genome.fa.s117.2.7.7.80.10.50.1000.9.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: Scaffold117
Parameters: 2 7 7 80 10 50 1000
Length:  3231771

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   

This is table  9  of  18  ( 2101 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)
1434532--1434568	8	4.5	8	86	6	56	86	0	13	0	0.57
1434532--1434568	17	2.2	17	90	4	58	86	0	13	0	0.57
1440856--1440896	20	2.0	21	85	4	57	48	0	0	51	1.00
1443598--1443741	48	3.0	48	93	0	234	20	14	26	38	1.91
1443649--1443724	24	3.2	24	66	7	73	17	15	26	40	1.89
1443643--1443722	27	3.2	27	62	26	66	20	13	27	38	1.90
1443667--1443743	24	3.2	24	66	14	68	20	11	31	36	1.89
1443811--1443906	48	2.0	48	93	0	165	18	16	28	36	1.93
1447870--1447989	64	1.9	64	91	0	195	26	6	29	37	1.82
1460523--1460574	14	3.5	15	75	17	54	57	3	0	38	1.17
1463985--1464012	2	14.0	2	100	0	56	50	0	0	50	1.00
1466299--1466847	273	2.0	275	92	0	922	34	17	16	31	1.92
1466874--1466977	31	3.3	30	69	28	90	36	16	8	38	1.79
1466858--1466981	63	2.0	63	95	0	221	37	16	8	37	1.78
1470245--1470285	21	2.0	21	95	0	73	43	0	7	48	1.30
1470258--1470306	26	1.9	25	83	4	62	34	0	10	55	1.34
1474777--1474855	28	2.9	29	85	9	103	25	7	16	50	1.71
1474809--1474864	26	2.2	26	83	0	67	25	5	16	53	1.63
1475052--1475097	22	2.1	22	95	0	83	43	15	6	34	1.72
1477062--1477104	15	2.9	15	85	0	59	25	9	20	44	1.81
1481302--1481336	12	2.6	14	86	13	56	40	0	0	60	0.97
1501849--1501880	2	16.0	2	93	0	55	46	0	3	50	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1503967--1504005	15	2.7	15	84	4	53	41	15	17	25	1.89
1504123--1504177	19	2.8	20	68	15	51	43	0	0	56	0.99
1504280--1504320	16	2.5	17	84	15	59	41	0	0	58	0.98
1506636--1506702	33	2.0	33	97	0	125	16	17	5	59	1.56
1510543--1510581	19	2.1	19	90	9	62	48	5	0	46	1.24
1511528--1511572	19	2.5	19	76	20	51	53	0	0	46	1.00
1511608--1511656	21	2.3	21	82	0	62	46	0	0	53	1.00
1511561--1511656	25	3.7	26	70	22	76	45	0	2	52	1.12
1515220--1515310	21	4.6	19	66	20	51	60	0	0	39	0.97
1515226--1515285	10	5.5	11	76	15	54	55	0	0	45	0.99
1515226--1515292	21	3.0	22	74	12	66	55	0	0	44	0.99
1516556--1516585	3	10.0	3	100	0	60	0	0	33	66	0.92
1518990--1519020	2	15.5	2	100	0	62	48	0	0	51	1.00
1519517--1519553	2	18.5	2	100	0	74	51	0	0	48	1.00
1519821--1519854	2	17.0	2	100	0	68	50	0	0	50	1.00
1520105--1520140	18	2.0	18	100	0	72	27	16	16	38	1.90
1524662--1524708	2	23.5	2	100	0	94	48	0	0	51	1.00
1526180--1526445	16	15.8	16	69	16	110	50	3	4	41	1.38
1526267--1526378	22	5.2	22	73	22	87	51	4	0	42	1.28
1529701--1529781	37	2.2	37	84	0	108	24	14	20	39	1.91
1536303--1536335	3	11.0	3	100	0	66	66	0	0	33	0.92
1536641--1536687	16	2.9	15	84	9	58	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1536662--1536722	22	3.1	18	76	13	50	47	0	0	52	1.00
1537559--1537591	7	4.6	7	96	3	57	36	0	0	63	0.95
1537553--1537623	15	4.6	15	81	12	65	35	1	0	63	1.03
1537553--1537625	30	2.3	32	80	13	89	35	1	0	63	1.04
1538585--1538625	2	21.0	2	85	5	57	46	0	4	48	1.23
1539799--1539864	22	3.0	21	77	14	71	42	1	1	54	1.18
1545558--1545590	12	2.5	13	90	9	50	48	3	15	33	1.60
1545741--1545781	4	10.2	4	89	0	55	51	7	0	41	1.30
1545741--1545781	6	6.8	6	91	0	55	51	7	0	41	1.30
1545741--1545781	10	4.1	10	90	0	55	51	7	0	41	1.30
1547588--1547634	13	3.4	13	83	16	67	63	0	0	36	0.94
1547588--1547632	14	3.1	14	85	14	65	64	0	0	35	0.94
1547594--1547642	14	3.4	14	76	15	55	55	0	0	44	0.99
1547739--1547796	29	2.1	29	81	15	70	36	0	5	58	1.20
