genome.fa.s8.2.7.7.80.10.50.1000.11.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   32   
          33   

This is table  11  of  33  ( 3942 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)
1467689--1467752	25	2.6	24	79	11	67	43	0	3	53	1.16
1468356--1468397	15	2.7	15	80	16	50	50	0	0	50	1.00
1468340--1468391	17	3.2	17	76	15	56	48	0	0	51	1.00
1468392--1468433	13	3.3	13	78	18	52	33	0	0	66	0.92
1471017--1471073	22	2.6	21	84	13	71	31	3	0	64	1.10
1471132--1471181	18	2.8	18	82	11	50	36	0	0	64	0.94
1471150--1471185	18	2.1	17	94	5	63	33	0	0	66	0.92
1471518--1471560	13	3.2	13	77	6	50	46	2	0	51	1.13
1471568--1471603	18	2.0	18	94	0	63	63	2	0	33	1.08
1472017--1472063	2	23.5	2	95	0	85	0	51	0	48	1.00
1473329--1473379	23	2.2	23	85	0	66	33	1	3	60	1.26
1474117--1474141	12	2.1	12	100	0	50	44	0	0	56	0.99
1474094--1474148	26	2.2	25	81	12	60	43	0	0	56	0.99
1477372--1477445	27	2.8	27	80	17	84	45	0	0	54	1.00
1477346--1477443	20	4.3	23	72	21	66	43	0	1	55	1.06
1477384--1477454	33	2.2	33	87	5	99	43	0	0	56	0.99
1477429--1477486	15	3.8	15	71	24	50	36	1	1	60	1.17
1478276--1478329	19	2.7	19	94	5	90	51	0	1	46	1.11
1478527--1478616	41	2.2	39	75	9	92	62	3	0	34	1.12
1478593--1478641	19	2.5	19	87	12	73	65	2	0	32	1.04
1479112--1479186	33	2.3	32	84	6	96	42	0	4	53	1.19
1479229--1479290	22	2.8	22	82	2	79	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)
1479230--1479304	31	2.4	30	78	6	87	40	0	0	60	0.97
1481103--1481128	3	8.7	3	100	0	52	34	0	0	65	0.93
1481330--1481367	14	2.6	15	87	4	51	47	0	2	50	1.15
1483326--1483366	20	2.1	20	86	4	57	51	2	0	46	1.14
1483725--1483764	15	2.6	15	80	4	53	52	2	0	45	1.14
1483749--1483788	19	2.0	20	85	4	55	47	0	2	50	1.14
1491539--1491599	31	1.9	32	83	9	81	32	1	4	60	1.28
1491612--1491669	22	2.7	20	76	17	55	44	0	0	55	0.99
1491645--1491687	12	3.5	12	83	3	50	55	0	0	44	0.99
1496538--1496663	62	2.0	62	87	0	180	49	6	8	35	1.59
1496976--1497002	3	9.0	3	100	0	54	0	33	33	33	1.58
1497507--1497552	2	23.0	2	100	0	92	50	0	0	50	1.00
1500374--1500406	2	16.5	2	100	0	66	51	0	0	48	1.00
1501527--1501556	13	2.3	13	100	0	60	63	0	0	36	0.95
1501523--1501565	21	2.0	21	86	0	59	65	0	0	34	0.93
1502727--1502766	21	1.9	21	85	10	55	40	0	0	60	0.97
1503121--1503160	20	2.0	20	85	5	53	47	0	2	50	1.14
1503133--1503192	30	2.0	30	83	9	77	51	0	3	45	1.17
1503828--1503876	18	2.8	18	74	17	50	42	2	2	53	1.24
1503874--1503970	35	2.8	37	81	10	98	32	2	0	64	1.05
1503904--1503966	26	2.6	25	87	7	85	28	0	0	71	0.86
1503874--1503970	23	4.1	24	77	16	87	32	2	0	64	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1505722--1505781	20	3.0	20	80	4	68	40	1	0	58	1.08
1505960--1505996	17	2.2	17	90	9	58	62	0	0	37	0.96
1506115--1506145	2	15.5	2	100	0	62	51	0	0	48	1.00
1506898--1506960	32	2.0	31	85	11	85	71	1	0	26	0.95
1511280--1511341	22	2.8	23	68	7	56	56	0	0	43	0.99
1511339--1511388	20	2.7	18	82	17	66	42	0	4	54	1.19
1517756--1517799	11	3.7	12	81	9	54	40	2	0	56	1.11
1518372--1518410	2	19.5	2	100	0	78	51	0	0	48	1.00
1519951--1520000	27	1.9	25	84	8	64	62	0	6	32	1.20
1520017--1520085	24	2.9	23	69	16	59	59	1	1	37	1.15
1520252--1520295	23	1.9	23	81	9	54	25	4	4	65	1.30
1520288--1520330	13	3.2	13	83	9	52	53	0	0	46	1.00
1520578--1520610	16	2.1	16	94	0	57	33	0	0	66	0.92
1520600--1520670	19	3.5	20	70	19	58	54	0	0	45	0.99
1521511--1521550	20	2.0	20	85	9	55	50	0	0	50	1.00
