genome.fa.s5.2.7.7.80.10.50.1000.9.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: Scaffold5
Parameters: 2 7 7 80 10 50 1000
Length:  1536239

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   

This is table  9  of  14  ( 1571 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)
1046510--1046549	11	3.3	12	82	10	55	72	0	0	27	0.85
1046874--1046941	26	2.6	24	73	15	64	55	1	0	42	1.08
1047587--1047639	25	2.1	25	82	0	61	32	1	1	64	1.15
1049769--1049807	12	3.2	13	85	10	55	41	0	0	58	0.98
1050102--1050159	29	2.1	27	81	18	66	50	0	0	50	1.00
1050140--1050182	22	2.0	22	90	9	70	60	0	0	39	0.97
1063796--1063851	20	2.7	21	76	20	64	32	3	0	64	1.11
1063809--1063958	19	7.8	19	67	21	82	36	0	0	63	1.00
1063825--1063952	17	7.7	18	68	21	66	37	0	0	62	0.95
1063817--1063952	63	2.2	60	81	11	170	36	0	0	63	0.95
1063951--1063991	15	2.7	16	81	11	59	53	0	2	43	1.13
1063856--1064010	85	1.8	82	81	10	188	40	0	0	59	1.02
1063856--1064010	84	1.8	85	81	10	194	40	0	0	59	1.02
1064270--1064327	21	2.8	21	82	10	66	62	0	0	37	0.96
1064327--1064383	19	3.2	17	76	13	53	47	7	0	45	1.30
1067859--1067916	24	2.4	24	100	0	116	25	22	18	32	1.97
1070046--1070081	16	2.2	16	90	0	54	36	2	2	58	1.27
1070221--1070267	19	2.5	19	82	6	60	44	2	0	53	1.12
1072776--1072836	16	4.1	16	73	16	58	63	1	0	34	1.04
1078401--1078495	46	2.0	47	82	13	117	45	1	2	51	1.20
1078671--1078716	16	3.1	15	84	9	58	52	0	0	47	1.00
1078764--1078806	22	2.0	22	90	4	70	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1078986--1079155	6	27.0	6	65	28	54	41	0	0	58	1.02
1078979--1079018	19	2.2	18	86	4	53	32	2	2	62	1.22
1078995--1079152	9	18.4	8	68	22	65	41	0	0	57	1.03
1078994--1079163	44	3.8	43	72	21	125	42	0	0	57	1.03
1079036--1079146	32	3.5	33	75	17	110	42	0	0	57	0.98
1079102--1079154	16	3.3	15	82	15	54	35	0	0	64	0.94
1079042--1079152	26	4.3	27	74	14	101	42	0	0	57	0.98
1078993--1079163	15	12.4	14	69	21	105	42	0	0	56	1.03
1079688--1079735	20	2.6	18	78	15	53	52	0	0	47	1.00
1079751--1079784	15	2.1	17	89	10	54	50	2	0	47	1.16
1080116--1080150	3	11.7	3	93	0	61	31	2	0	65	1.07
1080351--1080388	20	1.9	19	89	5	58	57	0	0	42	0.98
1080835--1080880	18	2.5	19	82	10	51	21	6	0	71	1.08
1081039--1081090	17	3.1	17	73	13	54	44	0	0	55	0.99
1081014--1081096	33	2.5	34	78	11	100	49	0	0	50	1.00
1081590--1081703	18	6.1	18	68	20	56	50	3	0	45	1.18
1082073--1082104	14	2.3	14	94	0	55	50	0	0	50	1.00
1082445--1082490	22	2.1	21	84	4	56	52	0	0	47	1.00
1083157--1083193	2	18.5	2	100	0	74	48	0	0	51	1.00
1088969--1089021	21	2.6	21	85	11	67	60	0	0	39	0.97
1088965--1089057	27	3.3	28	70	22	70	59	0	0	40	0.98
1089045--1089085	19	2.2	18	86	4	55	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1089358--1089425	22	3.1	22	77	22	72	55	0	0	44	0.99
1089339--1089428	22	3.5	27	70	21	68	54	0	0	45	0.99
1089616--1089687	31	2.3	30	83	9	81	55	1	2	40	1.23
1089605--1089663	11	5.3	11	83	2	64	59	1	3	35	1.24
1089649--1089694	23	1.9	23	82	8	56	52	0	2	45	1.13
1089950--1090046	13	6.8	14	69	19	58	44	1	1	53	1.14
1090486--1090692	69	3.0	67	80	9	247	36	18	27	17	1.93
1091049--1091085	20	2.0	19	85	15	51	56	0	0	43	0.99
1091248--1091280	16	2.1	16	94	0	57	63	0	0	36	0.95
1091409--1091456	22	2.3	21	85	7	62	41	0	4	54	1.20
1094916--1094940	13	1.9	13	100	0	50	24	4	8	64	1.38
1097646--1097706	31	2.0	31	90	0	95	36	11	13	39	1.80
1100006--1100050	16	2.9	16	80	3	56	62	0	2	35	1.08
1100007--1100070	21	3.0	21	72	4	65	60	0	3	35	1.12
