oyster.v9_M.fa.s1.2.7.7.80.10.50.500.5.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.04

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: scaffold22
Parameters: 2 7 7 80 10 50 500
Length:  1964558

Tables:   1   2   3   4   5   6   

This is table  5  of  6  ( 655 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)
1427535--1427603	2	34.5	2	100	0	138	0	50	0	49	1.00
1428423--1428480	2	29.0	2	100	0	116	0	50	0	50	1.00
1439527--1439587	30	2.1	29	87	9	88	26	18	11	44	1.83
1446896--1447136	84	3.1	77	78	12	229	35	37	4	22	1.76
1447369--1448452	180	6.0	180	95	0	1875	30	14	17	37	1.90
1449199--1449692	35	14.1	35	93	0	855	28	29	17	23	1.97
1454291--1454426	70	2.0	69	83	2	175	25	9	25	39	1.86
1458170--1458491	32	10.1	32	93	0	500	31	29	10	28	1.90
1458796--1458864	2	34.5	2	97	0	129	0	49	1	49	1.09
1463072--1463121	26	1.9	26	95	0	91	34	10	34	22	1.87
1464238--1464607	25	14.8	25	88	3	473	28	15	21	35	1.94
1464238--1464607	75	4.9	75	88	3	523	28	15	21	35	1.94
1469407--1469446	2	20.0	2	100	0	80	50	0	50	0	1.00
1473779--1473805	13	2.1	13	100	0	54	7	22	14	55	1.64
1476403--1476447	21	2.2	21	84	4	56	46	8	4	40	1.55
1477240--1477287	22	2.2	22	88	3	80	35	14	12	37	1.84
1490327--1490384	21	2.7	22	86	5	84	37	13	18	29	1.90
1490552--1490614	21	3.1	21	71	15	60	31	19	14	34	1.91
1490582--1490860	21	13.0	21	70	6	184	35	16	18	30	1.93
1490557--1490692	42	3.3	42	85	2	168	33	18	17	30	1.94
1490590--1490884	105	2.7	108	86	3	391	35	15	17	30	1.92
1490793--1490872	41	1.9	42	87	2	117	35	12	17	35	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1490945--1491024	42	1.9	42	87	5	117	26	20	15	38	1.91
1490941--1491026	21	4.1	21	75	7	86	25	18	13	41	1.88
1494090--1494142	2	26.5	2	100	0	106	49	0	50	0	1.00
1507103--1507183	2	40.5	2	100	0	162	50	0	49	0	1.00
1507240--1507267	2	14.0	2	100	0	56	50	0	50	0	1.00
1510805--1510852	2	24.0	2	100	0	96	50	0	50	0	1.00
1513670--1513877	4	52.5	4	95	1	375	49	0	25	25	1.54
1514788--1514862	8	9.4	8	89	0	78	0	30	25	44	1.55
1514801--1514862	4	15.5	4	93	0	106	0	27	25	46	1.53
1514867--1515283	146	2.9	146	95	0	728	29	19	22	29	1.98
1518660--1520035	54	25.6	54	89	0	1844	24	35	10	30	1.88
1518644--1520035	162	8.6	162	92	0	2033	24	35	10	29	1.88
1527927--1527960	2	17.0	2	100	0	68	50	0	50	0	1.00
1548896--1548967	22	3.3	22	84	3	92	15	31	13	38	1.87
1551443--1551513	22	3.2	22	84	4	90	14	29	15	40	1.86
1554999--1555023	9	2.8	9	100	0	50	32	12	24	32	1.91
1563549--1563574	13	2.0	13	100	0	52	23	0	30	46	1.53
1570584--1571123	180	3.0	180	96	1	1003	36	18	15	29	1.92
1593511--1593555	2	22.5	2	100	0	90	48	0	51	0	1.00
1593799--1593871	4	18.2	4	84	0	74	0	39	9	50	1.35
1593802--1593871	6	11.7	6	82	11	54	0	38	10	51	1.36
1593799--1593871	10	7.5	10	81	6	78	0	39	9	50	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1594367--1594433	7	9.6	7	83	0	89	26	22	14	35	1.93
1594367--1594433	21	3.2	21	86	0	98	26	22	14	35	1.93
1606768--1606829	4	15.8	4	86	3	63	41	24	32	1	1.64
1615919--1615958	2	20.0	2	85	10	55	2	0	52	45	1.14
1620527--1620579	12	4.4	12	90	0	70	28	24	45	1	1.64
1620527--1620562	16	2.2	16	95	0	63	33	25	41	0	1.55
1620536--1620579	4	11.0	4	85	0	61	25	25	47	2	1.63
1637210--1637271	2	31.0	2	100	0	124	0	50	0	50	1.00
1645408--1645456	2	24.5	2	100	0	98	0	48	0	51	1.00
1645839--1647128	437	2.9	434	85	3	1628	32	18	14	35	1.90
1650324--1650362	1	39.0	1	94	0	69	2	97	0	0	0.17
1658539--1658669	41	3.2	41	97	2	248	24	32	16	26	1.96
1660322--1660407	4	21.8	4	81	7	95	75	5	17	1	1.06
1660324--1660397	12	6.2	12	87	3	105	77	6	14	1	1.05
