genome.fa.s1279.2.7.7.80.10.50.1000.5.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

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   

This is table  5  of  29  ( 3433 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)
983349--983395	18	2.7	17	80	6	67	38	12	8	40	1.74
985046--985076	15	2.0	16	93	6	55	9	0	25	64	1.24
986738--986784	18	2.7	17	80	6	67	38	12	8	40	1.74
990111--990157	18	2.7	17	80	6	67	38	12	8	40	1.74
991848--991958	49	2.3	49	96	0	204	30	9	17	42	1.81
991987--992033	18	2.7	17	80	6	67	38	12	8	40	1.74
996484--996516	16	2.1	16	100	0	66	6	24	21	48	1.72
997313--997513	75	2.7	74	77	9	180	52	15	4	27	1.62
998489--998547	21	2.8	21	97	0	109	28	28	20	22	1.98
998704--998736	2	16.5	2	100	0	66	48	0	0	51	1.00
1009727--1009773	17	2.8	17	81	12	60	44	10	6	38	1.65
1010702--1010756	2	27.5	2	100	0	110	50	0	0	49	1.00
1023321--1023353	16	2.1	16	88	5	50	27	0	6	66	1.15
1024376--1024482	17	6.2	17	72	15	67	41	9	10	39	1.71
1026789--1026866	23	3.4	23	70	0	66	44	19	11	24	1.83
1039919--1040262	129	2.6	130	78	9	317	31	17	18	32	1.94
1041155--1041209	17	3.2	17	81	2	65	40	12	9	38	1.75
1042977--1043067	45	2.0	47	81	12	109	58	1	6	34	1.31
1043096--1043138	18	2.5	17	85	7	61	67	2	4	25	1.22
1043022--1043146	62	2.1	59	79	11	128	60	3	3	33	1.29
1044291--1044740	105	4.3	105	92	3	696	22	18	26	32	1.97
1045313--1045480	68	2.5	68	83	4	205	36	8	22	32	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1045510--1045735	37	6.4	37	75	14	199	40	13	18	26	1.88
1045505--1045693	102	1.9	102	88	2	290	40	13	17	28	1.88
1045615--1045735	36	3.3	36	90	2	197	41	13	19	25	1.88
1045413--1045783	138	2.7	139	83	3	450	39	12	19	29	1.88
1046701--1046744	22	2.0	22	91	8	72	27	6	22	43	1.78
1047342--1047400	12	5.0	11	79	18	57	0	11	5	83	0.81
1047332--1047409	22	3.6	22	73	20	67	0	16	6	76	0.98
1047342--1047394	9	6.2	8	78	18	54	0	11	5	83	0.81
1047341--1047402	30	2.0	31	84	9	83	0	14	6	79	0.93
1047366--1047402	18	2.0	19	89	5	58	0	13	8	78	0.96
1047332--1047414	23	3.8	22	73	20	68	1	16	6	75	1.06
1048585--1048615	15	2.1	15	93	0	53	58	12	16	12	1.64
1051729--1051771	18	2.5	17	85	7	61	67	2	4	25	1.22
1058323--1058367	23	2.0	23	95	0	81	53	8	2	35	1.45
1058326--1058375	23	2.2	23	88	0	73	52	10	2	36	1.47
1062853--1062877	12	2.1	12	100	0	50	76	0	8	16	1.02
1063884--1063943	27	2.3	26	85	2	75	51	5	8	35	1.54
1067294--1067320	12	2.2	12	100	0	54	62	7	22	7	1.46
1067342--1067397	28	2.0	27	82	3	67	62	16	16	5	1.50
1071608--1071668	28	2.2	28	82	5	70	63	14	16	4	1.46
1080519--1080604	20	4.2	21	75	10	79	33	19	17	29	1.95
1083471--1083855	190	2.0	191	94	0	682	38	19	7	35	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1092401--1092446	24	2.0	23	83	12	58	26	8	8	56	1.58
1102733--1102884	44	3.5	44	88	1	216	31	25	13	28	1.94
1108522--1108560	3	13.3	3	89	5	62	30	33	0	35	1.58
1110734--1110778	22	2.1	21	87	4	63	40	2	13	44	1.56
1110784--1111022	37	6.4	37	80	9	247	44	4	10	41	1.57
1110784--1111022	75	3.2	73	81	9	272	44	4	10	41	1.57
1110987--1111013	13	2.1	13	100	0	54	44	7	7	40	1.60
1111010--1111062	2	26.5	2	100	0	106	50	0	0	49	1.00
1110788--1111100	38	8.3	38	74	14	217	44	3	9	42	1.53
1111096--1111145	22	2.3	22	82	0	64	48	2	4	46	1.32
1110975--1111124	77	2.0	77	83	7	191	47	3	5	44	1.42
1111118--1111171	29	2.0	26	85	10	72	40	0	9	50	1.35
1118914--1118954	19	2.2	19	83	16	50	14	12	0	73	1.11
1127437--1127486	24	2.1	24	88	0	73	32	24	16	28	1.96
1134855--1134895	20	2.0	22	85	9	59	36	2	0	60	1.10
