oyster.v9_M.fa.s6.2.7.7.80.10.50.500.4.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: scaffold419
Parameters: 2 7 7 80 10 50 500
Length:  1725835

Tables:   1   2   3   4   5   

This is table  4  of  5  ( 535 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)
1032216--1032283	1	68.0	1	80	0	55	8	86	2	1	0.73
1039590--1039674	42	2.0	42	100	0	170	24	14	16	44	1.84
1071207--1071282	38	2.0	38	100	0	152	28	18	23	28	1.98
1075144--1075201	2	29.0	2	100	0	116	0	50	0	50	1.00
1080325--1080383	1	59.0	1	89	0	91	94	0	0	5	0.29
1088339--1089588	165	7.5	165	90	3	1821	32	14	25	26	1.95
1092208--1092239	2	16.0	2	100	0	64	0	0	50	50	1.00
1099798--1099828	2	15.5	2	100	0	62	48	0	0	51	1.00
1116675--1116724	2	25.5	2	93	4	84	46	0	54	0	1.00
1117575--1117931	115	3.0	117	86	9	467	14	21	17	46	1.83
1117814--1117922	53	2.1	53	98	0	209	13	22	18	44	1.85
1118094--1119379	436	3.0	433	89	2	1850	35	15	18	31	1.92
1139932--1139977	2	23.0	2	100	0	92	0	0	50	50	1.00
1143099--1143144	22	2.1	22	95	0	83	39	8	26	26	1.85
1145478--1145530	20	2.6	20	100	0	106	0	39	20	39	1.53
1145482--1145512	16	1.9	16	93	0	53	0	38	19	41	1.51
1145867--1146118	133	1.9	131	82	4	319	30	17	26	26	1.97
1149760--1149852	31	3.0	30	85	6	123	37	21	15	25	1.92
1152028--1152058	16	1.9	16	100	0	62	12	25	19	41	1.87
1153505--1153546	2	21.0	2	100	0	84	50	0	50	0	1.00
1165415--1165439	10	2.5	10	100	0	50	44	12	0	44	1.41
1166327--1166372	19	2.4	19	92	0	74	36	8	21	32	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1172390--1172461	21	3.4	21	96	1	126	43	38	16	1	1.57
1172390--1172461	11	6.7	11	93	4	121	43	38	16	1	1.57
1172615--1173320	173	4.1	173	94	1	1168	36	26	15	21	1.93
1177759--1177817	21	2.9	20	74	18	59	11	11	37	38	1.79
1177784--1177818	11	3.3	11	88	8	54	11	14	37	37	1.82
1178068--1178137	10	6.8	10	90	6	113	2	17	38	41	1.64
1178068--1178137	21	3.4	20	90	5	113	2	17	38	41	1.64
1178068--1178137	31	2.3	30	90	7	113	2	17	38	41	1.64
1184965--1184997	14	2.2	15	89	10	50	42	18	0	39	1.50
1193154--1193197	22	2.0	23	86	13	65	2	0	15	81	0.78
1199380--1199404	13	1.9	13	100	0	50	44	24	0	32	1.54
1206301--1206481	4	45.2	4	95	0	272	24	29	0	45	1.58
1207847--1207883	17	2.2	18	85	9	51	32	0	21	45	1.52
1209470--1209506	15	2.5	15	91	4	58	48	16	8	27	1.74
1211336--1211380	2	22.5	2	100	0	90	0	48	0	51	1.00
1215833--1215895	18	3.3	18	68	20	56	38	15	26	19	1.92
1215819--1215896	39	2.0	39	100	0	156	38	15	28	17	1.91
1217427--1217480	2	27.0	2	100	0	108	0	50	0	50	1.00
1226416--1226451	2	18.5	2	94	5	65	0	52	0	47	1.00
1226415--1226449	17	2.1	17	100	0	70	0	54	0	45	0.99
1231190--1231326	21	6.5	21	70	0	94	40	15	24	19	1.90
1231202--1231318	42	2.8	42	86	0	162	41	17	22	18	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1232344--1232392	21	2.2	21	85	7	62	38	20	24	16	1.92
1232359--1232430	21	3.5	20	81	7	81	40	22	23	13	1.90
1232361--1232460	42	2.4	42	89	3	148	40	21	23	16	1.91
1232382--1232454	21	3.5	21	78	0	92	41	20	21	16	1.90
1239206--1239276	31	2.3	31	95	0	133	25	29	16	28	1.97
1239206--1239296	31	2.9	31	88	3	119	28	26	18	26	1.98
1240726--1240770	19	2.2	20	84	11	56	26	2	22	48	1.62
1241621--1241705	36	2.5	33	86	7	118	27	17	30	24	1.97
1241689--1241722	17	2.0	17	88	0	50	35	11	35	17	1.87
1244489--1244519	16	1.9	16	100	0	62	45	25	19	9	1.81
1244527--1244602	16	4.9	16	85	6	111	9	18	25	47	1.78
1244522--1244602	30	2.6	31	90	3	119	9	19	23	46	1.80
1245996--1246042	2	23.5	2	100	0	94	0	48	0	51	1.00
1249310--1249794	166	3.1	153	80	11	462	28	22	15	34	1.94
