genome.fa.s16.2.7.7.80.10.50.1000.8.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

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: Scaffold16
Parameters: 2 7 7 80 10 50 1000
Length:  5287347

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   

This is table  8  of  35  ( 4175 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)
1064348--1064442	47	2.0	47	93	0	163	24	27	15	32	1.95
1064700--1064766	37	1.9	35	88	11	102	29	25	11	32	1.92
1065224--1065249	13	2.0	13	100	0	52	30	15	15	38	1.88
1065204--1065267	32	2.0	33	87	3	94	28	14	17	40	1.88
1065957--1066000	21	2.1	21	83	8	54	25	31	4	38	1.76
1068075--1068239	84	2.0	84	82	7	201	24	19	3	52	1.62
1070289--1070314	13	2.0	13	100	0	52	30	15	15	38	1.88
1070269--1070332	32	2.0	33	87	3	94	28	14	17	40	1.88
1071313--1071344	13	2.3	15	89	10	50	18	6	12	62	1.50
1071475--1072101	164	3.8	163	78	8	626	29	10	9	50	1.69
1071506--1072111	326	1.8	327	82	5	776	29	10	9	50	1.68
1072726--1072790	7	8.9	8	75	20	54	78	0	18	3	0.88
1072734--1072789	13	4.2	13	77	8	58	78	0	17	3	0.89
1072748--1072792	9	4.9	9	83	5	54	82	0	13	4	0.82
1072725--1072790	21	3.1	21	80	4	71	78	0	18	3	0.87
1072725--1072792	28	2.3	29	82	9	86	79	0	17	2	0.86
1073694--1074013	164	2.0	158	84	6	394	35	9	13	42	1.76
1078938--1079673	156	4.7	155	79	6	659	38	21	17	22	1.93
1081352--1081513	64	2.5	64	79	11	204	32	24	12	31	1.92
1081352--1081510	65	2.5	63	81	10	196	32	23	12	31	1.92
1081355--1081513	32	5.0	31	81	15	175	31	23	12	32	1.92
1081944--1081995	20	2.6	20	90	0	77	40	19	5	34	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1082174--1082213	20	1.9	21	90	10	64	37	5	7	50	1.53
1082990--1083016	14	1.9	14	100	0	54	11	7	0	81	0.87
1095154--1095209	8	6.8	8	78	15	51	83	10	1	3	0.83
1095152--1095209	18	3.4	16	78	19	55	84	10	1	3	0.81
1095156--1095209	24	2.2	24	83	3	63	83	11	1	3	0.85
1096444--1096610	28	6.0	28	84	4	187	28	28	18	24	1.98
1096444--1096610	56	3.0	56	87	0	226	28	28	18	24	1.98
1096870--1096906	11	3.5	11	92	3	58	0	10	0	89	0.49
1096870--1096906	10	3.6	10	96	3	65	0	10	0	89	0.49
1098673--1098725	20	2.6	21	84	3	72	28	16	15	39	1.89
1098713--1098741	13	2.2	13	100	0	58	37	13	17	31	1.89
1098726--1098777	20	2.6	20	87	0	68	36	13	15	34	1.87
1099294--1099337	21	2.0	21	86	4	61	31	29	2	36	1.70
1101019--1101057	20	1.9	19	85	10	51	43	2	20	33	1.65
1101193--1101229	13	2.8	13	87	0	56	35	13	21	29	1.92
1107503--1107531	13	2.2	13	100	0	58	37	13	17	31	1.89
1107516--1107567	20	2.6	20	87	0	68	36	13	15	34	1.87
1110737--1110762	13	2.0	13	100	0	52	30	15	15	38	1.88
1113277--1113302	13	2.0	13	100	0	52	38	15	15	30	1.88
1118627--1118652	13	2.0	13	100	0	52	30	15	15	38	1.88
1119095--1119146	19	2.7	19	100	0	104	40	17	15	26	1.89
1119135--1119159	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1119116--1119180	33	2.0	32	88	8	96	38	15	15	30	1.88
1120149--1120841	154	4.5	155	81	5	708	40	19	15	24	1.90
1120149--1120841	309	2.2	308	84	4	869	40	19	15	24	1.90
1120197--1120841	308	2.1	308	84	4	843	39	20	15	24	1.91
1121095--1121358	146	1.8	147	81	2	334	37	14	13	34	1.85
1122262--1122309	11	4.4	11	74	10	53	0	16	0	83	0.65
1122262--1122312	20	2.6	19	82	11	68	0	15	0	84	0.63
1122952--1123368	167	2.5	167	85	3	536	52	8	10	28	1.65
1122952--1123429	167	2.9	167	83	4	468	52	8	10	28	1.66
1125487--1125547	22	2.8	21	85	14	79	44	13	8	34	1.73
1125843--1125899	22	2.6	23	77	8	64	42	14	8	35	1.76
1126172--1126215	22	2.0	21	82	4	52	50	4	9	36	1.55
1126301--1126880	53	11.2	53	74	12	480	40	1	5	52	1.36
1126433--1126853	104	4.0	103	80	13	477	40	1	5	52	1.33
