genome.fa.s3.2.7.7.80.10.50.1000.9.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  9  of  32  ( 3795 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)
1050791--1050835	20	2.3	20	85	11	58	31	2	0	66	1.04
1050864--1050913	17	2.9	17	80	11	66	52	0	0	48	1.00
1051533--1051562	14	2.2	13	94	5	51	83	3	0	13	0.77
1051535--1051569	18	1.9	18	88	0	52	82	2	0	14	0.77
1052468--1052518	26	2.0	26	81	11	61	50	3	1	43	1.31
1053135--1053205	10	7.6	10	69	15	53	53	0	0	46	1.00
1053138--1053205	27	2.4	29	81	16	90	54	0	0	45	0.99
1054906--1054957	22	2.4	22	81	9	61	44	3	0	51	1.19
1055074--1055115	17	2.6	16	85	7	57	54	0	0	45	0.99
1055538--1055581	2	22.0	2	100	0	88	50	0	0	50	1.00
1056294--1056344	20	2.8	18	80	11	59	49	0	0	50	1.00
1056294--1056328	18	2.0	17	88	5	52	51	0	0	48	1.00
1056294--1056346	19	2.8	19	75	10	56	49	0	0	50	1.00
1058276--1058317	20	2.2	20	86	4	59	73	0	23	2	0.94
1064322--1064380	22	2.9	20	80	14	68	55	1	0	42	1.09
1069750--1069787	20	2.0	20	89	5	60	44	0	0	55	0.99
1071801--1071970	87	2.0	87	93	0	295	23	32	11	32	1.91
1074506--1074553	18	2.7	17	83	6	51	35	2	2	60	1.20
1074642--1074687	16	2.8	17	81	18	62	63	4	0	32	1.14
1074687--1074733	22	2.3	19	89	10	67	40	0	0	59	0.97
1074969--1075005	17	2.2	17	90	0	56	35	0	0	64	0.94
1075182--1075214	16	2.1	16	100	0	66	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1075677--1075742	18	3.3	20	77	14	66	40	0	1	57	1.08
1075706--1075754	18	3.1	16	81	16	50	46	0	0	53	1.00
1076334--1076385	20	2.7	20	82	5	63	38	0	0	61	0.96
1080987--1081022	16	2.3	15	85	4	54	36	0	0	63	0.94
1081534--1081611	19	3.8	20	76	20	74	66	5	0	28	1.12
1081534--1081596	9	6.3	9	74	16	54	68	6	0	25	1.13
1081591--1081693	33	3.5	28	68	25	70	55	0	0	42	1.13
1081595--1081682	33	2.9	31	75	20	87	53	1	1	44	1.15
1082273--1082303	15	2.1	15	93	0	53	35	0	0	64	0.94
1084251--1084312	32	2.0	32	87	9	94	43	0	0	56	0.99
1084248--1084316	29	2.4	27	76	19	77	42	0	0	57	0.98
1085576--1085620	16	2.8	16	80	16	56	55	0	0	44	0.99
1085583--1085622	16	2.5	17	84	12	57	57	0	0	42	0.98
1087086--1087158	14	5.2	14	71	15	62	64	0	0	35	0.94
1089398--1089427	2	15.0	2	100	0	60	0	50	0	50	1.00
1089752--1089797	14	3.4	14	79	11	60	43	0	0	56	0.99
1094431--1094460	7	4.1	7	91	8	51	73	0	0	26	0.84
1094432--1094556	47	2.4	55	78	16	142	60	0	0	39	1.03
1094484--1094550	24	2.8	24	81	6	82	59	0	0	40	0.97
1094430--1094587	54	2.9	54	78	16	132	58	1	0	39	1.11
1096921--1096971	20	2.5	20	77	0	57	47	0	0	52	1.00
1096968--1097005	17	2.2	18	90	4	60	65	2	0	31	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1098566--1098615	4	12.5	4	95	0	64	50	0	42	8	1.32
1104934--1104983	16	2.9	17	77	16	59	52	0	4	44	1.20
1104994--1105036	15	2.9	15	78	0	50	72	0	0	27	0.85
1106192--1106231	21	2.0	20	85	14	55	40	0	0	60	0.97
1108028--1108074	16	2.7	18	84	15	64	57	2	0	40	1.11
1109940--1109971	12	2.6	13	85	14	50	0	37	0	62	0.95
1111070--1111103	16	2.0	18	88	11	54	29	0	0	70	0.87
1111441--1111489	18	2.6	19	84	15	66	34	0	2	63	1.06
1111652--1111697	23	2.0	23	95	0	83	60	10	0	28	1.30
1111982--1112032	21	2.2	24	80	19	65	45	0	0	54	0.99
1112883--1112924	14	3.0	14	85	0	57	50	0	26	23	1.50
1116305--1116344	14	2.9	14	88	0	53	40	0	37	22	1.54
1116520--1116587	28	2.4	28	92	0	109	32	13	10	44	1.77
1116872--1116932	27	2.2	27	82	5	68	40	3	9	45	1.53
1117537--1117578	18	2.2	20	83	8	52	50	0	2	47	1.14
