genome.fa.s63.2.7.7.80.10.50.1000.11.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: Scaffold63
Parameters: 2 7 7 80 10 50 1000
Length:  2211945

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

This is table  11  of  16  ( 1834 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)
1577459--1577553	30	3.1	29	82	8	100	41	2	24	32	1.67
1577504--1577565	30	2.1	30	84	0	79	38	6	22	32	1.80
1577870--1577923	19	2.8	19	77	11	56	59	7	0	33	1.25
1583126--1583157	16	2.0	16	93	0	55	53	18	21	6	1.67
1584312--1584367	18	2.9	19	76	15	53	71	1	1	25	1.05
1584971--1585011	18	2.2	19	86	4	57	65	4	0	29	1.13
1586001--1586048	23	2.1	23	100	0	96	35	25	8	31	1.85
1590039--1590076	3	12.7	3	100	0	76	68	0	0	31	0.90
1590662--1590719	25	2.5	23	75	10	64	51	0	0	48	1.00
1590718--1590820	51	2.0	52	84	5	138	51	0	0	48	1.00
1591044--1591109	3	22.0	3	85	0	87	33	36	1	28	1.67
1591168--1591226	20	2.9	20	76	2	64	49	0	0	50	1.00
1591617--1591673	30	1.9	30	89	10	91	54	0	0	45	0.99
1591789--1591843	29	1.9	29	89	10	87	50	0	0	49	1.00
1591549--1591886	171	2.0	172	91	1	554	48	5	3	42	1.44
1592352--1592419	28	2.4	28	78	11	75	51	0	1	47	1.09
1594890--1595037	78	1.9	78	87	0	215	27	26	13	33	1.94
1595022--1595069	15	3.2	15	75	0	51	27	27	4	41	1.74
1595945--1595977	13	2.6	13	90	4	50	48	0	0	51	1.00
1596178--1596230	6	9.0	6	75	24	51	47	0	0	52	1.00
1596184--1596230	14	3.5	14	78	16	55	46	0	0	53	1.00
1596249--1596289	21	2.0	21	85	9	57	39	0	0	60	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1596279--1596365	15	5.7	15	71	16	56	56	0	0	43	0.99
1596352--1596385	18	1.9	18	94	5	61	44	0	0	55	0.99
1597180--1597213	17	1.9	18	88	5	52	88	0	11	0	0.52
1597437--1597462	7	3.7	7	100	0	52	84	0	0	15	0.62
1597674--1597712	13	2.9	13	80	3	51	51	0	0	48	1.00
1598717--1598760	19	2.3	18	85	11	61	75	2	0	22	0.92
1598716--1598757	5	8.6	5	80	15	52	76	2	0	21	0.90
1599262--1599287	2	13.0	2	100	0	52	50	0	0	50	1.00
1602804--1602869	27	2.6	24	77	15	69	48	1	0	50	1.10
1602817--1602874	27	2.1	28	90	3	91	51	0	0	48	1.00
1602817--1602892	28	2.7	27	82	9	91	55	0	0	44	0.99
1602862--1602893	17	1.9	17	93	6	57	65	0	0	34	0.93
1602862--1602902	18	2.3	18	88	12	59	60	0	0	39	0.96
1604569--1604596	13	2.2	13	100	0	56	46	0	21	32	1.52
1610307--1610338	2	16.0	2	100	0	64	50	0	0	50	1.00
1618840--1618890	26	2.0	26	92	0	84	35	25	1	37	1.67
1619339--1619427	20	4.4	20	94	0	142	25	6	23	43	1.78
1625646--1625696	25	2.1	25	88	3	77	45	1	31	21	1.63
1626098--1626149	3	17.3	3	100	0	104	32	0	0	67	0.91
1627770--1627795	7	3.7	7	100	0	52	11	0	0	88	0.52
1631130--1631170	21	2.0	21	95	0	73	46	17	4	31	1.69
1631201--1631234	18	1.9	17	94	5	59	41	0	5	52	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1631484--1631513	6	5.0	6	91	0	51	33	30	16	20	1.94
1632567--1632615	23	2.1	24	84	3	64	42	0	2	55	1.11
1632583--1632649	24	2.8	25	75	18	70	43	1	0	55	1.09
1632578--1632676	32	2.9	33	73	10	85	44	2	0	53	1.12
1632607--1632668	18	3.3	19	71	26	51	41	3	0	54	1.16
1634651--1634696	20	2.4	19	86	10	67	39	0	0	60	0.97
1634658--1634698	20	2.0	20	95	0	73	41	0	0	58	0.98
1634756--1634807	21	2.5	22	72	12	56	59	5	0	34	1.21
1634832--1634876	20	2.4	19	79	20	58	66	0	0	33	0.92
1635107--1635145	2	19.5	2	100	0	78	48	0	0	51	1.00
1635429--1635514	15	5.7	15	70	20	56	40	1	0	58	1.06
1635429--1635482	20	2.6	21	82	14	67	38	0	0	61	0.96
1635430--1635528	32	2.9	34	82	12	98	43	1	0	55	1.06
1635460--1635542	32	2.7	31	82	15	95	42	2	0	55	1.13
