genome.fa.s48.2.7.7.80.10.50.1000.8.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: Scaffold48
Parameters: 2 7 7 80 10 50 1000
Length:  4619657

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   

This is table  8  of  27  ( 3212 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)
1021982--1022027	19	2.4	20	82	7	60	71	2	4	21	1.14
1023420--1023460	15	2.7	16	77	7	50	39	0	0	60	0.96
1023938--1023984	17	2.8	16	75	18	51	38	0	0	61	0.96
1024751--1024802	17	2.9	17	85	5	59	42	0	0	57	0.98
1024739--1024803	26	2.5	27	85	9	91	43	0	0	56	0.99
1024849--1024889	17	2.4	17	95	4	55	43	0	0	56	0.99
1024853--1024885	9	3.8	9	84	8	50	45	0	0	54	0.99
1024893--1024928	12	3.1	12	88	8	56	75	0	0	25	0.81
1026770--1026807	19	2.0	19	85	10	51	47	2	0	50	1.15
1027600--1027667	19	3.8	17	81	18	84	33	0	1	64	1.02
1027600--1027664	27	2.4	28	81	5	87	35	0	1	63	1.04
1027712--1027780	27	2.5	28	75	15	72	52	2	0	44	1.16
1033729--1033783	22	2.5	21	82	8	65	47	0	3	49	1.19
1033719--1033754	16	2.2	16	95	0	63	52	0	0	47	1.00
1036321--1036348	2	14.0	2	100	0	56	0	0	50	50	1.00
1038826--1038854	2	14.5	2	100	0	58	51	48	0	0	1.00
1045822--1045875	27	2.0	27	88	0	81	38	0	3	57	1.17
1047731--1047765	11	3.1	11	88	8	52	82	2	8	5	0.91
1048957--1049028	33	2.2	33	85	4	94	44	0	0	55	0.99
1048981--1049048	33	2.1	33	86	5	93	42	0	0	57	0.98
1048981--1049051	32	2.2	33	85	7	92	43	0	0	56	0.99
1049047--1049087	22	2.0	21	85	9	57	41	2	0	56	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1054590--1054929	114	2.9	114	95	3	590	22	20	15	40	1.91
1062355--1062399	23	1.9	24	90	4	74	44	4	0	51	1.21
1062337--1062410	23	3.2	22	74	25	57	45	2	0	51	1.15
1068592--1068696	38	2.8	38	88	0	147	35	12	22	29	1.91
1073271--1073375	38	2.8	38	94	0	174	28	12	29	29	1.93
1074828--1074863	15	2.3	16	90	4	56	52	0	0	47	1.00
1075410--1075460	2	25.5	2	91	0	84	49	0	3	47	1.20
1075761--1075819	26	2.2	27	85	14	79	55	3	0	40	1.16
1076424--1076449	3	8.7	3	100	0	52	65	0	0	34	0.93
1078135--1078183	2	24.5	2	95	0	89	0	46	0	53	1.00
1079195--1079242	14	3.4	14	80	8	53	66	2	0	31	1.03
1078927--1079744	405	2.0	402	94	1	1453	42	8	6	42	1.61
1087523--1087557	17	2.1	17	88	0	52	34	0	0	65	0.93
1099478--1099518	19	2.2	19	90	0	64	4	17	9	68	1.35
1099597--1099650	2	27.5	2	84	3	74	46	3	1	48	1.30
1100065--1100124	22	2.8	22	72	20	56	38	3	1	56	1.26
1100178--1100265	43	2.1	40	83	10	106	25	3	6	64	1.34
1104117--1104166	19	2.5	21	81	15	61	54	0	2	44	1.11
1104118--1104181	21	3.0	21	84	4	67	48	0	1	50	1.10
1104131--1104206	16	5.1	14	74	15	64	43	0	1	55	1.08
1104127--1104205	15	5.2	16	74	20	64	43	0	1	55	1.07
1104150--1104209	21	2.6	25	87	10	76	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1104862--1104924	28	2.2	28	83	13	76	52	0	1	46	1.10
1105383--1105422	13	2.9	15	78	17	50	57	0	0	42	0.98
1105796--1105838	18	2.3	19	84	4	52	41	2	4	51	1.35
1106024--1106072	20	2.5	19	75	18	55	67	2	0	30	1.02
1106147--1106194	2	25.5	2	79	12	57	50	0	2	47	1.12
1108025--1108066	16	2.8	16	79	13	54	42	2	0	54	1.13
1108049--1108076	11	2.5	11	100	0	56	39	0	0	60	0.97
1108345--1108374	11	2.6	12	94	5	53	23	0	0	76	0.78
1110320--1110423	29	3.5	30	84	3	131	45	4	0	50	1.23
1110390--1110434	22	2.0	22	83	8	56	51	4	0	44	1.21
1111409--1111437	2	14.5	2	100	0	58	51	0	0	48	1.00
1112632--1112690	22	2.6	22	81	2	64	40	1	0	57	1.09
1112628--1112665	19	2.0	19	85	10	51	34	5	0	60	1.19
1116536--1116575	20	2.0	20	95	0	71	22	15	25	37	1.93
