genome.fa.s400.2.7.7.80.10.50.1000.9.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: Scaffold400
Parameters: 2 7 7 80 10 50 1000
Length:  2847997

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

This is table  9  of  17  ( 1977 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)
1238742--1238780	16	2.5	15	84	8	51	33	5	17	43	1.72
1240974--1241015	21	2.0	22	86	13	61	40	7	14	38	1.73
1241135--1241159	13	1.9	13	100	0	50	32	16	16	36	1.90
1241147--1241199	20	2.6	21	82	8	65	37	16	16	28	1.91
1241259--1241284	13	2.0	13	100	0	52	38	15	15	30	1.88
1241241--1241304	33	2.0	32	90	3	101	39	20	14	26	1.90
1247391--1247430	20	2.0	21	90	5	64	37	15	12	35	1.85
1247465--1247502	13	2.9	13	84	0	58	34	13	13	39	1.83
1247635--1247674	21	2.0	21	85	9	57	35	25	0	40	1.56
1249906--1249944	20	2.0	19	90	5	60	35	20	10	33	1.86
1250007--1250124	53	2.2	53	96	0	218	25	19	24	30	1.98
1250113--1250176	33	2.0	32	84	3	83	39	18	12	29	1.88
1256146--1256191	20	2.2	21	85	11	60	34	19	6	39	1.78
1263965--1264015	20	2.5	20	87	0	66	23	15	19	41	1.90
1265183--1265223	6	6.7	6	97	2	73	14	2	0	82	0.76
1266472--1266501	5	6.2	5	92	7	53	40	0	0	60	0.97
1266867--1266899	15	2.2	15	94	0	57	45	0	0	54	0.99
1266936--1267047	55	2.1	53	81	5	127	44	6	1	47	1.38
1267724--1267760	2	18.5	2	100	0	74	51	0	0	48	1.00
1269009--1269043	7	4.9	7	89	6	52	45	0	2	51	1.16
1269009--1269040	15	2.1	15	94	0	55	50	0	3	46	1.17
1271103--1271151	3	16.7	3	87	4	73	69	0	30	0	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1272692--1272745	28	1.9	28	88	0	81	53	3	3	38	1.36
1273571--1273615	2	22.5	2	95	0	81	46	0	2	51	1.13
1275138--1275189	2	26.0	2	100	0	104	50	0	0	50	1.00
1276079--1276221	75	1.9	76	83	9	186	29	15	15	39	1.88
1276380--1276417	19	2.0	19	94	0	67	44	0	0	55	0.99
1277028--1277071	18	2.4	18	80	0	52	34	0	11	54	1.36
1278474--1278517	11	3.8	11	81	6	52	43	2	0	54	1.12
1278451--1278511	29	2.2	27	79	5	68	42	1	1	54	1.20
1280003--1280045	21	2.1	20	91	4	68	53	2	0	44	1.13
1280336--1280496	79	2.0	79	98	0	313	44	12	13	29	1.80
1281030--1281072	2	21.5	2	100	0	86	51	0	0	48	1.00
1282947--1283002	24	2.6	21	78	15	60	55	0	0	44	0.99
1283724--1283779	17	3.6	16	76	9	53	48	0	0	51	1.00
1283723--1283773	17	3.2	17	75	10	54	52	0	0	47	1.00
1284438--1284657	111	2.0	111	91	2	363	46	9	3	41	1.51
1285221--1285267	22	2.1	23	84	11	62	29	2	4	63	1.25
1287595--1287657	32	1.9	33	87	3	92	44	1	0	53	1.10
1288886--1288918	13	2.6	13	90	4	50	30	0	9	60	1.27
1289345--1289402	16	3.6	17	77	9	59	44	0	5	50	1.24
1289481--1289534	20	2.7	21	72	16	53	57	1	0	40	1.09
1289966--1290016	20	2.5	19	81	15	50	50	1	0	47	1.12
1289990--1290053	20	3.3	20	69	20	55	54	0	1	43	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1291422--1291452	13	2.3	13	94	5	53	80	0	19	0	0.71
1292460--1292534	20	3.8	20	78	0	87	34	13	12	40	1.81
1292460--1292537	40	2.0	39	87	2	111	34	12	12	39	1.82
1293443--1293501	23	2.7	23	92	5	95	16	8	8	66	1.43
1299603--1299648	23	2.0	24	86	4	67	71	10	13	4	1.27
1301000--1301371	27	13.6	27	89	0	483	24	33	14	27	1.94
1301279--1302478	28	40.8	28	86	4	1135	28	32	17	21	1.96
1301298--1302529	145	8.3	145	83	8	1164	28	31	18	21	1.97
1303089--1303163	20	3.8	20	78	0	87	34	13	12	40	1.81
1303089--1303166	40	2.0	39	87	2	111	34	12	12	39	1.82
1304071--1304128	23	2.7	23	92	7	95	17	8	8	65	1.45
1306842--1306871	4	7.5	4	100	0	60	76	0	0	23	0.78
1306998--1307032	18	1.9	18	88	0	52	40	5	17	37	1.73
1307036--1307092	17	3.2	18	80	16	66	40	1	7	50	1.40
