genome.fa.s500.2.7.7.80.10.50.1000.8.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: Scaffold500
Parameters: 2 7 7 80 10 50 1000
Length:  2046043

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  8  of  10  ( 1137 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)
1382027--1382058	15	2.1	16	94	5	57	0	15	0	84	0.63
1382070--1382096	1	27.0	1	100	0	54	100	0	0	0	0.00
1382207--1382240	6	6.0	6	86	13	54	47	0	0	52	1.00
1382207--1382240	16	2.0	16	88	11	50	47	0	0	52	1.00
1382508--1382551	12	3.6	12	80	17	54	43	0	0	56	0.99
1382510--1382557	25	1.9	25	86	0	69	45	0	0	54	0.99
1383106--1383155	19	2.9	17	83	13	66	58	2	0	40	1.10
1383093--1383140	25	1.9	25	87	8	71	54	0	0	45	0.99
1383455--1383481	2	13.5	2	100	0	54	0	48	0	51	1.00
1390227--1390259	7	4.6	7	96	3	57	12	3	0	84	0.72
1393693--1393734	19	2.2	19	83	8	50	28	11	30	28	1.92
1398274--1398313	21	1.9	21	94	0	71	22	25	7	45	1.78
1398270--1398330	21	2.9	21	77	2	68	26	31	4	37	1.77
1405505--1405553	25	2.0	24	84	4	62	48	0	0	51	1.00
1407138--1407174	12	3.0	13	88	7	51	48	2	0	48	1.15
1409430--1409482	20	2.8	19	75	8	54	60	0	0	39	0.97
1409411--1409535	32	4.0	33	74	20	92	55	0	0	44	1.05
1409431--1409535	32	3.4	32	77	18	98	55	0	0	43	1.06
1409475--1409536	32	1.9	33	90	9	101	53	1	0	45	1.10
1409479--1409539	16	3.8	16	71	18	54	54	1	0	44	1.10
1409532--1409564	11	2.7	13	86	13	52	57	0	0	42	0.98
1416707--1416759	26	2.1	25	89	3	79	45	0	3	50	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1416713--1416756	13	3.4	13	84	12	63	40	0	4	54	1.21
1417849--1417967	28	4.2	27	74	16	89	57	0	1	40	1.15
1417920--1417980	26	2.4	26	86	13	83	54	0	0	45	1.00
1417920--1417980	27	2.3	25	84	15	79	54	0	0	45	1.00
1429571--1429629	30	2.0	31	83	12	79	49	1	0	49	1.11
1430474--1430506	9	3.7	9	92	8	50	0	12	0	87	0.53
1430475--1430507	14	2.4	14	94	0	57	0	12	0	87	0.53
1437262--1437293	5	6.4	5	100	0	64	81	0	0	18	0.70
1440065--1440211	48	2.9	50	73	11	131	44	0	2	53	1.15
1440119--1440162	17	2.6	16	82	7	52	38	0	0	61	0.96
1442504--1442560	3	19.0	3	100	0	114	0	33	0	66	0.92
1456283--1456314	2	16.0	2	100	0	64	50	0	50	0	1.00
1467154--1467860	351	2.0	351	99	0	1387	28	20	16	34	1.95
1480498--1480542	2	22.5	2	88	0	63	44	4	0	51	1.21
1480494--1480543	24	2.1	24	96	0	91	40	6	0	54	1.25
1486953--1487050	48	2.0	48	94	0	169	22	6	18	53	1.66
1500043--1500072	2	15.0	2	100	0	60	50	0	0	50	1.00
1503663--1503724	18	3.3	18	78	10	70	43	0	0	56	0.99
1504040--1504100	15	3.5	17	78	21	65	57	0	0	42	0.98
1504344--1504402	27	2.2	27	84	6	75	38	1	0	59	1.08
1504354--1504383	16	1.9	16	93	6	53	36	0	0	63	0.95
1504620--1504648	3	9.7	3	100	0	58	31	0	0	68	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1505093--1505157	26	2.5	28	73	16	68	63	1	0	35	1.04
1514887--1514970	9	8.2	10	71	23	68	64	0	1	34	1.02
1514887--1514956	19	3.7	19	75	12	63	64	0	1	34	1.03
1514911--1514977	10	6.3	10	74	19	55	62	0	0	37	0.95
1514869--1514977	35	3.0	35	77	15	105	61	0	1	36	1.07
1515379--1515413	2	18.0	2	94	5	63	48	0	0	51	1.00
1519491--1519533	21	2.0	22	81	4	52	65	0	2	32	1.06
1519498--1519537	21	1.9	21	85	10	55	65	0	2	32	1.06
1521448--1521477	2	15.5	2	93	6	53	46	0	53	0	1.00
1522839--1522878	21	1.9	21	100	0	80	25	15	32	27	1.95
1522840--1522886	21	2.2	21	92	0	76	23	14	34	27	1.94
1540849--1540895	2	23.5	2	95	0	85	48	2	0	48	1.13
1546669--1546698	2	15.0	2	100	0	60	50	0	0	50	1.00
1548716--1548763	2	24.5	2	91	4	80	45	0	2	52	1.12
