genome.fa.s47.2.7.7.80.10.50.1000.12.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: Scaffold47
Parameters: 2 7 7 80 10 50 1000
Length:  2157611

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

This is table  12  of  15  ( 1735 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)
1518686--1518748	32	2.0	32	93	0	108	36	12	14	36	1.84
1527719--1527769	22	2.3	22	93	0	84	43	7	0	49	1.32
1530427--1530542	51	2.3	51	84	3	144	34	12	19	33	1.89
1532927--1532981	24	2.3	24	100	0	110	34	14	20	30	1.92
1533157--1533252	20	4.8	20	87	5	131	42	12	14	30	1.83
1533267--1533296	13	2.3	13	100	0	60	40	13	16	30	1.87
1534375--1534442	34	2.0	34	97	0	127	32	10	11	45	1.74
1535046--1535114	34	2.0	34	100	0	138	31	8	11	47	1.70
1535751--1535813	29	2.2	29	82	5	74	38	6	9	46	1.62
1542283--1542337	28	2.0	27	96	3	101	29	30	14	25	1.95
1544603--1544644	22	2.0	22	90	4	68	52	2	0	45	1.13
1547402--1547439	21	2.0	20	85	15	53	42	5	28	23	1.76
1547835--1547875	17	2.4	17	91	0	73	68	0	0	31	0.90
1547975--1548055	24	3.2	26	73	21	73	49	0	1	49	1.08
1548128--1548189	16	3.9	16	73	21	51	50	1	0	48	1.10
1548100--1548189	32	2.8	32	84	6	101	54	2	0	43	1.12
1548118--1548185	18	4.1	17	73	22	63	54	1	0	44	1.09
1548128--1548187	15	3.9	15	76	18	61	50	1	0	48	1.11
1548129--1548216	32	2.8	31	79	11	90	48	3	2	45	1.31
1548460--1548521	22	2.8	23	76	20	78	50	0	0	50	1.00
1548460--1548523	20	3.0	20	75	18	67	50	0	0	50	1.00
1548508--1548547	18	2.3	18	87	8	57	62	0	0	37	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1548552--1548592	17	2.4	18	80	12	50	58	2	0	39	1.11
1549165--1549219	20	2.8	20	76	13	60	41	1	7	49	1.41
1549291--1549392	20	5.1	21	71	17	101	47	1	0	50	1.19
1553451--1553485	2	17.5	2	93	0	52	42	0	5	51	1.25
1553814--1553845	13	2.5	13	94	0	55	65	3	0	31	1.08
1557262--1557311	21	2.5	20	83	6	57	38	14	22	26	1.91
1558148--1558348	52	3.9	52	94	1	332	29	17	18	33	1.94
1558337--1558361	13	1.9	13	100	0	50	36	16	16	32	1.90
1558402--1558468	33	2.0	33	88	0	98	40	14	11	32	1.83
1558424--1558448	13	1.9	13	100	0	50	32	16	16	36	1.90
1560831--1560885	20	2.8	20	88	5	76	32	16	12	38	1.86
1563806--1563850	22	2.0	23	82	4	56	46	15	20	17	1.84
1564205--1564263	14	4.5	13	75	8	57	77	0	20	1	0.85
1572037--1572094	30	1.9	31	89	3	91	24	27	15	32	1.95
1572062--1572150	46	1.9	46	97	0	169	23	26	11	38	1.89
1572114--1572554	27	16.1	27	91	2	702	21	35	14	28	1.93
1572114--1572578	55	8.5	55	91	2	722	21	35	15	27	1.94
1572114--1572578	82	5.7	82	90	2	711	21	35	15	27	1.94
1572534--1575333	32	90.8	32	90	4	3834	30	32	18	18	1.95
1572534--1575333	399	7.0	405	91	3	4074	30	32	18	18	1.95
1575366--1575484	49	2.5	47	80	9	127	19	29	22	28	1.98
1576173--1576217	22	2.0	23	82	4	56	46	15	20	17	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1576593--1576628	17	2.1	17	89	0	54	83	0	16	0	0.65
1582782--1582837	21	2.8	21	81	8	71	37	0	0	62	0.95
1582762--1582837	32	2.3	31	82	13	89	35	0	0	64	0.94
1582756--1582837	38	2.2	35	82	12	101	37	0	0	62	0.96
1582911--1582964	24	2.2	24	90	3	81	5	24	22	48	1.72
1586234--1586265	2	16.0	2	100	0	64	50	50	0	0	1.00
1593666--1593706	21	2.0	21	95	0	73	34	21	24	19	1.97
1595579--1595648	27	2.6	27	82	13	90	27	7	15	50	1.70
1596273--1596331	19	3.1	19	76	13	59	54	1	1	42	1.20
1598236--1598310	28	2.8	26	88	6	98	37	0	2	60	1.11
1598236--1598310	17	4.3	16	71	22	53	37	0	2	60	1.11
1598236--1598321	28	3.2	28	81	4	79	36	2	3	58	1.28
1598331--1598375	17	2.6	17	85	0	63	44	4	0	51	1.21
