genome.fa.s1.2.7.7.80.10.50.1000.5.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: VEPZ01000001.1 Hibiscus syriacus cultivar Beakdansim tig00000002_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2159989

Tables:   1   2   3   4   5   6   7   8   

This is table  5  of  8  ( 891 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)
1057321--1057368	18	2.7	18	80	9	62	54	0	0	45	0.99
1057481--1057520	20	2.1	19	86	9	55	22	20	5	52	1.65
1057490--1057527	20	1.9	20	88	0	58	26	26	5	42	1.76
1068518--1068618	50	2.0	50	100	0	202	23	13	36	25	1.92
1069220--1069311	45	2.0	45	100	0	184	32	21	28	17	1.96
1072400--1072530	29	4.5	28	80	6	109	41	19	6	32	1.76
1072401--1072498	29	3.4	29	88	2	135	40	19	6	33	1.76
1072540--1072589	23	2.2	23	85	0	64	24	24	36	16	1.94
1078673--1078878	42	4.8	41	82	8	202	33	22	25	18	1.97
1078712--1078878	42	4.0	42	88	3	230	33	22	23	19	1.97
1079811--1079994	29	6.3	29	86	4	194	40	20	5	33	1.75
1079811--1079989	59	3.1	58	82	7	193	41	19	5	33	1.75
1079811--1079994	88	2.1	86	83	7	221	40	20	5	33	1.75
1083680--1083767	45	2.0	45	86	0	122	20	23	25	30	1.98
1091888--1091918	16	1.9	16	100	0	62	58	16	12	12	1.64
1091988--1092052	16	4.1	16	93	0	112	56	21	12	9	1.63
1091984--1092058	10	7.7	10	68	21	52	57	20	12	10	1.64
1093124--1093178	24	2.3	24	90	0	83	58	18	10	12	1.63
1093144--1093199	14	4.3	14	73	17	57	51	26	12	8	1.69
1093137--1093198	24	2.6	24	89	5	90	53	25	11	9	1.67
1094080--1094116	7	5.4	7	87	6	58	16	27	29	27	1.97
1094697--1096427	873	2.0	873	97	0	3257	27	12	19	40	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1102065--1102122	19	3.1	19	94	0	98	18	24	29	27	1.98
1102066--1102124	9	6.3	9	75	7	55	16	27	28	27	1.97
1102143--1102183	7	6.0	7	88	5	66	14	26	26	31	1.95
1102143--1102183	20	2.0	21	90	4	66	14	26	26	31	1.95
1105359--1105383	12	2.1	12	100	0	50	52	0	0	48	1.00
1110149--1110186	19	2.0	19	100	0	76	42	5	21	31	1.75
1118841--1118905	18	3.5	19	87	2	71	78	0	6	15	0.94
1118856--1118905	9	5.4	9	87	2	73	82	0	2	16	0.77
1119189--1119238	24	2.1	23	85	3	64	74	0	4	22	0.99
1119238--1119268	2	15.5	2	100	0	62	51	0	0	48	1.00
1119328--1119352	2	12.5	2	100	0	50	52	0	0	48	1.00
1119544--1119579	18	2.1	18	89	5	56	66	2	5	25	1.27
1119959--1120030	35	2.1	35	94	0	126	30	20	8	40	1.82
1120516--1120738	106	2.1	106	81	3	261	25	20	22	31	1.98
1120670--1120805	69	2.0	67	91	2	218	23	22	19	34	1.96
1120564--1120911	173	2.0	174	89	2	529	25	19	21	33	1.97
1120739--1121320	106	5.6	106	86	6	782	23	18	23	34	1.96
1122179--1122253	36	2.1	36	92	5	125	37	13	24	25	1.91
1122740--1122775	18	2.0	18	94	0	63	41	33	8	16	1.78
1123823--1123884	18	3.6	18	78	8	74	1	11	11	75	1.11
1123834--1123884	16	3.0	17	73	21	61	0	11	9	78	0.97
1127811--1127966	31	5.0	31	88	1	233	20	17	21	40	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1132245--1132400	31	5.0	31	92	0	249	20	17	21	40	1.91
1135120--1135167	4	11.2	4	88	6	60	75	0	4	20	0.97
1135103--1135167	21	3.0	21	82	8	69	73	0	7	18	1.06
1135125--1135179	17	3.4	17	85	9	62	70	0	7	21	1.11
1135208--1135236	2	14.5	2	100	0	58	51	0	0	48	1.00
1135229--1135308	40	2.0	40	83	9	103	56	8	5	30	1.51
1135665--1135780	54	2.2	54	81	10	132	57	1	5	35	1.31
1135786--1135821	18	2.1	18	89	5	56	66	2	5	25	1.27
1143284--1143322	21	1.9	21	89	5	62	35	2	0	61	1.10
1144969--1145003	2	17.5	2	100	0	70	48	0	0	51	1.00
1151440--1151531	46	2.0	46	93	0	157	36	26	14	22	1.92
1154413--1154459	2	23.5	2	100	0	94	51	0	0	48	1.00
1156642--1156692	23	2.3	22	82	3	66	43	3	0	52	1.19
1156649--1156698	23	2.2	23	81	0	55	42	6	0	52	1.26
