oyster.v9_M.fa.s20.2.7.7.80.10.50.500.3.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: scaffold481
Parameters: 2 7 7 80 10 50 500
Length:  1334154

Tables:   1   2   3   4   

This is table  3  of  4  ( 385 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)
733730--733823	30	3.1	30	89	3	152	24	24	9	41	1.84
735093--735342	35	7.1	35	73	5	227	34	8	28	29	1.87
735093--735368	140	2.0	141	88	0	410	33	9	28	28	1.88
735093--735330	70	3.4	70	91	0	377	34	8	28	28	1.87
740604--740649	21	2.2	21	84	7	58	32	26	4	36	1.76
750190--750248	2	30.0	2	96	3	111	0	50	0	49	1.00
757884--757929	2	23.0	2	100	0	92	50	0	50	0	1.00
763412--763474	4	15.8	4	100	0	126	25	25	0	49	1.51
763469--763511	20	2.1	20	100	0	86	34	18	13	32	1.90
763541--763571	16	1.9	16	100	0	62	22	19	12	45	1.84
763994--764061	4	17.0	4	100	0	136	25	25	0	50	1.50
771011--771057	2	23.5	2	100	0	94	0	48	0	51	1.00
771533--771580	20	2.4	20	96	0	87	39	0	10	50	1.37
779623--779647	2	12.5	2	100	0	50	52	0	0	48	1.00
793025--793064	2	20.0	2	100	0	80	0	50	0	50	1.00
796891--796934	21	2.1	21	82	0	52	15	18	18	47	1.83
797053--797106	21	2.5	22	79	8	58	18	18	20	42	1.89
797005--797107	42	2.5	42	70	3	100	19	17	22	40	1.91
799491--799521	2	15.5	2	100	0	62	0	51	0	48	1.00
801018--801103	2	43.5	2	97	2	165	0	51	0	48	1.00
803049--803095	21	2.2	21	80	0	58	72	23	2	2	1.06
805694--805814	22	5.5	22	87	2	163	36	9	35	18	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
806040--806080	2	20.5	2	100	0	82	48	0	51	0	1.00
808333--808374	4	10.8	4	89	5	68	0	0	23	76	0.79
808365--808399	1	35.0	1	94	0	61	0	0	2	97	0.19
808332--808400	7	9.0	8	85	7	65	0	0	15	84	0.63
808331--808399	12	6.0	12	83	5	63	0	0	14	85	0.60
813570--813611	21	2.0	21	85	0	57	35	4	0	59	1.19
820660--820706	2	23.5	2	95	0	85	48	0	51	0	1.00
830202--830253	2	26.0	2	100	0	104	50	0	50	0	1.00
830319--830653	167	2.0	167	100	0	670	28	15	10	45	1.80
835274--835310	2	18.5	2	94	0	65	54	0	45	0	1.00
843358--843415	19	3.1	19	100	0	116	63	5	25	5	1.36
844420--844450	15	2.1	15	100	0	62	32	6	19	41	1.77
850568--850649	41	2.0	42	90	2	130	54	4	8	31	1.52
861508--861571	32	2.0	32	96	0	119	15	17	29	37	1.91
863235--863272	19	1.9	20	94	5	69	15	10	10	63	1.52
863241--863279	19	2.1	19	90	0	60	15	15	10	58	1.62
864620--864812	32	5.8	31	68	14	89	32	14	17	36	1.90
864692--864817	32	3.9	32	78	5	128	30	15	15	37	1.90
864758--864907	53	2.8	53	94	0	264	28	14	18	38	1.90
864844--864886	21	2.0	21	86	0	59	32	16	13	37	1.88
864864--864935	32	2.2	32	85	9	94	27	12	19	40	1.88
866011--866071	2	30.5	2	100	0	122	0	49	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
872051--872101	8	6.4	8	90	0	84	43	25	31	0	1.55
872051--872101	4	12.8	4	82	0	66	43	25	31	0	1.55
872051--872101	16	3.2	16	97	0	93	43	25	31	0	1.55
877911--877937	13	2.1	13	100	0	54	44	7	22	25	1.79
878900--878924	10	2.5	10	100	0	50	60	8	0	32	1.26
890243--890405	53	3.1	52	89	8	260	25	15	19	40	1.90
890247--890400	49	3.1	49	93	4	254	24	16	20	38	1.92
894529--894560	2	16.0	2	100	0	64	50	0	50	0	1.00
901301--901350	2	25.0	2	100	0	100	50	0	50	0	1.00
904609--904635	9	3.0	9	100	0	54	55	0	0	44	0.99
905265--905298	2	17.0	2	100	0	68	50	0	50	0	1.00
913080--913150	9	8.0	9	80	14	69	76	19	1	2	0.99
913080--913150	19	4.0	18	77	15	69	76	19	1	2	0.99
916415--916757	174	2.0	173	97	1	634	35	14	15	33	1.88
917327--917362	4	9.0	4	100	0	72	50	0	25	25	1.50
