oyster.v9_M.fa.s4.2.7.7.80.10.50.500.3.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: scaffold1024
Parameters: 2 7 7 80 10 50 500
Length:  1774716

Tables:   1   2   3   4   5   

This is table  3  of  5  ( 509 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)
819786--819810	4	6.2	4	100	0	50	0	24	28	48	1.52
820624--820704	25	3.2	25	82	1	99	50	6	12	30	1.64
821121--821149	11	2.6	11	100	0	58	31	27	17	24	1.97
828029--828077	22	2.2	22	85	7	64	14	40	14	30	1.85
830731--830757	2	13.5	2	100	0	54	48	0	51	0	1.00
831869--832780	327	2.8	330	86	5	1183	37	13	18	30	1.89
831895--832780	166	5.4	165	85	5	1127	37	13	18	30	1.89
839505--839559	2	27.5	2	92	0	83	45	0	0	49	1.02
841345--841398	2	27.0	2	100	0	108	50	0	50	0	1.00
844841--844875	16	2.2	16	100	0	70	25	22	22	28	1.99
847031--847414	194	2.0	194	97	0	732	39	14	15	30	1.87
848887--848916	16	1.9	15	93	6	51	83	16	0	0	0.65
849266--849297	2	16.0	2	100	0	64	0	50	0	50	1.00
851311--851780	30	14.6	30	66	15	127	37	21	6	34	1.79
851249--851760	64	7.9	64	84	6	618	36	22	6	34	1.79
851249--851760	134	3.9	130	84	6	580	36	22	6	34	1.79
851278--851760	198	2.5	194	87	4	677	37	22	6	34	1.79
851668--852007	30	11.4	30	71	13	202	41	22	8	27	1.83
852061--852090	2	15.0	2	100	0	60	50	0	0	50	1.00
861879--862072	34	5.7	34	74	9	146	46	8	24	20	1.77
862002--862055	17	3.2	17	74	10	56	42	11	27	18	1.84
862010--862064	17	3.2	17	77	10	67	36	14	27	21	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
862017--862073	17	3.4	16	78	4	60	43	10	24	21	1.83
865065--865148	2	41.5	2	97	2	159	48	0	50	0	1.01
869229--869285	2	28.5	2	100	0	114	50	0	49	0	1.00
870525--870603	32	2.4	33	93	4	142	34	30	15	20	1.93
882637--882669	17	1.9	17	93	0	57	51	15	0	33	1.43
912974--913024	12	4.2	12	84	0	66	1	41	21	35	1.65
912964--913024	16	3.8	16	84	4	61	3	40	22	32	1.70
912964--913012	4	12.2	4	82	8	55	2	42	24	30	1.66
913651--913685	7	5.0	7	85	0	52	28	14	28	28	1.95
918464--918503	20	2.1	19	86	13	55	22	12	15	50	1.77
918990--919022	17	1.9	17	100	0	66	18	30	6	45	1.73
919037--919088	2	26.0	2	100	0	104	50	0	50	0	1.00
930545--930571	13	2.1	13	100	0	54	14	48	7	29	1.71
948633--948699	7	9.6	7	83	0	89	35	14	22	26	1.93
949195--949242	2	24.0	2	100	0	96	50	0	50	0	1.00
949240--949270	4	7.8	4	100	0	62	51	22	25	0	1.48
951677--951743	7	9.6	7	83	0	89	26	22	14	35	1.93
951677--951743	21	3.2	21	86	0	98	26	22	14	35	1.93
957327--957358	15	2.1	15	100	0	64	34	9	18	37	1.83
959694--959749	2	28.0	2	100	0	112	50	0	50	0	1.00
960345--960392	2	24.5	2	95	4	89	52	0	47	0	1.00
960964--960997	11	3.1	11	91	0	59	17	44	20	17	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
960993--961099	21	5.1	21	84	0	142	32	28	21	17	1.96
961488--961728	122	2.0	122	94	0	428	29	12	14	42	1.83
962689--962834	21	6.9	21	85	1	94	30	29	19	20	1.97
962744--962834	21	4.3	21	88	0	146	37	26	18	17	1.93
987865--987916	8	6.5	8	86	0	59	3	38	25	32	1.74
987865--987916	12	4.3	12	82	0	59	3	38	25	32	1.74
987864--987907	4	11.0	4	80	0	52	4	40	25	29	1.75
989970--990194	113	2.0	113	89	3	346	31	14	18	36	1.90
991917--991957	2	20.5	2	100	0	82	48	0	51	0	1.00
999133--999174	2	21.0	2	100	0	84	50	50	0	0	1.00
999365--999392	1	28.0	1	100	0	56	0	100	0	0	0.00
1000113--1000169	2	28.5	2	96	0	96	49	3	47	0	1.18
1004656--1004695	4	10.0	4	83	0	53	2	42	25	30	1.68
1004665--1004704	12	3.3	12	82	0	53	0	40	25	35	1.56
1006425--1006525	33	3.1	33	97	0	193	23	8	18	48	1.76