1549717--1549756	2	20.0	2	100	0	80	50	0	0	50	1.00
1549722--1549869	20	7.5	20	68	21	57	44	0	0	54	1.04
1549717--1549851	30	4.7	28	76	11	94	44	0	0	55	0.99
1549751--1549852	25	3.8	25	77	16	82	42	0	0	57	0.98
1554224--1554270	23	2.1	22	84	4	58	51	0	0	48	1.00
1554310--1554367	18	3.2	18	92	0	98	48	0	3	48	1.18
1554309--1554367	9	6.6	8	81	18	64	47	0	3	49	1.18
1554754--1554816	13	4.1	15	74	18	51	50	0	3	46	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1557678--1557707	2	15.0	2	100	0	60	50	0	0	50	1.00
1565162--1565215	24	2.2	26	80	12	69	48	1	0	50	1.11
1570761--1570798	17	2.1	19	85	9	53	55	5	5	34	1.45
1571392--1571442	17	2.9	18	74	11	52	54	1	0	43	1.11
1571412--1571472	9	6.6	9	74	20	54	62	0	1	36	1.05
1571755--1571796	21	2.0	20	86	4	57	42	0	2	54	1.13
1574035--1574066	4	7.8	4	93	6	55	25	0	0	75	0.81
1576985--1577018	1	34.0	1	93	0	59	97	0	2	0	0.19
1587841--1587884	22	2.0	21	86	4	61	52	0	0	47	1.00
1603143--1603253	49	2.2	53	84	11	142	39	0	0	60	0.97
1603139--1603253	32	3.7	31	71	17	94	40	0	0	60	0.97
1603184--1603261	26	3.0	26	76	19	81	41	1	0	57	1.07
1604301--1604355	13	3.9	14	74	13	51	49	0	0	50	1.00
1609974--1610017	14	3.1	14	93	0	79	29	22	11	36	1.89
1609648--1610649	354	2.8	354	99	0	1995	30	16	19	32	1.95
1610328--1610371	14	3.1	14	93	0	79	29	22	11	36	1.89
1610827--1610873	2	23.5	2	95	0	85	53	0	0	46	1.00
1612322--1612347	2	13.0	2	100	0	52	50	50	0	0	1.00
1620191--1620454	142	1.8	144	94	1	469	40	19	18	21	1.91
1623345--1623382	2	19.0	2	89	10	60	47	2	50	0	1.15
1632034--1632151	34	3.5	33	85	4	173	42	26	6	24	1.79
1633005--1633079	33	2.3	33	100	0	150	33	21	8	37	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1634210--1635486	637	2.0	636	96	0	2347	28	23	16	32	1.96
1636874--1636955	19	4.3	19	87	0	110	35	17	18	29	1.93
1637264--1637377	34	3.4	34	83	8	128	44	18	5	31	1.72
1637824--1637859	2	18.0	2	100	0	72	0	50	0	50	1.00
1646526--1646558	2	16.5	2	93	0	57	48	3	0	48	1.17
1646786--1646818	14	2.4	14	90	5	50	45	0	0	54	0.99
1655132--1655160	15	1.9	15	100	0	58	13	13	31	41	1.84
1657285--1657325	2	21.0	2	90	5	66	46	0	0	53	1.00
1661096--1661129	2	17.0	2	100	0	68	50	0	0	50	1.00
1663197--1663268	25	3.1	23	75	9	74	48	11	0	40	1.39
1663254--1663311	23	2.5	24	81	13	68	50	0	0	50	1.00
1663306--1663346	14	3.1	14	82	6	50	68	2	0	29	1.03
1663321--1663356	18	2.0	18	89	10	56	66	0	0	33	0.92
1667628--1667706	23	3.5	23	76	8	56	45	0	0	54	0.99
1667667--1667707	21	1.9	21	90	5	64	36	0	0	63	0.95
1668796--1668844	19	2.5	20	71	21	50	48	0	0	51	1.00
1673637--1673665	6	5.0	6	95	4	51	0	0	17	82	0.66
1675159--1675216	29	1.9	29	82	6	71	39	3	1	55	1.27
1680223--1680261	19	2.1	19	100	0	78	48	25	10	15	1.76
1681587--1681619	2	16.5	2	100	0	66	48	0	0	51	1.00
1683059--1683085	2	13.5	2	100	0	54	48	0	0	51	1.00
1689285--1689500	34	6.4	34	88	1	292	24	7	27	40	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1689285--1689502	67	3.2	67	88	1	319	24	7	27	40	1.82
1693911--1694128	34	6.5	34	87	1	287	24	7	27	40	1.81
1693911--1694130	67	3.3	67	87	1	314	24	7	27	40	1.81
1699465--1699555	1	91.0	1	77	0	74	0	7	5	86	0.69
1699466--1699549	32	2.7	32	98	1	161	0	7	5	86	0.69
1712828--1712869	17	2.6	17	85	7	52	28	4	0	66	1.12
1712828--1712859	17	1.9	17	93	6	57	28	0	0	71	0.86
1712865--1712917	26	2.0	26	82	13	65	52	0	0	47	1.00
1712987--1713016	15	2.0	15	100	0	60	46	0	13	40	1.43
1712915--1713021	42	2.6	41	84	11	148	55	0	10	34	1.34

Tables:   1   2   3   4   5   6   7   8   9   10