genome.fa.s5.2.7.7.80.10.50.1000.13.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: Scaffold5
Parameters: 2 7 7 80 10 50 1000
Length:  1536239

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

This is table  13  of  14  ( 1571 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)
1428811--1428949	16	7.8	18	72	18	80	38	0	2	59	1.09
1432132--1432351	111	2.0	108	94	2	386	21	15	22	40	1.91
1432420--1432461	21	2.0	21	95	0	75	28	16	14	40	1.88
1434148--1434191	2	22.0	2	100	0	88	0	50	0	50	1.00
1436455--1436599	77	1.9	77	92	0	245	22	11	22	43	1.85
1437334--1437400	26	2.7	24	82	11	80	29	0	8	61	1.27
1440008--1440076	17	3.9	18	75	22	58	49	0	0	50	1.00
1440049--1440112	29	2.3	27	81	10	74	40	3	1	54	1.25
1440556--1440597	21	2.0	22	90	4	68	69	0	0	30	0.89
1440865--1440891	4	6.8	4	100	0	54	77	0	0	22	0.76
1442101--1442152	20	2.4	21	84	12	70	48	0	0	51	1.00
1442282--1442345	27	2.3	26	81	10	65	46	1	1	50	1.20
1442402--1442459	28	2.1	28	87	9	84	62	0	1	36	1.06
1442804--1442836	11	2.9	12	86	13	52	30	0	0	69	0.88
1442924--1442966	14	3.1	14	77	16	54	53	0	0	46	1.00
1443531--1443604	7	11.0	7	73	20	52	54	1	4	40	1.28
1443750--1443845	49	2.0	49	95	0	174	32	17	21	28	1.96
1444724--1444770	22	2.1	22	88	0	67	17	4	25	53	1.62
1444790--1444895	34	3.1	34	70	0	104	23	4	26	45	1.72
1449318--1449364	22	2.1	22	92	0	76	14	8	27	48	1.73
1449340--1449489	34	4.4	34	74	5	142	24	5	28	42	1.76
1449340--1449489	68	2.2	68	86	2	212	24	5	28	42	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1450365--1450413	23	2.1	23	88	0	71	12	0	14	73	1.10
1451045--1451085	21	2.0	21	90	0	64	39	0	0	60	0.96
1451100--1451150	20	2.5	21	84	6	61	56	0	1	41	1.10
1451702--1451875	90	1.9	90	90	0	276	37	10	9	41	1.72
1452677--1452722	17	2.6	18	82	3	67	58	0	0	41	0.98
1452711--1452795	27	2.9	30	79	13	104	54	10	1	34	1.43
1452904--1452979	22	3.2	23	78	12	75	55	1	1	42	1.16
1453113--1453174	33	1.9	32	83	9	81	38	8	4	48	1.54
1453196--1453258	29	2.3	27	76	12	74	44	3	6	46	1.45
1454544--1454578	8	4.1	8	86	13	52	34	0	0	65	0.93
1454549--1454602	18	3.2	18	76	15	60	38	0	0	61	0.96
1454522--1454608	15	5.7	15	73	15	52	40	0	3	56	1.16
1454561--1454600	21	1.9	21	85	10	55	42	0	0	57	0.98
1455134--1455609	245	1.9	245	91	1	785	29	16	14	39	1.88
1461529--1461567	18	2.1	19	90	4	62	48	0	2	48	1.15
1462314--1462347	13	2.5	13	90	4	50	26	0	0	73	0.83
1463637--1463669	2	16.5	2	100	0	66	48	0	0	51	1.00
1463701--1463745	17	2.6	17	76	10	56	35	0	4	60	1.17
1468647--1468688	16	2.7	15	79	13	50	57	7	2	33	1.39
1468702--1468751	24	2.1	24	85	10	68	46	8	4	42	1.52
1472878--1472915	20	1.9	20	88	0	58	68	0	0	31	0.90
1473438--1473501	22	2.9	23	82	13	73	53	0	1	45	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1474319--1474347	2	14.5	2	100	0	58	51	0	0	48	1.00
1474598--1474656	13	4.6	13	81	8	68	64	0	0	35	0.94
1474598--1474650	7	7.9	7	76	16	58	66	0	0	33	0.92
1474834--1474891	14	4.1	14	70	20	50	60	1	0	37	1.07
1475142--1475184	7	5.9	7	78	10	50	44	0	0	55	0.99
1475143--1475196	14	3.7	15	81	13	69	44	0	0	55	0.99
1475376--1475438	12	5.3	12	69	17	51	39	0	0	60	0.97
1475379--1475438	23	2.6	23	79	10	68	40	0	0	60	0.97
1475881--1475954	25	3.4	23	67	22	61	47	0	1	51	1.09
1475881--1475935	20	2.9	19	78	19	62	47	0	1	50	1.11
1476333--1476370	19	2.0	19	89	0	58	63	2	0	34	1.09
1480827--1480888	2	31.0	2	86	0	88	1	46	3	48	1.28
1485679--1485735	24	2.5	24	83	10	68	47	0	0	52	1.00
1486287--1486325	19	2.1	19	90	0	60	23	17	7	51	1.71
