genome.fa.s4.2.7.7.80.10.50.1000.4.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   

This is table  4  of  31  ( 3628 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)
940299--940354	25	2.2	25	78	12	62	44	0	0	55	0.99
941618--941686	34	2.0	34	94	0	120	26	20	17	36	1.94
943255--943359	52	2.0	52	98	0	201	36	12	17	34	1.87
953064--953096	2	16.5	2	100	0	66	51	0	0	48	1.00
953400--953447	20	2.3	20	79	10	53	37	4	4	54	1.39
954162--954211	22	2.2	24	85	7	68	42	0	0	58	0.98
956190--956219	2	15.0	2	92	0	51	50	3	0	46	1.18
956735--956772	2	19.0	2	94	0	67	47	0	2	50	1.15
967660--967701	2	21.0	2	100	0	84	50	0	0	50	1.00
967740--967776	2	18.5	2	100	0	74	51	0	48	0	1.00
969114--969170	20	2.9	19	77	10	62	49	1	3	45	1.29
972386--972430	21	2.1	22	91	4	74	28	2	0	68	1.01
972390--972438	21	2.2	21	82	7	53	34	2	2	61	1.19
972440--972494	26	2.2	26	80	9	60	41	1	16	40	1.59
972725--972774	21	2.5	21	80	6	59	58	2	0	40	1.10
977513--977542	2	15.0	2	92	0	51	46	0	0	53	1.00
990441--990467	13	2.1	13	100	0	54	37	7	7	48	1.59
992890--992930	17	2.4	16	84	11	55	68	2	0	29	1.03
996260--996291	2	16.0	2	100	0	64	50	0	0	50	1.00
998428--998468	20	2.0	21	85	4	57	68	0	0	31	0.90
1004809--1004870	21	2.8	24	76	19	78	56	0	0	43	0.99
1005433--1005461	14	2.1	14	100	0	58	65	0	13	20	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1005504--1005562	19	3.2	18	86	9	82	54	3	0	42	1.17
1005603--1005661	11	5.2	11	76	13	57	61	0	1	37	1.07
1005602--1005661	23	2.7	23	80	16	65	60	0	1	38	1.07
1005602--1005678	34	2.3	34	84	4	93	55	0	1	42	1.07
1005745--1005790	19	2.5	19	82	6	60	67	2	0	30	1.03
1006283--1006331	21	2.3	20	80	16	55	40	0	0	59	0.98
1006604--1006801	50	4.0	50	86	5	265	29	19	18	32	1.96
1011253--1011450	50	4.0	50	87	1	263	28	16	20	33	1.95
1016989--1017039	24	2.1	24	100	0	102	68	7	0	23	1.15
1017240--1017265	2	13.0	2	100	0	52	50	0	50	0	1.00
1017416--1017558	19	7.4	20	66	18	61	37	0	0	61	1.01
1017483--1017568	37	2.4	35	86	9	120	34	0	0	65	0.93
1017482--1017558	29	2.6	28	80	11	75	32	0	0	67	0.91
1017446--1017566	17	5.7	20	71	17	77	36	0	0	63	0.95
1017925--1017983	24	2.5	23	76	17	59	57	0	0	42	0.98
1022327--1022361	3	11.7	3	100	0	70	68	0	0	31	0.90
1023281--1023308	14	2.0	14	100	0	56	42	7	7	42	1.59
1024374--1024481	30	3.6	29	81	5	126	37	4	2	54	1.36
1027044--1027072	15	1.9	15	100	0	58	27	0	0	72	0.85
1027305--1027344	3	13.3	3	100	0	80	65	0	0	35	0.93
1028165--1028214	25	2.0	25	84	3	66	46	2	0	52	1.12
1029077--1029346	139	2.0	137	96	1	495	37	20	25	17	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1029852--1029878	4	6.8	4	100	0	54	22	0	0	77	0.76
1030621--1030654	14	2.4	14	95	0	59	44	0	0	55	0.99
1030933--1030978	24	1.9	24	82	8	58	43	4	2	50	1.34
1033534--1033566	2	16.5	2	100	0	66	51	0	0	48	1.00
1036873--1036924	23	2.3	23	81	15	65	71	0	1	26	0.97
1036886--1036953	32	2.1	33	83	8	86	67	1	1	29	1.08
1038553--1038577	13	1.9	13	100	0	50	76	0	0	24	0.80
1038637--1038704	24	2.7	24	82	13	66	66	0	1	32	1.01
1039508--1039607	51	2.0	51	100	0	200	52	9	8	31	1.62
1039951--1040045	31	3.0	32	80	14	83	62	3	0	34	1.11
1039981--1040059	16	4.8	16	71	10	61	63	1	0	35	1.03
1040069--1040116	13	3.6	13	78	13	53	0	18	0	81	0.70
1040069--1040113	17	2.6	17	89	0	63	0	17	0	82	0.68
1043695--1043719	5	5.0	5	100	0	50	40	0	0	60	0.97
1044057--1044100	16	2.7	16	76	16	54	38	0	0	61	0.96