1523352--1523418	13	4.8	14	67	20	50	59	0	0	40	0.97
1523780--1523820	15	2.6	16	81	14	50	60	0	0	39	0.96
1524253--1524302	19	2.5	20	87	6	66	64	4	2	30	1.23
1524285--1524329	17	2.7	16	80	19	56	55	0	2	42	1.12
1525422--1525455	6	5.3	6	93	6	50	85	0	0	14	0.60
1525422--1525455	7	5.1	7	89	10	54	85	0	0	14	0.60
1525422--1525455	13	2.6	13	90	9	52	85	0	0	14	0.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1526852--1527286	86	5.0	87	74	10	239	45	8	6	40	1.60
1526792--1527270	260	1.9	257	84	4	642	44	8	6	41	1.60
1529330--1529366	16	2.3	16	90	0	56	56	8	8	27	1.56
1531756--1531800	6	7.5	6	100	0	90	33	0	15	51	1.44
1538925--1538960	18	2.1	17	89	5	54	47	5	0	47	1.25
1539600--1539625	9	2.9	9	100	0	52	92	0	7	0	0.39
1540588--1540682	32	3.1	32	75	15	85	40	0	1	58	1.05
1540565--1540682	58	2.0	61	82	11	147	36	0	0	61	1.08
1540650--1540690	14	2.8	15	85	10	50	43	0	0	56	0.99
1541048--1541127	5	17.6	5	69	17	50	61	0	0	38	0.96
1541067--1541130	11	6.2	11	74	20	57	57	0	0	42	0.98
1541061--1541128	20	3.4	19	75	15	66	60	0	0	39	0.97
1541050--1541126	40	1.9	40	87	10	113	61	0	0	38	0.96
1541068--1541181	33	3.4	32	74	18	92	57	0	0	42	1.05
1541058--1541147	40	2.2	39	82	11	110	60	0	1	38	1.04
1541694--1541728	2	17.5	2	90	0	52	42	0	2	54	1.15
1542078--1542103	3	8.7	3	100	0	52	69	0	0	30	0.89
1542207--1542245	16	2.4	17	86	4	53	64	0	0	35	0.94
1542209--1542248	17	2.4	16	87	4	53	62	0	0	37	0.95
1542202--1542254	26	2.0	26	85	7	70	60	0	0	39	0.97
1542240--1542277	19	2.0	20	94	5	69	55	0	0	44	0.99
1542260--1542338	29	2.7	29	80	9	88	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1542244--1542335	19	4.8	19	71	19	66	54	0	0	45	0.99
1542664--1542695	2	16.0	2	100	0	64	0	50	0	50	1.00
1549817--1549952	33	4.1	32	72	16	107	55	0	1	42	1.08
1549862--1549910	18	2.5	20	75	18	59	61	0	2	36	1.08
1551559--1551592	17	1.9	18	88	5	52	52	0	0	47	1.00
1551547--1551609	20	3.2	20	81	2	65	53	0	0	46	1.00
1552273--1552310	19	2.0	19	90	10	60	50	0	0	50	1.00
1552941--1553028	37	2.3	40	80	11	103	46	0	0	53	1.00
1554401--1554526	9	13.7	10	67	22	55	44	0	0	55	0.99
1554374--1554417	18	2.5	18	79	17	56	40	6	2	50	1.42
1554409--1554531	20	6.7	20	72	22	94	43	0	0	56	0.99
1554428--1554536	32	3.3	32	79	11	114	43	0	0	55	1.05
1554477--1554539	11	5.8	11	78	10	58	41	1	0	57	1.08
1554464--1554544	31	2.7	31	84	7	96	41	1	0	56	1.07
1554401--1554540	10	14.0	10	68	15	58	44	0	0	55	1.05
1555636--1555696	18	3.3	18	73	15	54	62	0	1	36	1.05
1555732--1555791	19	3.2	18	86	13	70	36	0	0	63	0.95
1555848--1555903	24	2.3	24	82	14	71	55	0	3	41	1.17
1556615--1556639	12	2.1	12	100	0	50	60	0	0	40	0.97
1558592--1558621	7	4.1	7	95	4	51	43	0	0	56	0.99
1559052--1559077	5	5.2	5	100	0	52	80	0	0	19	0.71
1560566--1560630	2	32.5	2	100	0	130	49	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1566229--1566274	24	2.0	22	84	16	58	52	0	2	45	1.13
1566957--1566981	2	12.5	2	100	0	50	0	52	0	48	1.00
1567899--1567944	22	2.1	21	84	4	56	45	4	2	47	1.34
1568849--1568896	24	2.0	24	87	0	69	37	6	6	50	1.53
1569305--1569333	2	14.5	2	100	0	58	48	0	0	51	1.00
1569676--1569700	2	12.5	2	100	0	50	0	0	48	52	1.00
1573706--1573751	23	2.0	23	100	0	92	21	17	17	43	1.88
1573710--1573762	23	2.3	23	87	6	72	22	18	18	39	1.92
1583984--1584011	2	14.0	2	100	0	56	50	0	0	50	1.00
1584796--1584824	2	14.5	2	100	0	58	48	0	0	51	1.00

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   32   
          33