genome.fa.s1465.2.7.7.80.10.50.1000.21.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: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11160956

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   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   

This is table  21  of  55  ( 6520 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)
4013324--4013409	40	2.2	40	81	12	106	53	2	3	40	1.31
4013563--4013858	35	8.4	34	76	7	259	24	22	16	36	1.94
4013563--4013834	71	3.8	71	81	0	337	25	22	16	36	1.94
4013563--4013835	142	1.9	142	89	1	422	25	21	16	36	1.94
4013595--4013865	142	1.9	142	87	3	368	25	22	15	36	1.94
4014059--4014586	62	8.6	62	85	3	608	34	16	22	26	1.95
4014059--4014575	247	2.1	244	84	3	662	35	16	22	26	1.95
4022991--4023039	25	1.9	25	87	4	71	12	10	30	46	1.74
4022991--4023047	24	2.4	25	77	8	66	17	8	28	45	1.78
4023041--4023096	5	10.6	5	76	16	51	57	0	1	41	1.09
4026405--4026640	130	1.8	131	87	4	352	40	13	11	34	1.80
4029330--4029985	232	2.8	231	87	1	936	33	17	15	32	1.92
4040119--4040383	131	2.0	131	89	2	408	39	14	11	33	1.83
4041193--4041447	110	2.3	110	84	4	313	46	19	15	19	1.84
4042166--4042213	23	2.1	23	92	0	78	4	12	41	41	1.62
4042169--4042227	23	2.6	23	86	0	73	5	16	44	33	1.70
4042203--4042268	29	2.3	29	84	5	80	12	9	37	40	1.74
4042552--4042989	133	3.3	132	80	7	499	31	18	19	30	1.96
4042493--4042989	133	3.7	133	79	7	489	30	18	19	30	1.96
4066908--4067023	43	2.6	45	77	13	105	63	4	12	19	1.44
4068867--4068901	3	11.7	3	93	0	61	37	0	0	62	0.95
4071991--4072055	31	2.1	31	97	0	121	27	40	1	30	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4072033--4072059	12	2.2	12	100	0	54	29	33	0	37	1.58
4074252--4074305	23	2.5	22	85	11	67	25	25	25	22	2.00
4074259--4074333	23	3.3	22	80	9	71	22	28	28	21	1.99
4080484--4080519	2	18.0	2	100	0	72	50	0	0	50	1.00
4085949--4086014	15	4.5	15	73	17	66	40	1	1	56	1.18
4085949--4086041	44	2.1	43	84	5	116	43	2	2	52	1.25
4087500--4087563	29	2.2	28	78	13	67	70	3	4	21	1.20
4092456--4092514	29	2.0	29	93	0	100	47	16	11	23	1.80
4097143--4097201	29	2.0	29	93	0	100	49	16	11	22	1.78
4112250--4112285	18	1.9	19	88	5	56	22	11	2	63	1.39
4117621--4117669	21	2.3	21	86	10	64	65	0	4	30	1.11
4117621--4117683	22	2.8	22	81	13	67	61	0	6	31	1.21
4117638--4117683	24	1.9	25	86	8	69	63	0	8	28	1.24
4122087--4122246	23	6.7	23	86	6	133	26	22	25	26	2.00
4122129--4122166	13	2.9	13	96	0	67	31	31	21	15	1.94
4122161--4122246	11	7.5	11	78	21	97	23	18	25	32	1.97
4122162--4122271	23	4.8	23	95	0	193	23	18	24	33	1.97
4122173--4122262	12	7.8	12	75	20	93	22	16	24	36	1.94
4124592--4124654	11	5.9	11	73	14	51	38	1	1	58	1.17
4129080--4129131	25	2.1	25	100	0	104	40	7	23	28	1.82
4133304--4133358	24	2.3	24	78	6	58	58	10	3	27	1.49
4133796--4133894	39	2.5	40	91	1	155	20	24	12	43	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4134531--4134634	52	2.0	53	86	5	149	45	18	8	27	1.79
4134705--4134977	55	4.8	55	78	7	260	43	13	9	33	1.75
4136819--4136947	9	13.4	10	70	21	64	2	18	1	77	0.96
4136819--4136947	51	2.5	52	82	8	156	2	18	1	77	0.96
4136820--4136948	11	11.9	11	72	17	83	2	18	1	77	0.96
4136908--4136971	24	2.7	24	85	11	87	6	17	3	73	1.17
4141332--4141377	16	2.8	17	77	12	51	45	4	0	50	1.21
4143050--4143153	3	34.0	3	84	3	127	59	2	0	37	1.12
4143044--4143162	15	7.8	15	73	21	81	57	2	0	39	1.12
4143126--4143169	15	2.9	15	90	6	54	59	0	0	40	0.98
4143284--4144840	76	20.4	76	97	0	2835	35	22	19	22	1.96
4143284--4144840	229	6.8	228	97	0	2853	35	22	19	22	1.96
4143284--4144840	305	5.1	304	97	0	2853	35	22	19	22	1.96
4145885--4146097	54	3.9	54	86	5	293	23	21	15	38	1.92
