genome.fa.s168.2.7.7.80.10.50.1000.13.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: Scaffold168
Parameters: 2 7 7 80 10 50 1000
Length:  2098754

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

This is table  13  of  16  ( 1854 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)
1444305--1444390	43	2.0	44	82	15	108	59	1	0	39	1.05
1444305--1444366	21	2.9	22	83	9	83	59	0	0	40	0.97
1444563--1444594	2	16.0	2	100	0	64	50	0	0	50	1.00
1446377--1446429	3	17.7	3	100	0	106	0	32	0	67	0.91
1448468--1448496	12	2.5	12	94	5	51	31	0	0	68	0.89
1455444--1455506	21	3.0	21	76	4	56	38	0	0	61	0.96
1455649--1455685	17	2.1	19	85	10	51	62	0	0	37	0.96
1455869--1455899	3	10.3	3	92	0	53	64	0	3	32	1.09
1456046--1456072	3	9.0	3	100	0	54	66	0	0	33	0.92
1456071--1456100	3	10.0	3	100	0	60	33	0	0	66	0.92
1456407--1456492	27	3.2	27	73	15	72	45	0	2	52	1.13
1456407--1456494	29	3.1	29	68	18	69	44	0	2	53	1.13
1459902--1459957	17	3.2	17	73	16	51	57	1	1	39	1.20
1460217--1460258	2	21.0	2	95	0	75	47	2	0	50	1.14
1460510--1460564	14	3.8	14	75	15	58	60	1	0	38	1.08
1473318--1473357	6	6.7	6	94	0	71	17	0	0	82	0.67
1473548--1473603	11	5.1	11	74	12	53	41	3	3	51	1.36
1473556--1473597	21	2.0	20	86	4	57	38	4	4	52	1.44
1475675--1475704	2	15.0	2	100	0	60	50	0	0	50	1.00
1476691--1476731	21	2.0	21	85	9	57	34	0	4	60	1.18
1476699--1476743	22	2.2	20	84	8	54	31	0	4	64	1.13
1477581--1477616	2	18.0	2	88	11	56	50	0	2	47	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1478609--1478670	28	2.3	26	80	8	61	46	1	0	51	1.10
1479803--1479838	2	18.0	2	100	0	72	50	0	50	0	1.00
1480033--1480097	32	2.1	31	85	8	87	40	0	1	58	1.07
1480262--1480319	20	3.0	20	82	14	68	55	0	0	44	0.99
1480944--1481000	22	2.5	22	85	2	69	42	0	3	54	1.17
1481553--1481701	28	5.2	28	75	15	119	38	0	0	60	1.02
1481555--1481701	57	2.6	59	76	10	160	39	0	0	59	1.02
1481553--1481687	48	2.8	47	75	11	121	40	0	0	59	1.03
1481553--1481699	18	7.8	19	65	22	69	38	0	0	60	1.02
1482659--1482754	29	3.4	28	78	17	101	54	2	0	43	1.12
1482659--1482724	16	4.2	16	79	13	75	54	3	0	42	1.15
1482679--1482783	37	2.7	39	82	7	117	56	0	0	42	1.06
1482685--1482730	9	5.1	9	79	15	51	58	0	0	41	0.98
1482674--1482845	15	12.7	14	70	19	75	54	1	0	43	1.15
1482674--1482873	15	13.3	15	70	22	70	55	2	0	42	1.15
1482700--1482774	22	3.4	21	78	14	80	54	0	0	45	0.99
1482680--1482783	38	2.7	38	81	11	124	56	0	0	42	1.05
1483363--1483407	23	1.9	24	86	4	65	37	0	0	62	0.96
1483346--1483410	23	3.0	22	76	12	64	33	0	0	66	0.92
1485603--1485639	2	19.5	2	89	10	60	51	0	0	48	1.00
1485887--1485933	13	3.4	14	82	11	62	44	0	0	55	0.99
1485887--1485941	7	8.3	7	76	15	55	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1485890--1485941	26	2.0	26	88	7	79	44	0	0	55	0.99
1485899--1485960	33	1.9	31	83	6	79	46	1	1	50	1.20
1486396--1486424	13	2.1	14	93	6	51	44	0	0	55	0.99
1487046--1487131	45	1.9	44	88	6	129	25	19	25	29	1.99
1487287--1487342	26	2.2	26	86	0	76	46	25	12	16	1.81
1492424--1492512	30	3.0	29	78	6	88	46	15	10	28	1.78
1493395--1493434	20	2.0	20	95	0	71	72	0	0	27	0.85
1494115--1494172	18	3.1	19	73	14	57	43	0	0	56	0.99
1494917--1494958	18	2.2	20	87	8	61	42	2	2	52	1.27
1495578--1495619	19	2.2	19	87	8	59	45	0	0	54	0.99
1495563--1495634	32	2.2	32	87	5	99	48	0	1	50	1.09
1495572--1495634	32	1.9	34	90	6	103	47	0	0	52	1.00
1495925--1495973	14	3.6	14	83	5	57	44	0	0	55	0.99
1495988--1496029	11	3.9	11	76	17	52	47	0	0	52	1.00
