oyster.v9_M.fa.s17.2.7.7.80.10.50.500.3.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: scaffold1213
Parameters: 2 7 7 80 10 50 500
Length:  1372454

Tables:   1   2   3   

This is table  3  of  3  ( 346 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)
896726--896835	58	1.9	57	94	3	195	33	16	19	30	1.94
896782--897093	86	3.6	86	97	0	579	29	18	20	32	1.96
897042--897149	58	1.9	57	96	3	200	32	16	19	31	1.94
917970--917998	2	14.5	2	100	0	58	48	0	0	51	1.00
926957--927012	2	28.0	2	100	0	112	0	50	0	50	1.00
933095--933218	21	6.0	21	74	7	119	22	12	24	41	1.88
933095--933219	41	3.0	40	87	3	151	23	12	24	40	1.88
933362--933449	21	4.2	21	88	0	122	39	29	6	23	1.81
943755--943786	2	16.0	2	100	0	64	50	0	50	0	1.00
945148--945548	200	2.0	200	100	0	802	36	18	13	31	1.90
947874--948044	62	2.7	62	89	2	254	32	17	13	36	1.89
953522--953573	15	3.4	15	76	10	52	32	13	1	51	1.52
958332--958483	44	3.5	44	91	1	225	9	21	17	52	1.71
958332--958483	66	2.3	66	88	2	216	9	21	17	52	1.71
958332--958452	22	5.5	22	98	0	224	6	19	18	56	1.63
958414--958497	22	3.8	23	82	7	75	10	25	14	50	1.75
958414--958497	44	1.9	44	85	0	114	10	25	14	50	1.75
958543--958581	14	2.8	14	92	0	60	7	25	10	56	1.59
958529--958599	37	1.9	37	85	5	99	9	25	11	53	1.67
958558--958696	22	6.2	22	79	10	113	11	23	15	49	1.77
973176--973240	18	3.6	18	85	0	76	36	26	12	24	1.91
983523--983585	2	31.5	2	100	0	126	0	50	0	49	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
986507--986568	2	31.0	2	100	0	124	0	50	0	50	1.00
990640--990669	14	2.1	14	93	0	51	46	16	0	36	1.47
994090--994116	11	2.5	11	100	0	54	25	18	7	48	1.74
995734--995788	23	2.4	23	90	0	83	47	20	9	23	1.78
1008074--1008807	177	4.2	165	83	10	690	23	16	26	33	1.96
1008182--1008807	177	3.5	175	89	2	871	23	16	26	33	1.96
1009750--1009836	15	5.9	15	69	10	54	40	5	10	43	1.63
1027628--1027686	2	29.5	2	92	0	100	0	45	0	54	0.99
1031338--1031392	22	2.5	22	84	0	74	29	16	43	10	1.82
1031338--1031399	22	2.8	22	78	9	63	29	16	45	9	1.79
1031415--1031463	22	2.2	22	85	0	62	10	40	12	36	1.77
1032179--1032506	21	15.9	21	85	5	393	41	6	7	43	1.59
1032183--1032506	142	2.2	142	86	6	438	41	6	8	43	1.60
1039589--1039672	20	4.0	20	82	11	98	39	0	10	50	1.37
1039618--1039695	35	2.2	35	86	4	104	38	1	12	47	1.50
1039535--1039656	15	8.2	15	76	8	106	38	1	11	48	1.49
1043684--1044069	170	2.3	167	84	8	476	31	23	14	30	1.94
1045314--1045346	16	2.1	16	94	0	57	54	6	15	24	1.63
1056651--1056811	23	7.0	23	100	0	322	39	17	17	26	1.91
1057618--1057647	11	2.7	11	89	0	51	73	0	23	3	0.98
1062337--1062367	16	1.9	16	100	0	62	45	25	22	6	1.76
1072029--1072060	16	2.0	16	100	0	64	87	0	12	0	0.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1089273--1089299	14	1.9	14	100	0	54	0	0	7	92	0.38
1090932--1090969	2	19.0	2	100	0	76	50	0	50	0	1.00
1091570--1091656	2	44.5	2	90	4	142	50	1	48	0	1.08
1091971--1092020	2	25.0	2	100	0	100	50	0	50	0	1.00
1118465--1118548	8	10.6	8	81	15	77	80	17	1	0	0.77
1118481--1118545	4	15.8	4	89	9	96	76	21	1	0	0.86
1118465--1118548	16	5.4	15	87	9	100	80	17	1	0	0.77
