genome.fa.s38.2.7.7.80.10.50.1000.9.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: Scaffold38
Parameters: 2 7 7 80 10 50 1000
Length:  2073527

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

This is table  9  of  15  ( 1750 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)
1245240--1245295	21	2.7	21	75	10	60	66	3	0	30	1.09
1245449--1245522	36	2.1	36	82	5	87	54	1	2	41	1.23
1245545--1245590	16	2.9	16	81	9	58	60	0	2	36	1.09
1245545--1245590	17	2.9	16	83	6	58	60	0	2	36	1.09
1246557--1246608	24	2.2	23	82	3	68	42	0	0	57	0.98
1246569--1246678	42	2.6	41	72	20	95	41	0	0	56	1.12
1246616--1246676	13	4.6	14	72	22	51	40	0	1	57	1.08
1247846--1248034	94	2.0	94	100	0	378	41	10	7	40	1.69
1248581--1248621	20	2.0	21	86	13	59	78	0	2	19	0.87
1248565--1248724	85	1.9	84	82	7	198	54	5	7	32	1.52
1249473--1249518	22	2.2	22	77	18	53	32	2	2	63	1.19
1250035--1250065	16	2.0	15	93	6	53	22	0	0	77	0.77
1250734--1250784	13	3.6	14	78	19	52	62	0	1	35	1.06
1250786--1250856	19	4.1	18	71	22	62	54	0	0	45	0.99
1250780--1250849	32	2.2	33	84	5	99	55	0	0	44	0.99
1250784--1250857	18	4.4	17	68	23	57	52	0	0	47	1.00
1254147--1254189	22	2.0	21	81	4	50	16	11	16	55	1.68
1256290--1256353	15	3.8	16	78	17	60	46	0	1	51	1.10
1258430--1258481	18	2.7	19	80	14	63	53	0	0	46	1.00
1258393--1258500	32	3.3	32	81	10	96	53	0	0	45	1.06
1258433--1258500	26	2.5	26	81	11	75	51	0	0	48	1.00
1258749--1258781	15	2.2	15	94	0	57	51	0	3	45	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1258772--1258820	21	2.3	22	82	10	66	38	0	0	61	0.96
1258787--1258828	21	2.0	21	82	13	52	45	0	0	54	0.99
1258841--1258870	13	2.3	13	94	0	51	60	0	0	40	0.97
1260197--1260221	13	1.9	13	100	0	50	48	0	4	48	1.20
1260617--1260669	26	2.0	26	82	7	63	52	0	1	45	1.11
1261921--1261989	25	2.7	25	82	14	79	46	0	0	53	1.00
1261920--1261986	18	3.6	19	77	16	61	46	0	0	53	1.00
1261939--1261986	6	7.7	6	80	15	53	41	0	0	58	0.98
1262142--1262209	22	3.1	22	79	8	68	58	0	0	41	0.98
1262379--1262417	20	2.0	20	85	10	53	64	0	0	35	0.94
1262390--1262544	31	4.5	33	75	14	118	57	0	1	41	1.07
1262392--1262511	7	16.9	7	69	17	70	56	0	0	42	1.05
1262404--1262533	50	2.7	45	80	11	152	56	0	1	42	1.09
1262404--1262539	8	15.4	9	72	18	85	56	0	1	41	1.08
1262709--1262733	6	4.2	6	100	0	50	64	0	0	36	0.94
1269905--1269935	2	15.5	2	100	0	62	48	0	0	51	1.00
1270665--1270689	2	12.5	2	100	0	50	52	0	0	48	1.00
1271264--1271306	21	2.0	21	82	8	52	32	0	2	65	1.06
1278434--1278467	17	2.0	17	88	11	52	44	0	0	55	0.99
1282422--1282531	35	3.5	32	77	20	99	55	0	0	43	1.06
1283556--1283597	15	2.9	15	75	3	50	57	0	0	42	0.99
1283616--1283660	21	2.1	22	83	4	56	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1284913--1284967	16	3.4	16	75	12	58	40	1	0	58	1.09
1285426--1285491	27	2.5	27	80	9	75	50	1	0	48	1.10
1286491--1286539	22	2.2	21	86	13	64	46	4	0	48	1.20
1287151--1287247	50	2.0	47	84	9	124	48	0	1	50	1.07
1287435--1287468	17	2.1	16	88	5	50	64	14	0	20	1.28
1287506--1287539	13	2.5	13	90	4	50	58	2	0	38	1.13
1289620--1289653	16	2.1	17	88	5	52	70	0	0	29	0.87
1289683--1289759	16	4.8	16	71	20	54	58	0	0	41	0.98
1289702--1289764	27	2.2	29	86	5	94	58	0	0	41	0.98
1289625--1289765	59	2.4	58	72	21	132	56	0	1	41	1.13
1289702--1289769	28	2.4	28	75	17	70	60	0	0	39	0.97
1289987--1290055	37	1.9	36	85	11	97	62	0	0	37	0.96
1289983--1290061	37	2.3	36	81	14	96	59	0	0	40	0.97
1290008--1290071	17	3.7	18	71	24	57	59	0	0	40	0.97
