genome.fa.s189.2.7.7.80.10.50.1000.5.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: Scaffold189
Parameters: 2 7 7 80 10 50 1000
Length:  2243555

Tables:   1   2   3   4   5   6   7   8   9   

This is table  5  of  9  ( 1067 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)
986037--986070	11	3.0	11	86	4	50	67	0	0	32	0.91
991129--991170	17	2.5	17	85	11	52	26	0	2	71	0.98
991136--991170	18	2.0	17	88	5	52	22	0	2	74	0.95
991935--991974	2	20.0	2	100	0	80	0	50	0	50	1.00
995921--995952	9	3.7	9	95	4	57	21	34	0	43	1.53
997638--997677	2	20.0	2	100	0	80	50	0	0	50	1.00
998122--998157	12	3.0	12	87	0	54	52	0	2	44	1.15
998382--998418	3	12.3	3	94	0	56	27	0	37	35	1.57
1004469--1004511	2	21.5	2	100	0	86	51	0	48	0	1.00
1007885--1007909	8	3.1	8	100	0	50	40	0	0	60	0.97
1013342--1013391	13	3.4	14	75	20	57	40	0	2	58	1.10
1015385--1015435	27	2.0	26	85	14	70	35	1	0	62	1.06
1017399--1017448	26	1.9	26	88	8	75	46	0	2	52	1.12
1017449--1017512	34	1.9	34	87	6	96	43	0	0	56	0.99
1017484--1017582	31	3.5	27	70	21	69	47	0	0	52	1.00
1017927--1017954	5	5.6	5	100	0	56	42	0	0	57	0.99
1018029--1018077	18	2.6	19	84	9	57	67	0	0	32	0.91
1018046--1018086	12	3.4	12	81	18	50	70	0	0	29	0.87
1020761--1020797	3	12.3	3	88	0	56	62	32	2	2	1.23
1023908--1023989	31	2.6	30	80	16	78	54	1	1	42	1.15
1029070--1029168	52	1.9	52	91	0	162	33	18	10	38	1.84
1030766--1030821	21	2.5	23	75	21	57	62	3	0	33	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1031026--1031085	25	2.4	25	83	2	68	80	3	15	1	0.93
1031046--1031085	12	3.3	12	82	0	53	85	0	12	2	0.71
1031045--1031085	22	1.9	21	90	5	64	82	0	14	2	0.76
1031019--1031086	21	3.3	21	72	15	61	77	2	16	2	1.00
1031103--1031155	22	2.4	23	85	14	76	35	0	0	64	0.94
1031785--1032070	136	2.1	137	89	4	436	28	7	8	55	1.56
1031831--1032124	136	2.2	133	80	8	326	28	6	10	54	1.59
1032700--1032779	35	2.3	35	79	10	92	30	2	1	66	1.13
1032800--1032858	27	2.1	27	81	9	66	47	0	0	52	1.00
1032834--1032876	15	2.7	16	79	13	52	46	0	0	53	1.00
1032834--1032876	17	2.6	17	82	10	54	46	0	0	53	1.00
1039282--1039321	20	2.0	20	100	0	80	55	0	0	45	0.99
1039285--1039328	20	2.2	20	87	0	61	61	0	0	38	0.96
1039379--1039455	22	3.4	22	75	19	68	42	1	7	48	1.40
1040407--1040477	37	1.9	37	94	0	124	32	26	15	25	1.95
1045144--1045237	37	2.5	37	84	3	118	34	26	15	23	1.95
1047415--1047444	13	2.2	14	94	5	53	66	13	0	20	1.24
1048676--1048707	16	2.0	16	93	0	55	28	6	3	62	1.34
1051744--1051782	15	2.5	15	87	8	51	48	0	5	46	1.24
1055209--1055239	14	2.2	14	94	0	53	51	0	0	48	1.00
1055417--1055465	22	2.3	21	83	13	64	46	0	0	53	1.00
1055423--1055473	20	2.5	21	75	12	52	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1056395--1056450	20	2.6	22	75	13	64	66	0	0	33	0.92
1062359--1062465	21	5.2	20	83	8	103	34	0	8	57	1.29
1062359--1062434	11	7.4	11	72	21	58	32	0	7	59	1.26
1062386--1062441	10	5.6	10	76	19	55	37	0	7	55	1.27
1062359--1062465	41	2.6	40	84	7	119	34	0	8	57	1.29
1066996--1067042	24	1.9	25	86	4	69	51	0	0	48	1.00
1070161--1070235	21	3.7	20	76	11	62	52	0	4	44	1.20
1070459--1070514	20	2.6	21	77	13	60	53	0	0	46	1.00
1081801--1081834	2	17.0	2	100	0	68	50	0	0	50	1.00
1081834--1081873	2	20.0	2	100	0	80	50	0	50	0	1.00
1084262--1084300	4	9.8	4	88	0	60	25	46	0	28	1.53
1084327--1084358	15	2.0	17	88	11	50	37	3	15	43	1.63
1085049--1085077	2	14.5	2	100	0	58	51	0	0	48	1.00
1085965--1085998	13	2.7	13	86	4	52	67	5	26	0	1.13
