oyster.v9_M.fa.s28.2.7.7.80.10.50.500.3.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: scaffold301
Parameters: 2 7 7 80 10 50 500
Length:  1229110

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)
810141--810721	166	3.5	165	77	9	576	32	15	23	28	1.95
830036--830120	36	2.5	33	86	7	118	27	17	30	24	1.97
830104--830137	17	2.0	17	88	0	50	35	11	35	17	1.87
830359--830406	16	3.0	16	93	0	87	35	25	39	0	1.56
830368--830415	4	12.0	4	86	0	60	31	25	41	2	1.67
830359--830414	12	4.7	12	86	0	58	33	25	39	1	1.66
832478--832505	2	14.0	2	100	0	56	50	0	50	0	1.00
835547--835843	26	11.5	26	93	2	462	30	25	22	21	1.99
835547--836097	52	10.9	52	86	6	726	31	25	21	21	1.98
835547--836097	78	7.2	78	82	9	683	31	25	21	21	1.98
835805--835884	40	2.0	40	92	0	133	28	27	20	23	1.99
835845--836097	26	9.7	26	88	3	316	33	25	18	22	1.97
837153--837215	26	2.4	26	94	0	108	30	22	20	26	1.98
837206--837232	14	1.9	14	100	0	54	33	29	14	22	1.94
837180--837258	40	2.0	40	97	0	149	31	26	17	24	1.97
838941--839313	167	2.2	167	91	1	597	30	21	15	31	1.94
846145--846173	15	1.9	15	100	0	58	0	58	0	41	0.98
847140--847390	138	1.8	138	96	1	468	39	15	16	29	1.89
865486--865938	168	2.7	168	87	3	662	31	19	19	30	1.96
868375--868399	10	2.5	10	100	0	50	32	28	0	40	1.57
872863--872960	50	2.0	49	97	0	178	27	17	21	32	1.95
876313--876337	10	2.5	10	100	0	50	32	28	0	40	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
881622--882260	161	3.9	161	89	2	902	35	20	13	31	1.91
881657--882260	327	1.8	327	90	2	962	35	20	12	31	1.90
882396--882429	12	2.8	12	86	0	50	38	23	35	2	1.70
883694--884061	180	2.0	180	96	0	673	36	17	15	29	1.91
885159--885688	166	3.2	166	92	2	868	26	23	15	34	1.95
888824--889693	166	5.2	166	96	1	1523	25	25	15	32	1.96
889855--889887	12	2.8	12	95	4	59	36	27	36	0	1.57
891383--891440	24	2.6	22	78	21	68	25	31	18	24	1.98
892792--892817	12	2.2	12	100	0	52	30	15	30	23	1.95
895194--895228	16	2.2	16	89	0	52	25	17	22	34	1.96
913582--913606	3	8.3	3	100	0	50	68	0	0	32	0.90
918448--918487	2	20.0	2	100	0	80	0	50	0	50	1.00
921411--921460	16	3.1	16	88	2	64	34	12	32	22	1.90
921505--921551	17	2.8	17	93	0	85	34	25	21	19	1.96
930547--930759	19	11.3	19	72	10	105	36	39	3	21	1.70
930527--930671	57	2.5	56	78	4	157	34	39	2	23	1.69
932083--932136	2	27.0	2	100	0	108	50	0	50	0	1.00
935606--935667	20	3.2	19	81	4	70	48	9	17	24	1.77
935561--935713	81	1.9	80	81	6	184	39	14	17	28	1.89
935709--935734	10	2.6	10	100	0	52	38	23	19	19	1.93
937252--937294	2	21.5	2	100	0	86	48	0	51	0	1.00
938143--938181	2	19.5	2	100	0	78	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)
940049--940101	11	4.6	11	77	9	61	7	20	26	45	1.78
950281--950704	214	2.0	213	100	0	839	37	18	8	34	1.83
955991--956374	192	2.0	191	99	0	759	37	17	9	35	1.83
983632--983669	2	19.0	2	100	0	76	50	0	50	0	1.00
985126--985285	83	1.9	83	83	2	205	25	23	15	35	1.94
986167--986348	91	2.0	91	97	0	346	49	13	12	24	1.76
991300--991345	21	2.2	21	92	0	74	21	10	28	39	1.87
993373--993442	22	3.2	21	82	6	77	25	21	11	41	1.86
993877--993916	12	3.2	12	85	3	53	0	2	12	85	0.71
993876--993916	15	2.7	15	84	3	55	0	4	12	82	0.81
999484--999515	16	2.0	16	93	0	55	3	40	25	31	1.71
1002713--1002756	2	22.0	2	100	0	88	0	50	0	50	1.00
1015348--1015383	13	2.7	14	91	8	58	0	0	22	77	0.76
1016431--1016479	2	24.5	2	100	0	98	48	0	51	0	1.00
1029505--1029624	20	6.0	20	86	0	168	27	35	23	13	1.92
1029504--1029623	40	3.0	40	90	0	186	27	36	23	12	1.91