921299--921450	18	8.4	18	94	2	270	23	11	32	32	1.90
922119--922155	18	2.0	19	89	5	58	48	10	8	32	1.67
926037--926062	2	13.0	2	100	0	52	0	50	0	50	1.00
937052--937090	2	20.0	2	84	5	53	56	0	43	0	0.99
937671--937695	12	2.1	12	100	0	50	40	8	8	44	1.63
944801--944888	36	2.4	36	86	0	122	29	29	17	23	1.97
947061--947095	2	17.5	2	93	0	61	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
952549--953918	437	3.1	436	90	1	2118	34	16	17	31	1.92
961564--961594	16	1.9	16	100	0	62	22	19	12	45	1.84
961864--961915	15	3.1	17	72	13	54	30	17	13	38	1.88
965681--966212	165	3.2	165	88	5	752	32	14	24	27	1.95
973310--973360	2	27.5	2	83	15	65	0	47	1	50	1.12
975364--975411	11	4.5	11	78	2	53	72	27	0	0	0.84
975364--975411	21	2.2	22	88	3	71	72	27	0	0	0.84
997607--997632	2	13.0	2	100	0	52	50	0	0	50	1.00
997993--998036	18	2.4	18	85	7	54	31	25	27	15	1.96
998816--998867	21	2.5	21	83	0	68	15	26	32	25	1.95
1000326--1000359	17	2.0	17	94	0	59	17	23	38	20	1.93
1004494--1004521	13	2.2	13	100	0	56	28	25	25	21	1.99
1011560--1011604	2	22.0	2	90	4	72	2	46	0	51	1.13
1021743--1021786	2	22.0	2	90	0	70	0	45	4	50	1.22
1023617--1023710	32	2.9	32	87	0	125	27	15	26	29	1.96
1026223--1026308	43	2.0	43	97	0	163	30	24	4	40	1.75
1030377--1030438	2	31.0	2	96	0	115	1	48	0	50	1.10
1043001--1043234	62	3.6	63	83	12	305	30	23	18	27	1.98
1043104--1043138	9	3.9	9	96	0	61	22	40	11	25	1.88
1043042--1043200	71	2.2	71	93	2	266	28	26	16	28	1.97
1043407--1043445	2	19.5	2	100	0	78	48	0	51	0	1.00
1049291--1049512	119	1.9	119	95	0	399	26	22	9	40	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1054669--1054749	10	7.8	10	93	6	135	1	17	40	40	1.57
1054669--1054749	21	3.9	20	93	4	135	1	17	40	40	1.57
1054664--1054749	31	2.7	31	91	7	138	2	17	39	40	1.62
1059083--1059115	14	2.4	14	94	0	57	42	6	30	21	1.77
1060926--1060951	2	13.0	2	100	0	52	0	0	50	50	1.00
1062180--1062683	162	3.1	161	87	2	692	37	20	14	27	1.91
1079019--1079084	32	2.1	32	91	0	105	21	15	18	45	1.85
1090102--1090154	2	26.5	2	100	0	106	0	50	0	49	1.00
1096214--1096269	28	2.0	28	96	0	103	42	8	21	26	1.82
1101470--1101521	2	26.0	2	100	0	104	50	0	50	0	1.00
1103983--1104045	31	2.0	31	96	0	117	39	20	9	30	1.84
1118833--1119041	105	2.0	104	94	0	364	38	12	15	32	1.86
1121644--1121684	2	20.5	2	100	0	82	0	48	0	51	1.00
1133851--1133932	33	2.5	33	86	7	121	31	21	20	25	1.98
1133955--1134838	65	13.6	65	86	4	1088	26	20	20	33	1.97
1152682--1152715	13	2.5	14	90	4	52	67	2	14	14	1.34
1152664--1152689	1	26.0	1	100	0	52	100	0	0	0	0.00
1153369--1153396	14	2.0	14	100	0	56	21	7	14	57	1.61
1155816--1156004	21	9.1	21	90	4	278	21	8	22	47	1.78
1155816--1156004	82	2.3	82	91	5	310	21	8	22	47	1.78
1156362--1156442	33	2.5	33	97	0	153	28	18	23	29	1.98
1161211--1161246	19	1.9	19	88	5	56	25	13	25	36	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1165002--1165030	2	14.5	2	100	0	58	51	0	0	48	1.00
1176018--1176074	2	28.5	2	100	0	114	50	0	49	0	1.00
1176403--1176451	2	24.5	2	100	0	98	0	48	0	51	1.00
1185429--1185834	201	2.0	202	94	1	708	22	14	16	45	1.84
1185890--1185924	3	11.7	3	87	0	52	60	0	2	37	1.12
1187353--1187385	2	16.5	2	93	0	57	51	0	48	0	1.00
1190633--1190861	115	2.0	115	95	0	413	34	8	19	37	1.82
1193841--1193871	12	2.5	13	94	5	55	25	6	32	35	1.82
1203780--1203823	21	2.1	21	86	0	61	22	25	13	38	1.91
1208221--1208342	42	2.9	42	93	0	199	47	15	22	14	1.82

Tables:   1   2   3   4