oyster.v9_M.fa.s13.2.7.7.80.10.50.500.3.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: scaffold1301
Parameters: 2 7 7 80 10 50 500
Length:  1559340

Tables:   1   2   3   4   

This is table  3  of  4  ( 397 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)
894610--895462	180	4.7	180	95	0	1463	30	16	16	36	1.91
894610--895462	361	2.4	361	94	0	1465	30	16	16	36	1.91
900783--900815	11	3.0	11	91	8	50	45	27	18	9	1.79
904221--904416	73	2.7	72	88	3	284	30	22	23	22	1.99
905841--905931	30	3.0	30	91	0	155	24	25	25	25	2.00
907873--907929	2	28.5	2	100	0	114	0	50	0	49	1.00
916121--916170	22	2.3	22	79	3	57	34	14	16	36	1.88
917875--918275	201	2.0	200	100	0	793	31	18	13	35	1.90
922775--922821	8	6.0	8	77	5	51	36	23	40	0	1.55
922768--922811	12	3.7	12	78	0	52	38	22	38	0	1.55
925987--926075	2	45.0	2	93	2	117	0	44	0	55	0.99
932257--932699	164	2.7	165	86	5	592	38	14	16	29	1.89
932242--932699	165	2.8	161	85	4	605	39	14	16	29	1.89
934231--934271	18	2.3	18	91	0	64	36	12	14	36	1.84
936041--936065	13	1.9	13	100	0	50	8	4	24	64	1.38
945397--945428	6	5.3	6	100	0	64	0	34	46	18	1.49
945545--946312	177	4.3	176	88	3	976	23	16	26	33	1.96
946361--946644	152	1.8	154	83	8	380	24	17	24	33	1.97
947007--947042	15	2.4	15	90	0	54	36	5	13	44	1.68
947008--947167	50	3.2	50	74	3	162	35	7	11	45	1.68
947076--947207	15	8.1	15	66	21	52	37	3	10	48	1.56
947253--947294	15	2.8	15	81	0	57	45	11	4	38	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
947302--947357	27	2.1	27	86	0	76	48	14	1	35	1.54
956843--956872	15	2.0	15	100	0	60	26	33	26	13	1.93
963260--964105	156	5.4	155	75	9	698	29	21	13	34	1.92
963303--964105	304	2.6	304	83	5	932	29	22	13	34	1.93
963610--964133	165	3.2	164	82	7	597	28	21	13	35	1.92
1005220--1006190	486	2.0	485	100	0	1933	30	18	16	34	1.93
1014472--1014534	2	32.5	2	90	6	103	0	50	0	49	1.00
1017471--1017519	20	2.4	20	79	3	53	30	14	8	46	1.73
1021800--1021829	15	2.0	15	100	0	60	26	6	20	46	1.75
1024974--1025016	19	2.3	19	88	8	61	37	11	11	39	1.78
1046704--1046731	14	2.0	14	100	0	56	28	21	7	42	1.79
1049129--1049153	2	12.5	2	100	0	50	52	48	0	0	1.00
1055523--1055550	14	2.0	14	100	0	56	57	0	7	35	1.26
1059583--1059607	12	2.1	12	100	0	50	84	0	0	16	0.63
1063554--1063619	33	2.0	33	96	0	123	27	19	9	43	1.81
1063746--1063805	25	2.4	26	75	13	63	56	10	8	25	1.60
1064291--1064886	61	9.7	61	85	3	711	39	21	11	27	1.88
1068159--1068188	2	15.0	2	100	0	60	50	0	50	0	1.00
1088810--1088842	17	1.9	17	100	0	66	24	21	24	30	1.99
1090736--1090826	19	4.6	19	74	12	94	38	9	8	42	1.69
1090736--1090826	41	2.3	37	76	12	92	38	9	8	42	1.69
1094306--1094381	2	38.0	2	97	0	143	1	50	0	48	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1097941--1097986	21	2.2	21	84	0	56	50	2	41	6	1.40
1103084--1103134	15	3.5	15	84	7	61	29	25	1	43	1.66
1106078--1106105	12	2.3	12	100	0	56	35	25	32	7	1.83
1112930--1113042	57	2.0	58	87	5	167	38	11	13	36	1.81
1113011--1113113	45	2.2	45	89	6	152	37	8	16	36	1.80
1113021--1113169	55	2.9	55	87	9	201	34	9	18	37	1.83
1113371--1113421	15	3.4	15	88	0	75	45	17	21	15	1.86
1114575--1114647	34	2.1	34	100	0	146	21	21	13	42	1.88
1118065--1118181	58	2.0	57	88	1	171	29	18	11	39	1.87
1129681--1129734	18	3.0	18	97	0	99	22	24	20	33	1.97
1170024--1170061	19	1.9	20	84	5	51	31	10	7	50	1.66
1174461--1174561	37	2.6	37	75	12	105	29	14	14	40	1.87
1179237--1179509	63	4.3	63	96	0	501	34	30	14	20	1.92
1179479--1179538	31	1.9	31	100	0	120	30	28	20	21	1.98
1181605--1181647	15	2.8	16	89	7	70	41	11	13	32	1.81