1032024--1032070	2	23.5	2	95	0	85	0	48	0	51	1.00
1034534--1034574	21	2.0	21	90	0	64	4	19	24	51	1.66
1034772--1034850	2	39.5	2	100	0	158	0	49	0	50	1.00
1047954--1047985	16	2.0	16	93	0	55	53	18	15	12	1.73
1047958--1048094	41	3.3	41	93	3	229	40	21	23	14	1.90
1048035--1048067	16	2.1	16	94	0	57	45	21	21	12	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1049327--1049374	22	2.2	22	92	0	78	25	33	12	29	1.92
1049375--1049647	64	4.3	64	97	0	510	23	25	15	35	1.94
1050864--1051250	157	2.4	156	83	5	440	36	11	30	21	1.89
1051109--1051294	73	2.5	73	94	0	318	36	10	30	22	1.88
1052160--1053435	437	2.9	436	89	2	1839	30	17	16	36	1.92
1054188--1055601	437	3.2	431	84	5	1646	30	17	16	35	1.92
1056037--1056174	66	2.1	66	93	2	233	47	13	22	16	1.81
1063447--1063505	21	2.8	21	84	5	75	23	32	18	25	1.97
1064670--1064786	22	5.5	22	88	8	188	40	41	5	12	1.68
1064713--1064774	13	5.4	13	64	28	50	38	41	6	12	1.69
1064673--1064786	40	2.7	43	93	5	189	39	41	6	13	1.69
1064694--1064807	31	3.7	32	69	17	87	40	40	6	13	1.69
1064660--1064792	40	3.2	41	77	12	146	42	39	5	12	1.66
1064660--1064795	62	2.2	61	85	3	209	43	38	5	12	1.65
1064673--1064805	44	3.1	44	80	6	141	39	41	6	12	1.68
1069805--1069834	2	15.0	2	100	0	60	0	50	0	50	1.00
1078418--1078457	2	20.0	2	100	0	80	50	50	0	0	1.00
1078457--1078482	2	13.0	2	100	0	52	50	0	0	50	1.00
1084319--1084358	2	20.0	2	100	0	80	0	50	0	50	1.00
1086228--1086294	31	2.2	31	97	2	127	14	32	8	43	1.77
1086542--1086867	48	6.8	48	93	1	512	36	12	6	44	1.67
1092542--1092620	2	39.5	2	92	0	122	0	50	5	44	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1093493--1093546	15	3.5	15	90	9	83	22	1	0	75	0.89
1093493--1093541	3	16.7	3	83	8	57	24	2	0	73	0.94
1093488--1093545	13	4.2	13	79	16	64	22	1	0	75	0.89
1097856--1097904	2	24.5	2	100	0	98	0	51	0	48	1.00
1101035--1101073	2	19.5	2	100	0	78	51	0	48	0	1.00
1109265--1109301	16	2.3	15	86	13	56	27	16	32	24	1.96
1110163--1110194	16	2.0	16	100	0	64	25	37	6	31	1.81
1113976--1114457	168	2.9	167	84	5	614	32	18	18	30	1.94
1115360--1115390	4	7.8	4	100	0	62	51	22	25	0	1.48
1123879--1123909	2	15.5	2	100	0	62	0	51	0	48	1.00
1124525--1124607	41	2.0	42	88	2	123	32	7	4	55	1.48
1125662--1125709	2	24.0	2	100	0	96	0	50	0	50	1.00
1126021--1126089	2	34.5	2	97	0	129	49	0	1	49	1.09
1132467--1132493	2	13.5	2	100	0	54	51	0	0	48	1.00
1133659--1133712	21	2.6	21	75	13	58	33	12	1	51	1.51
1133764--1133884	21	6.0	21	77	8	101	23	9	10	57	1.61
1134051--1134236	21	9.0	21	75	10	120	53	8	10	27	1.64
1134021--1134241	41	5.4	41	74	8	171	53	8	10	27	1.63
1140349--1140391	17	2.6	16	76	20	52	30	4	0	65	1.13
1148050--1148115	20	3.3	20	73	0	60	24	15	0	60	1.35
1148055--1148113	16	3.7	16	83	0	82	23	16	0	59	1.37
1151695--1152015	18	17.8	18	87	1	383	3	18	35	42	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1151696--1152022	54	6.1	54	89	1	431	3	18	35	43	1.66
1152209--1152252	18	2.4	18	84	0	61	4	13	34	47	1.63
1151979--1152437	230	2.0	229	96	0	846	12	13	28	44	1.81
1153152--1153201	24	2.1	24	88	0	73	16	30	14	40	1.87
1153137--1153303	39	4.1	39	81	13	163	13	26	18	41	1.87
1153195--1153285	24	3.8	24	95	0	155	10	24	20	43	1.84
1153195--1153384	48	4.0	48	78	4	233	11	24	20	44	1.83
1153133--1153321	15	13.2	15	72	21	147	13	25	18	41	1.88
1153305--1153384	24	3.3	24	87	0	124	8	23	20	47	1.77
1153137--1153378	39	6.2	39	73	11	124	12	25	18	43	1.85

Tables:   1   2   3   4