genome.fa.s38.2.7.7.80.10.50.1000.11.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: Scaffold38
Parameters: 2 7 7 80 10 50 1000
Length:  2073527

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

This is table  11  of  15  ( 1750 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)
1476895--1476919	3	8.3	3	100	0	50	64	0	0	36	0.94
1477058--1477088	2	15.5	2	100	0	62	51	0	0	48	1.00
1478635--1479112	232	2.1	232	95	0	866	35	16	14	32	1.90
1484606--1485071	233	2.0	233	98	0	896	27	19	15	37	1.92
1487522--1487566	20	2.2	20	80	0	54	60	2	2	35	1.22
1489384--1489428	2	22.5	2	100	0	90	51	0	0	48	1.00
1492464--1492494	6	5.0	6	92	7	53	80	0	0	19	0.71
1492464--1492545	40	2.0	40	81	4	94	63	1	1	34	1.10
1493292--1493382	36	2.6	34	74	19	89	52	1	0	46	1.07
1493279--1493382	39	2.8	36	78	12	95	51	0	0	47	1.07
1493311--1493382	35	2.0	35	84	12	94	48	1	0	50	1.09
1493699--1493759	26	2.4	25	86	8	79	42	1	1	54	1.20
1493755--1493792	20	1.9	20	94	0	67	55	0	0	44	0.99
1493757--1493800	20	2.2	20	83	0	52	61	0	0	38	0.96
1497289--1497315	14	1.9	14	100	0	54	48	0	7	44	1.31
1497805--1497890	28	2.8	32	76	18	103	63	0	0	36	0.94
1497805--1497920	26	4.0	29	75	18	82	62	0	0	37	0.95
1497841--1497919	8	9.0	9	74	16	60	63	0	0	36	0.95
1497805--1497930	60	2.0	62	82	15	154	61	0	0	38	0.96
1497856--1497930	16	4.6	16	70	17	55	58	0	0	41	0.98
1497926--1497962	19	1.9	19	88	0	56	56	5	0	37	1.22
1499335--1499379	22	2.0	22	95	0	81	33	0	8	57	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1503244--1503298	27	2.1	25	83	12	67	36	1	1	60	1.18
1510895--1510923	3	9.7	3	100	0	58	34	0	0	65	0.93
1512140--1512189	16	3.1	16	83	11	66	62	0	0	38	0.96
1512219--1512277	25	2.3	26	75	24	63	59	0	1	38	1.08
1518943--1519002	23	2.6	23	77	12	61	51	0	0	48	1.00
1518978--1519024	18	2.7	17	75	15	51	57	2	0	40	1.11
1518977--1519035	19	3.1	19	72	16	50	54	1	0	44	1.10
1519556--1519664	45	2.4	45	82	3	119	24	22	30	22	1.99
1519757--1519914	28	5.2	28	70	14	100	47	1	2	48	1.23
1519774--1519810	18	2.0	19	94	5	67	51	5	0	43	1.24
1519824--1519893	29	2.4	29	80	2	70	47	0	4	48	1.21
1519868--1519913	24	1.9	24	86	0	65	47	0	2	50	1.13
1520015--1520078	21	3.0	21	88	4	85	39	1	0	59	1.07
1520027--1520078	21	2.5	21	93	0	86	40	0	0	59	0.97
1521365--1521393	3	9.7	3	100	0	58	65	0	0	34	0.93
1521448--1521527	32	2.4	32	83	4	88	41	1	1	56	1.15
1521486--1521554	28	2.5	29	86	11	92	34	0	1	63	1.03
1521486--1521554	29	2.5	28	86	11	97	34	0	1	63	1.03
1522712--1522753	22	1.9	22	90	9	68	38	0	0	61	0.96
1523139--1523187	2	24.5	2	87	0	71	44	2	4	48	1.33
1523533--1523577	17	2.6	17	82	0	63	46	0	0	53	1.00
1524924--1524970	18	2.7	18	77	16	53	40	4	0	55	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1526341--1526387	3	16.3	3	91	8	80	34	0	0	65	0.93
1526496--1526620	15	8.3	15	68	17	55	45	0	0	54	0.99
1526486--1526529	20	2.2	20	84	8	54	36	0	0	63	0.95
1526502--1526580	37	2.1	38	79	11	92	44	0	0	55	0.99
1526538--1526612	31	2.4	31	86	4	96	46	0	0	53	1.00
1526538--1526612	32	2.3	32	84	8	91	46	0	0	53	1.00
1526526--1526603	31	2.8	26	73	19	84	47	0	0	52	1.00
1527144--1527196	19	2.6	22	75	25	62	33	0	0	66	0.92
1527464--1527492	11	2.5	12	88	11	51	41	0	0	58	0.98
1528767--1528836	29	2.4	28	86	13	90	45	0	0	54	0.99
1529509--1529567	13	4.5	13	81	14	68	44	0	0	55	0.99
1529519--1529595	24	3.2	24	84	1	100	40	0	1	58	1.06
1531093--1531141	17	2.9	17	76	8	55	24	0	8	67	1.18
1531111--1531162	19	2.9	18	83	16	56	28	0	1	69	0.99