1126439--1126857	209	2.0	209	83	9	534	39	1	5	53	1.34
1128277--1128315	21	1.9	21	89	5	62	20	17	12	48	1.80
1143325--1143473	52	2.9	51	88	4	226	30	16	18	33	1.94
1143462--1143486	13	1.9	13	100	0	50	36	16	16	32	1.90
1143527--1143593	33	2.0	33	88	0	98	40	14	11	32	1.83
1143549--1143573	13	1.9	13	100	0	50	32	16	16	36	1.90
1144164--1144625	166	2.8	163	85	6	610	29	9	7	53	1.61
1144624--1144661	14	2.8	14	88	4	60	34	2	0	63	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1144625--1144683	27	2.2	27	84	6	75	37	3	3	55	1.33
1144930--1144954	11	2.3	11	100	0	50	92	0	8	0	0.40
1145910--1146175	140	1.9	139	81	6	322	34	10	11	43	1.75
1146383--1146665	155	1.8	154	80	4	345	26	17	18	37	1.93
1147914--1148157	49	4.8	49	85	4	274	32	15	25	26	1.96
1148178--1148631	30	15.5	30	78	9	366	24	16	29	29	1.97
1148162--1148418	58	4.4	59	85	6	317	20	17	29	32	1.96
1148162--1148418	88	2.9	87	90	4	383	20	17	29	32	1.96
1148516--1148568	27	2.0	27	88	0	79	15	15	32	37	1.88
1148340--1148622	121	2.4	116	79	4	298	26	16	28	27	1.97
1150069--1150197	1	129.0	1	75	0	78	2	3	10	84	0.82
1150071--1150197	22	5.8	21	77	14	114	2	3	10	84	0.83
1150069--1150197	29	4.6	27	83	12	145	2	3	10	84	0.82
1159886--1159912	10	2.7	10	100	0	54	77	22	0	0	0.76
1164043--1164191	52	2.9	51	89	4	235	30	17	18	32	1.94
1164180--1164204	13	1.9	13	100	0	50	36	16	16	32	1.90
1164245--1164311	33	2.0	33	85	0	89	41	14	10	32	1.80
1164882--1165343	166	2.8	163	85	6	610	29	9	7	53	1.61
1165342--1165379	14	2.8	14	88	4	60	34	2	0	63	1.09
1165343--1165401	27	2.2	27	84	6	75	37	3	3	55	1.33
1165648--1165672	11	2.3	11	100	0	50	92	0	8	0	0.40
1166628--1166893	140	1.9	139	81	6	322	34	10	11	43	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1167101--1167383	155	1.8	154	80	4	345	26	17	18	37	1.93
1170288--1170788	165	3.1	164	83	6	576	27	11	9	50	1.70
1172662--1172734	20	3.6	20	81	3	101	35	13	19	31	1.91
1172680--1172755	21	3.7	21	78	3	91	40	11	17	30	1.85
1172662--1172755	41	2.3	41	96	0	170	38	12	18	30	1.88
1172794--1172819	13	2.0	13	100	0	52	38	15	15	30	1.88
1176881--1176911	15	2.1	15	93	0	53	48	16	22	12	1.80
1178990--1179028	13	3.0	13	96	0	69	30	17	15	35	1.91
1181468--1181540	20	3.6	20	81	3	101	35	13	19	31	1.91
1181486--1181561	21	3.7	21	78	3	91	40	11	17	30	1.85
1181468--1181561	41	2.3	41	96	0	170	38	12	18	30	1.88
1181600--1181625	13	2.0	13	100	0	52	38	15	15	30	1.88
1182373--1182898	161	3.3	162	92	1	871	35	11	13	39	1.81
1190831--1190882	19	2.6	20	93	6	88	26	11	15	46	1.80
1190913--1190969	21	2.7	21	100	0	114	26	19	10	43	1.83
1193394--1193431	13	2.9	13	96	0	67	31	15	18	34	1.92
1195513--1195543	15	2.1	15	93	0	53	12	22	16	48	1.80
1199611--1199636	13	2.0	13	100	0	52	30	15	15	38	1.88
1199590--1199654	32	2.0	33	93	6	114	27	12	15	44	1.82
1199590--1199654	19	3.6	19	73	26	70	27	12	15	44	1.82
1205940--1206121	51	3.8	50	75	16	213	40	13	18	28	1.88
1205988--1206115	20	5.8	20	71	21	96	40	12	17	29	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1205940--1206115	91	1.9	91	94	0	307	40	13	17	28	1.87
1207052--1207748	29	24.4	28	85	3	856	24	17	29	28	1.97
1207052--1207748	57	12.2	57	84	5	829	24	17	29	28	1.97
1208919--1208959	9	4.8	9	88	11	68	0	0	12	87	0.53
1208919--1208956	16	2.4	16	100	0	76	0	0	10	89	0.49
1215722--1215784	32	2.0	32	93	0	108	34	7	17	39	1.79
1223610--1223635	9	2.9	9	100	0	52	11	7	23	57	1.59
1226421--1226514	37	2.4	38	82	10	120	39	11	17	31	1.85
1226421--1226521	20	5.2	19	82	11	125	39	11	17	30	1.86
1229872--1230154	89	3.2	89	87	3	374	22	25	14	38	1.92

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35