1660909--1660958	2	25.0	2	100	0	100	0	50	0	50	1.00
1671116--1671740	165	3.8	166	87	4	877	39	15	17	27	1.90
1678320--1678475	83	1.9	83	87	0	231	25	24	17	33	1.96
1684803--1684866	24	2.5	26	85	7	78	28	12	15	43	1.83
1685979--1686015	2	18.5	2	100	0	74	0	51	0	48	1.00
1686106--1686143	2	19.0	2	100	0	76	0	50	0	50	1.00
1685979--1686219	128	1.9	125	93	5	416	24	21	9	44	1.81
1689092--1689126	2	17.5	2	93	0	61	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1691342--1691381	20	2.0	20	100	0	80	45	35	10	10	1.71
1695025--1695064	17	2.3	18	86	4	55	45	17	2	35	1.62
1696756--1696786	16	1.9	16	93	0	53	54	16	0	29	1.42
1700142--1700166	11	2.3	11	100	0	50	8	0	0	92	0.40
1700131--1700165	15	2.4	15	90	4	54	11	0	0	88	0.51
1700579--1700609	4	7.8	4	100	0	62	48	0	25	25	1.52
1700628--1700655	4	7.0	4	100	0	56	25	25	50	0	1.50
1706288--1706316	14	2.0	15	93	6	51	48	13	13	24	1.79
1709425--1709459	13	2.7	13	91	8	54	57	0	0	42	0.99
1710916--1710942	4	6.8	4	100	0	54	77	22	0	0	0.76
1711887--1711941	2	28.0	2	96	3	103	0	49	0	50	1.00
1712600--1712649	4	12.8	4	87	4	57	0	40	26	34	1.56
1712606--1712652	12	3.9	12	88	0	67	0	38	25	36	1.56
1712600--1712649	16	3.2	16	94	2	84	0	40	26	34	1.56
1717831--1717883	2	26.5	2	100	0	106	50	0	49	0	1.00
1722750--1723027	138	2.0	135	92	2	459	36	16	13	33	1.87
1736866--1736932	31	2.2	31	97	2	127	14	32	8	43	1.77
1737113--1737150	16	2.4	16	95	0	67	36	21	42	0	1.53
1739177--1739395	21	10.2	21	77	5	170	36	12	16	34	1.87
1739177--1739395	43	5.1	42	76	5	188	36	12	16	34	1.87
1739266--1739369	22	4.8	22	83	2	111	28	13	15	42	1.85
1740068--1740168	21	4.8	21	80	2	121	29	17	13	38	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1740068--1740198	64	2.0	64	86	5	185	33	18	12	35	1.89
1742640--1742687	23	2.1	23	84	0	60	54	2	22	20	1.55
1748210--1748264	2	27.5	2	100	0	110	49	0	50	0	1.00
1754552--1754577	12	2.2	12	100	0	52	46	15	7	30	1.74
1757725--1757758	16	2.1	17	88	5	52	41	14	8	35	1.77
1765849--1765901	2	27.0	2	92	3	90	0	49	0	50	1.00
1765944--1766463	260	2.0	259	99	0	1031	36	17	17	28	1.92
1770730--1770770	19	2.2	19	90	0	64	29	7	14	48	1.71
1776280--1777456	360	3.2	357	83	9	1487	32	13	16	37	1.88
1776275--1777019	180	4.1	180	94	1	1242	31	14	17	37	1.89
1776992--1777072	39	2.1	38	84	9	101	38	4	14	41	1.68
1777104--1777456	180	2.0	180	89	1	537	31	12	15	39	1.85
1787498--1787541	21	2.1	21	83	8	54	50	4	31	13	1.62
1789874--1789958	44	1.9	44	90	4	136	38	23	12	24	1.90
1796574--1796607	2	17.0	2	100	0	68	0	50	0	50	1.00
1800244--1800269	11	2.4	11	100	0	52	50	19	0	30	1.48
1808001--1808114	4	28.5	4	96	0	210	50	0	24	25	1.50
1811457--1811485	15	1.9	15	100	0	58	86	13	0	0	0.58
1815263--1815288	4	6.5	4	100	0	52	76	23	0	0	0.78
1816431--1816466	12	3.0	12	91	0	54	8	25	0	66	1.19
1816440--1816465	9	2.9	9	100	0	52	7	23	0	69	1.14
1816952--1817572	147	4.2	144	64	19	312	35	17	14	31	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1816494--1817619	441	2.6	441	98	0	2153	36	17	13	32	1.90
1820418--1820459	17	2.5	17	96	3	77	30	11	11	45	1.77
1821199--1821589	51	7.7	50	79	9	423	51	11	21	15	1.75
1821180--1821587	153	2.7	152	87	2	577	50	11	21	15	1.76
1822570--1823106	268	2.0	268	98	0	1047	35	16	20	27	1.95
1827698--1827760	27	2.4	27	97	2	119	63	7	19	9	1.48
1828564--1828604	16	2.4	17	88	8	57	46	21	4	26	1.72
1832820--1833580	165	4.6	166	86	2	1014	39	14	16	30	1.88
1832840--1833592	329	2.3	329	88	2	1093	39	14	16	30	1.88
1839208--1839579	79	4.7	79	77	5	311	40	15	19	23	1.90

Tables:   1   2   3   4   5   6