1533969--1534011	20	2.2	20	95	0	77	37	9	16	37	1.81
1536352--1536385	15	2.3	15	95	5	61	47	5	11	35	1.65
1541150--1541243	19	4.8	18	65	23	55	40	0	0	59	0.97
1541196--1541239	19	2.4	18	88	3	61	43	0	0	56	0.99
1542332--1542356	13	1.9	13	100	0	50	12	0	0	88	0.53
1542906--1542975	25	2.8	26	79	12	83	40	1	0	58	1.07
1543127--1543161	18	1.9	18	100	0	70	28	17	25	28	1.97
1547847--1547896	18	2.8	17	82	14	64	64	6	0	30	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1547863--1547935	16	4.2	18	76	18	66	56	4	0	39	1.19
1547858--1547944	16	5.1	16	74	18	61	59	3	0	36	1.14
1547868--1547944	33	2.3	33	86	8	104	57	3	0	38	1.17
1548200--1548986	197	4.0	198	90	1	1154	33	9	11	45	1.72
1550802--1550853	2	26.0	2	81	14	63	50	3	1	44	1.31
1551512--1551559	14	3.6	13	75	13	53	58	10	0	31	1.32
1553139--1553524	189	2.0	189	98	0	754	39	6	8	45	1.61
1553514--1553590	30	2.6	31	85	8	106	44	0	1	54	1.08
1553526--1553576	14	3.7	13	74	20	50	47	0	1	50	1.12
1554361--1554405	18	2.6	18	82	10	58	46	0	0	53	1.00
1554357--1554411	20	2.7	22	78	21	66	52	0	0	47	1.00
1554659--1554701	21	2.0	21	86	9	59	41	2	0	55	1.12
1558478--1558535	11	5.4	11	75	8	57	60	0	1	37	1.07
1558482--1558542	22	3.0	20	80	15	63	62	0	1	36	1.05
1558483--1558535	22	2.4	23	84	9	74	62	0	1	35	1.06
1558641--1558668	2	14.0	2	100	0	56	50	0	0	50	1.00
1564556--1564617	30	2.0	30	84	9	81	53	0	3	43	1.17
1564632--1564731	41	2.4	42	77	9	98	50	4	1	45	1.27
1564887--1564924	17	2.2	18	85	4	51	50	0	0	50	1.00
1564991--1565048	22	2.7	22	82	12	68	56	0	0	43	0.99
1572371--1572402	16	1.9	17	93	6	57	53	0	0	46	1.00
1572375--1572445	14	5.2	14	72	16	60	46	0	2	50	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1572409--1572512	9	11.1	9	68	13	50	37	3	1	56	1.28
1573399--1573941	154	3.5	154	80	5	585	42	11	14	31	1.82
1578198--1578228	2	15.5	2	100	0	62	51	0	0	48	1.00
1578984--1579078	30	3.2	30	79	8	95	47	1	14	36	1.52
1581024--1581092	23	3.0	23	82	16	90	44	0	0	55	0.99
1582519--1582566	18	2.7	18	80	6	62	33	2	6	58	1.35
1585638--1585673	18	2.0	18	100	0	72	44	11	0	44	1.39
1586204--1586252	19	2.4	21	80	10	57	55	0	0	44	0.99
1587724--1587821	26	3.7	26	71	22	87	43	0	0	56	0.99
1587735--1587852	32	3.7	31	75	13	98	43	0	0	55	1.05
1587735--1587812	31	2.5	30	84	12	95	43	0	0	56	0.99
1587756--1587845	15	6.2	14	72	21	62	43	1	0	55	1.07
1589135--1589173	12	3.1	13	81	7	53	30	5	0	64	1.15
1589620--1589696	31	2.5	31	89	2	111	57	2	3	36	1.31
1589690--1589806	60	2.0	60	81	10	141	56	5	0	36	1.30
1589986--1590037	21	2.6	19	82	14	61	40	1	0	57	1.10
1592396--1592440	23	2.0	23	95	0	81	33	11	13	42	1.79
1592399--1592448	23	2.2	23	85	7	66	36	12	14	38	1.83
1596303--1596334	16	2.0	16	100	0	64	37	0	0	62	0.95
1596305--1596341	16	2.3	16	90	0	56	37	0	2	59	1.12
1597515--1597564	18	2.8	18	78	3	57	46	2	2	50	1.24
1598152--1598204	25	2.1	25	83	13	65	43	1	3	50	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1598436--1598480	23	2.0	23	86	8	65	62	0	0	37	0.96
1599396--1599434	3	13.0	3	94	0	69	33	2	0	64	1.08
1599489--1599595	33	3.3	32	78	12	112	33	0	5	59	1.27
1599489--1599614	16	7.8	16	76	6	110	32	0	4	61	1.22
1599581--1599624	23	2.0	22	86	13	63	29	0	0	70	0.88
1599947--1599979	16	2.1	16	100	0	66	48	0	12	39	1.40
1601005--1601052	25	1.9	25	91	8	80	68	0	0	31	0.90
1603015--1603058	22	2.0	23	82	8	56	59	4	4	31	1.38
1603297--1603325	14	2.0	15	93	6	51	51	0	0	48	1.00
1603649--1603743	8	10.9	8	70	23	59	54	2	1	42	1.19

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