1487227--1487256	2	15.0	2	100	0	60	50	0	0	50	1.00
1489561--1489596	2	18.0	2	100	0	72	50	0	50	0	1.00
1490359--1490416	3	19.3	3	96	0	107	65	0	1	32	1.03
1491846--1491911	15	4.3	15	76	7	62	45	0	0	54	0.99
1491855--1491922	29	2.4	30	82	9	88	45	0	0	54	0.99
1491895--1491955	19	3.2	19	77	20	65	52	1	0	45	1.10
1493415--1493462	20	2.3	21	82	3	53	33	2	2	62	1.18
1493718--1493771	2	27.0	2	100	0	108	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)
1494879--1494921	19	2.3	19	88	8	61	55	2	0	41	1.12
1495027--1495099	8	9.4	8	75	24	59	36	0	0	63	0.95
1496606--1496663	16	3.6	16	77	9	64	36	3	1	58	1.25
1496679--1496704	9	2.9	9	100	0	52	46	0	0	53	1.00
1496719--1496758	18	2.3	17	83	8	53	20	5	5	70	1.26
1498366--1498414	26	1.9	26	84	12	66	38	2	2	57	1.22
1498417--1498472	24	2.3	25	78	9	62	53	0	1	44	1.11
1499496--1499538	12	3.5	12	78	6	50	44	0	0	55	0.99
1500221--1500272	24	2.1	26	89	7	81	42	0	1	55	1.10
1501521--1501572	21	2.5	20	78	6	59	51	0	0	48	1.00
1501551--1501593	15	3.1	14	81	12	54	65	0	0	34	0.93
1501681--1501742	16	3.6	16	72	18	52	64	0	0	35	0.94
1502117--1502154	20	1.9	19	89	5	58	28	0	0	71	0.87
1503617--1503681	33	1.9	35	90	6	107	55	0	3	41	1.15
1503663--1503705	19	2.2	19	83	8	50	55	2	2	39	1.25
1503704--1503756	20	2.5	22	81	12	65	30	11	1	56	1.45
1503701--1503746	20	2.3	20	88	3	67	34	10	2	52	1.49
1504424--1504523	35	3.0	32	78	18	98	36	1	2	61	1.14
1504460--1504523	22	2.7	24	72	16	62	32	1	0	65	1.02
1504469--1504557	35	2.4	36	82	14	103	30	3	3	62	1.27
1504647--1504692	24	2.0	23	82	4	56	32	4	2	60	1.28
1505164--1505289	49	2.6	50	77	13	129	34	0	4	61	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1505603--1505667	33	1.9	34	84	3	87	40	0	0	60	0.97
1505802--1505864	30	2.1	30	85	5	83	44	1	0	53	1.10
1505902--1505946	22	2.0	23	86	8	65	37	0	0	62	0.96
1506714--1506747	16	2.1	16	88	0	50	52	8	0	38	1.33
1506823--1506863	16	2.4	18	88	8	59	53	0	0	46	1.00
1506828--1506904	26	3.1	25	84	5	93	61	3	0	35	1.15
1506855--1506911	26	2.2	26	100	0	114	63	7	0	29	1.21
1507247--1507296	20	2.5	19	79	17	57	38	0	0	62	0.96
1507348--1507417	27	2.9	23	76	19	79	64	0	4	31	1.13
1507379--1507443	13	5.1	13	73	14	55	64	0	3	32	1.09
1507432--1507480	21	2.2	23	79	13	59	48	0	0	51	1.00
1514696--1514721	2	13.0	2	100	0	52	50	0	0	50	1.00
1514968--1515017	19	2.7	19	70	14	50	50	0	0	50	1.00
1517430--1517474	3	15.0	3	95	0	81	68	0	0	31	0.89
1520873--1520897	3	8.3	3	100	0	50	68	0	0	32	0.90
1521461--1521545	42	2.0	42	93	0	143	30	25	11	31	1.92
1521718--1521771	16	3.3	16	69	5	54	46	0	0	53	1.00
1521690--1521772	33	2.8	29	76	16	80	48	1	0	50	1.08
1521707--1521782	33	2.3	33	93	0	125	51	1	0	47	1.09
1521728--1521781	17	3.2	17	71	5	56	51	0	0	48	1.00
1522957--1522995	12	3.2	12	81	0	51	17	2	5	74	1.12
1522961--1523003	12	3.7	12	81	3	52	18	2	6	72	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1523183--1523236	21	2.5	22	78	9	56	40	0	0	59	0.98
1523175--1523290	35	3.3	35	75	22	86	38	0	0	61	0.96
1523217--1523263	15	3.0	16	77	22	55	40	0	0	59	0.97
1523181--1523283	28	3.6	28	74	17	95	39	0	0	60	0.97
1523210--1523263	16	3.3	16	75	19	58	38	0	0	61	0.96
1523237--1523287	24	2.1	24	82	13	61	39	0	0	60	0.97
1523164--1523290	11	12.1	11	72	20	69	37	0	0	61	1.02
1523837--1523863	7	3.9	7	100	0	54	40	0	0	59	0.98
1523912--1523938	2	13.5	2	100	0	54	51	0	0	48	1.00
1526225--1526288	27	2.4	28	79	10	80	35	0	0	64	0.94

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