4155028--4155070	9	4.9	9	81	13	54	67	0	2	30	1.03
4155065--4155107	18	2.5	17	85	14	61	74	0	4	20	1.00
4155791--4155825	18	1.9	18	88	0	52	40	2	2	54	1.30
4157129--4157232	3	34.0	3	84	3	118	58	2	0	38	1.13
4157205--4157248	15	2.9	15	90	6	54	59	0	0	40	0.98
4179758--4179809	24	2.2	24	82	6	61	9	13	26	50	1.72
4179768--4179823	14	4.3	14	78	17	66	8	14	25	51	1.70
4179769--4179843	24	3.1	24	86	3	89	12	12	21	54	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4180569--4180635	16	4.3	16	90	3	93	11	10	17	59	1.60
4180567--4180627	32	1.9	32	93	0	104	9	13	21	55	1.66
4180697--4180729	16	2.1	16	100	0	66	6	12	24	57	1.57
4181955--4182041	22	4.0	22	100	0	174	22	27	22	26	2.00
4184262--4184297	2	18.0	2	100	0	72	50	0	0	50	1.00
4198404--4198433	11	2.7	11	89	0	51	33	13	20	33	1.91
4201592--4201675	30	2.9	28	77	11	89	44	8	26	21	1.80
4203443--4203509	20	3.3	20	69	24	59	43	7	28	20	1.79
4213074--4213647	284	2.0	284	94	0	1015	38	10	10	40	1.74
4215082--4215113	15	2.1	15	100	0	64	12	34	18	34	1.89
4215785--4215821	18	2.1	18	100	0	74	45	0	5	48	1.25
4242143--4242174	3	10.7	3	100	0	64	68	0	31	0	0.90
4248000--4248040	21	1.9	22	95	5	75	39	14	19	26	1.90
4248667--4248719	19	2.8	20	77	5	65	41	1	1	54	1.22
4248859--4248896	17	2.2	17	86	9	51	42	0	0	57	0.98
4248902--4248945	19	2.3	19	84	7	54	43	0	2	54	1.12
4248819--4248954	57	2.4	56	73	15	134	41	0	5	52	1.29
4249225--4249329	29	3.5	29	84	6	129	33	10	11	44	1.75
4249225--4249326	31	3.4	30	85	8	127	32	9	11	46	1.73
4249248--4249326	16	5.2	15	73	7	61	27	10	12	49	1.73
4250564--4250611	18	2.6	19	86	6	62	45	8	2	43	1.45
4250599--4250658	30	2.0	30	90	3	93	35	6	0	58	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4252818--4252858	17	2.4	17	91	0	64	12	29	29	29	1.93
4255362--4255418	24	2.4	24	78	0	69	21	15	15	47	1.82
4255362--4255477	55	2.1	55	85	0	151	18	12	17	51	1.75
4255416--4255477	24	2.6	25	75	17	67	16	9	17	56	1.66
4257032--4257076	18	2.6	18	83	13	58	57	0	2	40	1.11
4257192--4257219	8	3.5	8	100	0	56	89	0	0	10	0.49
4258692--4258776	3	29.0	3	79	9	95	65	0	1	32	1.00
4259148--4259585	122	3.7	120	85	9	560	26	20	14	39	1.91
4259881--4259969	22	4.0	22	81	5	108	37	13	15	33	1.87
4259881--4259969	44	2.0	44	89	4	135	37	13	15	33	1.87
4260584--4260621	18	2.1	18	90	0	58	55	5	5	34	1.45
4265476--4265504	14	2.0	15	93	6	51	34	6	6	51	1.55
4269722--4269759	3	12.7	3	100	0	76	65	0	0	34	0.93
4271174--4271290	3	40.0	3	77	8	116	63	0	1	35	1.05
4271611--4271776	83	2.0	83	95	0	296	27	9	34	28	1.88
4284879--4285054	84	2.1	83	81	7	198	27	17	22	32	1.96
4285077--4285237	81	2.0	82	84	8	213	31	14	18	35	1.91
4285466--4285525	21	2.9	21	87	0	84	15	50	10	25	1.74
4288389--4288691	42	7.1	42	84	2	356	23	24	18	33	1.97
4288412--4288695	85	3.3	83	84	3	354	22	24	18	34	1.96
4290569--4290600	16	2.0	16	100	0	64	43	6	25	25	1.77
4290883--4290934	22	2.4	22	100	0	104	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4293365--4293395	13	2.4	13	94	0	53	51	12	6	29	1.65
4294837--4295273	217	2.0	217	93	0	739	38	15	25	20	1.92
4295681--4295707	12	2.2	12	100	0	54	62	0	0	37	0.95
4298064--4298566	124	4.0	124	85	5	613	26	14	24	34	1.94
4298351--4298757	190	2.1	190	83	3	532	26	15	24	33	1.95
4298521--4298629	34	3.3	34	67	10	98	26	13	22	36	1.92
4298489--4298633	66	2.2	66	86	2	202	27	14	22	35	1.93
4301604--4301629	3	8.7	3	100	0	52	69	0	0	30	0.89
4302866--4302899	14	2.5	13	86	9	50	67	2	8	20	1.31
4302857--4302896	21	2.0	20	85	14	55	65	5	10	20	1.42

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   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55