genome.fa.s9639.2.7.7.80.10.50.1000.23.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: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  15077257

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  23  of  62  ( 7398 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)
4975372--4975431	30	2.0	30	90	6	95	46	0	5	48	1.24
4989751--4989801	17	3.0	17	88	0	66	60	3	15	19	1.50
4990764--4990810	22	2.1	23	88	4	69	23	12	25	38	1.90
4998071--4998106	19	2.0	18	89	10	56	19	13	16	50	1.79
4998985--4999021	10	3.7	10	92	0	65	10	5	18	64	1.43
4999194--4999237	10	4.4	10	85	0	61	18	11	9	61	1.55
5004560--5004617	24	2.5	24	85	2	82	29	22	22	25	1.99
5004581--5004685	48	2.2	47	83	5	122	28	23	24	22	1.99
5004610--5004685	23	3.2	23	78	14	82	28	21	25	25	1.99
5005480--5005527	20	2.3	21	82	13	55	20	31	14	33	1.93
5010758--5010862	24	4.5	23	77	12	97	31	25	19	23	1.98
5010751--5010866	47	2.5	48	83	9	134	31	25	18	23	1.97
5010771--5010862	24	3.9	23	78	14	107	32	27	17	22	1.96
5011631--5011680	21	2.5	20	80	9	57	34	24	10	32	1.88
5013294--5013368	22	3.5	21	72	17	64	69	5	2	22	1.22
5013361--5013407	13	3.5	13	80	8	58	57	14	2	25	1.49
5013894--5013969	21	3.6	21	83	0	89	21	15	28	34	1.94
5014771--5014842	37	1.9	37	100	0	144	38	18	22	20	1.93
5015938--5016021	22	3.8	22	91	0	132	35	5	16	41	1.73
5018026--5018065	21	1.9	21	84	0	53	42	2	0	55	1.13
5018030--5018076	25	1.9	24	86	4	67	42	2	0	55	1.12
5024668--5024944	137	2.0	138	99	0	547	22	23	21	32	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5026111--5026149	14	2.7	15	80	19	55	51	5	0	43	1.24
5026299--5026377	2	40.0	2	97	2	151	49	0	0	50	1.00
5028541--5028612	36	2.0	36	100	0	144	30	25	5	38	1.78
5030817--5030904	7	12.4	7	70	11	63	38	1	6	53	1.35
5031369--5031635	45	6.0	45	85	3	288	29	20	9	39	1.85
5031377--5031635	135	1.9	134	82	5	317	28	20	10	40	1.85
5031603--5031669	34	1.9	35	84	3	91	28	25	8	37	1.86
5031993--5032033	21	1.9	22	90	5	66	24	31	24	19	1.98
5032028--5032062	11	3.2	11	87	0	52	25	28	17	28	1.97
5032678--5032758	21	3.9	21	95	3	146	27	29	19	23	1.98
5032678--5032758	41	2.0	42	95	2	146	27	29	19	23	1.98
5035600--5035624	2	12.5	2	100	0	50	52	0	0	48	1.00
5038411--5038467	24	2.4	24	90	0	87	57	12	8	21	1.61
5045644--5045924	153	1.8	152	89	6	444	37	29	12	20	1.90
5045948--5046065	48	2.5	47	79	4	121	50	16	11	21	1.76
5045982--5046065	24	3.5	24	85	1	107	51	16	11	20	1.76
5050728--5051034	90	3.4	90	88	0	434	30	21	9	38	1.85
5050706--5051033	135	2.4	135	82	2	435	31	21	9	38	1.84
5050728--5051073	45	7.7	46	87	3	336	30	22	9	37	1.86
5051011--5051162	79	1.9	79	86	2	216	29	25	9	36	1.87
5051755--5051798	20	2.2	20	100	0	88	25	27	18	29	1.98
5051755--5051806	20	2.6	20	93	0	77	26	28	15	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5052659--5052856	7	27.4	7	73	23	119	40	3	1	54	1.27
5052664--5052928	5	51.6	5	77	14	199	40	3	3	53	1.33
5058058--5058121	28	2.4	27	80	12	78	53	15	3	28	1.57
5082457--5082504	24	2.0	24	91	0	78	35	4	35	25	1.75
5087052--5089621	139	18.6	139	85	1	3281	34	16	20	27	1.94
5087052--5089621	967	2.7	966	85	3	3389	34	16	20	27	1.94
5094962--5094994	17	1.9	17	93	0	57	18	24	33	24	1.97
5095169--5095232	24	2.7	23	82	7	74	50	1	0	48	1.10
5103054--5103110	2	29.0	2	96	3	107	49	0	0	50	1.00
5108218--5108951	2	409.5	2	66	26	343	41	3	2	52	1.31
5108338--5109441	5	217.2	5	80	14	875	40	5	0	53	1.29
5108218--5109438	19	68.7	18	74	18	493	40	5	1	52	1.33
5108650--5109223	24	23.6	24	79	12	187	39	9	0	50	1.36
5111123--5111174	26	2.0	26	82	10	63	42	3	0	53	1.19