1120562--1120611	2	24.5	2	95	4	91	50	0	48	2	1.12
1121532--1121559	13	2.2	13	100	0	56	21	14	0	64	1.29
1127840--1128262	207	2.0	206	99	0	828	37	14	13	34	1.85
1130053--1130132	17	4.7	16	75	15	63	77	21	1	0	0.84
1130057--1130089	9	3.6	9	92	8	57	87	12	0	0	0.53
1130081--1130132	21	2.4	21	83	3	68	73	25	1	0	0.94
1130052--1130132	43	1.9	40	83	11	101	76	22	1	0	0.86
1131008--1131149	71	2.0	71	97	0	266	50	17	8	23	1.73
1138231--1138268	16	2.4	16	95	4	69	39	13	13	34	1.83
1177173--1177746	172	3.4	172	92	0	904	30	18	14	36	1.91
1182086--1182253	55	3.1	55	100	0	336	27	25	8	38	1.86
1207452--1207599	74	2.0	75	88	5	219	39	12	12	35	1.81
1212643--1212700	2	29.0	2	100	0	116	50	0	50	0	1.00
1212847--1212880	15	2.3	15	100	0	68	26	5	11	55	1.58
1213646--1214063	24	17.4	24	89	0	611	26	23	12	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1225098--1225135	17	2.4	16	86	8	51	21	28	15	34	1.94
1225185--1225233	17	3.0	17	82	8	66	18	28	16	36	1.92
1241881--1241912	15	2.1	15	100	0	64	31	6	12	50	1.65
1248765--1248812	22	2.2	21	82	7	60	8	0	12	79	0.94
1250905--1250953	17	2.9	17	85	11	57	8	2	12	77	1.07
1256753--1256782	11	2.6	12	94	5	53	86	13	0	0	0.57
1257332--1258053	166	4.4	163	80	5	756	27	22	15	34	1.95
1257327--1258053	329	2.2	329	83	3	885	27	22	15	34	1.94
1263050--1263147	34	2.8	35	80	6	110	41	23	15	19	1.89
1263134--1263992	32	26.6	32	85	8	996	38	22	16	22	1.93
1263134--1263992	292	3.0	291	90	4	1258	38	22	16	22	1.93
1263808--1263924	61	1.9	61	89	3	182	38	23	17	20	1.93
1266030--1266287	3	86.0	3	89	3	394	35	1	30	32	1.67
1279677--1279713	2	18.5	2	100	0	74	0	51	0	48	1.00
1279894--1279930	1	37.0	1	100	0	74	100	0	0	0	0.00
1283283--1283696	141	2.9	141	95	0	749	31	21	13	33	1.92
1287282--1287306	12	2.1	12	100	0	50	40	24	0	36	1.55
1300228--1300274	24	2.0	24	95	0	85	23	21	42	12	1.87
1300759--1301426	148	4.5	148	93	1	1107	37	20	11	30	1.87
1328752--1329142	196	2.0	195	100	0	773	30	15	14	39	1.87
1331570--1331596	3	9.0	3	100	0	54	33	0	0	66	0.92
1332529--1332568	16	2.5	16	91	0	62	2	40	25	32	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1339573--1339618	2	23.0	2	100	0	92	0	50	0	50	1.00
1343297--1343355	11	5.1	11	87	6	73	35	15	11	37	1.84
1343298--1343439	22	5.9	24	70	11	94	39	14	10	35	1.81
1343374--1343439	11	5.7	11	77	10	69	39	12	7	40	1.71
1343381--1343409	14	2.1	14	100	0	58	41	13	6	37	1.72
1343374--1343505	22	5.4	23	71	17	90	37	10	10	40	1.74
1344040--1344075	2	18.0	2	100	0	72	50	0	50	0	1.00
1345879--1346090	105	2.0	105	99	0	415	32	17	16	33	1.92
1346451--1346486	15	2.4	15	90	0	54	33	5	13	47	1.67
1347742--1347783	20	2.1	20	86	0	57	47	11	7	33	1.68
1348955--1348985	16	1.9	16	93	0	53	45	19	6	29	1.75
1356981--1357006	13	2.0	13	100	0	52	7	7	7	76	1.15
1361755--1362147	179	2.2	179	82	2	450	29	21	21	28	1.98
1363939--1364219	99	2.8	97	74	12	266	28	20	18	32	1.96
1364479--1364931	198	2.3	198	86	2	615	26	24	18	30	1.98
1364479--1364931	99	4.6	98	87	3	552	26	24	18	30	1.98
1366098--1366123	13	2.0	13	100	0	52	53	0	7	38	1.30
1370931--1370972	1	42.0	1	95	0	75	0	97	0	2	0.16

Tables:   1   2   3

The End!