genome.fa.s56.2.7.7.80.10.50.1000.9.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: Scaffold56
Parameters: 2 7 7 80 10 50 1000
Length:  1793205

Tables:   1   2   3   4   5   6   7   8   9   10   11   

This is table  9  of  11  ( 1274 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)
1419767--1419804	15	2.7	15	92	8	62	86	0	13	0	0.56
1419767--1419804	7	5.4	7	90	9	60	86	0	13	0	0.56
1420368--1420461	30	3.2	30	68	24	90	27	13	15	42	1.85
1420368--1420688	59	5.5	58	81	9	305	29	12	14	43	1.81
1420385--1420542	30	5.3	30	68	22	93	29	15	11	43	1.81
1420590--1420700	55	2.0	55	82	6	136	27	11	18	42	1.85
1420886--1420997	59	1.9	59	83	0	143	34	13	15	36	1.86
1423028--1423055	2	14.0	2	100	0	56	50	0	0	50	1.00
1423809--1423893	25	3.2	25	64	23	66	44	12	16	25	1.83
1423797--1423908	54	2.1	54	98	0	215	45	12	15	26	1.81
1423802--1423887	27	3.2	27	64	23	72	43	15	13	27	1.85
1425249--1425273	13	1.9	13	100	0	50	32	16	16	36	1.90
1425261--1425313	20	2.6	21	82	8	65	37	15	16	30	1.90
1425354--1425421	33	2.1	33	88	2	102	35	17	13	33	1.89
1425374--1425399	13	2.0	13	100	0	52	30	15	15	38	1.88
1432023--1432074	21	2.5	20	84	9	59	19	46	26	7	1.77
1434760--1434815	20	2.8	20	89	5	78	35	21	12	30	1.90
1434804--1434828	13	1.9	13	100	0	50	32	16	16	36	1.90
1434910--1434961	20	2.7	20	90	3	79	38	21	11	28	1.88
1443466--1443506	14	2.6	16	77	14	50	46	0	4	48	1.23
1445135--1445194	16	3.8	15	80	6	57	41	20	18	20	1.90
1446046--1446096	16	3.2	16	74	0	57	49	27	9	13	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1449264--1449313	20	2.5	20	90	0	73	40	10	16	34	1.81
1453187--1453274	19	4.9	19	77	17	89	39	15	15	28	1.89
1453227--1453282	13	4.8	13	72	28	63	41	14	16	28	1.87
1453208--1453304	32	3.0	32	90	4	142	42	13	15	28	1.85
1457891--1457937	20	2.4	20	82	3	60	76	2	2	19	0.99
1461905--1461946	2	21.0	2	100	0	84	50	0	0	50	1.00
1462521--1462547	1	27.0	1	100	0	54	0	0	0	100	0.00
1466915--1467209	59	5.0	57	72	10	193	44	13	11	29	1.80
1467143--1467211	30	2.3	31	80	12	81	46	11	8	33	1.71
1468283--1468741	78	5.9	79	82	6	465	34	13	23	28	1.92
1468283--1468741	157	2.9	154	82	9	522	34	13	23	28	1.92
1472085--1472134	22	2.2	22	85	3	64	38	12	8	42	1.71
1473240--1473274	17	1.9	17	88	11	52	0	11	5	82	0.82
1473781--1473833	21	2.6	21	90	3	81	39	15	15	30	1.87
1474855--1475000	76	1.9	76	81	5	179	31	11	15	41	1.82
1474845--1475058	38	5.6	37	72	10	135	29	9	17	43	1.80
1474863--1475096	77	3.1	77	78	7	176	29	8	17	44	1.78
1475616--1475686	20	3.5	20	86	7	83	42	12	14	30	1.82
1475844--1475868	12	2.1	12	100	0	50	24	24	16	36	1.94
1480054--1480254	52	3.9	52	94	1	332	29	17	18	33	1.94
1480243--1480267	13	1.9	13	100	0	50	36	16	16	32	1.90
1480331--1480355	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1480413--1480454	21	2.0	21	90	0	66	35	14	14	35	1.86
1486516--1486588	14	5.5	13	73	18	53	76	0	20	2	0.90
1486505--1486588	21	4.2	20	75	18	59	76	0	21	2	0.90
1486503--1486588	41	2.2	39	85	8	111	75	0	22	2	0.91
1487248--1487623	109	3.5	110	80	3	377	34	12	16	36	1.86
1490235--1490301	16	4.2	16	79	11	66	14	14	23	46	1.83
1491639--1491696	16	3.6	16	85	0	80	13	17	24	44	1.85
1494126--1494317	68	2.8	67	80	3	204	41	21	12	25	1.88
1494118--1494370	68	3.7	68	77	1	202	39	20	12	27	1.89
1494781--1494900	38	3.1	39	84	4	127	46	17	5	30	1.69
1494839--1495076	39	6.2	39	71	10	123	45	16	10	27	1.80
1496468--1496506	7	5.4	7	93	6	69	87	0	12	0	0.55
1497071--1497164	30	3.2	30	68	24	90	27	13	15	42	1.85
1497088--1497245	30	5.3	30	68	22	93	29	15	11	43	1.81
