oyster.v9_M.fa.s1.2.7.7.80.10.50.500.3.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: scaffold22
Parameters: 2 7 7 80 10 50 500
Length:  1964558

Tables:   1   2   3   4   5   6   

This is table  3  of  6  ( 655 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)
771216--771258	16	2.7	16	92	0	68	46	44	2	6	1.43
771267--771306	2	20.0	2	100	0	80	0	50	0	50	1.00
787472--787525	17	3.1	17	78	5	54	29	20	5	44	1.74
787772--787820	3	16.3	3	100	0	98	32	0	32	34	1.58
788824--788861	16	2.3	16	86	13	51	63	0	18	18	1.32
793426--793462	18	2.1	18	100	0	74	43	10	16	29	1.82
802528--802561	16	2.2	16	89	5	52	76	14	2	5	1.09
813152--813192	2	20.5	2	100	0	82	48	0	51	0	1.00
818982--819072	21	4.4	21	87	1	112	38	16	16	28	1.90
819983--820016	1	34.0	1	93	0	59	97	0	2	0	0.19
820105--820225	21	5.8	21	75	3	118	39	18	25	16	1.91
820121--820225	42	2.5	42	88	0	165	40	20	24	15	1.91
821210--821322	21	5.4	21	80	6	113	39	16	26	16	1.90
821965--821996	16	2.0	16	93	0	55	34	9	12	43	1.75
824906--824935	4	7.5	4	100	0	60	0	23	50	26	1.50
826391--826439	2	24.5	2	100	0	98	51	0	48	0	1.00
840170--840196	12	2.2	12	100	0	54	29	0	22	48	1.51
849127--849175	5	9.8	5	100	0	98	38	20	0	40	1.53
851345--851419	2	37.5	2	100	0	150	49	0	50	0	1.00
852040--852090	2	25.5	2	100	0	102	0	50	0	49	1.00
858691--859229	180	3.0	180	96	1	983	29	16	17	36	1.92
860244--860282	8	4.9	8	80	0	51	58	41	0	0	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
860243--860286	18	2.4	19	85	11	65	56	43	0	0	0.99
861240--861279	4	10.0	4	94	0	53	0	32	25	42	1.55
861241--861282	20	2.1	20	90	0	66	0	33	26	40	1.56
864849--865895	65	16.0	64	81	6	1001	31	11	26	29	1.92
866413--867210	166	4.8	166	88	2	1109	28	16	15	39	1.89
866413--867210	165	4.8	164	87	2	1069	28	16	15	39	1.89
871484--871526	2	21.5	2	90	0	59	41	0	58	0	0.98
871484--871526	18	2.4	18	96	0	77	41	0	58	0	0.98
871488--871531	14	3.1	14	90	0	61	38	0	61	0	0.96
877478--877524	22	2.1	22	96	0	85	27	14	27	29	1.96
879498--879566	35	2.0	35	100	0	138	39	11	23	26	1.88
879576--879601	1	26.0	1	100	0	52	0	0	100	0	0.00
891998--892080	43	1.9	43	95	0	148	50	20	7	21	1.72
892001--892067	19	3.3	19	73	18	71	50	19	7	22	1.72
897800--897837	4	9.8	4	88	5	60	28	26	44	0	1.54
905192--905223	12	2.6	13	85	14	50	0	31	50	18	1.48
905548--905587	19	2.1	19	90	0	62	22	2	37	37	1.68
905361--906230	176	4.9	176	91	2	1210	24	16	25	33	1.96
905257--906230	352	2.7	353	86	3	1266	24	17	24	33	1.96
906897--906939	20	2.1	20	87	8	61	41	4	11	41	1.62
907010--907044	18	1.9	18	88	11	54	31	2	17	48	1.61
907182--907328	15	9.3	15	72	15	73	37	4	12	44	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
907199--907365	50	3.4	47	76	9	165	37	4	13	44	1.64
907253--907287	18	1.9	18	94	0	61	40	0	8	51	1.33
907165--907371	98	2.1	97	90	4	319	37	5	11	45	1.63
907244--907373	15	8.1	15	72	18	93	37	3	12	46	1.60
907237--907388	50	3.1	50	73	17	156	36	5	11	46	1.63
907602--907627	13	2.0	13	100	0	52	46	0	15	38	1.46
910527--910576	18	2.6	20	81	9	68	36	4	10	50	1.55
910666--910702	19	2.0	19	89	5	58	35	0	10	54	1.36
910850--910894	16	2.9	16	90	6	67	28	11	28	31	1.91
911763--912063	21	14.3	21	86	4	401	35	22	17	24	1.96
913365--913427	29	2.1	30	97	2	119	50	26	7	14	1.70
913822--913872	21	2.5	20	75	18	59	37	7	31	23	1.83
916446--916836	21	18.6	21	85	4	522	22	19	23	35	1.96
916444--916829	42	9.2	42	88	3	582	22	18	23	34	1.96
924992--925036	20	2.2	20	100	0	90	66	15	0	17	1.25
