genome.fa.s190.2.7.7.80.10.50.1000.22.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: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  14308945

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   56   57   58   59   60   61   62   

This is table  22  of  62  ( 7381 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)
5268275--5268463	76	2.6	75	86	5	253	57	13	0	28	1.40
5268319--5268500	76	2.4	75	80	6	224	57	10	2	29	1.44
5273932--5273972	19	2.2	19	90	0	64	58	12	0	29	1.34
5276000--5276032	16	1.9	18	88	11	52	48	3	9	39	1.50
5279670--5279753	41	2.0	41	97	0	159	39	11	15	33	1.84
5281174--5281215	21	2.0	20	86	13	59	45	14	16	23	1.84
5283465--5283521	14	4.1	14	100	0	114	29	35	7	28	1.83
5297203--5297296	24	4.0	24	80	2	109	28	15	19	36	1.93
5297368--5297482	57	2.0	57	93	0	194	13	20	31	34	1.91
5303448--5303477	15	2.0	15	100	0	60	60	13	13	13	1.60
5304464--5304604	71	2.0	70	81	4	167	29	2	13	54	1.50
5314157--5314216	22	2.7	23	78	5	68	40	25	16	18	1.91
5320422--5320494	31	2.4	31	85	0	101	35	31	23	9	1.87
5331172--5331254	23	3.7	23	85	7	100	21	26	28	22	1.99
5338473--5338515	17	2.6	17	85	3	52	32	18	18	30	1.95
5344047--5344099	17	3.1	17	100	0	106	22	30	5	41	1.77
5344484--5344576	3	32.7	3	81	10	115	34	1	3	61	1.19
5347983--5348090	47	2.2	48	91	3	173	27	12	24	35	1.92
5355288--5355364	32	2.5	31	85	4	109	32	29	23	14	1.94
5359884--5361653	232	7.6	233	85	2	2247	32	16	17	32	1.93
5362006--5362296	134	2.2	133	83	4	363	32	21	15	29	1.94
5363148--5363220	30	2.4	30	90	0	119	23	26	20	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5366567--5366615	3	16.7	3	78	4	55	34	2	2	61	1.19
5367005--5367039	18	1.9	18	88	0	52	60	34	0	5	1.21
5372149--5372206	28	2.1	28	96	0	107	48	5	13	32	1.65
5378458--5378565	24	4.6	24	67	19	66	56	13	0	29	1.38
5378447--5378633	69	2.6	68	83	11	200	57	12	1	28	1.43
5379348--5379412	14	4.6	14	77	7	69	20	21	29	29	1.98
5380607--5380655	24	2.0	24	100	0	98	42	12	12	32	1.79
5406071--5407821	81	21.8	81	85	2	2260	29	21	11	37	1.89
5406059--5407821	323	5.5	322	86	2	2337	29	21	11	37	1.89
5407809--5408141	68	4.9	68	85	0	423	30	25	11	32	1.91
5408594--5408636	22	2.0	22	90	0	68	11	18	4	65	1.42
5415729--5415870	56	2.6	55	84	8	175	35	21	9	33	1.86
5420340--5420733	81	4.9	81	88	3	508	29	20	11	37	1.89
5420340--5420733	162	2.4	162	87	2	576	29	20	11	37	1.89
5420790--5421266	204	2.3	204	93	0	812	28	24	15	31	1.96
5420788--5421266	68	7.0	68	87	0	699	28	24	15	31	1.96
5437127--5437166	14	2.9	14	88	0	62	15	12	45	27	1.82
5442514--5442547	14	2.5	13	86	13	50	35	26	2	35	1.72
5444109--5444154	20	2.3	19	85	14	58	26	15	8	50	1.73
5457235--5457298	27	2.4	27	97	0	119	32	14	9	43	1.77
5460929--5461028	44	2.3	44	89	3	148	30	20	18	32	1.96
5467319--5467382	32	2.0	33	90	3	103	26	17	28	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5467479--5467524	24	1.9	24	95	0	83	43	15	13	28	1.83
5467503--5467591	44	2.0	46	91	4	146	38	8	21	31	1.84
5483461--5483780	54	5.9	54	82	3	374	30	18	19	31	1.96
5483461--5483780	108	3.0	108	85	2	428	30	18	19	31	1.96
5483465--5483772	162	1.9	163	88	2	467	30	18	19	31	1.96
5485561--5485606	20	2.3	19	85	14	58	26	15	8	50	1.73
5496738--5497020	140	2.0	140	100	0	566	36	4	24	35	1.75
5497527--5497804	59	4.7	59	82	3	317	36	10	23	29	1.89
5497527--5497837	118	2.6	118	82	3	349	36	11	23	29	1.89
5504255--5504301	19	2.5	19	90	10	71	25	21	25	27	1.99
5504703--5504981	59	4.7	59	77	7	253	37	9	21	30	1.86
5504708--5505028	118	2.7	118	77	5	301	38	10	20	30	1.87
5508597--5508642	24	1.9	24	86	0	65	43	13	15	28	1.83
5509951--5510403	106	4.4	105	83	3	537	33	24	18	23	1.97
