genome.fa.s43.2.7.7.80.10.50.1000.13.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: Scaffold43
Parameters: 2 7 7 80 10 50 1000
Length:  2559314

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   

This is table  13  of  19  ( 2200 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)
1496251--1496308	14	4.1	14	82	8	73	32	0	0	67	0.91
1499047--1499087	17	2.6	16	84	7	57	43	0	0	56	0.99
1499947--1499991	19	2.5	19	82	13	60	62	0	0	37	0.96
1499943--1500006	30	2.1	31	85	11	87	60	1	0	37	1.06
1499947--1499996	17	2.8	18	82	11	59	60	0	0	40	0.97
1499943--1499993	16	3.3	16	79	15	63	58	0	0	41	0.98
1499949--1500006	16	3.4	16	83	7	62	62	1	0	36	1.06
1500882--1500912	12	2.5	12	94	5	53	45	0	0	54	0.99
1500966--1500997	2	16.0	2	100	0	64	50	0	0	50	1.00
1502396--1502424	15	2.0	15	93	6	51	79	0	20	0	0.74
1504254--1504291	15	2.6	15	87	4	51	52	2	5	39	1.38
1504461--1504517	14	4.0	14	82	17	73	29	0	0	70	0.88
1504462--1504504	7	5.9	7	86	8	59	30	0	0	69	0.88
1504464--1504522	29	2.0	28	84	12	75	30	1	0	67	1.00
1507134--1507306	82	2.1	83	92	3	285	32	14	17	35	1.90
1508421--1508452	16	1.9	17	93	6	57	46	3	0	50	1.17
1508119--1508625	181	2.8	180	84	6	675	40	4	14	41	1.65
1508590--1508640	16	2.8	18	72	27	54	47	0	3	49	1.20
1509395--1509424	2	15.0	2	100	0	60	50	0	0	50	1.00
1510864--1510896	8	4.2	8	96	3	59	87	0	12	0	0.53
1511584--1511620	14	2.6	14	91	0	56	27	0	21	51	1.48
1514222--1514264	19	2.3	19	83	0	50	32	4	0	62	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1514263--1514306	15	3.0	15	78	18	56	47	0	2	50	1.13
1514264--1514311	14	3.4	14	78	16	53	50	0	2	47	1.12
1516643--1516705	25	2.5	25	79	7	65	53	3	0	42	1.16
1516650--1516702	16	3.4	16	77	15	56	50	3	0	45	1.19
1517342--1517402	22	2.8	22	75	24	67	44	1	1	52	1.20
1517150--1517576	144	3.0	143	86	7	602	43	3	7	45	1.50
1517497--1517546	22	2.2	24	74	25	56	38	2	2	58	1.21
1517673--1517772	6	14.9	7	70	20	63	43	1	0	56	1.06
1517673--1517771	17	5.9	17	73	19	59	43	1	0	55	1.06
1518326--1518368	23	2.0	23	86	9	63	65	0	0	34	0.93
1518334--1518383	21	2.2	21	86	10	64	64	0	0	36	0.94
1519665--1519725	27	2.3	26	82	17	74	54	1	0	44	1.10
1520807--1520850	24	1.9	24	86	9	65	45	0	0	54	0.99
1520803--1520872	30	2.4	30	81	11	83	47	0	0	52	1.00
1521100--1521203	30	3.5	30	81	1	120	43	0	2	53	1.15
1521531--1521592	29	2.2	28	79	2	70	35	1	3	59	1.23
1525787--1525835	22	2.2	22	89	7	73	51	0	0	48	1.00
1526186--1526228	22	2.0	22	90	9	70	39	0	0	60	0.97
1527440--1527486	21	2.2	21	85	7	60	51	0	0	48	1.00
1527511--1527552	15	2.7	15	85	3	57	59	2	0	38	1.10
1527509--1527554	20	2.3	20	80	0	56	56	2	0	41	1.11
1532856--1532913	6	9.2	6	74	10	53	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1532856--1532913	26	2.3	25	93	3	98	39	0	0	60	0.97
1532871--1532932	20	3.0	21	80	15	67	41	0	0	58	0.98
1536504--1536571	30	2.3	30	94	2	120	48	0	0	51	1.00
1537018--1537071	17	3.1	17	94	2	90	31	5	0	62	1.18
1540057--1540107	21	2.7	19	80	16	61	62	1	0	35	1.06
1541943--1542032	30	2.9	31	79	14	96	54	0	0	45	0.99
1545295--1545344	25	2.0	25	85	11	68	40	0	2	58	1.10
1545320--1545373	26	2.1	27	82	6	67	48	1	0	50	1.11
1545954--1545982	13	2.1	14	93	6	51	55	0	0	44	0.99
1546674--1546711	13	2.7	15	80	16	53	44	0	0	55	0.99
1547133--1547372	124	1.9	123	96	0	444	37	17	7	36	1.80
1548173--1548218	2	23.0	2	100	0	92	50	0	0	50	1.00
1548406--1548450	17	2.6	18	85	3	56	48	0	2	48	1.13
1549924--1550024	8	11.8	8	71	15	51	41	3	0	54	1.19