1181647--1181681	16	2.2	16	89	0	52	22	11	14	51	1.74
1190015--1190043	15	1.9	15	100	0	58	51	6	6	34	1.55
1200167--1200200	18	1.9	17	94	5	59	11	0	0	88	0.52
1206745--1206839	35	2.7	34	80	4	100	50	22	9	17	1.75
1209607--1209703	32	3.0	32	98	0	185	29	31	10	27	1.90
1213582--1213699	61	1.9	61	94	0	209	22	16	24	36	1.94
1213638--1213916	70	3.8	70	76	15	298	27	13	24	35	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1213861--1213980	61	2.0	61	94	0	213	24	15	25	35	1.94
1214397--1214783	160	2.4	159	89	2	560	28	13	21	35	1.92
1216197--1216244	20	2.4	21	79	10	55	27	12	8	52	1.67
1221070--1221109	21	1.9	21	94	0	71	15	25	22	37	1.93
1223902--1224007	21	5.1	21	75	4	108	20	27	17	33	1.96
1226923--1226957	16	2.2	16	90	10	54	54	8	17	20	1.68
1227113--1227138	11	2.4	11	100	0	52	26	0	26	46	1.53
1227683--1227723	18	2.3	18	86	0	55	39	12	14	34	1.84
1231805--1232146	172	2.0	170	98	0	648	35	19	10	35	1.86
1236108--1236241	50	2.7	50	90	0	205	37	15	16	30	1.90
1239440--1239795	34	10.3	34	80	4	329	34	17	17	29	1.94
1239551--1239611	15	3.9	14	71	24	50	40	16	11	31	1.84
1239566--1239625	19	3.4	19	70	25	67	41	16	13	28	1.86
1239445--1239795	102	3.4	102	80	4	364	34	18	17	29	1.94
1243965--1244334	187	2.0	186	99	0	722	32	18	15	33	1.92
1246042--1247460	39	36.0	39	87	4	2015	11	30	15	41	1.83
1249626--1249683	2	29.0	2	92	0	98	46	0	50	3	1.18
1250427--1250696	39	7.0	39	93	2	438	23	4	14	57	1.57
1250430--1250696	114	2.3	116	91	2	439	23	4	14	56	1.57
1250427--1250706	153	1.8	153	91	1	463	23	4	14	57	1.56
1250675--1250726	27	1.9	27	84	0	68	15	3	25	55	1.57
1252399--1252482	41	2.0	41	97	0	159	38	22	2	36	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1258491--1258562	2	36.0	2	85	0	99	48	6	44	0	1.29
1258816--1259221	5	79.4	5	74	14	231	38	21	3	36	1.70
1259038--1259063	12	2.2	12	100	0	52	50	15	0	34	1.45
1259372--1259403	17	1.9	17	93	6	57	37	12	18	31	1.88
1259541--1259616	40	1.9	40	97	0	143	39	17	14	28	1.89
1268661--1268785	30	4.2	30	91	0	196	20	19	25	34	1.96
1279207--1279607	200	2.0	200	100	0	802	45	21	9	23	1.81
1281487--1281533	2	23.5	2	100	0	94	51	0	48	0	1.00
1287927--1287971	2	22.5	2	100	0	90	51	0	48	0	1.00
1292536--1292607	35	2.1	35	97	0	135	50	15	13	20	1.78
1296824--1296877	26	2.1	26	96	0	99	42	14	12	29	1.83
1300414--1300483	10	6.8	10	90	6	113	2	17	38	41	1.64
1300414--1300483	21	3.4	20	90	5	113	2	17	38	41	1.64
1300414--1300483	31	2.3	31	94	0	122	2	17	38	41	1.64
1313609--1313784	88	2.0	88	97	0	334	29	21	13	35	1.91
1317521--1317545	12	2.1	12	100	0	50	16	40	0	44	1.47
1319277--1319978	26	27.3	26	81	4	746	38	22	8	30	1.83
1319582--1319707	8	14.7	9	63	25	51	38	21	7	31	1.82
1320190--1320224	17	2.1	16	89	5	52	20	37	17	25	1.94
1332568--1332607	18	2.2	18	95	0	71	5	12	30	52	1.60
1361462--1362369	168	5.4	165	88	2	1042	31	18	19	30	1.96
1361504--1362369	336	2.6	332	85	2	1147	31	18	19	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1362539--1362570	7	4.4	7	92	7	55	31	40	28	0	1.57
1362539--1362570	15	2.2	14	94	5	55	31	40	28	0	1.57
1364713--1364756	21	2.1	20	87	8	61	63	4	15	15	1.46
1370702--1370730	2	14.5	2	100	0	58	51	0	48	0	1.00
1377772--1378698	166	5.6	166	88	2	1303	26	24	15	32	1.96
1377772--1378698	333	2.8	328	87	4	1304	26	24	15	32	1.96
1385869--1385910	18	2.3	18	87	0	57	38	9	23	28	1.86
1399331--1399391	30	2.0	30	90	0	95	24	21	27	26	1.99
1399683--1400000	159	2.0	158	99	0	627	39	15	16	27	1.89
1402053--1402093	2	20.5	2	84	0	55	4	2	43	48	1.37

Tables:   1   2   3   4