1125051--1125131	28	2.8	30	74	9	80	39	19	9	30	1.84
1125095--1125235	45	3.2	44	83	9	155	42	23	9	24	1.83
1125288--1125388	30	3.4	29	73	10	78	42	21	6	28	1.79
1128116--1128156	21	1.9	21	85	5	55	63	4	21	9	1.44
1129186--1129224	20	2.0	20	85	5	53	58	5	0	35	1.20
1129526--1129553	2	14.0	2	100	0	56	50	0	0	50	1.00
1129658--1129687	15	2.0	15	93	0	51	56	0	0	43	0.99
1130073--1130117	16	2.8	15	80	12	54	53	4	0	42	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1130063--1130123	17	3.5	17	74	12	61	49	3	0	47	1.18
1131463--1131525	30	2.1	29	82	8	74	49	0	1	49	1.10
1131485--1131533	25	1.9	26	88	12	75	53	0	0	46	1.00
1131508--1131537	15	2.0	15	100	0	60	53	0	0	46	1.00
1131736--1131776	21	1.9	22	85	5	57	36	2	0	60	1.10
1132008--1132064	17	3.3	17	75	7	53	42	0	0	57	0.98
1135739--1135787	25	2.0	25	83	0	62	51	0	4	44	1.20
1135748--1135793	19	2.4	18	85	7	56	47	0	4	47	1.21
1136448--1136491	17	2.5	18	77	7	63	59	0	0	40	0.98
1137052--1137089	17	2.2	17	90	0	58	39	0	0	60	0.97
1137142--1137206	13	5.2	12	77	15	69	69	0	0	30	0.89
1137123--1137206	24	3.4	24	81	16	84	66	0	0	33	0.92
1137148--1137194	17	2.8	18	78	18	57	65	0	0	34	0.93
1137820--1137875	23	2.5	24	83	13	66	48	0	1	50	1.11
1137816--1137888	24	3.2	22	73	21	69	50	0	2	46	1.15
1138420--1138464	21	2.1	21	84	15	58	62	0	2	35	1.08
1138894--1138952	29	2.0	29	80	9	66	55	16	8	18	1.66
1139089--1139127	19	2.0	20	85	5	53	61	0	2	35	1.10
1139136--1139193	30	1.9	30	86	6	82	60	6	5	27	1.44
1139174--1139244	32	2.2	33	84	2	90	50	2	4	42	1.36
1140004--1140037	2	17.0	2	100	0	68	50	0	0	50	1.00
1140780--1140811	2	16.0	2	100	0	64	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1140888--1140916	2	14.5	2	100	0	58	51	0	0	48	1.00
1142880--1142915	3	12.3	3	94	5	65	30	0	0	69	0.89
1144032--1144060	2	14.5	2	100	0	58	48	0	0	51	1.00
1144292--1144397	18	5.5	19	68	20	60	36	1	1	59	1.19
1144292--1144334	20	2.2	20	84	8	54	32	0	4	62	1.15
1144302--1144412	27	3.9	28	70	10	82	39	1	0	58	1.09
1145502--1145536	13	2.6	13	90	4	52	57	0	0	42	0.99
1145898--1145974	30	2.7	29	80	11	95	38	0	1	59	1.06
1146059--1146131	23	3.3	23	78	14	82	57	0	0	42	0.98
1146075--1146116	22	1.9	22	90	9	68	54	0	0	45	0.99
1146449--1146489	21	2.0	21	95	0	73	48	0	0	51	1.00
1149170--1149208	18	2.2	17	86	4	51	51	0	0	48	1.00
1151554--1151578	2	12.5	2	100	0	50	52	0	0	48	1.00
1152250--1152291	2	21.0	2	95	0	75	47	0	2	50	1.14
1156002--1156036	17	2.1	17	89	10	54	37	2	0	60	1.12
1156010--1156069	24	2.5	24	84	10	79	38	0	0	61	0.96
1156025--1156083	30	2.0	30	86	6	84	44	0	0	55	0.99
1156248--1156289	16	2.7	16	85	3	59	54	0	0	45	0.99
1159635--1159697	29	2.2	29	80	5	74	39	1	3	55	1.25
1159987--1160022	4	9.0	4	100	0	72	75	0	0	25	0.81
1161122--1161167	24	1.9	23	83	16	58	36	4	0	58	1.18
1161327--1161361	18	1.9	18	88	0	52	42	2	2	51	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1168869--1168906	2	19.0	2	100	0	76	0	50	0	50	1.00
1175656--1175714	31	1.9	31	92	0	100	28	1	3	66	1.18
1176105--1176161	27	2.1	28	83	9	73	57	0	0	42	0.98
1176474--1176502	13	2.1	14	93	6	51	82	0	3	13	0.79
1176997--1177021	2	12.5	2	100	0	50	48	0	52	0	1.00
1177359--1177399	22	1.9	22	90	5	66	58	0	0	41	0.98
1178058--1178111	21	2.5	21	76	8	56	57	0	0	42	0.98
1178429--1178468	13	3.2	13	86	6	57	55	0	0	45	0.99
1179263--1179298	2	18.0	2	94	0	63	0	47	0	52	1.00
1180150--1180197	19	2.5	19	90	6	71	52	0	0	47	1.00

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