genome.fa.s125.2.7.7.80.10.50.1000.9.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: Scaffold125
Parameters: 2 7 7 80 10 50 1000
Length:  3608436

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   

This is table  9  of  18  ( 2131 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)
1368423--1368488	34	1.9	35	87	9	100	40	0	0	59	0.98
1368421--1368527	36	3.0	35	78	11	94	36	0	0	62	1.02
1370779--1370803	2	12.5	2	100	0	50	52	0	0	48	1.00
1370961--1371013	25	2.3	23	81	18	58	47	9	1	41	1.47
1371791--1371831	21	2.0	21	85	0	55	53	0	0	46	1.00
1372445--1372476	2	16.0	2	93	0	55	46	0	3	50	1.17
1382190--1382218	14	2.0	15	93	6	51	68	0	3	27	1.05
1383763--1383857	48	2.0	48	83	8	122	35	7	13	43	1.72
1396543--1396586	24	1.9	22	81	9	52	38	9	20	31	1.84
1397179--1397226	3	15.7	3	91	4	78	29	0	4	66	1.10
1397519--1397570	25	2.1	25	82	3	61	63	0	3	32	1.12
1403337--1403369	2	17.0	2	93	6	59	51	0	0	48	1.00
1408246--1408313	21	3.2	20	83	4	73	4	19	32	44	1.70
1408852--1408916	3	21.7	3	83	0	67	1	24	33	40	1.65
1408854--1408909	21	2.7	21	91	0	85	1	21	33	42	1.63
1408852--1408912	24	2.5	24	91	0	95	1	22	34	40	1.64
1408841--1408912	21	3.3	21	79	11	72	1	22	34	41	1.62
1409109--1409135	6	4.5	6	100	0	54	0	14	48	37	1.45
1415579--1415607	5	5.8	5	100	0	58	0	0	62	37	0.96
1434993--1435037	18	2.5	18	85	0	63	37	0	0	62	0.96
1435313--1435359	24	2.0	23	87	4	67	46	2	0	51	1.13
1439726--1439791	34	1.9	34	96	0	123	46	4	27	21	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1441710--1441764	10	5.4	10	76	18	51	45	0	0	54	0.99
1441709--1441776	20	3.2	22	80	14	63	47	0	1	51	1.09
1441731--1441778	10	4.6	10	82	15	53	45	0	2	52	1.12
1441716--1441778	20	3.0	21	79	9	65	47	0	1	50	1.10
1441867--1441906	14	2.9	14	85	3	55	50	0	0	50	1.00
1441890--1441959	29	2.4	29	80	2	88	48	0	0	51	1.00
1443085--1443147	21	3.1	21	73	15	60	58	0	0	41	0.98
1443091--1443148	11	5.2	11	80	10	64	62	0	0	37	0.96
1443184--1443239	28	2.0	28	82	6	69	55	0	0	44	0.99
1444351--1444388	14	2.7	15	84	8	53	55	0	0	44	0.99
1450239--1450263	13	1.9	13	100	0	50	32	4	8	56	1.47
1450655--1450717	23	2.7	22	78	19	74	52	0	0	47	1.00
1450656--1450736	26	3.3	24	81	13	87	50	0	0	49	1.00
1450677--1450810	59	2.3	58	75	15	132	49	0	0	50	1.00
1453593--1454145	183	3.0	183	96	0	1000	42	16	14	26	1.86
1455064--1455148	43	2.0	43	100	0	170	34	16	21	28	1.95
1458188--1458240	25	2.1	25	82	6	63	39	1	0	58	1.09
1460395--1460422	2	14.0	2	100	0	56	50	0	0	50	1.00
1461755--1462156	203	2.0	204	97	0	770	36	21	11	30	1.89
1463066--1463199	32	4.2	31	78	7	126	44	10	11	33	1.74
1463086--1463199	16	7.1	16	81	3	113	43	10	12	33	1.76
1463075--1463183	48	2.3	48	82	6	132	43	11	12	33	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1463831--1463881	14	3.4	15	81	8	59	45	0	1	52	1.12
1463877--1463909	9	3.8	9	88	4	50	60	0	0	39	0.97
1463951--1463988	18	2.2	18	86	13	53	34	0	2	63	1.09
1463948--1464005	16	3.6	16	70	25	50	39	0	1	58	1.08
1463948--1464028	32	2.6	29	83	14	99	41	1	1	55	1.15
1467372--1467399	2	14.0	2	100	0	56	50	0	0	50	1.00
1470549--1470631	26	3.1	26	71	8	76	53	0	2	44	1.13
1472273--1472306	17	2.0	17	94	0	59	38	0	0	61	0.96
1472247--1472310	28	2.2	29	86	5	85	43	0	1	54	1.09
1472294--1472346	23	2.2	22	87	12	70	50	0	0	49	1.00
1472290--1472360	35	2.0	35	83	8	90	50	0	0	49	1.00
1472306--1472384	40	2.0	41	82	7	99	54	0	0	45	0.99
1472700--1472735	3	11.7	3	94	5	63	36	0	0	63	0.94
1472702--1472732	16	1.9	16	100	0	62	35	0	0	64	0.94
