genome.fa.s258.2.7.7.80.10.50.1000.7.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: Scaffold258
Parameters: 2 7 7 80 10 50 1000
Length:  5730937

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   

This is table  7  of  25  ( 2900 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)
1360757--1360787	12	2.6	12	94	0	53	70	6	0	22	1.09
1363179--1363240	31	2.0	30	84	3	79	46	3	0	50	1.17
1376082--1376117	4	9.2	4	93	6	65	22	0	0	77	0.76
1376410--1376440	2	15.5	2	100	0	62	48	0	0	51	1.00
1377601--1377635	11	3.3	11	88	8	54	37	0	5	57	1.23
1377606--1377635	10	2.9	10	95	5	51	40	0	6	53	1.27
1377592--1377653	21	3.0	22	69	9	58	45	0	3	51	1.17
1382302--1382339	2	19.0	2	100	0	76	0	50	0	50	1.00
1382479--1382525	19	2.4	20	82	10	53	57	0	0	42	0.98
1383272--1383349	40	2.0	40	84	5	104	38	15	15	30	1.88
1386017--1386092	29	2.7	27	80	15	82	55	2	2	39	1.28
1386748--1386793	22	2.0	21	84	12	56	45	4	4	45	1.43
1389476--1389502	2	13.5	2	100	0	54	48	51	0	0	1.00
1395060--1395113	23	2.4	22	81	9	63	40	1	5	51	1.36
1395215--1395267	27	2.0	27	85	7	72	50	0	0	49	1.00
1400067--1400119	23	2.3	23	78	12	56	35	1	3	58	1.27
1402522--1402571	18	2.7	18	85	14	75	58	2	0	40	1.10
1403612--1403658	24	2.0	24	87	8	69	61	8	6	23	1.48
1404494--1404523	15	1.9	16	93	6	53	46	3	0	50	1.18
1404863--1404925	25	2.5	25	82	12	76	46	0	0	53	1.00
1408262--1408297	15	2.3	16	85	9	56	52	0	0	47	1.00
1408390--1408460	28	2.5	30	80	17	73	59	0	4	36	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1408408--1408460	26	1.9	29	85	11	76	58	0	3	37	1.16
1408673--1408759	23	3.5	24	80	12	79	40	1	0	58	1.05
1408695--1408784	32	2.8	31	77	14	94	37	1	0	61	1.04
1408689--1408802	7	15.0	8	69	25	54	36	0	0	62	1.02
1408674--1408778	41	2.6	41	80	15	112	38	1	0	60	1.08
1408750--1408806	20	2.9	19	84	7	69	33	1	0	64	1.04
1408717--1408815	32	3.2	32	72	18	50	36	1	0	62	1.02
1409610--1409644	16	2.2	16	90	5	54	20	0	8	71	1.11
1421851--1421885	17	2.0	18	88	5	54	74	0	0	25	0.82
1421851--1421885	18	2.1	16	89	10	52	74	0	0	25	0.82
1428975--1429020	21	2.2	21	85	11	60	41	2	6	50	1.40
1435430--1435497	19	3.9	19	78	21	85	35	11	14	38	1.83
1435432--1435494	32	2.0	32	96	0	117	34	12	15	36	1.86
1435451--1435475	13	1.9	13	100	0	50	36	16	16	32	1.90
1435537--1435562	13	2.0	13	100	0	52	30	15	15	38	1.88
1435517--1435583	33	2.0	33	88	0	98	25	14	16	43	1.86
1438080--1438249	52	3.3	51	78	8	182	29	24	12	32	1.93
1437913--1438248	104	3.2	102	71	13	286	30	25	12	32	1.92
1437911--1438303	211	1.9	212	88	3	605	28	26	13	31	1.94
1437971--1438387	107	3.9	105	72	13	309	27	27	14	30	1.95
1438264--1438461	79	2.5	79	84	3	229	25	28	16	30	1.96
1441304--1441382	29	2.7	29	75	9	79	45	2	2	49	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1444501--1444585	42	2.0	43	97	2	163	24	16	28	30	1.96
1466626--1466659	2	16.5	2	87	6	50	2	50	0	47	1.16
1468377--1468456	10	8.1	11	73	18	52	66	0	0	33	0.92
1468376--1468454	20	4.0	21	78	20	91	65	0	0	34	0.93
1468691--1468732	11	3.8	11	93	0	66	33	0	0	66	0.92
1468726--1468793	17	4.0	17	75	15	61	44	0	1	54	1.09
1468757--1468835	25	3.0	26	71	14	63	39	2	0	58	1.12
1468839--1468871	12	2.6	13	85	4	50	39	0	0	60	0.97
1468908--1468981	24	3.0	24	79	13	62	36	2	0	60	1.11
1468952--1469033	30	2.7	30	74	7	78	41	7	0	51	1.30
1473313--1473357	23	2.1	21	84	12	56	48	0	2	48	1.13
1473598--1473633	18	1.9	19	88	5	56	38	0	0	61	0.96
1473764--1473788	2	12.5	2	100	0	50	52	0	0	48	1.00
1474037--1474063	12	2.2	12	100	0	54	48	7	0	44	1.31