1550027--1550092	25	2.8	24	82	13	75	34	3	0	62	1.11
1549951--1550063	10	11.2	10	68	21	51	42	2	0	54	1.14
1551015--1551085	33	2.2	33	85	7	92	43	1	0	54	1.08
1551072--1551124	6	9.0	6	76	12	56	35	0	0	64	0.94
1551063--1551134	23	3.4	21	79	20	71	36	0	0	63	0.94
1551080--1551132	18	3.0	18	71	13	56	35	0	0	64	0.94
1551072--1551134	23	2.8	23	81	13	78	36	0	0	63	0.95
1552928--1552973	2	23.0	2	95	0	83	50	2	0	47	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1555007--1555045	2	19.5	2	94	0	69	46	0	2	51	1.14
1557094--1557148	18	3.3	17	76	18	62	40	1	0	58	1.09
1557100--1557155	18	3.2	18	75	7	62	37	1	0	60	1.07
1557754--1557798	19	2.4	19	92	0	72	0	13	4	82	0.82
1562071--1562118	18	2.7	18	80	0	51	39	0	0	60	0.97
1563045--1563079	17	2.1	17	94	5	63	40	0	2	57	1.14
1564451--1564475	2	12.5	2	100	0	50	52	0	0	48	1.00
1565397--1565427	10	3.2	10	90	9	55	54	0	0	45	0.99
1565366--1565427	19	3.2	19	80	8	70	56	0	0	43	0.99
1566077--1566127	17	3.1	17	74	20	54	41	0	0	58	0.98
1566268--1566308	20	2.1	20	90	4	66	51	0	0	48	1.00
1566246--1566323	20	3.8	21	75	13	63	51	0	1	47	1.09
1566271--1566323	22	2.5	19	79	14	52	56	0	0	43	0.99
1566754--1566811	23	2.8	20	75	14	62	58	0	0	41	0.98
1567215--1567293	27	3.0	26	78	7	72	65	0	3	30	1.10
1567261--1567299	14	2.6	14	84	11	51	71	0	0	28	0.86
1567266--1567298	16	2.1	16	88	11	50	69	0	0	30	0.88
1567243--1567300	19	3.2	19	73	26	54	68	0	0	31	0.89
1577798--1577835	3	12.7	3	100	0	76	31	0	0	68	0.90
1579906--1579932	2	13.5	2	100	0	54	48	0	0	51	1.00
1580039--1580303	139	1.9	139	94	0	467	35	17	16	29	1.92
1588395--1588427	2	16.5	2	93	0	57	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1595706--1595751	19	2.3	20	85	11	67	43	0	4	52	1.21
1596267--1596332	17	4.1	16	71	24	57	40	3	1	54	1.25
1596444--1596482	16	2.4	16	91	0	60	23	0	0	76	0.78
1596500--1596530	15	2.1	15	93	0	53	16	0	0	83	0.64
1603640--1603731	20	4.6	21	75	17	81	63	0	1	35	1.02
1603604--1603776	27	6.4	27	70	16	103	57	0	1	41	1.06
1603650--1603776	16	8.4	16	67	24	71	61	0	0	37	1.02
1603664--1603731	22	3.1	22	89	4	102	64	0	1	33	1.02
1603642--1603763	49	2.6	48	79	10	135	61	0	0	37	1.02
1603650--1603776	11	11.6	11	72	10	91	61	0	0	37	1.02
1603685--1603790	27	3.7	29	71	16	87	59	0	0	38	1.10
1604215--1604252	14	2.5	15	83	8	51	57	0	0	42	0.98
1608166--1608199	17	2.1	17	88	5	52	38	0	2	58	1.13
1608416--1608455	18	2.3	18	87	12	57	50	2	10	37	1.50
1609419--1609451	9	3.7	9	95	0	57	3	33	18	45	1.65
1609510--1609561	27	2.0	26	96	3	95	44	11	3	40	1.59
1609513--1609562	12	3.9	13	76	19	52	44	10	6	40	1.63
1614196--1614237	9	4.7	9	96	0	75	2	33	19	45	1.63
1614296--1614347	27	2.0	26	96	3	95	44	11	3	40	1.59
1614299--1614348	12	3.9	13	76	19	52	44	10	6	40	1.63
1614804--1614844	21	1.9	22	85	5	57	43	4	2	48	1.37
1615458--1615497	21	1.9	21	84	0	53	32	0	2	65	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1616385--1616532	34	4.3	35	72	19	107	61	0	1	36	1.09
1616407--1616465	25	2.3	26	80	11	68	59	1	3	35	1.24
1616421--1616483	9	7.1	9	71	10	58	63	1	0	34	1.04
1616419--1616483	19	3.6	19	70	16	57	63	1	0	35	1.04
1616400--1616540	36	4.1	34	73	22	109	60	0	1	36	1.10
1616423--1616483	25	2.5	25	82	15	74	63	1	0	34	1.04
1616421--1616487	26	2.5	26	79	13	75	62	1	0	35	1.04
1616447--1616540	24	3.8	24	71	19	68	62	0	0	37	0.95
1620232--1620271	11	3.6	11	89	0	53	65	2	0	32	1.06
1620225--1620257	16	2.0	17	88	5	50	66	0	0	33	0.92

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19