1290925--1290977	23	2.2	23	83	12	63	54	1	3	39	1.29
1291936--1291983	21	2.3	22	82	7	64	58	0	0	41	0.98
1292747--1292839	48	1.9	48	86	2	132	43	8	15	33	1.77
1293687--1293712	3	8.7	3	100	0	52	65	0	0	34	0.93
1294896--1294992	17	6.2	16	70	24	57	37	1	3	58	1.20
1295145--1295182	16	2.3	17	86	4	51	50	0	0	50	1.00
1295578--1295615	19	2.0	20	89	5	60	68	2	7	21	1.28
1295882--1295932	16	2.9	17	77	14	50	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1295889--1295932	19	2.4	18	81	7	54	52	0	0	47	1.00
1302571--1302726	78	2.0	78	93	2	269	32	23	24	20	1.98
1305852--1305878	2	13.5	2	100	0	54	51	0	0	48	1.00
1306244--1306287	23	2.0	22	86	4	61	50	0	0	50	1.00
1306876--1306948	32	2.3	32	79	11	80	47	1	1	49	1.18
1308959--1309015	24	2.3	25	80	17	66	40	5	1	52	1.34
1312517--1312560	19	2.4	19	85	14	65	59	0	0	40	0.98
1312993--1313022	2	15.0	2	100	0	60	50	0	0	50	1.00
1315941--1316047	39	2.8	37	77	12	101	59	3	0	36	1.15
1318021--1318062	2	21.0	2	100	0	84	0	50	0	50	1.00
1319169--1319195	13	2.1	13	100	0	54	51	14	0	33	1.43
1320401--1320440	20	2.0	21	90	5	64	30	10	0	60	1.30
1321647--1321897	133	1.9	133	90	0	403	32	11	16	39	1.85
1321780--1322070	150	1.9	150	85	1	404	30	12	17	39	1.86
1326317--1326381	29	2.2	28	82	15	78	46	0	0	53	1.00
1326330--1326402	35	2.1	35	84	5	94	45	0	1	53	1.09
1326637--1326673	18	2.1	18	90	10	58	43	0	0	56	0.99
1326703--1326741	19	2.1	18	85	4	51	43	2	0	53	1.14
1328973--1329027	26	2.2	25	83	3	65	45	0	0	54	0.99
1329717--1329766	27	1.9	25	88	8	73	60	0	0	40	0.97
1329724--1329781	21	2.8	21	80	17	75	62	0	0	37	0.96
1334189--1334213	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1334928--1334974	23	2.0	25	87	8	71	27	0	0	72	0.85
1339755--1339807	28	2.0	28	85	7	74	37	0	0	62	0.96
1339753--1339791	18	2.2	17	86	4	51	41	0	0	58	0.98
1340392--1340455	34	1.9	33	83	3	83	45	3	3	48	1.34
1340914--1340987	29	2.7	29	83	6	82	33	0	2	63	1.09
1340936--1340986	8	7.0	7	75	16	50	33	0	0	66	0.92
1340936--1340986	15	3.5	15	78	5	68	33	0	0	66	0.92
1341670--1341717	20	2.4	19	82	6	60	64	2	4	29	1.23
1343808--1343860	19	2.6	21	88	11	76	58	0	0	41	0.98
1345445--1345478	9	3.7	9	92	4	50	67	0	0	32	0.91
1345423--1345468	24	1.9	24	82	8	58	65	0	4	30	1.12
1345451--1345480	5	6.2	5	92	7	53	63	0	0	36	0.95
1346517--1346552	12	3.0	13	84	15	51	66	0	0	33	0.92
1346520--1346553	17	2.0	17	88	11	52	70	0	0	29	0.87
1346630--1346662	15	2.1	16	88	5	50	57	3	0	39	1.14
1347549--1347596	24	2.1	22	84	7	60	35	2	8	54	1.42
1348674--1348707	18	1.9	18	88	5	52	38	5	2	52	1.41
1350486--1350512	12	2.2	12	100	0	54	40	0	22	37	1.54
1354323--1354376	28	2.0	27	82	10	65	44	0	3	51	1.19
1354865--1354907	13	3.2	13	86	6	59	62	2	0	34	1.08
1354875--1354911	13	2.8	13	91	4	56	67	0	0	32	0.91
1355277--1355315	18	2.2	18	85	0	51	43	5	2	48	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1355269--1355307	14	2.8	14	88	0	51	43	5	2	48	1.38
1356638--1356669	2	16.5	2	93	6	57	50	0	0	50	1.00
1357559--1357595	17	2.1	18	90	5	58	51	16	0	32	1.45
1358086--1358168	32	2.9	27	70	18	76	45	1	0	53	1.08
1358092--1358177	33	2.6	34	78	14	90	45	1	0	53	1.07
1358082--1358176	27	3.7	26	68	14	63	46	1	0	52	1.07
1359171--1359226	19	3.1	18	75	15	62	42	1	0	55	1.10
1359153--1359226	36	2.1	35	82	7	87	43	2	0	54	1.14
1359098--1359213	26	4.6	26	69	17	75	49	0	0	50	1.06
1359370--1359447	18	4.2	18	72	26	65	38	0	0	61	0.96

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