genome.fa.s78.2.7.7.80.10.50.1000.10.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: Scaffold78
Parameters: 2 7 7 80 10 50 1000
Length:  2238306

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

This is table  10  of  15  ( 1751 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)
1356239--1356280	19	2.4	17	78	17	50	76	2	2	19	1.01
1356233--1356282	25	2.0	24	82	17	59	74	4	2	20	1.08
1356375--1356415	22	1.9	21	85	5	55	36	7	2	53	1.42
1357234--1357274	21	2.0	21	90	0	64	65	0	0	34	0.93
1357171--1357269	41	2.3	41	81	14	114	63	0	0	36	0.95
1357207--1357270	30	2.1	30	85	5	85	65	0	0	34	0.93
1358458--1358520	30	2.1	30	100	0	126	38	11	19	31	1.86
1358996--1359056	10	5.9	10	74	14	52	68	4	0	26	1.09
1358992--1359058	31	2.2	30	85	12	93	67	4	0	28	1.10
1359295--1359341	16	2.9	16	83	3	67	46	21	12	19	1.82
1360802--1360833	13	2.6	12	95	5	55	81	0	0	18	0.70
1362324--1362370	25	1.9	25	87	12	71	59	4	8	27	1.45
1363811--1363850	2	20.0	2	100	0	80	50	0	0	50	1.00
1364209--1364257	13	3.6	14	82	12	50	59	0	2	38	1.09
1367228--1367270	2	21.5	2	90	0	68	48	46	2	2	1.27
1367825--1367863	20	2.0	20	89	0	60	56	0	0	43	0.99
1369722--1369762	21	2.0	20	85	4	55	51	0	0	48	1.00
1370453--1370513	22	2.8	22	73	11	63	42	0	0	57	0.98
1371117--1371177	18	3.5	17	75	20	63	32	0	1	65	1.02
1371548--1371595	17	2.7	17	78	9	51	58	2	0	39	1.10
1371550--1371600	13	3.6	14	76	15	52	58	1	0	39	1.09
1372588--1372630	2	22.0	2	95	4	79	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1373123--1373162	18	2.2	18	86	8	55	50	0	0	50	1.00
1374053--1374107	15	3.5	15	76	13	58	78	0	0	21	0.76
1374053--1374101	16	3.1	16	80	17	57	77	0	0	22	0.77
1374060--1374118	21	2.7	22	79	7	59	69	1	0	28	0.98
1374994--1375031	16	2.4	16	90	0	67	34	5	7	52	1.53
1375933--1375967	19	1.9	19	88	11	56	34	8	5	51	1.56
1378328--1378391	21	2.8	23	77	13	62	46	0	7	45	1.32
1378443--1378477	17	1.9	19	88	11	56	40	2	0	57	1.14
1378638--1378683	21	2.1	21	84	11	58	52	0	0	47	1.00
1384099--1384141	2	21.5	2	100	0	86	51	0	0	48	1.00
1384780--1384837	29	2.0	30	96	3	109	46	5	10	37	1.60
1387668--1387727	26	2.4	24	73	10	66	51	1	0	46	1.10
1390916--1391217	149	2.0	151	88	5	457	44	13	7	34	1.72
1391354--1391382	14	2.0	15	93	6	51	55	0	6	37	1.27
1393121--1393161	18	2.4	17	92	8	73	56	2	0	41	1.13
1393346--1393411	31	2.1	32	85	2	89	48	33	9	9	1.66
1393374--1393456	16	5.2	16	73	0	76	48	25	13	13	1.78
1393346--1393516	32	5.4	33	72	6	129	47	28	11	12	1.77
1393370--1393516	64	2.3	64	86	3	197	47	25	12	13	1.79
1393812--1393857	23	2.0	23	91	8	76	47	4	8	39	1.54
1393880--1393950	34	2.1	33	84	7	90	42	2	0	54	1.14
1394223--1394280	9	6.7	9	73	13	50	50	1	0	48	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1394496--1394535	19	2.1	19	90	0	62	27	0	0	72	0.85
1398411--1398444	16	2.1	16	100	0	68	61	11	20	5	1.50
1398889--1398969	16	5.0	16	70	22	62	55	0	0	44	0.99
1398917--1398956	22	1.9	21	90	10	64	60	0	0	40	0.97
1398872--1398963	33	2.5	36	79	16	100	55	0	0	44	0.99
1399351--1399422	11	6.5	11	81	9	74	65	0	2	31	1.07
1399347--1399477	17	8.0	16	69	13	70	61	0	3	35	1.17
1399347--1399422	34	2.3	34	84	13	104	64	0	2	32	1.07
1399347--1399450	28	3.7	27	79	13	88	61	0	1	36	1.07
1399896--1399947	12	4.2	12	82	7	61	32	1	1	63	1.16
1400287--1400330	13	3.2	13	78	9	52	38	4	0	56	1.20
1400386--1400426	17	2.4	17	79	0	55	24	0	0	75	0.80
1401287--1401335	13	3.9	12	82	15	55	61	0	2	36	1.08
1401282--1401370	37	2.5	35	78	8	90	58	1	2	38	1.18