1474057--1474087	15	2.0	16	93	6	55	48	0	0	51	1.00
1480119--1480169	16	3.2	16	83	10	52	54	1	0	43	1.11
1481519--1481598	5	17.2	5	72	19	66	37	0	0	62	0.95
1481519--1481598	14	5.7	15	72	18	66	37	0	0	62	0.95
1481553--1481609	19	3.0	20	82	5	73	40	0	0	59	0.97
1481469--1481596	60	2.1	57	81	11	141	36	0	0	62	1.01
1481513--1481609	33	2.9	34	73	17	85	40	0	0	59	0.97
1482548--1482585	16	2.6	14	88	12	51	28	0	0	71	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1482549--1482606	27	2.2	26	82	11	73	32	0	0	67	0.91
1484846--1484876	3	10.3	3	92	0	53	64	0	35	0	0.94
1486667--1486963	151	2.0	151	91	1	488	27	21	15	35	1.93
1497056--1497114	22	2.8	21	75	12	59	66	1	0	32	1.02
1497829--1497863	5	7.0	5	93	0	61	57	20	2	20	1.54
1499751--1499784	2	17.0	2	93	0	59	50	2	0	47	1.16
1500006--1500051	23	2.0	23	83	8	58	32	4	2	60	1.28
1501313--1501377	18	3.6	18	74	12	69	53	0	0	46	1.00
1501335--1501413	15	4.5	16	70	27	54	54	0	0	45	0.99
1501321--1501424	38	2.7	38	91	5	158	52	0	0	47	1.00
1501415--1501450	8	4.5	8	89	0	54	27	0	0	72	0.85
1501780--1501867	31	2.8	32	84	5	99	46	0	1	52	1.08
1501777--1501880	33	3.2	32	76	16	99	44	0	0	54	1.06
1508792--1508853	24	2.7	23	82	5	79	35	0	0	64	0.94
1508817--1508869	23	2.2	24	83	10	63	28	0	5	66	1.15
1508793--1508870	24	3.3	23	80	7	66	32	0	3	64	1.12
1509582--1509639	22	2.6	23	74	15	59	48	0	0	51	1.00
1512303--1512359	27	2.1	28	83	9	73	36	3	0	59	1.14
1512289--1512373	44	1.9	44	83	9	111	37	4	0	57	1.20
1512318--1512375	21	2.8	20	76	7	53	43	1	0	55	1.10
1512290--1512386	44	2.2	45	80	9	110	39	4	0	56	1.18
1520843--1520869	14	1.9	14	100	0	54	59	25	0	14	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1523281--1523432	82	1.8	83	87	4	227	50	15	15	19	1.78
1524194--1524226	10	3.0	11	86	13	50	39	0	0	60	0.97
1524406--1524442	2	18.5	2	100	0	74	48	0	0	51	1.00
1527555--1527605	20	2.7	20	90	6	79	43	1	0	54	1.11
1528072--1528096	1	25.0	1	100	0	50	0	100	0	0	0.00
1531208--1531274	25	2.7	24	73	11	64	38	0	0	61	0.96
1531208--1531276	24	2.8	26	75	14	74	39	0	0	60	0.97
1531699--1531727	14	2.0	15	93	6	51	34	6	0	58	1.25
1538180--1538209	2	15.0	2	100	0	60	50	0	50	0	1.00
1538968--1539011	11	4.1	10	80	13	52	59	0	0	40	0.98
1541123--1541174	27	2.0	27	84	3	70	23	13	36	26	1.92
1543458--1543534	20	3.9	19	81	8	91	42	12	12	31	1.81
1545141--1545183	14	3.2	13	83	12	52	53	0	0	46	1.00
1552990--1553029	17	2.4	16	80	8	53	42	0	0	57	0.98
1553101--1553142	16	2.7	16	85	3	59	38	0	0	61	0.96
1553657--1553699	22	2.0	22	86	9	61	55	6	27	9	1.57
1558001--1558051	16	3.1	16	80	13	59	58	0	1	39	1.09
1558036--1558132	29	3.2	29	82	10	115	59	1	3	36	1.20
1558036--1558132	30	3.2	28	82	10	104	59	1	3	36	1.20
1562324--1562366	2	21.5	2	100	0	86	51	0	48	0	1.00
1562869--1562897	2	14.5	2	100	0	58	48	0	0	51	1.00
1566141--1566188	23	2.1	23	84	0	60	16	45	0	37	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1568823--1568852	15	2.0	15	100	0	60	53	20	0	26	1.46
1568823--1568875	6	9.3	6	76	15	51	50	16	0	32	1.46
1572121--1572174	16	3.4	17	78	19	62	40	0	0	59	0.98
1572516--1572557	13	2.9	15	83	16	54	54	0	0	45	0.99
1572558--1572618	29	2.2	28	82	11	72	47	6	1	44	1.39
1573398--1573422	2	12.5	2	100	0	50	48	0	0	52	1.00
1574868--1574918	26	1.9	28	84	11	72	45	0	0	54	0.99
1575497--1575534	7	5.6	7	85	14	53	0	15	0	84	0.63
1575497--1575534	13	2.8	13	92	4	58	0	15	0	84	0.63
1576990--1577023	15	2.3	15	89	0	50	50	14	35	0	1.44

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