1101999--1102032	2	17.0	2	93	0	59	52	0	47	0	1.00
1105262--1105298	2	19.0	2	94	5	67	51	0	0	48	1.00
1106361--1106391	14	2.2	14	100	0	62	58	0	0	41	0.98
1106618--1106728	35	3.3	34	74	16	106	44	0	0	55	0.99
1106628--1106692	16	4.3	15	72	18	55	43	0	0	56	0.99
1106706--1106769	29	2.2	28	81	8	76	53	0	0	46	1.00
1106721--1106769	22	2.4	19	86	10	62	59	0	0	40	0.98
1106620--1106755	67	2.0	67	79	13	147	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1106907--1106960	18	3.2	17	80	12	58	59	0	0	40	0.98
1107586--1107617	5	6.4	5	100	0	64	37	0	0	62	0.95
1107846--1107920	16	4.5	16	71	14	53	41	1	1	56	1.16
1108715--1108766	27	1.9	27	84	7	70	57	0	3	38	1.17
1108887--1108914	14	2.0	14	100	0	56	57	0	0	42	0.99
1109736--1109842	27	4.2	26	76	15	116	47	3	0	47	1.26
1110056--1110118	11	5.7	12	78	12	55	63	0	0	36	0.95
1110075--1110116	17	2.5	18	85	11	54	64	0	0	35	0.94
1110049--1110115	27	2.4	27	87	7	91	64	0	0	35	0.94
1110403--1110459	22	2.7	22	76	15	57	56	3	0	40	1.17
1111142--1111188	20	2.3	21	85	7	69	59	4	0	36	1.17
1111151--1111188	20	1.9	20	100	0	76	63	5	0	31	1.17
1111335--1111390	29	2.0	28	82	10	69	42	0	0	57	0.99
1111360--1111415	20	2.8	20	86	5	69	48	0	0	51	1.00
1111529--1111553	13	1.9	13	100	0	50	44	0	0	56	0.99
1111555--1111625	12	6.0	12	72	18	60	49	0	0	50	1.00
1111544--1111620	22	3.2	23	76	16	68	44	0	0	55	0.99
1111582--1111625	22	2.0	22	86	8	63	47	0	0	52	1.00
1112178--1112208	4	7.8	4	92	0	53	48	25	0	25	1.52
1113451--1113475	12	2.1	12	100	0	50	0	0	8	92	0.40
1124204--1124229	3	8.7	3	100	0	52	30	0	34	34	1.58
1124566--1124613	24	2.1	22	88	7	69	64	2	0	33	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1124703--1124763	22	2.8	22	80	14	81	40	0	0	59	0.98
1125803--1126077	116	2.5	108	83	9	333	53	1	1	42	1.20
1125963--1126045	32	2.6	32	83	14	109	50	0	2	46	1.14
1126050--1126108	21	2.8	22	78	17	70	61	0	3	35	1.13
1126373--1126718	129	2.8	128	85	8	462	41	2	2	54	1.23
1126373--1126716	128	2.7	124	84	11	427	41	2	2	54	1.23
1127099--1127149	2	25.5	2	100	0	102	49	0	0	50	1.00
1127516--1127554	19	2.1	19	85	0	51	53	0	0	46	1.00
1128025--1128076	27	1.9	27	84	0	68	59	0	1	38	1.08
1129066--1129154	39	2.4	37	92	7	144	44	16	16	21	1.86
1129706--1129748	18	2.4	19	80	11	54	62	0	0	37	0.95
1129748--1129792	23	2.0	23	82	8	56	37	6	4	51	1.49
1131610--1131693	36	2.3	37	82	15	95	40	2	1	55	1.20
1131817--1131867	13	3.8	13	89	2	75	58	0	0	41	0.98
1131821--1131873	18	2.9	18	74	2	52	62	0	0	37	0.96
1133771--1133855	39	2.2	38	77	10	91	36	12	27	23	1.91
1138368--1138402	17	2.1	17	88	0	52	37	0	2	60	1.12
1138505--1138547	22	2.0	22	90	0	68	39	0	0	60	0.97
1142910--1142948	20	2.0	20	85	5	53	38	0	2	58	1.12
1142910--1142949	21	2.0	20	85	5	53	40	0	2	57	1.12
1143667--1143730	23	2.9	21	81	6	65	34	1	12	51	1.49
1145189--1145236	24	2.0	23	92	4	78	64	2	4	29	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1146533--1146569	11	3.2	12	81	11	51	70	0	0	29	0.88
1146526--1146661	21	5.9	25	71	24	70	59	0	0	39	1.03
1146531--1146653	27	4.5	27	70	19	78	59	0	0	40	0.97
1146620--1146667	16	3.0	15	77	22	53	64	0	0	35	0.94
1146514--1146667	21	7.7	21	65	25	68	61	0	0	38	1.01
1147685--1147722	11	3.7	10	86	13	51	73	0	0	26	0.83
1147677--1147722	20	2.2	20	84	11	56	71	2	0	26	0.97
1147714--1147748	16	2.3	16	90	9	56	65	0	2	31	1.07
1147702--1147740	8	4.8	8	81	6	51	69	0	2	28	1.02
1147695--1147750	17	3.0	19	74	25	57	67	0	1	30	1.01

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14