genome.fa.s25.2.7.7.80.10.50.1000.8.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  8  of  56  ( 6609 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)
1546113--1546161	23	2.2	22	85	3	62	57	0	0	42	0.99
1546700--1546738	17	2.2	19	86	9	55	41	0	0	58	0.98
1547316--1547388	10	7.0	10	75	18	69	65	0	1	32	1.01
1547331--1547388	22	2.9	19	80	10	55	65	0	1	32	1.03
1547336--1547397	28	2.2	29	80	8	74	66	1	1	30	1.11
1547336--1547399	29	2.2	30	78	15	73	65	1	1	31	1.11
1551789--1551825	3	12.3	3	94	0	65	67	2	0	29	1.04
1553309--1553430	39	3.3	38	65	22	96	51	5	3	39	1.42
1553360--1553410	19	2.8	18	85	5	59	56	5	0	37	1.23
1553362--1553410	17	2.8	17	82	11	55	55	6	0	38	1.25
1553331--1553422	24	3.8	25	67	16	66	54	5	4	35	1.43
1554429--1554455	6	4.5	6	100	0	54	0	51	14	33	1.43
1562210--1562234	2	12.5	2	100	0	50	52	48	0	0	1.00
1567389--1567445	16	3.5	16	71	4	60	38	0	1	59	1.08
1567379--1567449	33	2.2	33	97	0	133	43	0	1	54	1.08
1567793--1567842	16	3.1	16	71	21	50	42	4	0	54	1.19
1567775--1567844	32	2.2	32	92	0	113	50	2	0	47	1.16
1569211--1569252	2	21.0	2	95	0	75	47	0	0	52	1.00
1569472--1569510	2	19.5	2	100	0	78	48	0	0	51	1.00
1570016--1570052	19	1.9	19	100	0	74	37	10	13	37	1.80
1570513--1570574	32	1.9	33	83	9	83	53	0	6	40	1.27
1592583--1592609	2	13.5	2	100	0	54	0	0	48	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1593368--1593439	36	2.0	37	81	13	87	50	2	0	47	1.15
1594163--1594239	41	1.9	41	89	5	122	55	1	7	35	1.37
1594287--1594342	28	2.0	28	82	6	69	57	3	0	39	1.16
1599137--1599188	26	1.9	26	84	7	68	48	0	0	51	1.00
1602252--1602327	33	2.3	33	88	4	109	67	7	1	23	1.25
1602485--1602564	38	2.1	39	83	9	101	36	1	1	61	1.12
1604412--1604447	2	18.0	2	94	0	63	52	0	0	47	1.00
1606029--1606253	113	2.0	112	94	0	396	27	19	24	28	1.98
1608153--1608185	2	16.5	2	93	0	57	45	0	0	54	0.99
1615936--1615999	12	4.6	13	72	25	51	57	0	3	39	1.14
1615933--1616016	30	2.8	30	77	15	86	57	0	2	40	1.12
1615959--1616027	29	2.3	29	85	2	84	57	0	1	40	1.07
1615991--1616119	35	3.7	35	75	13	140	54	0	0	44	1.05
1616052--1616139	31	3.1	27	80	13	97	48	0	1	50	1.08
1615944--1616139	69	3.0	64	76	16	186	52	0	2	45	1.12
1616047--1616124	31	2.6	30	86	11	99	52	0	0	47	1.00
1616508--1616542	2	17.5	2	87	0	52	51	5	0	42	1.25
1626856--1626902	3	15.3	3	82	12	60	63	0	2	34	1.06
1627855--1627948	38	2.5	37	76	6	100	60	2	4	32	1.28
1627866--1627912	17	2.5	19	76	16	53	63	2	4	29	1.25
1627883--1627961	17	4.3	18	74	16	65	62	3	5	29	1.34
1627867--1627949	38	2.2	39	89	4	125	63	2	4	28	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1627967--1628092	10	12.5	10	70	13	64	57	0	0	42	1.04
1628044--1628091	6	7.6	7	73	21	52	60	0	0	39	0.97
1627967--1628079	48	2.2	52	86	6	162	57	0	0	41	1.05
1628021--1628091	31	2.4	28	82	15	90	59	0	0	40	0.98
1629363--1629418	5	11.4	5	83	11	71	41	0	0	58	0.98
1631463--1631503	19	2.2	19	86	8	57	63	0	2	34	1.08
1631485--1631531	24	2.0	24	91	4	78	51	0	0	48	1.00
1642213--1642237	3	8.3	3	100	0	50	36	32	0	32	1.58
1650252--1650280	6	4.8	6	100	0	58	0	34	34	31	1.58
1650472--1650498	2	13.5	2	100	0	54	51	0	48	0	1.00
1650945--1650996	11	4.5	11	80	7	50	57	11	1	28	1.44
1651162--1651254	34	2.6	35	77	14	93	66	2	1	30	1.10
1651267--1651303	15	2.5	14	87	12	56	0	16	0	83	0.64
1651864--1651897	8	4.1	8	96	3	59	0	14	0	85	0.60
1651867--1651906	16	2.4	17	83	8	55	2	20	0	77	0.88
1652204--1652260	12	4.7	12	81	12	62	0	22	0	77	0.77