1497071--1497391	59	5.5	58	80	9	296	29	12	14	43	1.82
1497293--1497403	55	2.0	55	81	6	127	27	12	18	41	1.86
1497590--1497701	59	1.9	59	83	0	143	34	13	15	36	1.86
1499732--1499769	2	19.0	2	100	0	76	50	0	0	50	1.00
1500519--1500603	25	3.2	25	64	23	66	44	12	16	25	1.83
1500507--1500618	54	2.1	54	98	0	215	45	12	15	26	1.81
1500512--1500597	27	3.2	27	64	23	72	43	15	13	27	1.85
1501958--1501982	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1501970--1502022	20	2.6	21	82	8	65	37	15	16	30	1.90
1502063--1502130	33	2.1	33	88	2	102	35	17	13	33	1.89
1502083--1502108	13	2.0	13	100	0	52	30	15	15	38	1.88
1508272--1508309	13	2.9	13	96	0	67	31	15	18	34	1.92
1508744--1508795	21	2.5	20	84	9	59	19	48	26	5	1.71
1510692--1510747	20	2.8	20	89	5	78	35	21	12	30	1.90
1510736--1510760	13	1.9	13	100	0	50	32	16	16	36	1.90
1510842--1510893	20	2.7	20	90	3	79	38	21	11	28	1.88
1517042--1517096	27	2.0	27	100	0	110	29	3	29	38	1.74
1519442--1519482	14	2.6	16	77	14	50	46	0	4	48	1.23
1521107--1521166	16	3.8	15	80	6	57	41	18	18	21	1.90
1522011--1522061	16	3.2	16	74	0	57	49	27	9	13	1.74
1525230--1525279	20	2.5	20	90	0	73	40	10	16	34	1.81
1527985--1528040	23	2.3	25	78	6	62	14	1	17	66	1.34
1529150--1529237	19	4.9	19	77	17	89	39	15	15	28	1.89
1529190--1529245	13	4.8	13	72	28	63	41	14	16	28	1.87
1529171--1529267	32	3.0	32	90	4	142	42	13	15	28	1.85
1532508--1532532	11	2.3	11	100	0	50	40	0	0	60	0.97
1533838--1533884	20	2.5	19	86	6	60	74	2	2	21	1.03
1537844--1537871	2	14.0	2	100	0	56	50	0	0	50	1.00
1538483--1538507	1	25.0	1	100	0	50	0	0	0	100	0.00
1542875--1543169	59	5.0	57	72	10	193	44	13	11	29	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1543103--1543171	30	2.3	31	80	12	81	46	11	8	33	1.71
1544256--1544644	78	5.0	78	82	4	374	34	14	23	27	1.93
1544243--1544622	79	4.8	78	81	7	389	34	13	23	27	1.93
1544240--1544644	157	2.6	157	79	8	407	34	14	23	27	1.94
1549121--1549156	18	1.9	18	88	5	54	0	11	5	83	0.80
1549663--1549715	21	2.6	21	90	3	81	39	15	15	30	1.87
1550738--1550883	76	1.9	76	81	5	179	31	11	15	41	1.82
1550728--1550941	38	5.6	37	72	10	135	29	9	17	43	1.80
1550746--1550979	77	3.1	77	78	7	176	29	8	17	44	1.78
1551499--1551569	20	3.5	20	86	7	83	42	12	14	30	1.82
1551727--1551751	12	2.1	12	100	0	50	24	24	16	36	1.94
1558717--1558801	38	2.1	42	85	10	117	75	0	22	2	0.92
1558742--1558801	21	2.8	20	74	20	59	78	0	20	1	0.84
1559459--1559834	109	3.5	110	80	3	377	34	12	16	36	1.86
1562433--1562483	16	3.2	16	75	5	50	13	11	25	49	1.76
1562840--1562883	12	4.2	10	78	21	54	59	0	0	40	0.98
1562841--1562882	20	2.0	20	86	13	57	57	0	0	42	0.99
1563839--1563879	16	2.6	16	88	0	64	14	14	21	48	1.80
1566403--1566454	25	2.1	24	96	3	95	44	15	13	26	1.84
1566567--1566608	21	2.0	21	95	0	75	26	16	14	42	1.86
1566577--1566622	21	2.2	21	84	0	56	34	19	8	36	1.83
1579247--1579308	32	1.9	33	86	3	90	40	16	12	30	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1579343--1579382	20	2.0	20	95	4	73	45	15	10	30	1.78
1581107--1581132	13	2.0	13	100	0	52	30	15	15	38	1.88
1581087--1581148	32	1.9	33	90	3	99	27	12	16	43	1.84
1583690--1583731	13	3.2	13	93	0	75	28	14	19	38	1.90
1589791--1589816	13	2.0	13	100	0	52	30	15	15	38	1.88
1589771--1589834	33	2.0	32	87	9	94	28	14	17	40	1.88
1589771--1589834	32	2.0	33	87	9	96	28	14	17	40	1.88
1595311--1595335	13	1.9	13	100	0	50	32	20	16	32	1.94
1595456--1595502	21	2.3	20	78	10	51	34	19	2	44	1.62
1597115--1597175	23	2.7	23	94	0	104	31	1	22	44	1.63

Tables:   1   2   3   4   5   6   7   8   9   10   11