1044078--1044128	14	3.9	13	78	12	52	45	0	0	54	0.99
1044882--1044939	20	2.9	20	84	5	73	58	0	1	39	1.08
1045619--1045684	31	2.1	32	83	11	82	39	6	3	51	1.42
1045680--1045719	20	2.0	20	85	0	53	50	5	0	45	1.23
1047045--1047083	18	2.2	17	86	4	51	43	0	5	51	1.24
1048654--1048697	21	2.2	20	87	4	61	6	11	2	79	1.01
1051931--1051969	19	2.1	19	95	0	69	41	7	10	41	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1061539--1061579	2	20.5	2	89	0	64	43	0	4	51	1.23
1061790--1061831	22	1.9	22	85	0	57	52	9	4	33	1.55
1063801--1063849	16	3.0	16	79	5	53	46	0	2	51	1.12
1063952--1063981	2	15.0	2	100	0	60	50	0	0	50	1.00
1065022--1065046	2	12.5	2	100	0	50	52	0	0	48	1.00
1066128--1066161	17	2.0	17	94	0	59	50	0	0	50	1.00
1066178--1066223	19	2.4	19	85	3	56	60	2	2	34	1.21
1066788--1066819	15	2.0	17	88	11	50	62	18	3	15	1.45
1067207--1067250	2	21.5	2	81	4	52	45	4	0	50	1.22
1077575--1077604	2	15.0	2	100	0	60	0	50	0	50	1.00
1078602--1078686	29	3.0	29	78	11	70	37	1	3	57	1.23
1078609--1078696	28	3.1	27	79	15	81	34	1	4	60	1.25
1078737--1078800	22	2.8	23	77	17	80	54	0	3	42	1.16
1078764--1078832	30	2.3	30	85	2	95	53	0	7	39	1.29
1078845--1078945	26	4.0	25	75	17	84	60	0	1	36	1.15
1085800--1085862	31	2.0	31	96	0	117	25	14	15	44	1.84
1087811--1087883	11	7.3	11	73	17	52	36	1	0	61	1.05
1087823--1087877	16	3.2	18	72	15	53	34	1	0	63	1.05
1087808--1087875	25	2.9	24	79	16	79	35	1	0	63	1.04
1088129--1088206	33	2.6	31	82	13	92	42	0	1	56	1.07
1088141--1088191	15	3.3	15	74	17	50	45	0	1	52	1.12
1088694--1088727	12	2.8	12	95	0	59	8	38	5	47	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1088693--1088736	12	3.7	12	81	9	54	6	40	4	47	1.50
1092421--1092450	15	2.0	15	93	0	51	26	23	0	50	1.50
1095914--1095961	18	2.4	20	86	13	64	58	2	0	39	1.10
1097507--1097548	16	2.6	16	77	7	50	38	0	0	61	0.96
1097530--1097608	24	3.4	22	75	16	61	44	0	0	55	0.99
1097983--1098035	22	2.4	22	87	0	70	50	3	3	41	1.38
1098769--1098825	17	3.2	18	76	14	55	52	0	3	43	1.18
1099998--1100035	19	2.1	18	90	5	58	36	2	0	60	1.11
1100456--1100488	2	16.5	2	100	0	66	48	0	0	51	1.00
1103860--1103890	15	2.0	16	93	6	55	45	0	0	54	0.99
1103982--1104048	25	2.6	25	79	11	66	47	1	0	50	1.10
1104570--1104608	19	2.1	18	90	4	60	51	0	0	48	1.00
1111685--1111711	2	13.5	2	100	0	54	51	0	0	48	1.00
1126160--1126252	46	2.0	46	93	0	159	35	21	15	27	1.93
1128844--1128881	19	2.1	18	85	9	51	47	0	0	52	1.00
1129550--1129591	21	2.0	21	90	4	66	40	0	4	54	1.21
1129661--1129708	25	2.0	25	84	15	66	62	4	2	31	1.26
1130207--1130254	17	2.7	18	83	6	62	31	0	0	68	0.90
1130239--1130294	27	2.1	27	86	0	76	35	0	1	62	1.06
1130207--1130285	41	1.9	41	85	10	108	34	0	1	64	1.02
1139906--1139937	2	16.0	2	93	0	55	50	3	0	46	1.17
1142601--1142665	19	3.0	22	72	21	66	16	1	3	78	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1143689--1143731	11	3.8	11	81	12	52	30	4	2	62	1.28
1143693--1143732	21	1.9	21	85	10	55	27	5	2	65	1.27
1144916--1144975	24	2.6	22	81	7	66	66	0	1	31	1.01
1144914--1145026	33	3.6	32	77	12	92	60	0	1	38	1.07
1146727--1146796	26	3.0	22	71	21	61	54	0	0	45	0.99
1147209--1147244	3	12.0	3	100	0	72	33	0	0	66	0.92
1148473--1148519	8	5.8	8	78	14	51	53	0	0	46	1.00
1148485--1148531	18	2.7	18	83	3	60	61	0	0	38	0.96
1151344--1151412	20	3.2	20	66	15	57	46	5	1	46	1.35
1152490--1152516	3	9.0	3	100	0	54	33	0	0	66	0.92

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31