genome.fa.s4.2.7.7.80.10.50.1000.6.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  6  of  31  ( 3628 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)
1432550--1432601	18	2.9	18	81	18	65	36	0	0	63	0.95
1432546--1432619	29	2.6	30	81	10	86	40	0	0	59	0.97
1432606--1432673	17	3.9	19	68	26	53	44	1	0	54	1.09
1432563--1432644	17	5.2	16	70	24	59	40	0	0	59	0.97
1433194--1433218	12	2.1	12	100	0	50	60	0	0	40	0.97
1433226--1433260	18	1.9	18	88	0	52	48	5	0	45	1.26
1433261--1433304	23	1.9	23	86	9	63	45	0	0	54	0.99
1433281--1433319	19	2.1	18	90	4	60	58	0	0	41	0.98
1433776--1433820	21	2.1	21	87	0	63	60	0	0	40	0.97
1437217--1437257	5	8.0	5	92	7	57	43	0	0	56	0.99
1437217--1437256	21	1.9	21	90	10	64	45	0	0	55	0.99
1437289--1437351	16	3.9	16	77	8	56	42	15	14	26	1.86
1437295--1437359	32	2.0	32	85	5	87	40	20	15	24	1.91
1438023--1438108	16	5.4	16	80	5	86	40	20	16	22	1.91
1438023--1438108	32	2.7	32	83	7	111	40	20	16	22	1.91
1439170--1439209	16	2.5	17	84	12	57	40	20	20	20	1.92
1439158--1439216	16	3.7	16	76	0	55	35	23	18	22	1.96
1439270--1439323	15	3.5	15	80	9	56	50	11	1	37	1.49
1443069--1443093	4	6.2	4	100	0	50	48	0	0	52	1.00
1443588--1443622	15	2.2	16	90	10	54	42	0	0	57	0.99
1443592--1443642	19	2.8	19	75	16	54	49	0	0	50	1.00
1453774--1454109	175	1.9	175	90	1	539	50	11	20	17	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1454790--1454838	22	2.3	21	83	16	66	53	0	2	44	1.12
1454790--1454838	21	2.3	21	83	16	66	53	0	2	44	1.12
1454933--1455240	153	2.0	152	83	6	383	45	4	4	45	1.45
1456378--1456440	30	2.1	30	82	11	76	49	0	4	46	1.23
1456457--1456533	31	2.4	32	80	8	95	50	1	1	46	1.17
1456433--1456499	25	2.5	26	78	9	82	47	1	1	49	1.19
1456388--1456547	47	3.3	46	73	12	128	50	1	1	46	1.17
1456391--1456526	15	8.9	14	73	16	76	50	0	0	47	1.11
1456433--1456547	53	2.2	53	81	12	130	49	1	1	46	1.22
1456661--1456868	16	13.5	16	70	13	107	56	6	0	36	1.31
1460431--1460772	173	2.0	171	94	2	596	49	12	21	16	1.78
1460841--1460906	29	2.3	29	91	0	105	46	4	0	48	1.22
1461020--1461467	172	2.7	169	82	10	499	45	4	3	46	1.40
1461340--1461375	19	1.9	19	88	5	56	44	0	0	55	0.99
1461361--1461401	20	2.0	21	85	4	57	48	2	2	46	1.28
1461020--1461555	170	3.2	170	79	9	463	44	5	3	46	1.46
1461707--1461751	21	2.1	21	88	8	65	53	0	2	44	1.13
1461888--1461929	21	2.0	21	81	9	50	42	0	4	52	1.22
1461625--1462152	175	3.0	169	79	9	487	47	3	4	44	1.40
1462088--1462126	18	2.3	18	86	8	55	56	0	2	41	1.13
1462667--1462796	5	25.6	5	67	12	59	51	1	0	46	1.10
1462673--1462815	16	9.2	16	73	15	97	52	1	0	45	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1462667--1462841	31	5.7	31	71	15	80	52	1	1	44	1.21
1462726--1462793	9	7.3	9	73	17	59	51	1	0	47	1.09
1462901--1462933	15	2.3	15	89	5	50	51	9	0	39	1.34
1462921--1462978	16	3.6	16	86	4	73	53	5	0	41	1.23
1467483--1467539	14	3.9	15	72	22	50	50	0	0	49	1.00
1467480--1467537	28	2.1	28	84	12	75	51	0	0	48	1.00
1468256--1468292	2	18.5	2	100	0	74	51	0	0	48	1.00
1468429--1468532	50	2.1	50	96	1	192	22	21	19	37	1.94
1477738--1477795	29	2.0	27	83	16	71	51	1	1	44	1.21
1482304--1482351	18	2.6	18	76	3	51	56	2	0	41	1.11
1487675--1487710	2	18.0	2	100	0	72	50	0	0	50	1.00
1488381--1488415	3	11.7	3	93	0	61	62	2	0	34	1.10
1496145--1496190	12	3.9	12	83	13	51	0	13	4	82	0.81
1496146--1496190	22	2.0	22	82	0	54	0	11	4	84	0.76
1506911--1506946	2	18.5	2	88	5	56	0	47	2	50	1.15
