	0	1.00
1009849--1009889	2	20.5	2	100	0	82	0	51	0	48	1.00
1009889--1009930	2	21.0	2	100	0	84	50	50	0	0	1.00
1019442--1019486	2	22.5	2	90	0	72	48	2	48	0	1.13
1019525--1019593	2	35.0	2	97	2	131	0	49	0	50	1.00
1022545--1022581	12	3.1	12	88	0	56	0	0	86	13	0.57
1023352--1023380	14	2.1	14	100	0	58	0	0	13	86	0.58
1028009--1028036	1	28.0	1	100	0	56	0	100	0	0	0.00
1042198--1042252	14	3.9	14	85	4	67	56	1	41	0	1.10
1042198--1042252	16	3.6	15	83	9	67	56	1	41	0	1.10
1050507--1050841	40	8.5	40	88	3	468	17	0	24	58	1.41
1050608--1050641	15	2.2	16	94	5	61	5	0	23	70	1.09
1050623--1050785	24	7.8	24	62	31	79	16	0	25	57	1.43
1050731--1050761	15	2.0	16	93	6	55	12	0	22	64	1.27
1050507--1050841	79	4.3	80	91	2	477	17	0	24	58	1.41
1056142--1057024	172	5.2	171	86	6	1160	26	25	15	32	1.95
1057186--1057231	20	2.4	19	88	3	65	41	26	32	0	1.56
1086073--1086102	2	15.0	2	92	0	51	0	46	0	53	1.00
1086146--1086180	17	2.1	17	100	0	70	31	11	11	45	1.76
1086343--1086463	5	24.4	5	80	8	140	4	16	23	56	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1089783--1089915	2	65.5	2	92	3	221	0	48	3	48	1.19
1091136--1091162	2	13.5	2	100	0	54	0	51	0	48	1.00
1093593--1093617	2	12.5	2	100	0	50	0	52	0	48	1.00
1096215--1096243	15	1.9	15	100	0	58	24	0	48	27	1.51
1101666--1101727	2	31.0	2	100	0	124	0	50	0	50	1.00
1103561--1104029	166	2.8	164	83	5	586	26	24	16	32	1.96
1117120--1117176	2	28.5	2	100	0	114	0	50	0	49	1.00
1117773--1117804	11	3.1	11	86	13	50	46	0	9	43	1.35
1119649--1119681	16	2.1	16	94	0	57	30	12	21	36	1.90
1124087--1124123	15	2.4	16	86	9	58	24	27	13	35	1.93
1137119--1137185	20	3.4	20	83	4	91	53	5	14	25	1.64
1153989--1154112	20	6.6	20	67	16	77	34	18	16	30	1.93
1154016--1154075	31	1.9	31	86	6	86	31	20	15	33	1.93
1159646--1159712	7	9.6	7	80	0	80	37	14	20	26	1.92
1159646--1159712	21	3.2	21	84	0	89	37	14	20	26	1.92
1162285--1162331	2	23.5	2	100	0	94	48	0	51	0	1.00
1162521--1162570	8	6.2	8	90	0	55	0	36	12	52	1.39
1162541--1162570	2	15.0	2	92	0	51	0	46	3	50	1.18
1162521--1162570	12	4.2	12	86	0	55	0	36	12	52	1.39
1163065--1163131	7	9.6	7	78	0	71	26	19	14	38	1.91
1163065--1163131	21	3.2	21	82	0	80	26	19	14	38	1.91
1170375--1170403	2	14.5	2	100	0	58	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1170698--1170724	2	13.5	2	100	0	54	0	48	0	51	1.00
1176542--1176604	2	31.5	2	96	0	117	49	0	50	0	1.00
1176847--1176888	22	1.9	22	100	0	84	33	19	19	28	1.96
1184541--1184571	16	1.9	16	93	0	53	29	22	19	29	1.98
1185013--1185056	24	1.9	23	90	9	72	38	11	9	40	1.73
1185043--1185155	15	7.5	15	67	18	65	42	12	6	38	1.68
1185276--1186205	177	5.3	177	87	2	1370	33	25	18	23	1.96
1185596--1185632	19	1.9	19	88	0	56	40	32	5	21	1.76
1185276--1186205	353	2.6	353	97	0	1729	33	25	18	23	1.96
1185949--1185985	19	1.9	19	88	0	56	40	32	5	21	1.76
1186130--1186169	19	2.1	19	85	0	53	35	40	2	22	1.68
1187293--1187327	12	2.9	12	86	0	52	54	0	42	2	1.15
1187995--1188037	20	2.1	20	95	0	77	53	9	6	30	1.59
1197867--1198973	168	6.7	168	86	5	1281	30	18	19	31	1.96
1197867--1198973	323	3.3	335	83	4	1345	30	18	19	31	1.96
1199143--1199178	7	5.0	7	86	6	54	38	41	19	0	1.52
1199143--1199178	15	2.5	14	86	8	54	38	41	19	0	1.52
1201667--1201706	18	2.2	18	86	8	55	50	15	15	20	1.79
1204270--1204316	12	4.2	12	76	15	55	48	4	0	46	1.21
1204270--1204328	16	3.6	16	76	13	66	47	3	1	47	1.29
1204283--1204326	21	2.1	21	91	0	70	45	2	2	50	1.27
1205705--1205859	77	2.0	77	98	0	301	34	23	7	34	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1218432--1218456	11	2.3	11	100	0	50	56	0	16	28	1.41
1218708--1219093	189	2.0	192	94	1	679	36	15	13	33	1.88
1220041--1220098	2	29.0	2	100	0	116	50	0	50	0	1.00
1223295--1223350	23	2.6	22	83	10	71	21	7	19	51	1.70
1223864--1223895	12	2.7	12	95	0	55	53	15	9	21	1.70
1226511--1226552	21	2.0	21	100	0	84	61	4	23	9	1.45
1227358--1227387	14	2.1	14	93	0	51	0	3	20	76	0.92
1227543--1227602	31	1.9	32	89	3	95	20	21	26	31	1.98
1230780--1230847	2	34.0	2	100	0	136	0	50	0	50	1.00
1234547--1234590	21	2.1	21	87	8	63	15	15	36	31	1.90

Tables:   1   2   3   4