oyster.v9_M.fa.s5.2.7.7.80.10.50.500.4.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.04

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: scaffold102
Parameters: 2 7 7 80 10 50 500
Length:  1727112

Tables:   1   2   3   4   5   

This is table  4  of  5  ( 549 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)
1097932--1098392	230	2.0	229	99	0	913	38	16	18	26	1.91
1099601--1099651	23	2.2	23	86	6	68	35	27	9	27	1.88
1099900--1100980	166	6.5	165	85	4	1304	33	16	23	26	1.95
1108493--1108546	27	2.0	27	100	0	108	44	7	11	37	1.68
1109603--1109660	22	2.6	22	80	0	71	29	25	13	31	1.94
1109709--1109746	20	1.9	20	94	0	67	36	10	18	34	1.85
1115766--1115800	2	18.0	2	88	5	54	48	0	0	51	1.00
1121935--1122575	167	3.9	165	92	1	1021	37	19	18	24	1.94
1123144--1124696	165	9.5	165	66	16	449	36	15	18	29	1.92
1128857--1128886	14	2.1	14	100	0	60	26	23	13	36	1.92
1144054--1144094	21	2.0	21	95	0	73	39	19	12	29	1.88
1144940--1145052	37	3.1	37	92	0	181	30	7	11	50	1.67
1164742--1164775	1	34.0	1	100	0	68	0	0	100	0	0.00
1166645--1166705	30	2.0	30	100	0	122	22	27	26	22	1.99
1168108--1168266	43	3.7	43	96	0	300	38	16	18	26	1.92
1183812--1183864	2	26.5	2	100	0	106	50	0	49	0	1.00
1184833--1185195	166	2.2	166	88	2	543	33	15	24	26	1.96
1187528--1187604	18	4.3	18	88	0	109	23	20	35	20	1.96
1188695--1188729	18	1.9	18	100	0	70	22	22	28	25	1.99
1196895--1197633	366	2.0	369	95	1	1340	31	17	18	32	1.94
1198210--1198271	30	2.1	30	96	0	115	50	9	8	32	1.65
1211614--1211649	14	2.6	14	86	13	56	66	0	16	16	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1211616--1211649	13	2.5	13	95	4	59	67	0	14	17	1.23
1217938--1218430	161	3.1	161	87	2	697	30	13	19	35	1.91
1220265--1220569	152	2.0	152	98	0	592	41	15	12	29	1.84
1238362--1238387	2	13.0	2	100	0	52	50	0	50	0	1.00
1239155--1240060	168	5.4	167	86	1	1127	31	19	18	31	1.96
1261490--1261548	21	2.8	21	89	0	91	8	8	55	27	1.58
1262293--1262347	10	5.3	10	87	8	83	49	27	9	14	1.73
1262294--1262347	21	2.6	21	93	0	99	48	27	9	14	1.75
1263671--1263737	7	9.6	7	83	0	89	35	14	22	26	1.93
1264232--1264275	2	22.0	2	100	0	88	50	0	50	0	1.00
1264273--1264302	4	7.5	4	100	0	60	50	23	26	0	1.50
1264481--1264526	2	23.0	2	95	0	83	0	47	0	52	1.00
1266578--1266644	7	9.6	7	83	0	89	26	22	14	35	1.93
1266578--1266644	21	3.2	21	86	0	98	26	22	14	35	1.93
1272226--1272277	20	2.7	19	77	14	54	53	5	7	32	1.53
1272308--1272368	21	2.9	22	80	14	65	45	9	6	37	1.63
1272299--1272368	22	3.2	22	76	15	74	40	10	7	42	1.66
1272308--1272384	22	3.6	21	77	10	66	48	7	5	38	1.55
1272922--1272981	20	2.9	21	87	5	77	40	13	10	36	1.78
1273723--1274173	34	13.3	34	93	1	717	31	24	10	33	1.89
1274864--1274904	20	2.0	20	100	0	82	46	19	9	24	1.80
1275063--1275088	2	13.0	2	100	0	52	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)
1286553--1286829	42	6.6	41	85	5	315	35	27	11	24	1.91
1286549--1286801	84	3.0	83	87	6	359	35	28	12	23	1.91
1286553--1286791	126	1.9	126	89	3	374	36	28	12	23	1.90
1286553--1286829	126	2.2	126	85	3	362	35	27	11	24	1.91
1288290--1288336	2	23.5	2	100	0	94	0	48	0	51	1.00
1290485--1290524	18	2.3	18	91	4	64	55	0	0	45	0.99
1298207--1298505	27	10.7	27	77	7	285	13	6	35	45	1.67
1298334--1298408	39	1.9	39	81	5	89	16	6	36	41	1.74
1298386--1298432	24	2.0	24	86	0	67	14	8	34	42	1.77
1298261--1298520	117	2.2	118	86	2	351	13	6	35	44	1.70
1298619--1298905	66	4.3	66	85	1	324	11	7	41	39	1.70
1298685--1298856	33	5.2	33	66	13	111	13	8	40	37	1.75
1298618--1298860	132	1.8	132	88	0	369	12	7	40	39	1.71