930440--930483	21	2.1	21	95	0	79	13	6	38	40	1.71
935126--935317	10	18.0	10	69	19	79	19	16	38	25	1.92
935187--935230	23	1.9	23	86	9	63	15	15	40	27	1.88
935220--935282	33	1.9	33	87	6	92	22	15	38	23	1.93
935125--935318	43	4.5	45	78	10	160	20	16	38	25	1.93
936579--936608	15	2.0	15	93	0	51	6	30	36	26	1.82
937648--937704	28	2.0	28	100	0	114	21	35	10	33	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
943786--943815	15	2.0	15	93	0	51	30	6	20	43	1.77
945540--945854	22	14.3	22	85	1	353	30	16	20	32	1.95
981027--981071	2	22.5	2	100	0	90	48	0	51	0	1.00
985634--985721	2	44.0	2	97	0	167	0	48	1	50	1.08
987592--987652	2	30.5	2	100	0	122	0	49	0	50	1.00
990393--990417	4	6.2	4	100	0	50	76	0	0	24	0.80
998709--998746	2	19.0	2	100	0	76	50	0	50	0	1.00
1007568--1007618	2	25.5	2	100	0	102	0	50	0	49	1.00
1037023--1037073	2	25.5	2	100	0	102	0	50	0	49	1.00
1037451--1037499	2	24.5	2	100	0	98	51	0	48	0	1.00
1041331--1041375	2	22.5	2	100	0	90	51	0	48	0	1.00
1044339--1044369	4	7.8	4	100	0	62	22	25	0	51	1.48
1049713--1049768	2	28.0	2	100	0	112	50	0	50	0	1.00
1051468--1051599	46	2.8	46	90	1	192	31	10	21	36	1.88
1056777--1056911	46	2.8	48	91	6	202	45	8	11	34	1.70
1057587--1057611	1	25.0	1	100	0	50	100	0	0	0	0.00
1060790--1061577	168	4.7	168	85	5	949	30	18	18	31	1.95
1060887--1061543	168	3.9	168	90	3	1002	30	18	18	32	1.95
1060889--1061535	335	1.9	336	91	3	1063	31	18	18	31	1.95
1061748--1061786	7	5.4	7	87	6	60	33	41	25	0	1.56
1061747--1061786	15	2.8	14	92	7	71	35	40	25	0	1.56
1064602--1064709	57	1.9	57	92	0	180	50	20	4	25	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1065018--1065065	16	3.0	16	100	0	96	43	25	25	6	1.77
1065075--1065134	31	1.9	31	96	0	111	28	26	21	23	1.99
1065980--1066029	16	3.1	16	94	0	91	6	22	26	46	1.74
1066205--1066288	10	8.1	10	74	12	71	45	23	20	10	1.82
1067165--1067237	10	7.1	10	79	11	76	12	19	24	43	1.85
1067165--1067237	21	3.5	20	73	12	76	12	19	24	43	1.85
1069415--1069842	22	19.8	22	77	9	348	32	17	16	33	1.93
1069407--1069842	44	10.1	44	79	7	421	33	18	15	33	1.92
1069407--1069842	66	6.7	66	80	7	430	33	18	15	33	1.92
1069742--1069771	15	2.0	15	100	0	60	33	6	20	40	1.78
1069698--1069816	59	2.0	59	83	0	148	33	14	16	35	1.89
1069676--1069837	81	2.0	81	85	4	220	33	14	16	34	1.90
1070044--1070137	2	47.0	2	89	8	147	2	46	1	50	1.20
1077063--1077096	1	34.0	1	93	0	59	0	0	2	97	0.19
1077787--1077838	3	18.0	3	80	7	63	36	1	28	32	1.69
1077861--1077895	10	3.5	10	92	0	52	2	0	37	60	1.12
1092844--1092899	16	3.5	16	90	0	76	33	25	39	1	1.66
1092844--1092887	20	2.2	20	95	0	79	36	25	38	0	1.56
1092853--1092900	12	4.0	12	88	0	69	31	25	41	2	1.67
1092857--1092900	4	11.0	4	90	0	61	29	25	43	2	1.67
1093123--1093174	2	26.0	2	100	0	104	0	50	0	50	1.00
1101974--1102018	2	22.5	2	100	0	90	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1102252--1102323	2	36.0	2	100	0	144	0	50	0	50	1.00
1105790--1105870	41	2.0	42	90	2	128	37	2	9	50	1.49
1105830--1107115	134	9.7	134	84	4	1621	34	12	12	40	1.80
1105699--1106043	176	2.0	175	79	9	380	35	12	11	40	1.79
1105830--1107115	267	4.9	266	84	5	1585	34	12	12	40	1.80
1106376--1106413	19	2.0	19	89	0	58	44	0	2	52	1.14
1105830--1107115	401	3.2	399	85	4	1685	34	12	12	40	1.80
1108962--1109091	64	2.0	64	91	4	210	16	20	14	47	1.82
1109516--1110937	433	3.3	437	91	2	2152	34	15	18	31	1.93
1111254--1111362	53	2.1	53	94	3	193	14	22	17	44	1.85

Tables:   1   2   3   4   5   6