genome.fa.s9000.2.7.7.80.10.50.1000.6.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: VEPZ01009000.1 Hibiscus syriacus cultivar Beakdansim tig00112382_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1742898

Tables:   1   2   3   4   5   6   7   8   9   

This is table  6  of  9  ( 1003 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)
1092067--1092137	31	2.2	32	83	14	94	4	15	2	77	1.04
1092073--1092137	18	3.5	18	76	15	53	3	15	3	78	1.00
1092128--1092171	14	3.1	14	80	6	52	4	11	6	77	1.11
1094082--1094111	10	3.0	10	90	0	51	80	3	6	10	1.01
1095681--1095749	3	23.3	3	97	2	131	65	0	0	34	0.93
1095748--1095773	3	8.7	3	100	0	52	34	0	30	34	1.58
1097135--1097159	4	6.2	4	100	0	50	28	0	24	48	1.52
1101509--1101547	3	12.7	3	83	5	51	30	0	5	64	1.15
1102825--1102963	51	2.8	48	85	4	154	48	13	9	28	1.74
1102856--1102963	51	2.1	50	89	1	162	47	13	11	27	1.77
1103246--1103316	29	2.4	29	81	6	81	42	5	19	32	1.75
1104520--1104559	20	2.0	21	85	5	55	72	0	10	17	1.11
1104799--1104887	28	3.1	28	80	6	90	69	1	2	26	1.07
1104839--1104898	19	3.0	19	85	9	75	66	0	1	31	1.01
1104840--1104941	21	5.1	19	70	15	55	64	1	1	31	1.15
1105463--1105564	37	2.8	37	84	0	123	31	12	13	42	1.82
1106107--1106737	105	6.0	105	90	3	880	22	17	26	33	1.96
1106937--1107008	36	2.0	36	86	0	99	38	13	20	26	1.90
1106912--1107231	106	3.1	103	89	4	477	37	11	20	30	1.88
1107134--1107208	39	1.9	39	83	5	98	37	13	22	26	1.91
1107348--1107461	36	3.2	36	73	2	113	43	14	16	25	1.85
1107302--1107477	72	2.4	74	83	7	207	42	12	18	26	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1108621--1109153	183	2.9	183	93	0	906	31	20	19	27	1.97
1114802--1114838	3	12.7	3	88	11	51	70	0	2	27	1.01
1114799--1114841	9	4.6	9	83	11	50	74	0	2	23	0.93
1114797--1114844	10	4.9	10	85	10	55	72	0	2	25	0.95
1115101--1115143	18	2.5	17	85	7	61	67	2	4	25	1.22
1115033--1115151	58	2.1	55	80	12	125	61	3	3	31	1.29
1117742--1117780	19	2.1	19	95	0	69	30	30	15	23	1.95
1117731--1117890	65	2.5	65	84	7	193	31	21	18	28	1.97
1123270--1123364	23	4.4	21	77	9	86	27	26	22	24	2.00
1123289--1123369	23	3.7	23	77	8	96	25	25	24	23	2.00
1123270--1123364	44	2.2	42	87	7	129	27	26	22	24	2.00
1123288--1123387	43	2.3	42	80	8	112	27	26	25	22	2.00
1125975--1126133	65	2.5	63	82	9	189	31	22	17	28	1.96
1129760--1129789	10	3.0	10	100	0	60	30	0	0	70	0.88
1130115--1130168	26	2.0	27	89	10	85	50	3	0	46	1.19
1130402--1130449	24	2.0	23	84	4	60	25	6	6	62	1.42
1132389--1132747	177	2.0	179	89	6	550	45	9	3	42	1.51
1134309--1134382	31	2.4	31	86	0	103	52	14	13	18	1.74
1134506--1134557	20	2.6	20	78	0	59	40	25	26	7	1.82
1137597--1137633	13	2.8	13	91	0	65	16	48	21	13	1.80
1137593--1137657	31	2.1	31	91	0	103	18	47	18	15	1.82
1137611--1137651	18	2.3	18	91	0	64	19	48	19	12	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1137632--1137673	15	2.9	15	82	6	52	19	38	21	21	1.94
1140176--1140245	12	5.8	12	74	12	63	17	15	17	50	1.79
1140139--1140247	24	4.5	24	78	11	116	19	17	15	47	1.82
1140139--1140247	48	2.3	48	85	6	141	19	17	15	47	1.82
1142356--1142402	10	5.5	8	85	14	51	17	34	25	23	1.96
1142359--1142392	15	2.1	16	89	10	52	14	35	26	23	1.94
1143684--1143724	18	2.3	18	86	0	55	53	2	17	26	1.56
1144888--1144956	12	5.8	12	70	16	54	17	14	17	50	1.78
1144888--1144958	24	3.0	23	84	12	99	18	14	16	50	1.78
1151155--1151231	29	2.5	31	79	12	88	33	19	7	38	1.81
1153521--1153561	15	2.7	15	80	0	55	36	43	2	17	1.62
1159871--1160053	95	1.9	94	82	5	226	35	10	24	29	1.89
1160407--1160747	54	6.4	53	83	7	390	35	19	18	26	1.95
1160407--1160747	108	3.2	106	88	5	472	35	19	18	26	1.95