1087607--1087653	21	2.2	20	85	7	58	46	0	0	53	1.00
1088277--1088326	5	10.8	5	75	16	54	42	2	0	56	1.11
1088857--1088885	6	4.8	6	100	0	58	0	34	0	65	0.93
1093173--1093205	2	16.5	2	93	0	57	48	3	0	48	1.17
1096540--1096569	2	15.0	2	100	0	60	50	0	0	50	1.00
1096712--1096748	14	2.5	15	86	8	58	40	0	0	59	0.97
1097417--1097450	16	2.1	17	88	5	52	35	0	0	64	0.94
1106692--1106758	14	4.9	14	66	15	50	38	1	0	59	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1106706--1106755	18	2.8	18	76	11	57	40	2	0	58	1.10
1112688--1112716	2	14.5	2	100	0	58	48	0	0	51	1.00
1116262--1116312	20	2.5	20	78	9	59	50	1	0	47	1.12
1117671--1117983	158	2.0	158	95	0	563	38	21	15	24	1.92
1124265--1124291	14	1.9	14	100	0	54	0	11	0	88	0.50
1127551--1127708	11	15.6	10	68	23	84	54	0	1	43	1.13
1127551--1127708	21	7.8	21	77	14	154	54	0	1	43	1.13
1127613--1127708	20	4.9	19	75	19	83	56	0	2	41	1.11
1130570--1130630	29	2.1	30	81	9	72	44	0	0	55	0.99
1130620--1130671	26	2.0	26	84	3	68	51	0	0	48	1.00
1131288--1131448	59	2.6	60	82	5	180	29	13	7	50	1.68
1131477--1131512	2	17.5	2	94	5	63	47	2	0	50	1.15
1131745--1131794	18	2.5	19	81	15	57	34	2	0	64	1.05
1131745--1131813	29	2.4	30	83	7	81	36	1	1	60	1.14
1131744--1131853	47	2.3	46	74	19	102	38	0	1	59	1.15
1131787--1131843	16	3.5	15	78	19	60	38	0	3	57	1.16
1148832--1148870	14	2.8	13	85	14	51	41	2	0	56	1.13
1150437--1150480	18	2.4	18	85	11	54	54	2	0	43	1.12
1153258--1153322	11	6.3	10	76	16	62	40	0	1	58	1.07
1156911--1156946	16	2.2	17	90	5	56	44	0	2	52	1.15
1161103--1161135	2	16.5	2	93	0	57	0	48	0	51	1.00
1162530--1162591	30	2.1	30	85	11	83	46	0	1	51	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1170267--1170306	15	2.7	15	88	7	55	35	2	20	42	1.65
1175189--1175230	15	2.7	15	88	3	66	23	52	9	14	1.71
1175189--1175226	16	2.4	16	91	4	60	23	50	10	15	1.75
1175324--1175380	27	2.1	27	86	0	78	26	43	3	26	1.70
1175653--1175804	75	2.0	75	85	9	204	32	9	20	38	1.84
1181253--1181281	5	5.8	5	100	0	58	62	0	0	37	0.96
1183692--1183717	3	8.7	3	100	0	52	30	0	0	69	0.89
1184491--1184537	15	3.0	15	82	11	67	65	0	0	34	0.93
1184491--1184534	17	2.8	15	83	12	61	65	0	0	34	0.93
1184481--1184587	34	3.0	34	80	9	108	68	0	2	28	1.04
1184742--1184808	25	2.7	25	86	9	84	34	7	0	58	1.26
1185803--1185827	2	12.5	2	100	0	50	52	0	0	48	1.00
1188760--1188799	21	1.9	21	84	0	53	75	5	5	15	1.15
1189303--1189339	18	2.0	20	89	10	60	51	0	0	48	1.00
1189330--1189387	17	3.5	17	76	21	61	58	0	0	41	0.98
1189327--1189376	21	2.3	20	83	10	55	62	0	0	38	0.96
1189300--1189391	18	5.3	18	71	20	56	56	0	0	43	0.99
1189309--1189413	13	8.2	13	68	24	55	57	0	0	42	0.99
1189342--1189411	28	2.5	28	93	6	117	58	0	0	41	0.98
1189289--1189410	34	3.8	31	73	14	97	55	0	0	44	0.99
1191976--1192049	33	2.2	32	81	11	87	43	0	0	56	0.99
1191987--1192089	44	2.4	43	78	9	104	41	0	0	57	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1191990--1192056	32	2.1	33	85	2	91	43	0	1	55	1.09
1193213--1193238	2	13.0	2	100	0	52	0	50	0	50	1.00
1203607--1203635	3	9.7	3	100	0	58	68	0	0	31	0.89
1204109--1204143	11	3.2	11	91	0	52	68	0	2	28	1.04
1204106--1204150	17	2.5	19	79	17	60	68	0	2	28	1.01
1204190--1204220	15	2.0	16	93	6	55	38	12	12	35	1.82
1204436--1204486	17	3.1	16	75	16	50	66	0	0	33	0.92
1205723--1205761	12	3.3	12	96	3	71	79	0	15	5	0.90
1206020--1206071	19	2.7	20	72	6	52	40	0	3	55	1.18
1207001--1207025	2	12.5	2	100	0	50	52	0	0	48	1.00

Tables:   1   2   3   4   5   6   7   8   9