1472700--1472736	19	1.9	19	100	0	74	37	0	0	62	0.96
1487649--1487683	17	2.1	17	100	0	70	22	11	17	48	1.79
1490346--1490505	77	2.1	77	91	2	259	37	11	12	38	1.80
1492046--1492104	19	3.0	19	80	5	55	40	1	0	57	1.09
1492065--1492106	15	2.9	15	89	6	61	45	0	0	54	0.99
1492170--1492217	22	2.2	21	85	3	60	47	0	2	50	1.12
1492207--1492264	30	1.9	30	83	13	75	46	0	1	51	1.11
1492272--1492352	32	2.6	32	76	14	80	40	0	1	58	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1499086--1499110	3	8.3	3	100	0	50	32	0	0	68	0.90
1499328--1499381	26	2.1	25	83	10	65	29	0	1	68	1.00
1501758--1502041	148	1.9	148	89	1	444	35	10	13	40	1.78
1503055--1503120	2	35.5	2	77	19	72	50	1	0	48	1.10
1503055--1503123	22	3.1	22	84	12	97	50	1	0	47	1.09
1509008--1509042	2	17.5	2	100	0	70	0	48	0	51	1.00
1509729--1509754	2	13.0	2	100	0	52	50	0	0	50	1.00
1509758--1510069	167	1.9	165	93	2	536	30	20	16	31	1.95
1514851--1514900	27	1.9	25	84	15	66	48	12	4	36	1.59
1516012--1516037	2	13.0	2	100	0	52	50	0	0	50	1.00
1517892--1517953	21	3.3	19	77	16	67	43	0	0	56	0.99
1520957--1520993	16	2.4	16	86	13	51	56	0	0	43	0.99
1522232--1522269	6	6.3	6	88	11	60	50	0	0	50	1.00
1522895--1522961	27	2.5	26	76	7	71	40	0	0	59	0.97
1522894--1522969	22	3.4	22	81	13	77	38	0	0	61	0.96
1522890--1522977	32	3.1	28	76	17	83	39	0	0	60	0.97
1522939--1523016	29	2.7	29	82	4	77	47	0	0	52	1.00
1523002--1523049	17	2.9	17	84	6	62	62	0	2	35	1.07
1522994--1523044	17	3.1	16	83	8	66	62	0	1	35	1.06
1522994--1523069	33	2.2	36	82	15	90	60	0	1	38	1.05
1523035--1523090	21	2.7	21	78	13	62	58	1	0	39	1.08
1523097--1523150	21	2.6	20	75	13	56	48	0	1	50	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1523266--1523308	21	2.0	21	91	8	70	55	2	0	41	1.12
1523745--1523777	3	11.0	3	100	0	66	66	0	0	33	0.92
1529035--1529079	23	2.0	23	90	0	72	24	8	15	51	1.72
1532898--1532937	2	20.0	2	89	0	62	50	0	5	45	1.23
1534895--1534935	20	2.1	20	86	13	59	26	0	0	73	0.84
1536752--1536776	2	12.5	2	100	0	50	0	48	0	52	1.00
1538066--1538108	15	2.7	16	82	7	52	65	0	0	34	0.93
1538090--1538114	11	2.3	11	100	0	50	68	0	0	32	0.90
1538066--1538113	21	2.3	21	77	0	51	64	0	0	35	0.94
1539380--1539449	32	2.1	33	80	17	83	45	1	0	52	1.09
1539428--1539468	20	2.0	20	90	0	64	51	0	0	48	1.00
1540639--1540710	36	2.0	36	83	0	90	37	6	9	45	1.64
1546819--1546871	23	2.4	22	77	3	61	43	0	1	54	1.11
1546967--1547084	36	3.1	38	77	10	100	55	1	0	42	1.09
1547015--1547083	8	8.1	9	70	20	51	50	1	0	47	1.09
1546950--1547081	17	7.8	17	63	28	52	55	1	0	42	1.14
1547276--1547326	26	2.0	27	84	7	70	62	0	1	35	1.06
1547314--1547383	28	2.4	29	81	9	81	57	1	2	38	1.23
1550450--1550479	13	2.3	13	100	0	60	43	0	20	36	1.52
1551215--1551271	30	1.9	30	86	13	82	47	0	8	43	1.34
1551614--1551665	21	2.5	21	79	17	63	57	0	0	42	0.98
1551614--1551666	22	2.5	23	80	14	62	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)
1562096--1562415	106	3.0	106	96	1	597	30	13	13	42	1.83
1565320--1565417	50	2.0	50	89	4	153	28	10	26	34	1.89
1565867--1565919	23	2.3	23	93	3	88	43	0	7	49	1.31
1565875--1565923	23	2.1	23	100	0	98	40	0	4	55	1.19
1574483--1574548	32	2.1	32	85	5	89	50	0	0	50	1.00
1579926--1579964	3	13.0	3	100	0	78	33	0	0	66	0.92
1580445--1580482	2	19.0	2	100	0	76	50	0	0	50	1.00
1587369--1587456	17	5.0	17	72	13	70	39	0	0	60	0.97
1587413--1587511	28	3.3	30	74	8	94	41	0	2	56	1.11
1587399--1587511	58	1.9	57	82	7	129	41	0	1	56	1.09

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18