1160380--1160746	160	2.3	161	82	5	458	35	18	17	28	1.94
1166810--1167006	94	2.1	94	81	3	236	35	12	22	29	1.91
1167402--1167844	54	8.2	54	87	1	449	37	19	16	26	1.93
1167402--1167844	108	4.1	108	85	1	532	37	19	16	26	1.93
1167402--1167774	162	2.3	162	87	0	539	37	20	16	25	1.93
1167402--1167844	162	2.7	160	82	6	532	37	19	16	26	1.93
1170029--1170075	4	11.5	4	79	20	53	72	0	0	27	0.85
1170022--1170089	17	4.2	16	87	9	86	69	0	0	30	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1170103--1170141	17	2.5	15	80	15	51	43	5	5	46	1.48
1170176--1170408	77	3.0	76	77	14	235	40	12	4	42	1.63
1170171--1170410	37	6.4	36	77	15	170	41	12	4	41	1.63
1170359--1170441	37	2.3	37	81	6	89	44	13	4	37	1.65
1171020--1171160	72	2.0	72	84	2	185	23	15	24	36	1.94
1185376--1185424	21	2.3	22	80	20	59	34	28	12	24	1.91
1185404--1185477	23	3.2	23	84	0	103	22	21	16	39	1.92
1186113--1186154	22	1.9	22	90	9	68	19	26	14	40	1.89
1192794--1192838	19	2.3	20	84	3	65	71	0	0	28	0.87
1192923--1192969	23	2.2	22	88	11	71	44	10	4	40	1.59
1192872--1192983	57	1.9	59	82	10	140	46	9	3	40	1.54
1193027--1193129	38	2.7	38	86	4	136	42	11	3	41	1.59
1193062--1193145	38	2.3	36	83	8	98	45	13	3	38	1.60
1194588--1194648	25	2.4	26	78	10	72	39	1	0	59	1.08
1194808--1194860	24	2.2	24	82	3	61	43	1	0	54	1.11
1200747--1200844	35	2.8	35	84	1	135	38	14	21	25	1.91
1205842--1205933	21	4.6	21	69	17	70	46	30	0	22	1.52
1205890--1205940	21	2.5	22	78	12	63	47	25	0	27	1.53
1206812--1206874	22	2.9	22	90	0	99	46	25	9	19	1.80
1207022--1207057	16	2.2	17	90	5	56	47	0	2	50	1.15
1218692--1218744	25	2.1	25	85	0	70	26	0	3	69	1.05
1223536--1223614	39	2.0	39	80	4	88	32	17	12	36	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1223621--1224150	78	7.1	77	77	13	401	27	18	16	37	1.92
1223675--1223849	76	2.4	76	82	8	209	30	14	14	40	1.87
1223821--1224213	39	10.5	39	86	8	437	26	18	16	38	1.92
1224003--1224060	30	1.9	30	92	0	98	27	22	12	37	1.89
1223964--1224099	69	2.0	68	94	1	236	26	19	16	36	1.94
1223925--1224126	108	1.9	108	91	2	334	27	19	16	36	1.93
1224051--1224213	36	4.4	36	91	2	245	23	19	15	41	1.89
1224113--1224234	21	6.4	21	69	21	106	24	18	13	43	1.86
1224149--1224270	57	2.1	57	89	0	181	25	18	13	43	1.85
1224113--1224305	93	2.1	92	93	2	325	25	19	12	41	1.87
1224218--1224286	36	1.9	36	88	2	104	27	17	13	42	1.86
1224209--1224323	35	3.3	35	82	2	151	29	20	12	38	1.88
1224210--1224419	71	2.9	73	81	9	207	30	18	13	37	1.89
1224762--1224887	64	2.0	64	93	0	216	36	18	19	25	1.94
1224824--1225030	91	2.3	92	89	1	319	36	17	22	23	1.95
1226460--1226551	9	9.4	10	72	13	50	23	0	4	71	1.03
1226460--1226490	16	1.9	16	100	0	62	16	0	6	77	0.97
1226478--1226541	9	7.6	8	75	19	51	25	0	4	70	1.06
1226478--1226530	25	2.1	25	85	0	70	24	0	3	71	1.02
1229539--1229595	13	4.3	13	78	12	62	70	5	17	7	1.29
1229550--1229613	27	2.4	27	81	2	76	71	6	17	4	1.24
1229539--1229608	12	5.3	14	79	14	69	72	5	15	5	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1230834--1230895	18	3.2	20	63	28	53	25	16	16	41	1.88
1230841--1230925	36	2.3	37	84	6	102	27	20	15	37	1.92
1231041--1231229	65	2.9	67	87	7	280	28	15	12	42	1.84
1231112--1231330	120	1.8	118	91	3	359	25	16	15	42	1.88
1231048--1231395	185	1.9	184	87	2	509	25	17	14	42	1.87
1231232--1231463	65	3.5	65	89	1	329	23	19	15	41	1.90
1231281--1231462	29	5.4	35	66	23	122	23	20	15	40	1.90
1231475--1231857	134	2.9	133	85	3	486	27	29	17	25	1.98
1231465--1231857	131	3.0	132	85	4	499	27	29	17	25	1.97
1232351--1232391	20	2.0	21	90	4	66	60	21	12	4	1.50

Tables:   1   2   3   4   5   6   7   8   9