1547740--1547796	28	2.0	28	83	16	73	35	0	5	59	1.20
1547842--1547887	19	2.5	19	85	3	58	56	4	2	36	1.31
1548228--1548319	40	2.4	36	75	13	94	50	2	3	44	1.30
1548227--1548349	43	3.0	42	75	11	119	51	1	2	44	1.24
1548691--1548744	18	3.2	18	78	19	55	40	0	0	59	0.98
1548714--1548742	14	2.0	15	93	6	51	48	0	0	51	1.00
1548919--1548960	16	2.6	18	82	17	56	42	0	0	57	0.99
1549477--1549540	30	2.1	30	91	5	103	26	14	10	48	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1549639--1549717	24	3.5	23	73	19	69	55	0	0	44	0.99
1549646--1549730	43	2.0	44	82	13	106	50	0	0	49	1.00
1549748--1549789	21	2.0	21	86	9	59	45	2	2	50	1.27
1552569--1552599	2	15.5	2	100	0	62	51	0	0	48	1.00
1553090--1553141	21	2.6	20	78	6	61	44	0	0	55	0.99
1555008--1555204	96	2.1	96	90	1	306	19	25	18	36	1.95
1556287--1556324	3	12.7	3	100	0	76	31	0	34	34	1.58
1556714--1556788	31	2.3	32	82	8	91	33	1	1	64	1.11
1561042--1561075	3	11.3	3	100	0	68	64	0	0	35	0.94
1561918--1562090	17	11.2	15	66	22	67	35	1	2	61	1.16
1561943--1561988	9	5.1	9	82	10	58	28	0	0	71	0.86
1561928--1562052	27	4.6	28	78	13	109	32	0	1	64	1.08
1562011--1562070	28	2.1	28	81	6	68	35	3	1	60	1.23
1562999--1563071	25	3.0	24	75	18	62	41	0	0	58	0.98
1562989--1563055	32	2.2	29	84	7	89	43	0	0	56	0.99
1562999--1563118	29	4.5	27	66	18	72	40	0	0	59	1.03
1563037--1563119	15	5.1	15	68	21	51	37	0	1	61	1.04
1564480--1564527	14	3.4	14	77	11	53	60	0	0	39	0.97
1564490--1564534	23	2.0	23	86	0	63	57	0	4	37	1.19
1566443--1566494	24	2.1	26	85	7	72	61	1	0	36	1.07
1571817--1571889	3	25.0	3	73	15	55	41	0	0	58	0.98
1571834--1571886	20	2.6	20	87	3	70	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1571825--1571883	17	3.8	16	80	15	61	44	0	0	55	0.99
1571828--1571902	23	3.2	23	84	7	89	46	0	0	53	1.00
1572222--1572248	3	9.0	3	100	0	54	33	0	0	66	0.92
1577906--1577931	2	13.0	2	100	0	52	0	0	50	50	1.00
1582610--1582762	77	2.0	77	100	0	306	30	14	23	31	1.94
1593921--1593952	3	10.7	3	100	0	64	68	0	0	31	0.90
1594258--1594326	29	2.3	32	78	12	74	40	0	2	56	1.14
1594297--1594375	41	2.0	41	82	7	99	45	0	0	54	0.99
1594303--1594382	32	2.5	33	84	10	103	46	0	0	53	1.00
1594358--1594416	30	1.9	32	86	6	86	42	1	1	54	1.20
1594337--1594455	27	4.1	30	71	15	90	41	0	0	57	1.10
1595282--1595350	18	3.6	19	75	21	63	53	0	0	46	1.00
1595301--1595361	24	2.4	26	76	15	65	59	0	0	40	0.98
1595418--1595461	23	1.9	23	90	0	70	65	6	6	20	1.39
1596098--1596131	18	1.9	17	88	5	50	41	5	0	52	1.25
1596731--1596777	16	3.0	15	77	17	51	53	0	0	46	1.00
1596743--1596795	19	2.7	19	80	11	54	58	0	0	41	0.98
1597743--1597784	21	2.0	22	85	4	59	59	2	2	35	1.23
1597757--1597788	16	1.9	17	93	6	57	56	0	3	40	1.15
1609659--1609705	23	2.1	23	84	11	62	34	0	4	61	1.15
1609805--1609858	26	2.3	24	79	17	60	53	3	0	42	1.18
1609710--1610031	169	1.9	169	93	2	558	42	3	6	47	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1610002--1610041	19	2.0	21	90	9	66	50	0	0	50	1.00
1612294--1612339	20	2.3	20	82	10	58	39	2	2	56	1.24
1612292--1612353	32	1.9	33	86	3	90	43	1	1	53	1.20
1616818--1616844	2	13.5	2	100	0	54	51	0	48	0	1.00
1619506--1619544	12	3.2	12	88	0	60	30	23	46	0	1.53
1619506--1619544	6	6.5	6	84	0	51	30	23	46	0	1.53
1621340--1621368	3	9.7	3	100	0	58	0	0	65	34	0.93
1623805--1623839	18	1.9	18	88	0	52	37	11	45	5	1.64
1628390--1628421	8	4.2	8	84	15	50	0	9	50	40	1.35
1628393--1628424	14	2.3	14	100	0	64	0	6	50	43	1.27

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18