5111182--5111240	25	2.4	24	83	5	73	42	3	3	50	1.35
5111302--5111379	30	2.6	30	89	2	111	55	7	7	29	1.56
5111976--5112016	21	1.9	22	85	5	57	58	7	0	34	1.26
5112148--5112398	116	2.1	115	84	6	308	33	19	19	27	1.96
5114837--5114960	5	25.4	5	93	4	218	58	0	0	40	1.03
5121176--5121339	45	3.8	44	71	16	144	18	14	14	53	1.73
5121152--5121322	85	2.0	86	93	5	294	18	14	14	52	1.75
5121273--5121346	14	6.1	14	68	28	62	16	13	14	55	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5121186--5121329	10	13.5	10	70	12	65	18	13	13	54	1.70
5122398--5122447	26	2.0	25	84	11	66	60	0	2	38	1.09
5125403--5125435	15	2.2	15	100	0	66	75	0	0	24	0.80
5126560--5126614	19	2.8	19	80	5	65	34	23	16	25	1.95
5128102--5128311	103	2.0	103	83	5	264	41	12	8	36	1.74
5131332--5131364	16	2.1	15	94	5	57	48	15	0	36	1.45
5135610--5135669	21	2.7	22	75	12	61	56	6	23	13	1.60
5137335--5137377	18	2.4	19	84	7	54	18	6	4	69	1.29
5137747--5137875	32	4.0	32	82	2	134	27	17	15	39	1.90
5142241--5142278	20	1.9	20	88	0	58	26	26	5	42	1.76
5144374--5144445	33	2.2	33	87	5	101	27	12	26	33	1.92
5144946--5145056	7	16.7	7	68	22	53	50	1	3	44	1.30
5145193--5145247	21	2.7	19	79	20	58	49	1	3	45	1.30
5145231--5145296	29	2.3	28	80	12	71	48	6	1	43	1.36
5145262--5145304	18	2.3	18	84	8	50	48	4	2	44	1.36
5145435--5145503	2	35.0	2	94	2	122	49	1	0	49	1.09
5146154--5146195	20	2.1	20	100	0	84	16	35	28	19	1.93
5146885--5146926	7	6.0	7	85	0	57	40	38	2	19	1.64
5146957--5146995	20	2.0	20	100	0	78	46	5	0	48	1.24
5147111--5147243	17	7.0	18	74	18	78	45	4	4	45	1.44
5147132--5147254	13	9.2	13	70	16	56	46	4	2	46	1.37
5147132--5147194	25	2.5	25	92	2	99	50	1	0	47	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5147132--5147194	2	32.0	2	84	9	85	50	1	0	47	1.10
5147284--5147330	21	2.2	21	77	7	51	40	6	6	46	1.55
5147363--5147455	37	2.6	35	77	6	105	41	3	8	46	1.50
5148109--5148345	118	2.0	118	98	0	456	30	13	18	37	1.89
5148955--5148996	19	2.2	19	83	8	50	9	9	0	80	0.89
5152175--5152382	99	2.1	99	84	4	269	35	16	17	30	1.92
5153323--5153546	64	3.6	62	83	12	291	34	20	13	30	1.92
5153323--5153546	121	1.9	121	89	1	351	34	20	13	30	1.92
5153630--5154221	124	4.8	124	89	0	884	35	25	13	26	1.92
5154303--5154461	85	1.9	85	84	2	212	32	19	20	27	1.97
5156596--5156687	9	10.1	9	70	17	66	21	4	1	72	1.08
5157375--5157445	34	2.1	34	84	2	90	25	26	15	32	1.95
5157648--5157705	20	2.8	20	84	5	80	13	10	39	36	1.79
5157828--5157928	34	2.9	35	81	11	100	24	20	29	24	1.99
5157849--5157928	19	4.4	19	81	12	105	23	21	32	22	1.98
5161211--5161252	20	2.0	21	90	4	68	23	23	35	16	1.95
5161277--5161360	19	4.6	19	78	13	95	27	21	27	23	1.99
5163235--5163384	3	50.7	3	94	5	270	0	32	0	68	0.90
5164374--5164444	34	2.1	33	86	2	97	23	28	15	32	1.95
5165105--5165159	21	2.5	23	88	5	78	50	1	1	45	1.22
5165921--5165994	6	12.5	6	79	2	78	41	52	4	1	1.28
5165902--5165990	12	7.5	11	71	14	61	41	50	3	4	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5165921--5165994	18	4.2	18	87	1	87	41	52	4	1	1.28
5168451--5168492	20	2.1	20	100	0	84	26	19	19	35	1.95
5173834--5173914	23	3.9	21	78	9	85	28	20	19	30	1.97
5176555--5176596	18	2.3	19	91	4	68	30	23	21	23	1.99
5177172--5177213	20	2.1	20	95	0	75	26	14	9	50	1.73
5177612--5177650	11	3.5	11	83	13	53	41	7	5	46	1.55
5177892--5177945	24	2.2	24	90	6	83	51	7	1	38	1.41
5178156--5178197	16	2.7	16	85	3	59	42	9	19	28	1.82
5182305--5182421	40	2.9	40	79	5	119	18	39	12	29	1.88
5184108--5184134	6	4.5	6	100	0	54	14	14	33	37	1.88

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