1401381--1401412	16	2.0	16	93	0	55	56	12	3	28	1.51
1402068--1402096	2	14.5	2	100	0	58	48	0	0	51	1.00
1404625--1404665	20	2.1	20	86	4	57	48	2	0	48	1.14
1405001--1405053	24	2.2	24	80	9	65	45	0	0	54	0.99
1406614--1406638	2	12.5	2	100	0	50	52	0	0	48	1.00
1408523--1409235	93	7.6	94	82	6	706	12	26	22	38	1.90
1408928--1409008	36	2.2	36	82	4	92	11	27	20	40	1.86
1410452--1410505	16	3.4	16	86	0	72	35	0	3	61	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1410444--1410503	32	1.9	30	86	6	84	33	0	3	63	1.11
1410672--1410710	5	7.8	5	100	0	78	58	0	0	41	0.98
1410924--1410963	21	1.9	21	85	10	55	40	0	0	60	0.97
1412156--1412229	14	5.4	14	77	8	80	58	0	0	41	0.98
1414178--1414221	2	22.0	2	95	0	79	52	0	0	47	1.00
1416164--1416219	24	2.4	24	77	14	62	33	28	21	16	1.95
1416448--1416491	20	2.1	21	84	12	56	43	0	6	50	1.29
1417909--1417967	6	9.7	6	90	1	55	74	0	3	22	0.96
1417911--1417951	3	13.7	3	94	0	73	70	0	0	29	0.87
1419442--1419484	16	2.8	16	80	16	54	46	0	0	53	1.00
1420312--1420373	16	3.9	16	72	10	56	48	3	0	48	1.17
1420386--1420452	30	2.2	30	78	7	73	41	1	14	41	1.55
1428452--1428495	17	2.6	17	81	0	52	59	2	2	36	1.23
1429544--1429568	13	1.9	13	100	0	50	44	0	0	56	0.99
1429540--1429594	28	2.0	28	89	7	85	40	0	1	58	1.09
1431480--1431508	7	4.1	7	100	0	58	44	0	0	55	0.99
1431849--1431886	17	2.2	17	86	9	51	50	2	0	47	1.15
1434033--1434093	29	2.0	31	84	6	81	44	3	1	50	1.28
1434078--1434121	18	2.5	18	81	3	54	61	0	0	38	0.96
1434858--1434886	2	14.5	2	100	0	58	51	0	0	48	1.00
1436436--1436494	17	3.5	17	71	17	52	42	0	3	54	1.17
1436442--1436506	32	2.0	34	84	6	89	41	0	3	55	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1436529--1436567	11	3.4	11	80	13	51	38	2	0	58	1.12
1437293--1437369	37	2.1	37	95	0	136	35	3	6	54	1.45
1438393--1438435	19	2.3	19	92	4	70	48	0	0	51	1.00
1439454--1439494	15	2.7	15	88	0	55	36	0	0	63	0.95
1439569--1439632	28	2.2	28	78	8	67	51	0	4	43	1.22
1439615--1439661	24	2.0	24	83	8	60	65	4	2	27	1.22
1439672--1439705	3	11.3	3	100	0	68	32	0	0	67	0.91
1440022--1440066	21	2.1	21	84	8	56	53	4	4	37	1.41
1442154--1442190	5	7.6	5	90	6	58	62	0	0	37	0.96
1442154--1442244	10	8.8	11	73	14	52	56	0	0	43	0.99
1442955--1443024	21	3.1	22	79	8	79	62	0	0	37	0.95
1442969--1443090	17	7.6	16	67	23	53	57	0	0	42	0.98
1443027--1443119	29	3.0	29	81	12	98	53	0	0	46	1.00
1443263--1443296	14	2.5	14	90	4	52	44	0	0	55	0.99
1443270--1443324	22	2.6	21	78	16	60	47	0	0	52	1.00
1443431--1443494	23	2.9	22	81	6	58	59	1	0	39	1.07
1443453--1443494	22	1.9	22	90	9	68	57	0	0	42	0.99
1443453--1443499	22	2.1	22	84	11	60	55	0	2	42	1.12
1443480--1443539	24	2.4	25	81	10	70	55	0	1	43	1.10
1443913--1443954	22	1.9	22	90	0	66	61	0	0	38	0.96
1443871--1444208	178	1.9	177	93	3	590	46	4	7	41	1.52
1444864--1444895	2	16.0	2	100	0	64	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1446041--1446079	17	2.4	16	84	12	53	61	5	0	33	1.18
1446045--1446083	17	2.4	17	86	4	53	58	2	0	38	1.12
1447041--1447080	21	1.9	21	89	0	62	55	0	5	40	1.22
1447641--1447686	21	2.1	23	84	8	60	39	0	2	58	1.10
1447732--1447791	25	2.3	26	82	2	77	68	1	0	30	0.99
1447704--1447809	51	2.1	52	82	8	128	65	1	1	31	1.14
1448220--1448289	2	37.0	2	75	16	51	41	0	2	55	1.14
1450556--1450591	2	18.0	2	100	0	72	50	0	0	50	1.00
1451585--1451614	15	2.0	15	93	0	51	43	0	0	56	0.99
1460895--1460951	22	2.4	24	82	11	64	42	7	3	47	1.47

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