1158969--1159020	2	26.0	2	100	0	104	50	0	0	50	1.00
1166518--1166561	18	2.4	18	88	0	70	36	13	29	20	1.91
1175084--1175109	10	2.6	10	100	0	52	53	19	0	26	1.45
1185188--1185270	41	2.0	41	100	0	166	39	19	19	21	1.92
1188225--1188267	21	2.0	21	100	0	86	25	13	18	41	1.88
1194954--1195086	35	3.8	35	89	4	196	34	18	14	33	1.90
1194954--1195086	71	1.9	70	87	4	196	34	18	14	33	1.90
1195060--1195305	108	2.3	108	91	3	410	30	15	12	42	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1195937--1196081	64	2.3	62	81	9	166	28	14	15	41	1.86
1196315--1196396	28	2.9	28	83	3	94	24	12	13	50	1.76
1196414--1196572	46	3.7	42	80	9	180	22	34	21	21	1.97
1196407--1196786	134	2.9	132	85	5	456	25	31	18	24	1.98
1196407--1196786	130	2.9	131	84	5	450	25	31	18	24	1.98
1199858--1199934	31	2.5	31	82	0	100	23	11	18	46	1.81
1205216--1205254	17	2.4	17	95	4	71	43	0	5	51	1.24
1206014--1206052	14	2.8	14	84	0	51	35	28	12	23	1.91
1206733--1206763	16	2.0	16	93	6	55	58	6	0	35	1.24
1207552--1207576	3	8.3	3	100	0	50	32	0	0	68	0.90
1209288--1209337	22	2.1	22	85	10	64	40	0	2	58	1.10
1210444--1210501	26	2.2	27	84	3	73	36	5	0	58	1.20
1215927--1215975	24	2.0	24	88	7	73	32	10	8	48	1.66
1216993--1217019	13	2.1	13	100	0	54	37	14	25	22	1.93
1217232--1217386	77	2.0	78	86	7	217	38	10	10	39	1.76
1219228--1219259	3	10.7	3	93	0	55	31	3	0	65	1.08
1223020--1223060	21	2.1	20	86	13	59	36	0	17	46	1.48
1226355--1226478	60	2.1	60	100	0	248	28	19	19	33	1.96
1233804--1233834	2	15.0	2	93	6	53	48	3	0	48	1.17
1236091--1236134	2	22.0	2	100	0	88	50	0	0	50	1.00
1236845--1236898	18	3.1	17	81	5	65	48	3	0	48	1.19
1240488--1240631	72	2.0	72	100	0	288	36	18	18	27	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1242170--1242210	20	2.0	20	100	0	82	39	31	0	29	1.57
1243851--1243895	10	4.3	10	78	10	54	73	8	0	17	1.08
1243844--1243895	22	2.4	22	90	0	77	73	7	0	19	1.07
1243839--1243905	26	2.6	26	83	6	91	74	8	0	16	1.05
1243844--1243910	27	2.4	27	78	11	82	74	7	0	17	1.04
1243918--1243958	15	2.7	16	88	7	59	78	0	0	21	0.76
1243918--1243958	8	5.4	8	83	16	52	78	0	0	21	0.76
1244832--1244926	32	3.1	31	86	13	128	38	6	1	53	1.33
1249574--1249961	185	2.1	185	92	3	642	45	8	3	43	1.50
1250090--1250118	15	1.9	15	100	0	58	24	6	20	48	1.74
1253303--1253370	19	3.3	19	67	25	57	45	23	8	22	1.80
1253295--1253393	43	2.3	43	100	0	198	45	24	10	20	1.81
1253322--1253393	24	3.2	24	67	25	75	43	27	8	20	1.81
1253653--1253714	24	2.6	24	84	0	88	30	20	17	30	1.96
1264035--1264086	20	2.6	20	100	0	104	36	30	9	23	1.87
1264273--1264301	2	14.5	2	100	0	58	48	0	0	51	1.00
1264382--1264429	20	2.4	20	86	6	62	27	20	29	22	1.99
1264416--1264531	20	5.7	20	71	8	54	26	18	25	28	1.98
1264486--1264532	20	2.4	20	82	3	60	27	21	25	25	1.99
1264557--1264646	41	2.2	41	81	0	99	22	14	30	33	1.93
1264599--1264646	20	2.3	20	86	10	62	25	14	25	35	1.94
1265170--1265226	30	1.9	30	85	0	78	45	8	1	43	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1265324--1265414	41	2.3	41	86	7	125	48	2	3	46	1.31
1265267--1265414	39	3.6	40	77	9	147	46	1	4	47	1.29
1271807--1271852	2	23.0	2	100	0	92	50	0	0	50	1.00
1273797--1273834	17	2.3	16	83	16	51	76	2	7	13	1.11
1273806--1273852	19	2.5	19	82	10	60	76	4	10	8	1.13
1273831--1273878	13	3.7	13	94	0	78	81	6	6	6	0.99
1273813--1273902	31	3.0	30	77	18	96	78	5	4	11	1.05
1273849--1273901	18	2.9	18	83	13	72	81	5	1	11	0.94
1273958--1273985	14	2.0	14	100	0	56	50	7	14	28	1.69
1281336--1281375	21	1.9	21	84	0	53	25	12	15	47	1.80

Tables:   1   2   3   4   5   6   7   8