oyster.v9_M.fa.s2.2.7.7.80.10.50.500.4.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: scaffold1009
Parameters: 2 7 7 80 10 50 500
Length:  1861391

Tables:   1   2   3   4   5   

This is table  4  of  5  ( 553 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)
1041209--1041407	21	9.5	21	70	10	86	29	18	19	32	1.96
1056941--1056976	2	18.0	2	100	0	72	0	50	0	50	1.00
1063493--1063564	21	3.4	21	100	0	144	20	9	44	25	1.82
1069959--1070391	168	2.6	168	94	1	735	32	19	19	28	1.96
1071748--1071824	36	2.1	36	83	4	93	28	23	12	35	1.92
1071829--1072313	36	13.4	36	81	6	424	26	27	13	32	1.94
1074260--1074309	2	25.0	2	100	0	100	0	50	0	50	1.00
1076896--1077938	41	25.0	41	81	5	982	35	16	17	31	1.92
1076885--1077938	85	12.6	82	81	4	988	35	16	17	30	1.92
1077026--1077127	40	2.6	40	82	1	116	40	10	16	32	1.83
1078187--1078295	44	2.5	44	83	0	137	34	17	18	29	1.94
1084656--1084826	57	3.0	57	97	1	317	30	21	23	25	1.99
1085983--1086871	41	21.8	41	88	3	1141	39	13	15	32	1.86
1092606--1092632	14	1.9	14	100	0	54	66	0	33	0	0.92
1101705--1101745	17	2.5	17	84	7	50	48	12	12	26	1.75
1109276--1109331	12	4.6	12	84	4	76	0	32	25	42	1.55
1109276--1109328	8	6.5	8	86	4	70	0	33	24	41	1.55
1109289--1109331	4	10.5	4	85	5	59	0	27	25	46	1.53
1109285--1109329	17	2.7	17	86	3	65	0	31	24	44	1.54
1109336--1109878	146	3.7	146	94	1	928	29	19	22	28	1.98
1110472--1110518	23	2.0	23	95	0	85	36	31	0	31	1.58
1110477--1110518	12	3.6	12	74	6	50	30	35	0	33	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1123021--1123093	23	3.3	23	73	19	84	26	16	26	31	1.96
1127656--1127752	27	3.6	27	75	8	97	41	18	30	9	1.82
1130204--1130242	2	19.5	2	94	0	69	51	0	48	0	1.00
1135056--1135086	10	3.0	10	95	4	53	0	3	67	29	1.06
1140350--1140461	55	2.0	55	98	0	215	23	39	10	26	1.87
1147428--1147470	17	2.6	17	77	3	52	74	23	2	0	0.93
1148292--1148816	40	13.3	40	86	4	658	19	21	19	40	1.92
1151439--1151536	44	2.2	44	81	0	124	23	22	15	38	1.92
1151848--1152008	41	4.0	41	90	0	216	42	17	10	29	1.82
1153036--1153063	13	2.2	13	100	0	56	21	17	28	32	1.96
1160761--1160792	2	16.0	2	100	0	64	50	0	0	50	1.00
1160792--1160840	2	24.5	2	100	0	98	51	0	48	0	1.00
1161598--1161637	9	4.4	9	84	9	55	47	0	10	42	1.37
1164543--1164626	21	4.0	21	79	1	98	40	13	19	27	1.88
1164701--1164955	21	12.1	21	86	0	321	30	18	13	38	1.89
1164701--1164927	63	3.6	63	97	0	418	29	18	13	38	1.89
1164954--1165141	42	4.5	42	81	0	232	35	15	14	34	1.89
1164954--1165143	21	9.0	21	75	4	150	35	15	14	33	1.89
1164954--1165143	63	3.0	63	77	5	231	35	15	14	33	1.89
1165227--1165311	42	2.0	42	90	0	134	28	16	14	41	1.87
1165228--1165314	21	4.2	21	83	1	113	26	16	13	43	1.85
1179731--1179824	46	2.0	47	93	2	163	40	6	22	30	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1179808--1179872	2	32.5	2	96	0	121	52	0	47	0	1.00
1180237--1180279	14	3.1	14	86	6	52	23	2	6	67	1.27
1180313--1180371	2	29.5	2	100	0	118	49	50	0	0	1.00
1183898--1183955	2	29.0	2	100	0	116	0	50	0	50	1.00
1191114--1191500	144	2.8	144	78	10	383	30	17	21	30	1.96
1193941--1193981	2	20.5	2	100	0	82	48	0	51	0	1.00
1207261--1207444	102	1.8	102	86	0	269	31	21	21	26	1.98
1207345--1207580	62	3.8	61	80	3	247	27	22	22	27	1.99
1208467--1208512	23	2.0	23	100	0	92	26	26	30	17	1.97
1208490--1209292	62	13.1	62	76	4	635	24	22	24	29	1.99
1213894--1213919	13	2.0	13	100	0	52	53	0	15	30	1.42
1219322--1219367	2	23.5	2	93	4	76	45	0	2	52	1.13
1233413--1233522	30	3.7	30	96	2	204	34	4	20	40	1.73
1243349--1243381	12	2.8	12	95	4	59	0	36	27	36	1.57
