genome.fa.s8430.2.7.7.80.10.50.1000.5.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: VEPZ01008430.1 Hibiscus syriacus cultivar Beakdansim tig00111220_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1186098

Tables:   1   2   3   4   5   6   

This is table  5  of  6  ( 614 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)
1029033--1029188	31	5.0	31	89	1	233	35	21	21	21	1.96
1029044--1029188	62	2.3	62	96	0	263	35	21	21	21	1.96
1029404--1029450	23	2.0	24	91	4	78	34	21	0	44	1.52
1029976--1030021	21	2.2	21	92	0	74	17	26	26	30	1.97
1033218--1033373	31	5.0	31	89	1	233	35	21	21	21	1.96
1033229--1033373	62	2.3	62	96	0	263	35	21	21	21	1.96
1033589--1033635	23	2.0	24	91	4	78	34	21	0	44	1.52
1034168--1034213	21	2.2	21	88	0	65	15	26	28	30	1.96
1037683--1037733	22	2.3	22	100	0	102	29	35	17	17	1.93
1040261--1040331	22	3.3	22	68	4	72	53	15	2	28	1.56
1040247--1040342	43	2.2	43	98	0	183	51	16	2	30	1.56
1040610--1040716	31	3.5	31	96	0	196	38	19	18	23	1.93
1040796--1040863	33	2.1	32	89	8	102	30	16	10	42	1.81
1043429--1043874	41	10.8	41	86	1	500	27	17	18	36	1.94
1043431--1043874	166	2.7	166	85	2	563	27	17	18	36	1.94
1047508--1047672	42	3.9	42	81	6	188	27	25	14	32	1.95
1047504--1047683	43	4.2	42	82	2	198	25	24	18	31	1.97
1047714--1047788	34	2.2	35	90	4	118	21	22	14	41	1.89
1054271--1054351	20	3.9	21	78	12	78	22	34	25	17	1.95
1058006--1058069	23	2.8	23	85	0	83	15	23	25	35	1.94
1058441--1058484	19	2.3	19	96	0	79	31	2	31	34	1.70
1070145--1070223	38	2.1	38	97	0	149	35	22	15	26	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1073894--1073963	2	35.0	2	100	0	140	50	0	0	50	1.00
1078461--1078501	21	1.9	21	85	5	55	19	29	31	19	1.96
1079128--1079221	38	2.5	38	89	0	143	24	22	27	25	2.00
1079378--1079473	20	5.1	20	70	24	73	42	6	13	37	1.70
1079389--1079502	54	2.1	54	100	0	228	42	6	15	35	1.72
1081995--1082075	30	2.7	30	92	0	126	51	9	14	23	1.72
1082510--1082548	2	19.5	2	83	0	51	0	43	7	48	1.31
1082511--1082548	10	3.8	10	100	0	76	0	42	7	50	1.31
1088219--1088252	18	2.0	16	88	11	50	52	11	0	35	1.38
1094225--1094304	35	2.4	34	80	16	94	38	0	1	60	1.05
1094247--1094284	18	2.0	20	85	10	53	39	0	2	57	1.12
1094444--1094497	17	3.2	17	72	0	54	31	0	3	64	1.11
1096029--1096076	21	2.3	21	85	0	60	25	39	12	22	1.89
1096081--1096152	21	3.4	21	88	7	110	18	33	27	20	1.96
1096675--1096771	33	2.9	34	85	3	133	55	4	3	37	1.35
1096673--1096778	34	3.2	33	82	8	133	54	4	2	37	1.36
1097066--1097805	128	5.8	128	91	1	1216	31	20	25	22	1.98
1097066--1097805	383	1.9	384	98	0	1419	31	20	25	22	1.98
1097070--1097810	255	2.9	256	92	1	1218	31	20	25	22	1.98
1097883--1097923	8	5.2	8	82	5	57	36	29	0	34	1.58
1101319--1101480	30	5.4	30	99	0	315	32	23	19	24	1.97
1101319--1101505	90	2.1	91	92	1	313	33	24	19	22	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1101466--1101558	31	3.0	31	79	3	98	33	22	17	26	1.96
1102364--1102415	21	2.5	21	96	0	95	19	32	19	28	1.96
1110318--1110374	19	2.9	19	84	2	69	35	19	8	36	1.83
1110449--1110503	22	2.5	22	84	0	83	16	45	18	20	1.86
1112379--1112477	42	2.4	42	87	0	144	28	33	19	19	1.96
1112842--1112875	4	8.5	4	86	0	50	26	0	2	70	1.01
1113020--1113071	21	2.5	21	90	0	77	21	42	17	19	1.89
1117001--1117052	24	2.2	23	86	3	77	38	15	19	26	1.91
1117884--1117945	27	2.3	27	97	0	115	25	0	30	43	1.55
1117971--1118092	40	3.0	40	77	8	133	37	12	21	28	1.89
1118065--1118155	20	4.5	20	73	14	62	28	13	26	31	1.93
1120248--1120276	3	9.7	3	100	0	58	34	0	0	65	0.93
1122247--1122280	2	17.0	2	100	0	68	50	0	0	50	1.00
