oyster.v9_M.fa.s14.2.7.7.80.10.50.500.3.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: scaffold962
Parameters: 2 7 7 80 10 50 500
Length:  1469792

Tables:   1   2   3   4   

This is table  3  of  4  ( 424 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)
885507--886011	126	3.9	126	85	9	714	34	28	6	31	1.82
885507--886011	187	2.6	190	90	3	773	34	28	6	31	1.82
885872--885901	12	2.5	12	100	0	60	33	26	6	33	1.83
885810--885962	73	2.1	73	96	0	279	33	28	5	31	1.81
885745--885997	134	1.9	136	92	3	429	34	28	6	30	1.82
889246--889295	4	12.8	4	91	4	66	32	26	42	0	1.56
892233--892282	2	25.0	2	100	0	100	0	50	0	50	1.00
893011--893083	24	3.0	24	93	0	128	2	41	24	31	1.69
893011--893074	4	16.0	4	86	0	83	3	42	25	29	1.70
894909--894952	4	11.0	4	85	0	61	2	47	22	27	1.63
894909--894961	12	4.4	12	85	0	70	1	45	22	30	1.63
903631--903923	21	14.0	21	81	2	320	36	13	18	32	1.89
903664--903926	42	6.3	42	90	0	368	36	12	18	33	1.88
905048--905081	17	1.9	18	88	5	52	35	29	5	29	1.81
905066--905409	20	16.9	20	75	9	200	35	24	12	27	1.92
905094--905369	20	13.6	20	80	7	229	35	25	13	26	1.93
905094--905409	41	7.8	40	76	7	235	35	25	13	26	1.93
905066--905369	163	1.9	163	85	2	423	35	24	12	27	1.92
905130--905409	122	2.3	121	82	1	326	35	24	13	27	1.92
905069--905409	163	2.1	163	82	3	409	35	24	12	26	1.92
906208--906241	16	2.0	16	88	11	50	64	5	5	23	1.38
917836--917868	13	2.5	13	95	5	57	30	12	30	27	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
919450--919474	1	25.0	1	100	0	50	0	100	0	0	0.00
926619--926650	15	2.1	15	94	0	55	34	0	0	65	0.93
929006--929081	2	39.0	2	92	5	129	50	1	48	0	1.09
932529--932835	62	4.9	62	74	10	219	33	14	21	30	1.93
932495--932736	129	1.9	131	83	6	323	34	14	21	29	1.93
932529--932798	62	4.3	62	75	10	222	33	14	20	31	1.93
932816--932880	25	2.6	25	85	2	87	29	15	27	27	1.96
934154--934178	4	6.2	4	100	0	50	52	24	24	0	1.48
936003--936058	28	2.0	28	96	0	103	23	21	16	39	1.92
936648--936791	34	4.4	34	74	16	160	31	14	25	28	1.95
936648--936823	96	1.8	96	92	2	300	31	15	24	28	1.95
936810--936863	25	2.2	24	83	12	65	27	12	29	29	1.94
938433--938621	30	6.3	30	91	0	288	34	48	3	13	1.60
938427--938643	30	7.2	30	84	4	150	35	47	3	13	1.59
938658--938841	93	2.0	93	85	2	253	33	40	1	24	1.65
938965--939052	21	4.2	21	97	0	149	47	28	14	9	1.75
940335--940369	16	2.2	16	90	10	54	51	11	11	25	1.71
940427--940515	42	2.1	43	93	4	153	26	15	10	47	1.78
940627--941087	41	11.6	41	77	10	408	18	34	8	37	1.82
940627--940860	81	2.9	82	82	6	244	20	36	7	35	1.81
940650--941083	122	3.7	119	80	6	440	18	34	8	38	1.82
940972--941064	38	2.4	38	100	0	186	17	30	8	44	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
945759--945800	18	2.3	18	100	0	84	21	38	14	26	1.91
951340--951365	3	8.7	3	100	0	52	69	0	0	30	0.89
954298--954353	21	2.7	21	85	0	76	26	32	10	30	1.90
955916--955941	2	13.0	2	100	0	52	50	0	0	50	1.00
980218--980280	29	2.1	30	91	2	101	42	1	23	31	1.64
988202--988229	14	2.0	14	100	0	56	35	21	14	28	1.92
988179--988254	37	2.1	37	94	0	134	32	17	19	30	1.95
988216--989187	23	44.0	23	81	9	877	32	14	19	33	1.91
988174--989187	65	15.4	65	79	9	773	32	14	19	34	1.91
988217--989187	130	7.3	130	84	7	949	32	14	19	33	1.91
995728--995771	2	22.0	2	100	0	88	50	0	50	0	1.00
1001312--1001414	32	3.2	32	78	5	109	36	20	7	34	1.81
1001376--1002195	32	25.6	31	82	5	867	29	23	13	33	1.93
1001301--1001486	64	2.9	64	81	3	176	37	20	9	32	1.84
1010809--1011199	167	2.4	167	82	5	467	33	20	15	30	1.93