1635912--1635959	22	2.2	22	85	14	64	45	0	0	54	0.99
1635908--1635967	25	2.6	24	82	10	72	46	0	0	53	1.00
1635925--1635976	25	2.1	25	81	0	59	50	0	0	50	1.00
1636004--1636050	17	2.6	17	83	10	58	31	2	0	65	1.04
1636491--1636531	20	2.1	20	86	4	57	51	2	0	46	1.14
1636657--1636713	26	2.2	26	87	9	82	31	7	0	61	1.23
1636657--1636714	25	2.3	26	85	11	77	31	8	0	60	1.27
1638382--1638407	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1638971--1639000	2	15.0	2	100	0	60	50	0	50	0	1.00
1645363--1645397	18	2.0	17	88	5	52	45	2	0	51	1.16
1645535--1645576	17	2.5	17	77	22	52	40	0	0	59	0.97
1646092--1646125	15	2.1	16	89	10	52	61	0	0	38	0.96
1646144--1646174	15	2.1	15	100	0	62	45	0	0	54	0.99
1646281--1646328	20	2.4	19	76	13	51	50	0	0	50	1.00
1646399--1646442	16	2.7	16	82	3	52	40	0	0	59	0.98
1647710--1647768	29	2.0	30	83	9	77	64	1	3	30	1.20
1647715--1647778	29	2.3	27	72	15	67	67	1	1	29	1.09
1647776--1647835	16	3.7	15	72	18	50	50	1	0	48	1.11
1647772--1647835	32	2.0	33	87	9	96	51	1	0	46	1.10
1647762--1647878	39	3.0	39	78	13	98	53	0	0	44	1.12
1647805--1647881	39	1.9	41	86	5	113	53	0	1	45	1.08
1648179--1648219	14	2.9	15	79	20	52	53	0	0	46	1.00
1648233--1648295	24	2.7	25	83	11	80	55	0	1	42	1.09
1649150--1649186	12	3.1	12	88	0	56	48	0	0	51	1.00
1649137--1649186	25	2.0	25	84	7	66	52	0	0	48	1.00
1649164--1649257	35	2.7	35	77	9	84	39	1	1	58	1.12
1649274--1649314	19	2.2	19	86	8	57	46	0	2	51	1.14
1651515--1651566	26	2.0	26	88	7	79	48	7	0	44	1.31
1653846--1653877	5	6.8	5	92	7	50	43	0	0	56	0.99
1655641--1655688	23	2.1	22	85	11	62	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1655641--1655703	24	2.7	23	83	11	67	39	0	1	58	1.07
1655645--1655717	24	3.0	25	77	15	66	38	0	1	60	1.06
1655735--1655766	15	2.1	16	94	5	57	75	0	0	25	0.81
1655894--1658584	339	8.0	340	90	4	4014	37	8	14	39	1.77
1658166--1658231	24	2.7	23	81	11	62	48	0	0	51	1.00
1655894--1658584	991	2.6	998	89	5	3960	37	8	14	39	1.77
1658193--1658245	25	2.1	25	83	13	65	41	0	1	56	1.10
1657312--1658584	674	1.9	677	92	2	2175	37	8	14	39	1.77
1658621--1658682	27	2.3	29	76	21	71	29	0	9	61	1.28
1659657--1659725	27	2.6	25	74	14	66	31	0	7	60	1.24
1660145--1660197	24	2.4	21	78	9	61	26	1	1	69	1.09
1662330--1662378	23	2.1	23	84	3	62	38	0	0	61	0.96
1662272--1662541	133	2.1	131	88	3	400	41	2	1	54	1.22
1664354--1664390	2	18.5	2	100	0	74	51	0	0	48	1.00
1670696--1670733	2	19.0	2	100	0	76	50	0	0	50	1.00
1674011--1674066	30	1.9	28	89	7	85	48	1	0	50	1.11
1676781--1676813	14	2.3	15	94	5	59	54	0	0	45	0.99
1676780--1676814	15	2.3	16	85	14	56	51	0	0	48	1.00
1681002--1681042	2	20.5	2	94	0	73	51	0	0	48	1.00
1681142--1681185	2	23.0	2	90	9	74	50	0	0	50	1.00
1682346--1682397	22	2.4	22	80	6	61	57	0	0	42	0.98
1684763--1684803	19	2.2	19	86	8	57	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)
1687983--1688029	3	15.7	3	100	0	94	65	0	0	34	0.93
1689067--1689108	21	2.0	21	86	4	59	35	0	0	64	0.94
1689643--1689686	24	1.9	23	86	9	63	38	0	0	61	0.96
1689673--1689723	13	4.1	13	77	10	61	43	3	0	52	1.19
1689857--1689899	2	21.5	2	100	0	86	48	0	0	51	1.00
1689902--1689934	2	16.5	2	100	0	66	51	0	48	0	1.00
1690190--1690242	17	2.7	20	75	25	58	67	0	0	32	0.91
1690428--1690505	30	2.5	31	77	8	86	65	0	0	34	0.93
1692762--1692809	21	2.3	22	75	17	57	41	0	2	56	1.11
1694347--1694381	16	2.2	16	89	0	52	31	5	5	57	1.46

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