1122410--1122439	12	2.5	12	94	0	51	66	3	0	30	1.07
1122484--1122595	39	2.9	38	77	4	107	49	0	15	34	1.51
1122998--1123079	41	2.0	41	100	0	164	21	4	29	43	1.73
1123084--1123128	22	2.0	22	100	0	90	0	26	51	22	1.49
1123090--1123126	18	2.1	18	100	0	74	0	27	51	21	1.48
1124985--1125029	19	2.4	19	100	0	90	35	0	22	42	1.54
1125412--1125500	20	4.4	20	75	12	83	34	10	26	28	1.89
1125430--1125520	40	2.3	40	100	0	182	38	9	28	23	1.86
1125452--1125520	20	3.5	20	73	15	79	40	10	27	21	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1126169--1126236	23	3.0	23	91	0	109	27	23	22	26	1.99
1126362--1126405	23	1.9	23	100	0	88	36	4	13	45	1.64
1129603--1129807	102	2.0	103	87	2	295	26	22	21	29	1.99
1134844--1134958	20	5.7	20	80	6	106	32	24	18	25	1.97
1134841--1134972	61	2.2	61	84	0	174	35	23	16	24	1.95
1135433--1135496	20	3.2	20	86	0	83	15	18	21	43	1.87
1135633--1135687	25	2.2	24	78	15	58	20	7	18	54	1.66
1136816--1136860	18	2.5	18	88	0	72	26	44	15	13	1.83
1137342--1137387	20	2.3	20	84	0	56	36	23	21	17	1.94
1137353--1137397	20	2.3	20	84	3	65	37	20	24	17	1.93
1137381--1137439	19	3.4	19	68	22	65	47	20	20	11	1.81
1137397--1137453	14	3.7	14	72	20	51	50	22	17	8	1.73
1137381--1137459	33	2.4	33	97	0	149	46	21	20	11	1.81
1137459--1137626	19	9.6	18	71	21	108	14	20	21	44	1.86
1137479--1137567	14	5.6	14	71	23	61	12	16	21	49	1.78
1137460--1137584	33	3.8	33	96	0	223	13	19	20	46	1.83
1137569--1137624	20	2.8	19	86	7	76	16	25	23	35	1.94
1140133--1140263	19	7.1	19	80	10	155	45	19	22	12	1.83
1140134--1140264	52	2.4	56	84	8	171	45	19	21	12	1.84
1140259--1140306	20	2.5	19	77	12	53	10	16	27	45	1.80
1140826--1140879	20	2.7	19	88	5	72	22	18	22	37	1.95
1140847--1140896	20	2.5	20	86	3	64	18	26	20	36	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1140893--1140959	21	3.2	21	76	4	73	37	14	22	25	1.93
1140818--1141039	123	1.8	123	81	5	279	30	18	19	31	1.96
1143496--1143590	32	2.9	32	85	9	104	44	18	4	32	1.69
1143520--1143590	32	2.2	32	90	2	117	42	21	2	33	1.67
1143754--1143821	20	3.4	20	79	15	61	77	2	5	13	1.06
1143830--1143888	16	3.6	16	79	4	55	72	6	5	15	1.23
1144627--1144667	19	2.2	19	86	8	57	75	12	0	12	1.05
1144634--1144709	26	2.9	26	71	7	64	75	10	3	10	1.18
1144672--1144717	19	2.3	21	82	14	62	73	4	8	13	1.21
1144783--1144821	2	19.5	2	100	0	78	51	0	0	48	1.00
1145280--1145452	28	5.9	28	70	14	91	45	7	5	41	1.55
1145321--1145390	33	2.1	33	83	0	86	44	5	5	44	1.51
1145362--1145407	23	2.0	24	95	4	85	43	4	4	47	1.42
1145378--1145465	21	4.2	20	71	11	59	47	5	4	42	1.47
1146174--1146997	9	102.5	8	67	18	174	44	4	4	46	1.44
1146133--1146355	69	3.1	71	76	18	210	43	3	2	49	1.33
1146168--1146337	13	12.3	13	73	14	110	43	3	1	51	1.29
1146134--1146301	89	1.9	89	90	7	270	41	4	3	50	1.41
1146173--1146341	15	11.1	15	71	20	88	43	2	1	51	1.27
1146143--1146342	89	2.3	90	85	9	245	43	3	3	50	1.34
1146268--1146438	17	10.9	15	68	18	64	47	3	2	46	1.32
1146174--1146538	35	10.3	35	70	19	165	44	4	3	47	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1146409--1146734	11	30.4	11	66	20	97	41	3	7	48	1.47
1146556--1146655	13	7.3	13	68	22	62	37	2	8	53	1.42
1146935--1147016	28	3.0	28	83	5	96	46	1	1	51	1.16
1146935--1147007	8	8.9	9	80	17	63	45	1	1	52	1.18
1146174--1146997	2	410.0	2	63	20	174	44	4	4	46	1.44
1148370--1148488	57	2.1	56	83	10	145	32	20	18	28	1.96
1148380--1148488	56	1.9	56	85	9	150	32	20	18	29	1.96
1148469--1148517	19	2.6	19	84	9	57	24	28	20	26	1.99
1154245--1154288	21	2.1	21	83	8	54	43	6	6	43	1.57
1158226--1158255	2	15.0	2	100	0	60	50	0	0	50	1.00

Tables:   1   2   3   4   5   6