genome.fa.s6.2.7.7.80.10.50.1000.10.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

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: Scaffold6
Parameters: 2 7 7 80 10 50 1000
Length:  1308201

Tables:   1   2   3   4   5   6   7   8   9   10   11   

This is table  10  of  11  ( 1316 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)
1068999--1069448	113	3.9	113	85	5	570	42	1	3	52	1.26
1069159--1069229	22	3.1	23	76	13	76	43	0	1	54	1.08
1069045--1069448	113	3.5	114	88	5	593	41	1	2	54	1.24
1069359--1069383	13	1.9	13	100	0	50	24	0	0	76	0.80
1069459--1069511	18	2.9	18	75	13	54	43	0	0	56	0.99
1069638--1069686	14	3.3	15	73	23	50	51	4	0	44	1.20
1069947--1069984	18	2.0	19	90	10	60	44	0	0	55	0.99
1070079--1070118	19	2.1	19	90	9	64	37	0	2	60	1.11
1070400--1070445	19	2.5	19	82	6	60	69	0	2	28	1.00
1070382--1070452	10	6.8	10	72	15	63	66	0	2	30	1.06
1070513--1070594	30	2.7	30	86	3	112	57	1	1	40	1.14
1070869--1070902	6	5.7	6	96	0	59	44	0	2	52	1.16
1070856--1070920	20	3.3	20	79	14	73	44	0	1	53	1.09
1079263--1079336	32	2.4	31	80	8	87	50	9	12	28	1.71
1081185--1081222	16	2.4	16	86	8	51	36	10	10	42	1.74
1082432--1082478	25	2.0	23	83	8	58	44	2	0	53	1.12
1082603--1082647	17	2.6	17	76	13	56	51	8	0	40	1.33
1085089--1085114	3	8.7	3	100	0	52	69	0	0	30	0.89
1085691--1085748	24	2.5	23	83	10	73	74	1	6	17	1.12
1086689--1086722	14	2.5	14	95	4	61	44	0	0	55	0.99
1086669--1086714	22	2.0	24	87	8	69	43	0	0	56	0.99
1086672--1086723	22	2.5	19	77	22	59	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1087443--1087537	34	2.5	39	81	13	119	53	2	1	43	1.19
1087540--1087600	15	4.2	15	73	14	56	59	0	1	39	1.08
1088116--1088158	15	2.9	15	83	10	52	46	0	0	53	1.00
1088149--1088187	11	3.6	11	82	6	53	25	0	0	74	0.82
1088130--1088209	35	2.3	35	85	8	101	33	0	0	66	0.92
1088430--1088478	25	1.9	26	95	4	91	53	0	0	46	1.00
1088430--1088529	13	7.5	13	72	21	57	56	0	0	44	0.99
1088785--1088837	20	2.6	22	82	14	69	30	0	0	69	0.88
1088779--1088837	19	3.4	19	68	27	58	28	0	0	71	0.87
1088828--1088907	25	3.2	24	73	18	74	41	0	2	56	1.13
1088890--1088948	33	1.9	30	83	16	77	49	1	0	49	1.11
1088848--1089035	95	2.0	94	83	8	238	44	2	2	51	1.25
1088851--1089083	95	2.5	93	80	10	235	42	1	1	53	1.21
1088973--1089068	33	2.8	34	78	13	117	41	1	2	55	1.18
1089159--1089200	18	2.2	20	87	8	61	33	9	2	54	1.46
1090156--1090421	136	2.0	136	95	0	478	34	16	7	40	1.78
1091836--1091883	21	2.3	20	79	10	53	39	2	2	56	1.23
1096918--1096972	23	2.4	24	75	9	60	32	1	0	65	1.03
1097092--1097133	22	1.9	23	85	9	61	69	0	0	30	0.89
1097134--1097174	17	2.4	18	84	8	50	41	0	2	56	1.13
1102198--1102222	13	1.9	13	100	0	50	36	16	16	32	1.90
1102285--1102309	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1102318--1102498	52	3.5	52	98	0	344	34	19	17	28	1.95
1106626--1106652	10	2.7	10	100	0	54	0	0	22	77	0.76
1115890--1115933	22	2.0	22	95	0	79	36	2	9	52	1.46
1116963--1117008	22	2.1	22	84	4	58	41	13	6	39	1.70
1117993--1118035	15	2.8	16	78	3	52	20	13	27	37	1.91
1118533--1118565	17	1.9	17	93	0	57	66	0	0	33	0.92
1119017--1119077	16	3.8	16	80	4	70	18	19	24	37	1.94
1119016--1119085	32	2.2	32	79	5	79	18	18	22	40	1.92
1119281--1119318	12	2.9	14	81	18	55	63	0	5	31	1.17
1120686--1120742	21	2.8	21	78	5	55	54	1	1	42	1.21
1124500--1124533	14	2.5	14	90	4	52	41	0	0	58	0.98
1124965--1125017	23	2.4	22	81	6	61	52	1	0	45	1.11
1125052--1125105	18	2.9	18	79	12	56	61	5	0	33	1.19
1125591--1125668	14	4.8	16	72	17	54	57	1	0	41	1.07
