genome.fa.s1.2.7.7.80.10.50.1000.9.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  9  of  52  ( 6211 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)
1468021--1468070	16	3.2	16	88	5	77	2	0	12	86	0.67
1468022--1468070	10	4.8	10	78	12	55	2	0	12	85	0.68
1473853--1473904	20	2.5	20	81	9	61	32	15	7	44	1.75
1475315--1475365	21	2.4	22	83	9	70	50	27	7	13	1.69
1482623--1482746	20	5.7	20	68	23	81	30	16	11	41	1.84
1482621--1482695	39	1.9	39	91	0	123	34	14	12	38	1.83
1484900--1484957	30	1.9	30	100	0	116	17	39	18	24	1.92
1484904--1484973	30	2.4	30	88	6	101	22	38	17	21	1.93
1498070--1498469	28	13.6	28	77	12	315	30	30	16	23	1.96
1498070--1498487	62	7.1	58	77	12	374	30	29	16	23	1.96
1498072--1498487	85	4.7	84	76	13	322	30	29	16	23	1.96
1498428--1498505	32	2.4	32	82	2	93	33	28	14	24	1.94
1499428--1499502	20	3.8	19	82	3	87	33	12	12	42	1.79
1499378--1499552	90	2.0	89	86	5	246	31	14	11	42	1.82
1505777--1505801	13	1.9	13	100	0	50	32	16	16	36	1.90
1506481--1506524	21	2.1	21	83	8	54	25	31	4	38	1.76
1508334--1508383	13	3.8	13	100	0	100	40	16	14	30	1.87
1510462--1510492	15	2.1	15	93	0	53	12	22	16	48	1.80
1512295--1512339	21	2.1	21	84	8	56	22	20	4	53	1.63
1514555--1514580	13	2.0	13	100	0	52	30	15	15	38	1.88
1518379--1518404	13	2.0	13	100	0	52	30	15	15	38	1.88
1519111--1519154	21	2.1	21	83	8	54	25	31	4	38	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1520960--1520985	13	2.0	13	100	0	52	38	15	15	30	1.88
1523062--1523092	15	2.1	15	93	0	53	12	22	16	48	1.80
1524891--1524935	21	2.1	21	84	8	56	22	20	4	53	1.63
1526103--1526128	13	2.0	13	100	0	52	30	15	15	38	1.88
1527083--1527199	20	5.8	20	72	7	85	33	13	11	41	1.81
1527090--1527189	40	2.5	40	90	0	146	34	15	12	39	1.84
1532681--1532746	21	3.3	21	72	12	75	42	15	21	21	1.89
1540983--1541014	13	2.5	13	94	0	55	87	9	0	3	0.64
1541854--1541904	26	1.9	27	84	4	68	33	19	19	27	1.96
1542307--1542806	179	2.8	178	84	3	594	31	29	16	23	1.96
1542296--1542787	149	3.3	144	80	8	519	31	29	15	23	1.95
1542297--1542792	28	16.8	28	76	9	355	31	29	16	23	1.96
1542880--1543005	49	2.6	49	82	2	164	19	28	19	31	1.97
1543639--1543804	20	7.8	20	72	16	127	31	16	12	39	1.86
1543679--1543854	51	3.7	50	75	16	192	31	17	11	39	1.85
1543628--1543854	91	2.5	91	88	0	337	31	16	11	40	1.84
1548582--1548607	13	2.0	13	100	0	52	30	15	15	38	1.88
1548562--1548625	32	2.0	33	90	3	103	28	14	15	42	1.86
1551179--1551203	13	1.9	13	100	0	50	32	16	16	36	1.90
1553275--1553305	15	2.1	15	93	0	53	12	22	16	48	1.80
1557337--1557364	10	2.8	10	100	0	56	10	28	21	39	1.87
1557394--1557419	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1557374--1557437	32	2.0	33	90	3	103	28	14	15	42	1.86
1557489--1557544	20	2.8	20	88	0	76	30	16	16	37	1.90
1557950--1558074	52	2.3	52	90	4	187	23	22	14	40	1.90
1557950--1558098	52	2.8	52	86	3	154	22	24	15	37	1.93
1558905--1558929	13	1.9	13	100	0	50	36	16	16	32	1.90
1558885--1558951	33	2.0	33	88	0	98	32	11	14	40	1.83
1558992--1559019	13	2.2	13	100	0	56	28	14	17	39	1.89
1559025--1559149	52	2.4	52	95	0	223	36	18	17	28	1.94
1567326--1567453	52	2.5	52	93	3	215	30	17	18	32	1.95
1567326--1567473	52	2.9	50	85	12	185	31	17	18	31	1.95
1567462--1567486	13	1.9	13	100	0	50	36	16	16	32	1.90
1567550--1567574	13	1.9	13	100	0	50	32	16	16	36	1.90
1568336--1568462	67	1.9	68	85	1	175	37	13	25	23	1.91
1568475--1569653	49	24.7	49	82	6	1440	30	17	26	25	1.98
1568475--1569658	190	6.2	190	94	0	1990	30	17	26	25	1.97