5511344--5511374	2	15.5	2	100	0	62	48	0	0	51	1.00
5515696--5515728	14	2.4	14	94	0	57	42	18	6	33	1.75
5516044--5516091	9	5.3	9	82	7	62	83	2	14	0	0.74
5516044--5516091	18	2.7	18	90	6	71	83	2	14	0	0.74
5516038--5516099	30	2.1	30	85	11	83	82	3	14	0	0.80
5516041--5516100	19	3.2	19	77	15	70	83	3	13	0	0.77
5516041--5516120	13	6.2	13	74	9	58	81	5	11	2	0.95
5516733--5516802	22	3.2	22	95	0	131	37	25	14	22	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5517641--5518787	106	10.9	106	86	2	1496	33	24	17	23	1.96
5517628--5518787	211	5.5	212	87	2	1515	33	24	17	23	1.96
5519518--5519622	37	2.8	37	83	0	138	40	15	12	31	1.84
5520141--5520190	21	2.6	19	76	14	57	18	10	0	72	1.12
5520995--5521033	19	2.1	19	100	0	78	5	33	15	46	1.68
5533241--5533401	36	4.5	35	69	17	118	42	1	9	45	1.47
5533231--5533401	70	2.4	71	76	11	170	43	2	9	45	1.49
5533266--5533389	34	3.6	34	82	8	146	44	2	10	42	1.52
5533277--5533599	38	8.6	38	78	13	268	45	2	8	42	1.48
5533311--5533628	156	2.1	151	82	9	387	44	1	8	44	1.46
5533607--5533641	12	3.1	12	88	12	56	40	0	0	60	0.97
5533632--5533679	10	4.9	10	90	10	73	18	0	0	81	0.70
5533638--5533677	13	3.2	12	86	10	53	17	0	0	82	0.67
5534629--5534709	15	5.6	14	75	13	58	20	7	0	71	1.10
5534667--5534725	15	4.2	15	75	16	54	23	5	0	71	1.06
5534672--5534764	14	7.0	13	75	20	61	17	6	1	75	1.07
5534699--5534763	20	3.2	20	72	8	60	15	4	1	78	0.99
5536474--5536500	6	4.5	6	100	0	54	14	0	0	85	0.61
5537107--5537440	54	6.2	54	89	1	465	27	18	20	33	1.96
5539048--5539091	14	3.1	14	80	9	54	27	29	20	22	1.99
5543326--5543358	12	2.8	12	100	0	66	51	0	42	6	1.26
5544492--5544548	24	2.4	25	85	5	73	47	1	5	45	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5544586--5544628	11	4.1	11	88	5	63	53	2	0	44	1.13
5544522--5544619	20	4.8	20	74	7	81	47	6	4	41	1.47
5544662--5544745	33	2.6	33	83	12	111	45	3	5	45	1.45
5544665--5544745	15	5.3	15	68	24	53	44	3	6	45	1.46
5544842--5544913	20	3.5	20	75	17	67	44	9	5	40	1.61
5544845--5544929	22	4.0	21	77	11	77	47	9	5	37	1.60
5546368--5546397	13	2.3	13	100	0	60	53	6	0	40	1.27
5547441--5547473	16	2.1	16	94	0	57	39	0	15	45	1.46
5547500--5548113	55	11.2	55	86	3	774	36	19	17	26	1.94
5547511--5548092	219	2.7	220	89	1	846	36	19	17	26	1.94
5547500--5548104	274	2.2	275	86	1	831	36	19	17	26	1.94
5570997--5571061	21	3.3	21	64	27	61	40	9	9	41	1.69
5570983--5571065	37	2.2	37	97	0	157	40	8	10	39	1.70
5572075--5572120	2	23.0	2	100	0	92	50	0	0	50	1.00
5572120--5572158	2	19.5	2	89	0	60	2	2	43	51	1.29
5572323--5572393	24	3.0	24	82	0	97	50	18	11	19	1.76
5572325--5572393	12	5.8	12	69	6	50	50	18	11	18	1.76
5572321--5572414	48	2.0	48	85	8	129	48	15	10	24	1.77
5577000--5577110	48	2.3	48	83	6	136	48	17	11	22	1.79
5577003--5577108	24	4.4	24	70	11	83	47	17	12	22	1.81
5579464--5579503	10	3.8	10	81	12	53	22	27	27	22	1.99
5579488--5579526	17	2.3	17	86	8	53	30	28	25	15	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5590758--5590970	106	2.0	106	91	0	345	27	14	17	40	1.88
5593521--5593551	11	2.8	11	100	0	62	25	6	9	58	1.54
5598904--5598950	21	2.3	21	88	3	69	17	17	23	42	1.88
5598976--5599019	22	2.0	23	83	16	58	22	13	22	40	1.89
5602014--5602063	19	2.5	20	90	3	75	30	16	28	26	1.96
5602371--5602817	58	7.7	58	87	5	622	33	12	19	34	1.89
5602371--5602817	230	1.9	231	91	2	738	33	12	19	34	1.89
5607022--5607074	25	2.1	25	96	0	97	26	13	18	41	1.87
5609012--5609083	19	3.5	20	83	9	92	31	13	25	29	1.94
5609413--5609860	58	7.7	58	84	2	544	33	12	20	34	1.90

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   56   57   58   59   60   61   62