1652201--1652251	7	7.0	7	78	8	57	0	19	0	80	0.71
1652201--1652260	21	2.6	23	82	12	70	0	21	0	78	0.75
1652328--1652358	16	1.9	16	93	0	53	54	0	12	32	1.38
1652350--1652399	19	2.7	18	84	9	64	70	0	2	28	0.99
1652344--1652401	20	2.7	22	82	15	77	67	0	1	31	1.01
1652566--1652657	29	3.4	27	71	19	68	65	1	0	33	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1656833--1656858	2	13.0	2	100	0	52	50	0	0	50	1.00
1657512--1657537	13	2.0	13	100	0	52	30	23	23	23	1.99
1665338--1665407	27	2.6	27	88	0	95	27	32	15	24	1.95
1669751--1669794	13	3.3	14	78	12	56	27	6	0	65	1.17
1673387--1673411	2	12.5	2	100	0	50	48	0	0	52	1.00
1673711--1673754	16	2.6	17	80	13	56	52	2	0	45	1.13
1673711--1673752	17	2.5	17	85	11	52	54	2	0	42	1.13
1674782--1674832	26	2.0	25	84	3	66	41	1	0	56	1.10
1674820--1674861	22	2.0	22	86	9	61	54	7	0	38	1.28
1674870--1674906	17	2.2	17	90	9	58	70	0	0	29	0.88
1675600--1675633	13	2.5	13	90	4	50	44	0	0	55	0.99
1675843--1675875	5	6.8	5	86	6	50	63	0	0	36	0.95
1675843--1675875	14	2.3	15	89	5	50	63	0	0	36	0.95
1677487--1677541	19	2.8	19	80	5	56	65	3	0	30	1.10
1678170--1678197	14	2.0	14	100	0	56	28	0	0	71	0.86
1678228--1678274	25	2.0	23	83	8	58	40	4	0	55	1.19
1678697--1678755	15	4.0	14	80	12	57	66	0	0	33	0.92
1678698--1678755	22	2.6	23	76	20	68	65	0	0	34	0.93
1678698--1678746	7	6.5	8	75	13	50	63	0	0	36	0.95
1678732--1678768	18	2.1	18	89	0	56	70	2	0	27	1.01
1678841--1678896	16	3.7	15	77	17	53	37	1	0	60	1.07
1678835--1678890	16	3.7	15	76	17	53	37	1	0	60	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1678829--1678896	14	4.7	14	73	18	59	35	1	0	63	1.04
1679441--1679513	15	4.4	17	70	18	64	42	0	1	56	1.08
1679567--1679600	10	3.4	10	88	12	52	64	0	0	35	0.94
1691881--1691951	31	2.2	32	85	9	92	49	5	8	36	1.57
1692094--1692123	13	2.3	13	94	0	51	76	3	0	20	0.92
1692231--1692276	19	2.4	19	82	7	58	13	13	0	73	1.09
1692239--1692285	25	1.9	25	82	4	60	8	19	0	72	1.10
1692245--1692306	25	2.4	25	86	7	81	3	22	0	74	0.96
1692272--1692314	10	4.4	10	82	2	52	0	25	0	74	0.82
1692977--1693015	19	2.0	20	90	5	62	61	0	0	38	0.96
1692966--1693016	19	2.7	19	76	11	59	58	0	0	41	0.98
1693331--1693366	14	2.7	13	91	8	63	77	0	0	22	0.76
1693449--1693484	18	1.9	19	88	5	56	69	2	0	27	1.02
1693446--1693505	27	2.1	30	87	12	90	70	3	0	26	1.03
1693651--1693699	18	2.6	19	83	9	64	65	0	0	34	0.93
1693652--1693708	25	2.2	26	81	9	64	63	0	0	36	0.95
1694224--1694286	13	4.4	15	77	18	64	46	1	0	52	1.10
1694224--1694286	15	4.4	14	77	16	67	46	1	0	52	1.10
1694540--1694576	18	2.1	18	90	5	58	67	8	0	24	1.17
1694649--1694681	10	3.3	10	100	0	66	0	0	9	90	0.44
1694649--1694691	20	2.2	20	86	0	59	2	4	6	86	0.79
1694838--1694992	11	13.2	11	66	22	59	60	1	2	35	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1696014--1696228	113	1.9	112	86	1	306	34	11	16	37	1.85
1705040--1705399	180	2.0	179	85	3	483	44	16	8	30	1.78
1721403--1721461	19	3.1	19	85	7	66	54	8	0	37	1.31
1721429--1721469	2	20.5	2	100	0	82	51	0	0	48	1.00
1725459--1725505	22	2.3	19	82	17	51	57	0	0	42	0.98
1725984--1726017	11	3.2	11	87	8	52	70	0	2	26	1.01
1726246--1726286	20	2.0	21	90	4	66	65	0	0	34	0.93
1726362--1726397	17	2.1	17	89	0	54	47	0	0	52	1.00
1729366--1729450	40	2.2	38	82	16	102	52	1	0	45	1.08
1729432--1729461	15	2.0	15	93	0	51	63	0	0	36	0.95

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   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56