1298618--1298926	132	2.3	132	82	3	363	11	7	41	39	1.71
1299107--1299170	2	32.0	2	96	0	119	0	48	0	51	1.00
1300999--1301137	33	4.2	33	93	1	226	38	17	13	29	1.89
1303439--1303537	32	3.1	32	91	0	153	37	11	17	34	1.85
1305084--1305112	2	14.5	2	100	0	58	0	48	0	51	1.00
1313801--1313843	19	2.2	19	83	4	50	44	16	6	32	1.74
1314245--1314291	23	2.0	23	100	0	94	42	17	12	27	1.85
1315852--1315898	18	2.6	17	90	9	76	57	6	36	0	1.24
1319811--1319857	2	23.5	2	100	0	94	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1325519--1325851	167	2.0	166	100	0	657	35	12	17	34	1.87
1333221--1333723	67	7.5	67	87	0	691	25	20	17	36	1.94
1336475--1336692	99	2.2	99	81	4	253	33	19	20	26	1.96
1336772--1337048	93	3.0	92	83	2	315	46	10	17	24	1.80
1339543--1339636	21	4.5	20	75	7	55	38	12	15	32	1.86
1339533--1339636	42	2.5	42	75	12	106	36	15	15	32	1.89
1339600--1339675	21	3.6	21	77	11	66	39	18	9	32	1.82
1349720--1349775	3	18.7	3	84	0	76	37	1	30	30	1.68
1352593--1352651	2	29.5	2	100	0	118	50	0	49	0	1.00
1354904--1354950	4	11.8	4	81	0	58	0	40	25	34	1.56
1354905--1354950	8	5.8	8	89	0	65	0	39	26	34	1.57
1354913--1354950	12	3.2	12	100	0	76	0	39	26	34	1.57
1355418--1355455	20	2.1	18	85	14	51	28	5	21	44	1.73
1362004--1362038	12	2.9	12	95	0	61	0	34	25	40	1.56
1384495--1384522	3	9.3	3	100	0	56	0	0	35	64	0.94
1387024--1387089	32	2.1	32	85	5	89	25	22	30	21	1.99
1389357--1389395	19	2.0	20	95	5	71	28	15	0	56	1.40
1392188--1392242	2	28.0	2	96	3	103	0	49	0	50	1.00
1393599--1393642	2	22.0	2	100	0	88	0	50	0	50	1.00
1396181--1396237	28	2.0	28	89	0	87	28	40	22	8	1.84
1397068--1397119	2	26.0	2	100	0	104	0	50	0	50	1.00
1406694--1406718	1	25.0	1	100	0	50	0	0	0	100	0.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1408299--1408359	17	3.5	17	78	13	70	36	9	3	50	1.52
1411636--1411665	1	30.0	1	93	0	51	0	0	3	96	0.21
1416811--1416835	1	25.0	1	100	0	50	0	0	0	100	0.00
1417359--1417429	36	2.0	36	89	5	110	14	25	4	56	1.56
1417416--1417455	16	2.5	16	95	0	71	17	10	0	72	1.11
1420208--1420269	2	31.0	2	100	0	124	50	0	50	0	1.00
1420475--1420504	15	2.0	15	93	0	51	30	33	26	10	1.89
1433537--1433992	227	2.0	228	95	0	815	38	13	10	38	1.79
1434204--1434629	205	2.1	205	98	0	816	23	29	22	23	1.99
1434847--1435064	109	2.0	109	99	0	427	24	17	16	41	1.90
1439005--1439037	14	2.4	14	100	0	66	27	24	21	27	1.99
1439019--1439148	37	3.5	37	85	4	199	36	16	23	22	1.94
1442081--1442412	183	1.8	183	91	1	549	38	12	17	30	1.88
1442600--1442632	14	2.4	14	94	0	57	30	24	24	21	1.99
1443552--1443632	41	2.0	40	85	9	110	30	9	6	53	1.59
1450611--1450650	16	2.5	16	87	0	53	15	25	20	40	1.90
1450701--1450743	20	2.1	21	86	4	61	9	9	23	58	1.58
1462342--1462394	4	12.8	4	94	6	88	0	0	22	77	0.77
1463912--1463936	5	5.0	5	100	0	50	20	0	0	80	0.72
1464408--1464447	17	2.4	17	91	0	62	20	7	22	50	1.73
1472501--1472554	2	27.0	2	100	0	108	50	0	50	0	1.00
1474370--1474406	18	2.1	18	100	0	74	37	21	10	29	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1474889--1474913	11	2.3	11	100	0	50	52	0	16	32	1.44
1478348--1478803	173	2.6	172	94	1	797	36	14	19	29	1.92
1492959--1492994	18	2.0	18	94	0	63	58	5	36	0	1.22
1497843--1497872	16	1.9	15	93	6	51	30	6	0	63	1.20
1507255--1507287	9	3.7	9	91	0	57	0	24	33	42	1.55
1507460--1508658	165	7.4	166	88	3	1649	33	15	23	28	1.95
1516242--1516275	17	2.0	17	100	0	68	29	17	23	29	1.97
1516930--1516967	16	2.4	16	95	0	67	0	42	21	36	1.53
1517147--1517213	31	2.2	31	97	2	127	43	8	32	14	1.77
1517499--1517607	55	2.0	54	98	0	200	25	13	12	46	1.79

Tables:   1   2   3   4   5