1011063--1011346	144	2.0	145	89	2	435	33	18	16	31	1.93
1026132--1026254	18	6.9	18	82	4	151	40	18	30	10	1.84
1026132--1026254	36	3.4	36	96	1	230	40	18	30	10	1.84
1029904--1029951	18	2.8	17	81	6	60	72	22	2	2	1.05
1030551--1030656	17	6.0	17	87	8	158	26	47	14	12	1.79
1030551--1030655	55	1.9	55	96	0	192	26	46	14	12	1.80
1030823--1030866	15	2.9	15	96	0	79	31	6	22	38	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1031173--1031389	43	4.9	44	81	11	257	36	11	12	39	1.79
1031192--1031368	92	1.9	92	88	0	264	37	11	11	38	1.79
1031171--1031439	43	6.0	43	79	10	254	36	10	11	40	1.77
1031863--1032191	22	14.8	22	74	12	176	40	8	10	40	1.70
1031863--1032236	43	8.5	43	77	10	287	39	8	10	41	1.69
1031907--1032236	21	15.2	21	74	8	207	39	8	10	41	1.69
1031914--1032236	22	14.8	21	71	16	171	39	8	10	42	1.69
1032853--1032927	30	2.5	30	77	0	96	25	25	24	25	2.00
1042728--1042791	33	1.9	33	83	0	83	29	21	14	34	1.93
1042764--1042878	29	4.0	29	73	4	106	30	20	20	28	1.98
1045703--1045819	45	2.6	45	89	5	166	23	17	17	41	1.91
1050503--1050737	18	13.1	18	97	0	416	17	30	11	41	1.83
1059841--1060082	82	3.0	82	97	0	457	19	21	22	36	1.95
1062008--1062103	2	48.0	2	100	0	192	50	0	50	0	1.00
1065968--1066021	23	2.3	23	87	0	72	20	12	27	38	1.89
1066641--1066875	32	7.2	32	75	9	201	31	6	16	45	1.73
1066641--1066875	63	3.6	65	77	11	173	31	6	16	45	1.73
1066654--1066873	95	2.2	96	81	9	257	31	6	16	45	1.73
1066641--1067034	32	12.3	30	71	15	192	30	8	17	43	1.78
1071008--1071050	2	21.5	2	100	0	86	51	0	48	0	1.00
1071936--1071970	16	2.2	16	94	0	61	91	0	8	0	0.42
1071939--1071966	13	2.2	13	100	0	56	92	0	7	0	0.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1073555--1073601	2	23.5	2	100	0	94	51	0	48	0	1.00
1075005--1075632	56	11.2	56	93	0	1022	40	21	12	26	1.88
1075005--1075737	112	6.5	112	91	2	1069	39	21	12	26	1.89
1075004--1075740	168	4.4	168	90	2	1057	39	21	12	26	1.89
1076340--1076468	45	2.8	45	85	5	170	30	41	11	17	1.85
1077224--1077347	51	2.4	51	85	5	169	35	29	21	12	1.91
1077667--1077845	93	1.9	93	86	2	252	26	29	18	25	1.98
1077667--1077893	93	2.4	93	80	2	215	25	29	19	25	1.99
1077970--1078151	93	2.0	93	80	2	204	26	28	20	25	1.99
1080678--1080706	14	2.1	14	93	6	51	75	6	0	17	1.01
1080756--1080789	9	3.8	9	92	0	59	11	11	29	47	1.76
1092454--1092503	8	6.4	8	86	4	75	0	36	26	38	1.57
1095605--1095631	1	27.0	1	100	0	54	100	0	0	0	0.00
1101802--1102646	20	42.0	20	85	1	1026	12	28	20	38	1.89
1105742--1105770	2	14.5	2	100	0	58	0	48	0	51	1.00
1105984--1106110	37	3.6	36	77	11	118	60	9	23	6	1.50
1106981--1107025	12	3.9	11	81	18	56	26	20	24	28	1.99
1109044--1109407	178	2.0	178	86	7	515	31	15	18	34	1.92
1109617--1109664	24	2.0	24	95	0	87	52	16	12	18	1.75
1110569--1110666	50	2.0	50	95	0	178	32	10	13	43	1.77
1129031--1129574	179	3.0	178	84	4	630	35	19	15	29	1.92
1130033--1130079	18	2.5	19	86	6	60	40	6	12	40	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1130155--1130206	20	2.6	20	76	11	61	40	7	13	38	1.73
1130433--1130479	15	3.1	15	73	11	51	42	12	6	38	1.69
1130608--1130645	20	1.9	20	88	0	58	47	13	7	31	1.71
1133248--1133651	165	2.4	165	81	3	456	30	18	14	36	1.91
1134029--1134078	4	12.8	4	91	4	75	30	26	44	0	1.55
1142025--1142060	18	2.0	18	88	0	54	25	13	5	55	1.60
1145267--1145295	2	14.5	2	100	0	58	0	51	0	48	1.00
1145675--1145848	84	2.1	84	98	0	339	37	12	14	34	1.85
1161313--1162598	167	7.8	166	89	2	1849	39	15	17	27	1.90
1161313--1162598	333	3.9	332	88	2	1885	39	15	17	27	1.90

Tables:   1   2   3   4