1496580--1496679	22	4.4	23	72	14	66	56	0	1	43	1.06
1496800--1496831	16	2.0	16	100	0	64	56	6	25	12	1.59
1496972--1497014	11	3.9	11	85	8	52	62	2	0	34	1.08
1497206--1497284	36	2.3	34	81	14	90	43	3	0	53	1.19
1498358--1498403	21	2.2	20	84	3	56	41	4	0	54	1.20
1499298--1499383	35	2.4	38	83	11	103	56	0	0	43	0.99
1499315--1499384	20	3.7	21	78	17	75	60	0	0	40	0.97
1499341--1499396	17	3.3	17	75	20	55	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)
1499488--1499527	18	2.1	19	90	9	64	25	5	0	70	1.08
1500345--1500389	17	2.6	17	85	3	63	64	0	2	33	1.06
1500594--1500622	2	14.5	2	100	0	58	0	48	0	51	1.00
1505200--1505316	41	2.9	40	77	10	105	49	0	0	50	1.00
1505263--1505333	30	2.3	30	78	7	81	45	0	0	54	0.99
1510109--1510159	4	12.8	4	91	0	57	49	15	0	35	1.45
1510109--1510172	32	2.0	32	96	0	119	48	12	0	39	1.41
1510125--1510172	2	24.0	2	79	8	53	47	8	0	43	1.33
1520517--1520545	2	14.5	2	100	0	58	51	0	48	0	1.00
1524765--1524792	2	14.0	2	100	0	56	50	0	0	50	1.00
1525628--1525766	69	2.0	69	90	2	217	39	11	17	31	1.85
1534814--1534907	16	5.6	17	70	20	56	48	0	2	48	1.13
1534814--1534883	32	2.2	33	84	7	90	48	0	2	48	1.16
1534847--1534917	28	2.6	27	78	10	83	50	0	1	47	1.09
1535657--1535697	22	1.9	22	85	5	57	43	2	0	53	1.13
1535700--1535730	16	1.9	16	93	0	53	54	0	0	45	0.99
1542227--1542266	17	2.4	17	87	4	55	52	0	2	45	1.14
1542271--1542318	19	2.5	20	87	12	66	27	0	0	72	0.84
1542272--1542329	6	9.3	6	78	10	55	32	0	0	67	0.91
1542706--1542768	31	2.0	31	84	0	81	44	0	0	55	0.99
1542689--1542779	39	2.3	39	79	7	96	46	1	0	52	1.07
1543078--1543118	20	2.0	20	78	21	50	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1543075--1543118	19	2.3	20	85	14	58	40	0	0	59	0.98
1543085--1543127	15	2.8	16	78	7	52	51	0	0	48	1.00
1543122--1543206	43	2.0	43	81	4	100	40	5	1	52	1.33
1544197--1544278	16	5.2	16	76	8	87	40	1	2	56	1.20
1544197--1544275	21	3.5	21	72	16	68	40	1	2	55	1.21
1544253--1544281	15	2.0	15	93	6	51	44	0	0	55	0.99
1547376--1547404	2	14.5	2	100	0	58	48	0	0	51	1.00
1551730--1551760	2	15.5	2	100	0	62	48	0	0	51	1.00
1551768--1551826	29	2.0	29	83	6	75	37	0	5	57	1.21
1554168--1554199	2	16.0	2	100	0	64	50	0	0	50	1.00
1554372--1554403	10	3.1	10	95	4	55	56	0	3	40	1.15
1554380--1554463	32	3.1	26	72	21	73	52	1	0	46	1.08
1554791--1554823	2	16.5	2	100	0	66	48	0	0	51	1.00
1554963--1554993	3	10.3	3	100	0	62	64	0	35	0	0.94
1555342--1555378	2	18.5	2	88	0	56	51	2	0	45	1.15
1556026--1556060	2	17.5	2	93	0	61	54	0	0	45	0.99
1556176--1556208	2	17.0	2	87	6	50	51	0	0	48	1.00
1557707--1557744	2	19.0	2	94	0	67	0	47	0	52	1.00
1557808--1557865	19	3.0	19	73	12	55	37	3	3	55	1.34
1559030--1559058	14	2.1	14	93	6	51	58	0	3	37	1.15
1560199--1560224	2	13.0	2	100	0	52	50	50	0	0	1.00
1560224--1560250	2	13.5	2	100	0	54	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)
1561153--1561200	19	2.6	18	80	9	60	64	0	0	35	0.94
1562134--1562186	19	2.8	18	80	5	52	24	0	1	73	0.93
1562165--1562210	17	2.8	17	78	15	51	41	0	0	58	0.98
1563572--1563804	116	2.0	116	93	0	394	48	6	6	37	1.57
1564944--1564968	1	25.0	1	100	0	50	100	0	0	0	0.00
1565093--1565146	16	3.4	16	77	12	58	50	0	0	50	1.00
1565081--1565134	16	3.1	18	76	13	58	46	0	0	53	1.00
1568683--1568723	20	2.0	20	100	0	82	41	0	4	53	1.22
1569417--1569485	16	4.2	16	72	9	50	52	8	5	33	1.56
1569415--1569476	32	1.9	32	83	0	79	50	8	8	33	1.61

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