1012498--1012523	10	2.6	10	100	0	52	26	30	0	42	1.56
1018966--1018997	2	16.0	2	100	0	64	50	0	50	0	1.00
1024453--1024500	17	2.9	16	78	12	53	58	10	12	18	1.62
1025579--1025607	7	4.3	7	91	8	51	0	10	0	89	0.48
1025582--1025608	13	2.1	13	100	0	54	0	7	0	92	0.38
1032558--1032642	19	4.5	19	92	0	125	23	31	24	20	1.98
1032687--1032720	2	17.0	2	100	0	68	50	0	50	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1032722--1032794	19	3.8	19	92	0	110	23	31	23	21	1.98
1032840--1032900	2	31.0	2	83	9	72	44	1	50	1	1.21
1032568--1032873	153	2.0	152	99	0	603	30	21	27	20	1.98
1032855--1032909	29	1.9	29	88	3	85	36	1	56	3	1.28
1035014--1035046	14	2.4	14	94	0	57	36	18	0	45	1.49
1035590--1035631	2	21.0	2	100	0	84	50	0	50	0	1.00
1036847--1036982	25	5.4	25	85	0	191	16	30	11	41	1.83
1036847--1037198	50	6.8	50	80	7	398	15	30	13	40	1.85
1036847--1037209	75	4.7	75	78	8	377	15	30	13	41	1.85
1036947--1037018	36	2.0	36	88	0	108	16	33	11	38	1.84
1036922--1037043	61	2.0	61	91	0	199	15	32	10	40	1.82
1036897--1037069	86	2.0	86	89	0	265	16	31	10	42	1.81
1036872--1037093	111	2.0	111	89	0	336	15	31	11	40	1.83
1036847--1037102	136	1.9	136	91	0	422	15	31	11	41	1.83
1036983--1037198	25	8.6	25	87	2	290	13	31	14	40	1.86
1037306--1037402	25	3.7	25	80	10	113	15	28	12	43	1.83
1038722--1038748	2	13.5	2	100	0	54	48	0	51	0	1.00
1040671--1040695	12	2.1	12	100	0	50	24	8	20	48	1.76
1047179--1047232	19	2.8	19	80	0	72	24	24	16	35	1.95
1062622--1062795	86	2.0	86	85	2	233	17	19	13	50	1.78
1065550--1065665	42	2.7	42	79	10	130	24	19	16	39	1.91
1067257--1067299	22	2.0	22	95	0	77	30	20	11	37	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1072075--1072109	2	17.5	2	100	0	70	51	0	48	0	1.00
1082614--1083360	381	2.0	377	96	1	1377	37	13	12	36	1.83
1088624--1088665	1	42.0	1	100	0	84	0	0	0	100	0.00
1098371--1098990	166	3.8	165	90	2	933	33	15	25	25	1.95
1098369--1098990	330	1.9	332	89	2	984	33	16	24	25	1.96
1104822--1104887	2	33.0	2	96	0	123	48	0	50	1	1.10
1105059--1105093	3	11.7	3	93	0	52	60	0	0	40	0.97
1117090--1117121	16	1.9	17	93	6	57	53	9	37	0	1.34
1122274--1122389	32	3.8	32	78	9	141	43	19	8	28	1.81
1122368--1122412	23	2.0	23	90	0	72	48	20	4	26	1.68
1122276--1122419	60	2.5	57	84	7	186	45	19	9	26	1.80
1127045--1127081	2	19.0	2	91	5	58	45	0	54	0	1.00
1131080--1131554	238	2.0	237	100	0	941	23	13	16	45	1.84
1134668--1134862	31	6.3	31	89	1	291	43	18	7	30	1.78
1134668--1134862	94	2.1	94	90	0	302	43	18	7	30	1.78
1135139--1135180	22	2.0	21	95	4	75	76	23	0	0	0.79
1136771--1137225	85	5.3	85	81	5	531	28	24	9	38	1.86
1136765--1137225	172	2.7	174	89	3	664	28	24	9	38	1.86
1137121--1137171	21	2.5	20	84	12	59	25	19	11	43	1.85
1137228--1137280	23	2.3	23	86	0	70	33	20	7	37	1.81
1139331--1139426	18	5.2	18	70	17	63	60	26	2	11	1.42
1139359--1139412	18	2.9	19	84	15	69	59	24	3	12	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1139367--1139523	21	7.1	21	69	16	68	54	31	4	9	1.53
1139414--1139497	13	6.7	12	68	27	50	52	36	3	7	1.46
1139484--1139552	18	3.7	18	84	11	86	53	31	7	7	1.56
1143251--1143320	2	36.5	2	91	8	119	51	0	0	48	1.00
1151832--1152111	43	6.4	43	82	6	323	30	16	29	23	1.96
1151834--1152099	90	3.0	90	86	5	346	30	16	29	23	1.96
1151832--1152111	133	2.1	129	94	2	488	30	16	29	23	1.96
1152378--1153106	43	17.0	43	76	6	494	30	13	30	25	1.93
1160202--1160240	2	19.5	2	100	0	78	0	48	0	51	1.00
1160485--1160553	2	34.5	2	100	0	138	0	50	0	49	1.00

Tables:   1   2   3   4   5