1516634--1516666	2	16.5	2	100	0	66	0	51	0	48	1.00
1519291--1519342	2	26.0	2	88	0	77	44	0	5	50	1.26
1519291--1519342	16	3.2	16	91	0	86	44	0	5	50	1.26
1523413--1523456	22	2.0	22	100	0	88	31	18	13	36	1.90
1532555--1532595	21	2.0	20	86	13	57	56	2	0	41	1.13
1532649--1532703	28	2.0	26	86	13	76	54	0	0	45	0.99
1533005--1533074	27	2.6	27	77	6	79	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1533035--1533094	25	2.5	23	77	22	61	31	3	0	65	1.09
1542564--1542593	15	1.9	16	93	6	53	40	0	0	60	0.97
1542567--1542621	28	1.9	29	82	10	69	30	0	0	69	0.89
1542714--1542738	13	1.9	13	100	0	50	40	12	0	48	1.40
1546034--1546486	227	2.0	223	93	1	780	20	18	18	42	1.89
1554525--1554784	50	5.2	50	88	5	391	30	19	21	29	1.97
1554525--1554784	101	2.6	100	93	2	441	30	19	21	29	1.97
1559177--1559435	50	5.2	50	88	4	389	30	18	20	29	1.97
1559177--1559435	100	2.6	100	93	1	439	30	18	20	29	1.97
1560043--1560140	29	3.3	27	69	22	70	51	0	1	47	1.07
1560134--1560163	5	6.2	5	92	7	53	43	0	0	56	0.99
1560629--1560674	2	23.0	2	86	0	65	43	0	6	50	1.28
1561572--1561618	20	2.6	18	78	15	51	74	2	2	21	1.03
1561761--1561804	23	2.0	22	83	12	56	56	0	0	43	0.99
1562130--1562169	19	2.2	19	90	4	64	75	0	0	25	0.81
1562107--1562197	47	1.9	48	90	2	148	62	2	0	35	1.07
1562407--1562435	14	2.1	14	93	6	51	68	6	0	24	1.13
1562781--1562824	17	2.6	18	82	10	56	65	0	0	34	0.93
1562781--1562823	18	2.4	18	84	7	52	67	0	0	32	0.91
1565833--1565911	8	9.9	8	76	14	65	36	0	0	63	0.95
1565846--1565937	27	3.5	27	72	23	72	33	1	0	65	1.00
1569948--1570001	24	2.2	26	80	16	69	31	0	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1569962--1569996	15	2.4	15	90	4	54	28	0	0	71	0.86
1569956--1570014	23	2.6	23	84	12	70	30	0	0	69	0.89
1570026--1570108	43	1.9	44	80	11	100	43	2	0	54	1.13
1570715--1570756	16	2.6	16	88	3	57	57	0	2	40	1.12
1571128--1571153	2	13.0	2	100	0	52	50	0	50	0	1.00
1571550--1571580	16	1.9	16	93	0	53	38	3	0	58	1.15
1572102--1572150	22	2.2	22	92	7	82	34	14	2	48	1.55
1573956--1573994	14	2.7	14	84	4	51	61	0	0	38	0.96
1575828--1575990	76	2.1	77	83	7	208	30	7	15	46	1.73
1579611--1579778	86	2.0	83	90	3	264	37	18	13	30	1.90
1579933--1579994	21	2.9	21	78	7	63	33	9	4	51	1.56
1580398--1580456	30	2.0	30	86	0	82	33	6	10	49	1.63
1580566--1580616	23	2.2	24	85	3	68	11	11	3	72	1.25
1581037--1581313	114	2.5	110	83	8	310	46	7	3	42	1.51
1585180--1585221	22	1.9	22	100	0	84	19	19	35	26	1.95
1591425--1591455	2	15.5	2	100	0	62	48	0	0	51	1.00
1591880--1591909	6	5.0	6	100	0	60	16	16	66	0	1.25
1591880--1591915	18	2.0	18	88	0	54	22	16	61	0	1.35
1599976--1600005	2	15.0	2	92	0	51	50	3	0	46	1.18
1600796--1600834	2	19.5	2	94	0	69	46	0	2	51	1.14
1601372--1601401	12	2.5	12	94	0	51	6	43	0	50	1.28
1601403--1601443	14	2.9	14	92	0	64	48	7	0	43	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1601406--1601443	16	2.4	16	95	0	67	50	7	0	42	1.31
1601403--1601434	2	16.0	2	93	0	55	50	3	0	46	1.17
1602498--1602534	19	1.9	19	89	10	58	40	0	8	51	1.32
1612863--1613250	195	2.0	195	97	0	731	26	22	22	29	1.99
1613578--1613609	11	2.8	12	90	9	50	37	0	0	62	0.95
1614113--1614164	18	2.8	17	75	16	50	50	0	0	50	1.00
1614103--1614157	20	2.7	20	78	13	58	52	0	0	47	1.00
1615062--1615118	29	2.0	29	85	0	78	52	3	5	38	1.41
1616467--1616506	20	2.1	19	90	4	62	37	0	0	62	0.95
1624816--1624859	14	3.1	14	83	6	54	47	0	2	50	1.13

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