1307036--1307092	18	3.2	18	82	12	73	40	1	7	50	1.40
1307863--1307890	14	2.0	14	100	0	56	42	0	0	57	0.99
1308539--1308584	2	23.0	2	100	0	92	50	0	0	50	1.00
1308584--1308632	2	24.5	2	87	0	71	2	4	46	46	1.33
1309425--1309750	158	2.1	158	88	1	476	38	9	13	38	1.77
1311147--1311177	2	15.5	2	100	0	62	51	0	0	48	1.00
1313244--1313289	18	2.5	17	83	16	56	60	0	0	39	0.97
1314073--1314116	13	3.4	13	87	0	70	47	6	0	45	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1318933--1318962	15	2.0	15	100	0	60	66	6	0	26	1.16
1323196--1323227	3	10.7	3	100	0	64	68	0	0	31	0.90
1323582--1323627	14	3.2	15	81	9	51	34	0	0	65	0.93
1323576--1323631	24	2.3	24	87	0	76	37	0	0	62	0.95
1324642--1324669	3	9.3	3	100	0	56	64	0	0	35	0.94
1326613--1326646	4	8.2	4	93	6	59	47	2	0	50	1.16
1334445--1334495	26	2.0	26	92	0	84	21	17	13	47	1.82
1335063--1335207	31	4.7	30	72	13	98	58	0	0	40	1.03
1335084--1335244	16	9.6	17	68	20	58	56	0	0	42	1.03
1335130--1335231	18	5.9	19	73	24	75	57	0	0	42	0.98
1335091--1335230	29	5.0	29	71	17	100	58	0	0	41	0.98
1335098--1335231	18	6.9	19	66	20	73	57	0	0	42	0.98
1335477--1335508	2	15.5	2	93	6	55	46	0	3	50	1.17
1335598--1335654	24	2.4	25	85	11	75	42	0	0	57	0.98
1337583--1337614	2	16.0	2	100	0	64	50	0	0	50	1.00
1340498--1340607	29	3.9	28	75	10	98	38	17	12	31	1.87
1343521--1343715	37	5.2	37	85	2	194	23	20	21	34	1.96
1343700--1343732	17	1.9	17	100	0	66	30	3	18	48	1.63
1351301--1351377	6	12.8	6	90	0	82	32	7	15	44	1.75
1358151--1358216	28	2.4	28	100	0	132	56	3	13	27	1.52
1364516--1364567	13	3.8	14	82	12	72	71	1	7	19	1.20
1364643--1364680	16	2.5	15	84	16	51	76	2	0	21	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1364895--1364963	21	3.4	20	76	9	68	43	1	2	52	1.25
1365337--1365387	14	3.6	14	77	15	59	49	1	1	47	1.24
1366107--1366147	4	10.2	4	89	10	66	75	0	24	0	0.80
1366100--1366143	21	2.1	21	91	0	70	75	2	22	0	0.92
1366192--1366250	27	2.2	27	85	11	77	33	0	1	64	1.04
1366534--1366582	19	2.5	20	81	15	59	34	6	2	57	1.35
1366624--1366669	22	2.1	22	84	8	58	26	6	8	58	1.52
1367392--1367431	20	2.0	20	90	4	64	50	0	2	47	1.14
1367646--1367725	40	2.0	42	87	5	119	50	8	1	40	1.42
1370629--1370790	80	2.0	80	96	0	297	45	22	8	24	1.79
1377957--1378456	250	2.0	250	91	1	806	32	17	12	37	1.88
1380126--1380177	18	2.7	18	82	14	59	51	0	0	48	1.00
1380822--1380861	18	2.4	17	87	8	55	50	2	0	47	1.14
1392386--1392496	39	2.8	39	80	4	134	49	14	7	28	1.70
1396730--1396781	20	2.5	21	90	3	79	46	11	11	30	1.76
1403360--1403384	13	1.9	13	100	0	50	36	16	16	32	1.90
1403340--1403405	32	2.0	33	88	2	98	33	12	15	39	1.84
1403340--1403523	86	2.2	86	96	1	352	35	13	14	36	1.85
1403423--1403491	33	2.1	33	86	0	93	34	10	14	40	1.80
1403445--1403469	13	1.9	13	100	0	50	36	16	16	32	1.90
1403531--1403732	52	3.9	51	90	2	289	35	16	16	31	1.92
1405851--1405901	27	2.0	27	85	11	72	25	39	15	19	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1408791--1409064	42	6.5	42	77	8	229	24	23	13	39	1.90
1408826--1409103	85	3.4	82	78	9	255	23	21	12	41	1.88
1408835--1409103	42	6.6	41	77	9	221	24	21	13	40	1.89
1409425--1409943	87	6.0	87	85	1	650	30	21	22	25	1.99
1411695--1411743	24	2.0	24	100	0	98	28	12	22	36	1.90
1413237--1414645	706	2.0	706	100	0	2818	30	20	15	33	1.93
1416030--1416101	34	2.1	34	86	0	99	16	23	11	48	1.78
1416200--1416455	42	6.4	42	80	6	282	24	23	11	39	1.88
1416191--1416464	120	2.3	119	83	3	325	23	23	12	40	1.88
1416782--1417298	87	6.0	87	84	2	628	30	21	22	25	1.98

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