1137740--1138018	99	2.8	98	82	5	328	37	12	18	32	1.88
1137941--1138246	66	4.6	65	80	5	305	37	15	17	30	1.90
1137935--1138246	132	2.4	130	80	5	340	38	15	16	29	1.90
1138188--1138292	36	2.9	36	92	0	183	40	16	19	23	1.90
1143173--1143328	64	2.4	64	80	5	181	26	19	21	32	1.97
1145447--1145488	12	3.2	13	83	10	59	47	4	11	35	1.61
1145445--1145484	13	3.2	13	85	7	64	47	7	12	32	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1147034--1147101	23	3.0	22	71	16	68	26	22	25	26	2.00
1147026--1147087	21	2.8	22	74	13	56	27	22	20	29	1.99
1154066--1154102	16	2.2	17	90	4	58	62	5	5	27	1.39
1160652--1160683	13	2.5	13	94	0	55	34	15	21	28	1.94
1161999--1162055	21	2.8	21	97	2	107	19	19	22	38	1.93
1164112--1164150	20	2.0	20	100	0	78	41	12	41	5	1.65
1165198--1165259	2	31.0	2	100	0	124	50	0	0	50	1.00
1168539--1168584	22	2.0	23	84	12	60	23	13	8	54	1.66
1169722--1169812	41	2.2	42	84	9	116	73	1	16	8	1.13
1170936--1171022	32	2.7	32	78	8	88	70	1	10	18	1.22
1171002--1171192	4	47.5	4	67	19	60	70	1	2	26	1.05
1171006--1171109	13	7.5	13	70	19	59	74	0	2	23	0.96
1171006--1171097	23	4.1	21	74	19	80	73	0	2	23	0.94
1171138--1171204	20	3.1	21	76	8	73	65	2	1	29	1.16
1172614--1173147	106	5.0	106	88	7	783	22	19	23	34	1.97
1172574--1173147	219	2.7	219	92	3	934	21	19	24	34	1.97
1175620--1175657	14	2.8	14	84	4	51	0	13	5	81	0.85
1175613--1175674	10	5.5	10	77	20	52	1	12	3	82	0.87
1175619--1175674	22	2.4	23	82	11	62	0	14	3	82	0.81
1180158--1180189	15	2.2	15	94	5	57	81	0	6	12	0.87
1180151--1180195	15	2.9	14	84	15	54	77	2	6	13	1.05
1180174--1180247	32	2.3	33	81	9	91	70	1	12	16	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1180304--1180429	42	3.0	42	81	14	154	66	2	1	29	1.13
1180327--1180421	37	2.5	36	75	18	95	65	3	1	30	1.15
1180447--1180497	21	2.4	22	83	9	70	66	1	3	27	1.20
1182498--1182579	42	2.0	42	85	0	110	26	19	21	31	1.97
1182353--1183325	234	4.2	234	90	1	1477	31	15	18	34	1.92
1183198--1183290	42	2.2	41	82	1	114	27	19	21	31	1.97
1182359--1183309	467	2.0	467	90	2	1480	31	15	18	33	1.92
1183587--1183720	48	2.8	48	90	0	205	31	22	14	31	1.94
1183748--1183882	48	2.8	48	89	1	198	28	21	18	31	1.97
1183586--1183973	161	2.4	162	84	2	494	28	24	16	30	1.96
1184332--1184384	3	17.7	3	100	0	106	33	0	0	66	0.92
1185873--1185915	2	21.5	2	100	0	86	48	0	0	51	1.00
1188127--1188198	20	3.5	20	90	3	108	33	18	26	22	1.96
1188268--1188317	21	2.4	21	93	0	82	22	16	40	22	1.91
1188401--1188460	30	2.0	30	90	6	95	43	13	6	36	1.70
1191474--1191513	21	1.9	22	90	10	66	12	5	40	42	1.64
1191604--1191674	20	3.5	21	90	3	101	32	18	28	21	1.96
1191700--1191744	12	4.0	12	75	24	53	24	15	28	31	1.96
1191697--1191815	20	5.8	20	84	8	123	25	16	33	24	1.96
1191696--1191752	28	2.0	28	83	12	73	24	15	29	29	1.96
1191698--1191773	8	10.9	7	74	23	63	26	15	30	27	1.96
1191897--1191954	30	2.0	29	86	10	82	44	18	5	31	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1191897--1191956	29	2.0	30	90	6	95	43	18	6	31	1.76
1195157--1195231	20	3.7	20	91	3	105	33	17	29	20	1.95
1195251--1195351	21	4.8	21	77	12	100	24	17	33	23	1.96
1195432--1195489	30	2.0	29	90	10	91	46	15	5	32	1.68
1195432--1195491	29	2.0	30	93	6	104	45	15	6	33	1.72
1195551--1195598	24	1.9	26	87	8	73	52	4	0	43	1.20
1196872--1196931	16	3.8	16	88	0	84	11	15	28	45	1.81
1196891--1196951	16	3.8	16	86	0	59	13	13	27	45	1.80
1196873--1196952	32	2.5	32	82	8	83	12	13	28	45	1.80
1197652--1197718	31	2.2	30	82	10	75	47	8	1	41	1.44

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