1248913--1249813	321	2.8	316	79	9	919	28	21	14	35	1.93
1249465--1249846	166	2.3	165	91	1	604	28	21	14	35	1.93
1250848--1250891	18	2.3	20	84	7	56	56	4	13	25	1.56
1258417--1258858	165	2.7	166	90	2	669	28	22	15	33	1.95
1263016--1263070	24	2.4	22	88	11	92	25	25	7	41	1.81
1263023--1263070	24	2.0	24	100	0	96	25	29	8	37	1.85
1273045--1273121	36	2.1	38	83	16	99	33	9	6	50	1.60
1277072--1277141	9	7.7	9	75	1	68	2	21	35	40	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1277316--1278203	162	5.4	164	86	5	1117	35	15	21	27	1.93
1277316--1278203	328	2.7	326	85	5	1206	35	15	21	27	1.93
1278596--1279037	224	2.0	223	99	0	866	32	12	25	29	1.92
1285268--1285309	4	10.5	4	94	0	75	0	47	23	28	1.52
1285844--1286234	163	2.4	162	88	2	570	35	13	17	32	1.90
1286274--1286651	189	2.0	188	98	0	738	23	20	26	29	1.98
1286485--1286769	134	2.1	135	84	5	373	25	20	26	28	1.99
1306121--1306148	2	14.0	2	100	0	56	50	0	50	0	1.00
1341746--1342293	273	2.0	273	99	0	1087	31	15	14	38	1.88
1342875--1343417	146	3.7	146	95	1	955	28	20	22	28	1.99
1350488--1350681	107	1.8	107	85	5	275	42	12	12	32	1.81
1354424--1354878	180	2.6	179	92	2	756	39	15	20	24	1.91
1355451--1355504	28	1.9	28	100	0	108	40	11	18	29	1.85
1367870--1368014	55	2.7	55	93	1	238	31	10	24	33	1.89
1367870--1368037	55	3.1	55	83	5	137	32	10	23	33	1.88
1370609--1370659	21	2.4	21	90	6	77	13	15	39	31	1.87
1371660--1371715	11	5.3	11	82	8	71	10	21	30	37	1.87
1371657--1371715	21	2.8	21	97	0	109	10	20	32	37	1.86
1371657--1371711	10	5.3	10	82	8	65	9	20	34	36	1.84
1373184--1373809	48	13.0	48	91	1	932	12	22	37	27	1.90
1373789--1373909	48	2.5	48	81	9	140	14	31	31	23	1.94
1373802--1373960	48	3.3	48	80	6	171	13	31	33	21	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1374025--1374059	13	2.8	13	91	4	54	65	0	0	34	0.93
1375968--1376210	126	1.9	126	88	0	360	39	18	15	26	1.90
1376440--1376497	30	1.9	30	86	6	82	34	24	10	31	1.89
1380888--1380917	2	15.0	2	100	0	60	50	0	50	0	1.00
1396998--1397783	180	4.4	180	88	3	1120	37	16	14	31	1.88
1408293--1408325	17	1.9	17	93	0	57	27	12	15	45	1.81
1409787--1409891	51	2.1	51	89	1	158	39	7	10	42	1.68
1411090--1411426	134	2.5	134	90	2	502	35	20	9	35	1.85
1412735--1413154	166	2.5	166	93	1	709	26	24	15	33	1.95
1413304--1413349	8	5.8	8	94	0	83	39	26	34	0	1.57
1413307--1413357	4	13.0	4	81	4	59	41	25	33	0	1.56
1433648--1433689	20	2.1	20	90	0	66	0	33	26	40	1.56
1433713--1434022	157	2.0	157	90	1	496	29	15	16	38	1.90
1434024--1434334	164	1.9	164	83	5	405	29	16	14	38	1.89
1436716--1436749	12	2.8	12	95	0	59	38	26	35	0	1.57
1436719--1436754	12	3.0	12	91	0	54	33	25	41	0	1.55
1447106--1447210	32	3.2	32	84	1	129	29	19	26	24	1.98
1447269--1447344	30	2.5	30	91	0	125	23	25	25	26	2.00
1451479--1451526	21	2.3	21	96	0	87	37	12	12	37	1.81
1455326--1455377	20	2.6	20	90	6	79	42	0	51	5	1.25
1455327--1455377	18	2.9	17	83	11	66	41	0	52	5	1.25
1465358--1465446	20	4.7	18	70	14	63	47	7	14	30	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1465471--1465507	2	18.5	2	100	0	74	51	48	0	0	1.00
1495256--1495297	21	2.0	21	85	4	57	23	9	16	50	1.75
1497449--1497486	2	19.0	2	100	0	76	0	50	0	50	1.00
1499414--1499467	25	2.1	25	86	3	72	46	14	9	29	1.76
1500653--1500682	14	2.2	13	94	5	51	0	0	10	90	0.47
1503533--1503565	1	33.0	1	100	0	66	0	0	0	100	0.00
1515585--1515772	62	3.0	62	94	0	331	43	11	13	31	1.80
1533864--1533932	21	3.3	21	87	4	95	23	39	26	11	1.88
1534005--1534304	21	14.3	21	86	0	384	26	42	21	9	1.83
1533796--1534072	140	2.0	139	93	1	466	23	41	20	14	1.89

Tables:   1   2   3   4   5