1118292--1118352	21	2.9	20	80	9	59	57	1	0	40	1.08
1119456--1119513	17	3.4	17	79	9	55	24	0	1	74	0.92
1119456--1119518	18	3.5	18	82	4	65	23	0	1	74	0.90
1119475--1119528	16	3.5	15	80	10	65	25	0	0	74	0.83
1119769--1119794	4	6.5	4	100	0	52	76	0	0	23	0.78
1125716--1125760	24	2.0	24	83	16	60	62	0	0	37	0.96
1126479--1126529	23	2.1	25	85	7	70	50	0	3	45	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1129567--1129594	2	14.0	2	100	0	56	50	0	0	50	1.00
1133925--1133955	6	5.0	6	96	4	53	48	3	0	48	1.17
1133939--1133979	17	2.6	16	75	24	50	53	7	0	39	1.29
1135315--1135351	2	18.5	2	100	0	74	51	0	0	48	1.00
1136055--1136098	16	2.9	15	75	18	54	40	0	0	59	0.98
1136095--1136147	27	2.0	27	85	7	72	30	1	3	64	1.22
1137420--1137462	22	2.0	22	90	9	70	58	0	0	41	0.98
1138764--1138826	26	2.5	24	75	12	65	60	0	0	39	0.97
1141516--1141542	2	13.5	2	100	0	54	51	0	0	48	1.00
1143154--1143203	20	2.5	19	77	6	55	46	0	2	52	1.12
1144452--1144533	40	2.1	39	81	6	94	58	1	0	40	1.06
1144505--1144585	17	5.1	15	72	18	56	48	2	2	46	1.28
1144513--1144622	24	4.6	24	68	15	75	44	1	1	51	1.22
1144639--1144677	2	19.5	2	100	0	78	51	0	0	48	1.00
1145555--1145623	13	5.1	13	71	20	52	33	1	0	65	1.02
1148363--1148387	2	12.5	2	100	0	50	52	0	0	48	1.00
1148389--1148420	2	16.0	2	100	0	64	50	0	50	0	1.00
1149624--1149707	21	4.0	22	75	6	75	54	1	1	42	1.15
1149907--1149946	8	4.8	8	85	11	53	20	0	0	80	0.72
1157480--1157530	2	25.5	2	100	0	102	0	50	0	49	1.00
1159300--1159342	22	1.9	23	90	4	70	51	0	0	48	1.00
1161125--1161171	2	23.5	2	100	0	94	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1161364--1161426	29	2.3	28	81	10	76	30	0	0	69	0.88
1161463--1161565	33	3.0	33	72	12	84	49	2	0	47	1.16
1166327--1166380	19	2.9	19	75	10	58	48	0	3	48	1.19
1166345--1166386	12	3.6	12	81	18	61	47	0	2	50	1.14
1168797--1168822	3	8.7	3	100	0	52	0	0	34	65	0.93
1169585--1169615	4	7.5	4	92	7	53	70	3	0	25	1.02
1169713--1169756	2	22.0	2	100	0	88	50	0	0	50	1.00
1169915--1169993	29	2.8	28	77	16	74	45	0	0	54	0.99
1169915--1169983	29	2.4	30	83	9	83	46	0	0	53	1.00
1169967--1170016	21	2.5	20	80	6	64	40	2	0	58	1.10
1170915--1170993	34	2.3	35	76	6	90	45	0	3	50	1.19
1171008--1171041	11	3.0	11	91	4	50	41	0	0	58	0.98
1171013--1171055	17	2.6	17	85	7	54	46	0	0	53	1.00
1175966--1176007	22	2.1	19	86	13	57	42	0	0	57	0.99
1179213--1179307	30	3.2	29	75	5	93	45	5	1	48	1.32
1179397--1179434	15	2.5	15	87	8	51	63	2	5	28	1.30
1179730--1179804	26	3.2	24	76	14	68	65	0	4	30	1.11
1179788--1179813	12	2.2	12	100	0	52	73	0	0	26	0.84
1180312--1180348	10	3.8	10	83	16	51	40	0	0	59	0.97
1180511--1180561	16	3.2	15	78	15	50	49	0	0	50	1.00
1185926--1185983	20	2.9	20	84	0	62	32	12	13	41	1.82
1194865--1194907	20	2.2	19	83	4	50	34	9	6	48	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1195288--1195380	30	3.1	28	77	20	91	46	6	2	45	1.41
1196441--1196543	52	2.0	51	88	1	152	45	16	8	29	1.77
1196584--1196680	24	4.1	24	73	13	85	58	0	2	39	1.10
1196586--1196715	14	9.2	15	70	16	73	56	0	2	40	1.12
1196646--1196715	2	37.5	2	74	18	53	54	0	2	42	1.15
1197175--1197237	10	6.7	10	71	20	55	31	1	1	65	1.12
1197201--1197248	9	5.1	9	78	9	51	37	4	0	58	1.18
1197175--1197239	19	3.5	19	75	6	62	32	1	1	64	1.12
1197199--1197254	29	1.9	29	88	0	85	35	5	1	57	1.32
1197282--1197325	22	2.0	21	82	4	52	20	4	2	72	1.13

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