1247687--1247735	23	2.2	23	85	3	64	34	10	12	42	1.76
1248369--1248432	8	8.5	8	80	13	82	0	35	25	39	1.56
1248374--1248435	12	5.2	12	88	0	79	0	33	25	40	1.56
1263821--1263878	20	3.0	19	80	9	73	31	10	13	44	1.78
1270030--1271055	166	6.3	165	87	4	1321	34	15	21	28	1.94
1270028--1271055	488	2.1	486	86	3	1427	34	15	21	28	1.94
1272241--1272274	9	3.7	9	92	4	50	0	17	32	50	1.47
1272444--1273277	166	5.0	165	83	3	915	34	14	22	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1272451--1273277	333	2.5	331	85	2	1122	33	14	22	28	1.94
1274052--1274103	26	2.0	26	92	0	86	7	17	21	53	1.68
1274110--1274162	22	2.4	21	84	6	61	7	1	60	30	1.35
1276792--1276823	2	16.0	2	100	0	64	0	50	0	50	1.00
1294372--1294406	17	2.1	16	89	5	52	20	37	17	25	1.94
1294463--1294497	17	2.1	16	89	5	52	25	17	37	20	1.94
1298797--1298821	5	5.0	5	100	0	50	40	0	40	20	1.52
1298856--1298891	5	7.4	5	87	6	56	22	38	0	38	1.54
1308461--1308505	16	2.8	16	89	0	72	33	26	37	2	1.69
1308513--1308568	15	3.9	15	74	6	62	30	26	30	12	1.93
1309988--1310255	147	1.8	147	84	7	371	36	18	13	31	1.89
1310110--1310675	180	3.2	178	85	5	746	36	17	16	30	1.92
1317489--1317533	11	4.5	11	76	21	53	48	22	0	28	1.50
1318307--1318405	21	4.7	21	78	0	99	39	15	27	18	1.90
1321531--1321664	21	6.4	21	76	6	110	39	18	23	17	1.92
1321540--1321644	42	2.5	42	93	0	183	40	20	22	16	1.91
1335835--1336227	202	2.0	201	100	0	777	24	25	15	34	1.95
1338764--1338805	20	2.0	20	86	4	57	19	23	14	42	1.87
1341583--1341616	2	17.0	2	100	0	68	50	0	50	0	1.00
1342310--1342334	13	1.9	13	100	0	50	84	0	0	16	0.63
1343748--1343776	13	2.2	13	100	0	58	75	24	0	0	0.80
1343749--1343779	16	2.0	15	93	6	53	77	22	0	0	0.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1347106--1347154	17	3.1	16	80	11	55	26	20	10	42	1.84
1352707--1352736	14	2.1	14	93	0	51	40	10	36	13	1.78
1360931--1360971	13	3.1	13	89	3	64	80	19	0	0	0.71
1360931--1360966	16	2.2	16	90	0	54	83	16	0	0	0.65
1364449--1364477	13	2.1	14	93	6	51	31	10	37	20	1.86
1379960--1380387	173	2.5	171	83	5	535	28	20	19	31	1.97
1382721--1382785	21	3.1	21	79	0	76	26	20	35	18	1.95
1382837--1382908	32	2.2	32	95	0	126	26	31	15	26	1.95
1382837--1382928	32	2.8	32	85	6	114	29	28	17	25	1.97
1391611--1391742	43	3.0	42	80	8	149	21	14	22	40	1.90
1391723--1391777	28	2.0	28	85	0	74	23	14	32	29	1.94
1396273--1396313	17	2.4	17	100	0	82	24	24	4	46	1.72
1402391--1402510	43	2.8	43	93	0	195	35	10	17	36	1.83
1407586--1407618	11	3.2	11	83	16	52	45	18	0	36	1.49
1416377--1416426	21	2.4	21	89	0	73	30	30	6	34	1.81
1417681--1417749	34	2.0	34	88	5	104	24	18	2	53	1.58
1418055--1418081	2	13.5	2	100	0	54	48	0	0	51	1.00
1421654--1421710	28	2.0	28	96	0	105	49	14	7	29	1.69
1422594--1422850	131	2.0	131	96	1	471	36	11	20	31	1.89
1432295--1432320	12	2.2	12	100	0	52	23	15	0	61	1.33
1450268--1450315	20	2.4	20	85	0	69	29	14	27	29	1.95
1455819--1455844	1	26.0	1	100	0	52	0	100	0	0	0.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1462869--1462910	14	3.0	14	89	0	66	47	11	9	30	1.72
1462850--1462910	28	2.2	28	84	0	77	44	14	8	32	1.75
1463355--1463400	17	2.8	16	87	9	65	76	2	19	2	1.00
1479724--1479905	27	6.7	27	94	0	301	36	24	17	21	1.95
1488502--1489342	421	2.0	420	98	0	1610	20	26	25	27	1.99
1499098--1499127	15	2.0	15	100	0	60	13	26	33	26	1.93
1504501--1504594	35	2.7	36	83	5	111	42	8	17	31	1.79
1506356--1506442	42	2.1	42	93	0	147	26	25	8	40	1.83
1509204--1509232	14	2.1	14	100	0	58	44	13	13	27	1.82
1517664--1517689	11	2.4	11	100	0	52	69	15	0	15	1.20

Tables:   1   2   3   4   5