1125849--1125892	19	2.3	19	85	11	63	63	2	0	34	1.07
1126825--1126853	2	14.5	2	100	0	58	51	0	48	0	1.00
1127067--1127102	3	12.0	3	87	0	54	61	0	36	2	1.11
1127336--1127382	17	2.7	19	78	15	57	51	0	0	48	1.00
1127336--1127383	18	2.7	18	84	12	64	52	0	0	47	1.00
1127436--1127500	25	2.6	27	80	9	75	63	0	0	36	0.95
1127560--1127599	19	2.2	18	86	4	53	55	0	2	42	1.13
1128220--1128287	31	2.3	30	80	12	77	45	5	4	44	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1129054--1129095	22	1.9	22	90	9	68	61	0	0	38	0.96
1129148--1129193	23	2.0	23	95	0	83	36	30	8	23	1.85
1129273--1129331	22	2.7	21	87	10	75	40	0	0	59	0.97
1130143--1130206	23	2.8	23	77	15	69	51	0	1	46	1.10
1131565--1131612	24	1.9	26	84	16	66	52	0	0	47	1.00
1132307--1132351	22	2.0	24	86	8	67	46	2	2	48	1.26
1132477--1132529	27	2.0	26	85	10	72	73	1	5	18	1.12
1132477--1132529	26	2.0	27	85	10	74	73	1	5	18	1.12
1137907--1137962	17	3.4	18	73	26	61	55	7	0	37	1.27
1138974--1139006	9	3.3	10	87	12	50	21	0	3	75	0.93
1139758--1139793	19	1.9	18	88	5	54	75	0	0	25	0.81
1139822--1139847	13	2.0	13	100	0	52	69	0	0	30	0.89
1140028--1140069	2	21.0	2	100	0	84	50	0	0	50	1.00
1140336--1140387	19	2.7	19	85	8	61	44	0	0	55	0.99
1142810--1142850	11	3.9	11	78	9	50	82	0	17	0	0.66
1149243--1149279	14	2.6	15	83	12	51	56	0	0	43	0.99
1153728--1153811	28	3.1	28	76	11	77	33	4	4	57	1.41
1156035--1156142	22	4.8	22	85	6	144	33	2	25	38	1.70
1156035--1156142	47	2.4	44	85	4	144	33	2	25	38	1.70
1159765--1159839	20	3.8	20	78	0	87	34	13	12	40	1.81
1159765--1159842	40	2.0	39	87	2	111	34	12	12	39	1.82
1160754--1160809	22	2.5	23	94	5	105	17	10	8	62	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1160762--1160816	22	2.6	21	88	5	58	20	9	9	61	1.52
1164320--1164369	22	2.3	22	89	0	82	36	4	22	38	1.73
1164248--1164347	34	2.8	38	76	8	111	32	2	28	38	1.68
1165665--1165729	30	2.2	30	91	8	107	52	0	3	44	1.16
1167875--1167934	21	2.9	21	80	5	68	21	20	1	56	1.51
1167906--1167948	10	4.3	10	78	0	50	20	25	2	51	1.60
1170768--1170812	23	2.0	23	91	8	74	37	0	4	57	1.19
1171143--1171168	13	2.0	13	100	0	52	38	15	15	30	1.88
1174086--1174128	11	4.1	11	77	22	56	37	0	27	34	1.57
1174097--1174162	20	3.0	20	72	19	69	43	3	24	28	1.69
1174036--1174180	45	3.1	45	72	16	159	45	9	19	25	1.80
1176638--1177276	319	2.0	318	96	0	1188	31	17	14	37	1.90
1180360--1180386	13	2.1	13	100	0	54	40	14	14	29	1.86
1182545--1182601	19	2.8	21	89	7	82	42	12	19	26	1.86
1182545--1182626	20	4.0	21	83	9	89	37	12	17	32	1.86
1183495--1183519	13	1.9	13	100	0	50	56	0	4	40	1.18
1183675--1183775	50	2.0	50	98	0	193	42	3	8	44	1.54
1183921--1183964	23	1.9	23	85	0	61	36	15	15	31	1.90
1187296--1187340	23	2.0	23	86	0	63	51	2	0	46	1.13
1187510--1187674	71	2.3	69	80	10	172	53	12	1	32	1.48
1187692--1187850	84	1.9	84	98	0	309	49	13	3	33	1.60
1187510--1187950	73	6.0	73	69	18	195	53	11	2	32	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1187776--1187950	73	2.4	73	84	3	221	54	12	1	32	1.47
1187943--1188067	54	2.3	52	79	11	137	55	2	1	40	1.23
1188436--1188466	11	2.8	11	95	0	53	0	6	3	90	0.55
1188426--1188467	12	3.3	12	81	18	50	0	9	4	85	0.72
1188479--1188506	2	14.0	2	100	0	56	50	0	0	50	1.00
1188701--1188730	10	2.9	10	95	5	51	70	0	0	30	0.88
1188704--1188736	11	3.1	11	91	4	50	66	0	0	33	0.92
1188918--1188966	10	5.0	10	81	18	59	71	0	0	28	0.86
1188926--1188983	9	6.9	9	78	9	52	70	3	0	25	1.03
1188920--1188966	19	2.4	19	86	13	69	72	0	0	27	0.85

Tables:   1   2   3   4   5   6   7   8   9   10   11