1569694--1570391	34	20.8	34	85	8	803	32	12	34	21	1.90
1570140--1570200	27	2.3	27	85	0	77	27	13	37	21	1.90
1570340--1570484	31	4.7	29	85	11	157	26	17	32	24	1.97
1569759--1570484	102	7.3	94	81	11	315	31	12	34	21	1.91
1571429--1571454	9	2.9	9	100	0	52	0	0	7	92	0.39
1571428--1571457	10	3.1	10	90	9	53	0	0	10	90	0.47
1575475--1575517	21	2.0	21	100	0	86	27	20	23	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1578740--1578867	52	2.5	52	92	3	206	30	17	18	33	1.94
1578740--1578887	52	2.9	50	84	12	176	31	16	18	32	1.94
1578876--1578900	13	1.9	13	100	0	50	36	16	16	32	1.90
1579135--1579269	50	2.6	51	88	2	191	42	12	17	28	1.85
1579236--1579288	20	2.6	21	84	3	72	52	7	13	26	1.66
1579236--1579290	21	2.7	20	85	2	74	52	9	12	25	1.68
1590209--1590259	21	2.4	22	80	6	59	25	0	9	64	1.24
1590213--1590261	11	4.5	11	82	5	55	28	0	10	61	1.29
1590351--1590395	23	2.0	23	86	8	65	55	2	2	40	1.24
1597082--1597116	18	1.9	18	100	0	70	51	5	8	34	1.56
1598903--1598927	13	1.9	13	100	0	50	32	20	16	32	1.94
1598991--1599031	21	2.0	21	100	0	82	34	9	26	29	1.88
1599033--1599063	16	1.9	16	93	0	53	38	3	32	25	1.72
1599089--1599223	53	2.5	53	91	1	216	28	17	16	37	1.91
1599193--1599263	20	3.5	20	77	11	74	30	12	15	40	1.85
1599303--1599343	21	2.0	21	85	9	57	39	9	12	39	1.76
1599642--1600055	79	5.2	77	81	6	413	34	12	24	28	1.92
1599642--1600035	157	2.5	157	82	3	461	34	12	24	28	1.92
1602338--1602492	70	2.2	70	83	2	195	42	12	16	29	1.84
1603092--1603203	42	2.7	41	84	6	127	39	12	25	22	1.89
1603093--1603232	41	3.3	42	83	7	151	35	15	27	21	1.93
1603214--1603816	300	2.0	302	86	4	853	27	18	27	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1603213--1603841	61	10.4	61	84	6	773	27	19	27	26	1.99
1604791--1604846	29	2.0	29	85	3	78	3	5	12	78	1.05
1610480--1610545	33	2.0	33	93	0	114	36	13	12	37	1.82
1615889--1615919	4	7.8	4	92	0	53	74	0	3	22	0.96
1619509--1619603	45	2.1	45	98	0	181	36	21	0	42	1.53
1626143--1626168	13	2.0	13	100	0	52	38	15	15	30	1.88
1630233--1630271	15	2.6	15	91	0	60	51	15	20	12	1.76
1632280--1632357	20	3.6	21	73	15	70	25	12	16	44	1.83
1632344--1632382	13	3.0	13	96	0	69	30	17	15	35	1.91
1634188--1634233	16	2.8	16	93	6	74	28	2	39	30	1.69
1634932--1634957	13	2.0	13	100	0	52	38	15	15	30	1.88
1638061--1638132	28	2.6	28	91	6	119	27	22	26	23	1.99
1637980--1638211	107	2.2	107	86	3	324	31	17	25	26	1.97
1638090--1638667	79	7.3	79	85	3	707	32	13	26	27	1.94
1640989--1641094	20	4.8	20	75	20	77	41	12	16	30	1.84
1640990--1641144	70	2.2	70	89	2	231	41	13	16	28	1.86
1645737--1645812	37	2.1	37	90	5	118	32	15	18	32	1.93
1646359--1646914	167	3.3	164	83	4	634	27	12	9	50	1.72
1647519--1647546	10	2.8	10	100	0	56	71	0	17	10	1.14
1654682--1654728	20	2.3	20	88	3	67	42	8	14	34	1.77
1658311--1658383	21	3.5	22	85	7	98	41	9	23	26	1.85
1658407--1658443	19	2.0	19	94	5	67	27	10	16	45	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1658407--1658543	53	2.6	53	92	1	229	27	17	16	37	1.92
1658513--1658583	20	3.5	20	79	11	83	30	14	15	39	1.87
1658623--1658663	21	2.0	21	85	9	57	39	9	12	39	1.76
1659166--1659190	13	1.9	13	100	0	50	32	16	16	36	1.90
1659240--1659295	19	2.9	19	86	2	67	33	16	17	32	1.92
1663578--1663603	13	2.0	13	100	0	52	38	15	15	30	1.88
1668689--1668768	20	3.8	20	75	15	79	26	15	15	43	1.85
1668754--1668792	13	3.0	13	96	0	69	30	17	15	35	1.91
1671313--1671338	13	2.0	13	100	0	52	38	15	15	30	1.88
1675175--1675205	15	2.1	15	93	0	53	29	25	0	45	1.54

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