1601613--1601667	24	2.3	22	82	14	65	56	9	0	34	1.31
1602996--1603048	25	2.1	25	85	0	70	24	1	1	71	1.06
1603000--1603050	17	2.9	16	80	13	57	23	3	1	70	1.14
1604743--1604782	17	2.4	17	91	4	64	30	0	12	57	1.36
1604966--1604992	14	1.9	14	100	0	54	62	0	0	37	0.95
1608279--1608367	42	2.2	40	82	11	108	51	5	3	39	1.42
1608290--1608376	42	2.1	41	81	12	97	52	4	4	37	1.43
1609407--1609440	17	2.0	17	94	0	59	67	0	0	32	0.91
1609485--1609525	21	2.0	22	85	9	59	65	2	4	26	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1609964--1610013	21	2.4	20	80	12	57	46	8	6	40	1.58
1610483--1610601	21	5.9	21	70	15	81	48	0	0	49	1.12
1610490--1610601	60	1.9	59	83	5	145	47	0	0	50	1.13
1610570--1610602	12	2.6	13	85	9	50	54	0	0	45	0.99
1610505--1610587	33	2.5	34	81	13	93	48	1	1	49	1.16
1610555--1610602	25	1.9	25	84	16	64	54	0	0	45	0.99
1611128--1611188	16	3.9	15	85	10	86	62	4	0	32	1.17
1611123--1611188	32	2.1	32	97	0	123	59	4	0	36	1.18
1612868--1612900	15	2.1	16	88	5	50	18	0	0	81	0.68
1613743--1613871	23	5.7	23	71	12	63	53	3	3	39	1.35
1614004--1614037	10	3.4	10	87	0	50	64	0	0	35	0.94
1614006--1614051	20	2.3	20	85	3	58	65	0	0	34	0.93
1625692--1625716	1	25.0	1	100	0	50	0	100	0	0	0.00
1628222--1628263	16	2.6	16	92	0	66	14	11	9	64	1.50
1632548--1632608	29	2.1	30	96	3	115	49	13	21	16	1.79
1638346--1638394	13	3.6	13	77	17	55	48	4	0	46	1.20
1638374--1638410	18	2.0	19	89	5	58	48	0	0	51	1.00
1639188--1639221	2	17.5	2	93	6	61	47	0	0	52	1.00
1641663--1641725	31	2.1	31	82	11	78	55	0	0	44	0.99
1647155--1647180	9	2.9	9	100	0	52	0	23	0	76	0.78
1652532--1652579	25	1.9	25	100	0	96	14	25	16	43	1.86
1658601--1658647	23	2.1	22	84	11	60	40	2	4	53	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1663721--1663755	4	8.8	4	93	0	61	25	0	22	51	1.48
1668358--1668395	20	2.0	20	89	5	60	50	0	0	50	1.00
1669199--1669250	19	2.8	19	74	11	54	63	7	0	28	1.22
1669598--1669627	1	30.0	1	93	0	51	0	96	3	0	0.21
1674410--1674441	5	6.4	5	100	0	64	43	0	18	37	1.51
1678134--1678177	20	2.2	20	85	14	65	38	0	0	61	0.96
1678134--1678184	20	2.6	20	79	14	61	39	0	0	60	0.97
1678484--1678541	29	2.0	30	89	3	91	34	1	0	63	1.04
1678773--1678822	14	3.5	14	82	15	66	64	0	0	36	0.94
1678780--1678823	8	5.9	8	75	24	51	61	0	0	38	0.96
1678760--1678823	29	2.1	31	88	5	96	59	0	0	40	0.97
1679386--1679412	14	1.9	14	100	0	54	37	14	29	18	1.91
1679586--1679631	22	2.0	23	87	4	67	34	0	0	65	0.93
1687820--1687870	16	3.4	14	89	10	66	60	0	0	39	0.97
1687818--1687877	15	3.9	16	83	16	74	60	0	0	40	0.97
1692174--1692203	2	15.0	2	92	0	51	46	3	50	0	1.18
1694281--1694306	2	13.0	2	100	0	52	50	0	50	0	1.00
1695020--1695081	29	2.2	28	79	2	70	43	0	3	53	1.17
1695027--1695080	14	3.8	14	76	11	56	38	0	1	59	1.08
1695187--1695244	22	2.5	22	81	13	64	44	0	0	55	0.99
1695196--1695254	22	2.7	21	84	7	64	38	0	0	61	0.96
1695441--1695522	28	3.0	27	82	7	78	50	2	0	47	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1695462--1695516	13	4.2	13	85	2	74	52	0	0	47	1.00
1695462--1695523	28	2.3	27	85	2	79	53	0	0	46	1.00
1695714--1695766	12	4.5	11	77	13	52	33	0	3	62	1.13
1695781--1695827	18	2.3	20	75	20	53	44	0	0	55	0.99
1695756--1695863	48	2.2	48	77	6	112	48	0	0	51	1.00
1696117--1696170	26	2.1	25	82	3	63	37	5	0	57	1.22
1696159--1696233	22	3.3	23	76	9	75	56	0	1	42	1.08
1698434--1698475	21	2.0	21	100	0	84	23	19	9	47	1.78
1700314--1700347	2	17.0	2	100	0	68	50	0	50	0	1.00
1700905--1700951	24	2.0	24	86	0	67	17	31	21	29	1.96

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