genome.fa.s9585.2.7.7.80.10.50.1000.23.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: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8285662

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   

This is table  23  of  35  ( 4106 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)
5095317--5095349	2	17.5	2	87	12	52	54	0	0	45	0.99
5104424--5104498	2	38.0	2	97	2	143	50	0	0	49	1.00
5108635--5108685	20	2.5	20	79	14	52	39	3	1	54	1.30
5110425--5110454	3	10.0	3	100	0	60	0	33	0	66	0.92
5121207--5121584	186	2.0	190	97	2	719	34	18	15	30	1.93
5131543--5131599	25	2.2	26	93	6	98	14	19	10	56	1.67
5145431--5145501	35	2.0	35	100	0	142	29	22	5	42	1.76
5147125--5147490	187	2.0	179	95	4	660	33	9	12	44	1.74
5153277--5153953	338	2.0	337	98	1	1304	28	20	22	29	1.98
5155283--5155343	20	2.9	21	87	7	79	18	26	34	21	1.96
5174942--5174998	19	2.7	22	78	15	75	31	5	28	35	1.79
5175436--5175619	19	9.5	19	70	12	115	38	18	19	23	1.93
5175421--5175572	40	3.8	40	92	0	241	34	21	21	23	1.96
5175421--5175564	21	7.1	21	69	9	102	34	22	20	22	1.97
5175425--5175637	80	2.8	75	86	3	264	37	19	19	23	1.94
5175436--5175637	75	2.6	79	85	3	259	37	18	19	23	1.94
5178671--5178704	16	2.2	15	89	5	50	44	5	2	47	1.42
5182825--5182877	23	2.3	23	100	0	106	20	0	13	66	1.25
5189653--5189680	2	14.0	2	100	0	56	50	0	50	0	1.00
5193242--5193305	23	2.8	23	90	0	101	35	4	21	37	1.75
5193722--5193785	23	2.8	23	87	0	92	37	4	20	37	1.74
5194201--5194264	23	2.8	23	90	0	101	35	4	21	37	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5192833--5194275	481	3.0	481	98	1	2779	40	7	11	40	1.69
5193892--5194656	381	2.0	381	98	0	1469	42	6	10	39	1.67
5194582--5194645	23	2.8	23	87	0	92	37	4	20	37	1.74
5194273--5195522	476	2.6	477	96	1	2265	41	7	10	40	1.67
5195066--5195121	23	2.4	23	88	5	87	35	5	19	39	1.75
5200247--5200349	33	3.1	33	81	1	107	58	17	14	9	1.63
5200454--5200512	14	4.2	14	86	0	91	62	15	10	11	1.54
5203806--5203902	47	2.1	47	94	0	167	27	19	6	46	1.74
5215413--5215463	23	2.2	23	86	6	68	41	0	1	56	1.10
5218873--5218913	21	1.9	22	85	5	57	24	17	17	41	1.89
5219128--5219173	20	2.3	20	85	7	58	34	17	17	30	1.93
5219226--5219262	11	3.5	11	78	14	51	37	8	10	43	1.69
5219224--5219277	20	2.7	20	97	0	99	40	11	9	38	1.73
5221044--5221136	32	2.8	33	87	11	136	32	3	9	54	1.49
5221044--5221145	34	3.0	34	85	11	147	31	3	8	55	1.49
5225674--5225750	32	2.4	33	93	2	129	11	11	37	38	1.78
5227792--5227821	2	15.0	2	100	0	60	50	0	0	50	1.00
5233143--5233211	23	3.1	22	73	8	59	31	1	5	60	1.29
5236280--5236367	25	3.5	25	98	0	167	31	14	18	35	1.91
5236527--5236559	16	2.1	16	100	0	66	57	24	12	6	1.57
5236625--5236699	10	7.7	10	68	21	52	57	21	10	10	1.62
5236629--5236693	16	4.1	16	89	0	103	58	21	10	9	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5237680--5237733	24	2.2	25	83	9	76	59	14	11	14	1.62
5237700--5237755	14	4.3	14	73	17	57	50	23	16	10	1.76
5237693--5237754	24	2.6	24	86	0	88	51	22	14	11	1.74
5246077--5246126	21	2.4	21	89	0	73	22	12	40	26	1.88
5250870--5250998	66	2.0	66	92	0	213	44	14	10	30	1.80
5255782--5255814	13	2.5	13	85	14	50	54	0	0	45	0.99
5260017--5260053	18	2.1	18	94	0	65	45	5	8	40	1.56
5267502--5267547	18	2.6	18	77	19	51	54	2	0	43	1.12
5269258--5269318	33	1.9	30	90	9	95	65	6	0	27	1.17
5269259--5269321	15	3.9	16	75	24	62	65	7	0	26	1.20
5272861--5272917	19	3.0	19	85	10	64	33	31	19	15	1.93
5272851--5272917	9	7.1	9	75	9	62	32	31	20	14	1.93
5287691--5287722	17	1.9	17	93	6	57	62	0	3	34	1.11
5287741--5287777	17	2.2	17	86	13	51	37	8	0	54	1.30
5295457--5295483	6	4.5	6	100	0	54	0	14	33	51	1.43
5303158--5303187	15	2.0	15	93	0	51	56	0	26	16	1.40
5305731--5305774	20	2.3	19	84	4	52	27	27	27	18	1.98
5310033--5310072	21	1.9	21	89	0	62	10	22	12	55	1.67
5314557--5314628	30	2.4	30	88	0	99	41	1	13	43	1.53
5328642--5328695	25	2.1	25	83	10	65	22	11	27	38	1.88
5333165--5333346	30	6.1	30	98	0	355	33	23	19	23	1.97
5334384--5334420	19	1.9	19	88	0	56	10	29	35	24	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5337561--5337693	30	4.4	30	100	0	266	32	24	20	23	1.98
5338711--5338747	19	1.9	19	88	0	56	10	29	35	24	1.89
5338774--5338815	21	2.0	21	85	0	57	19	19	28	33	1.96
5345765--5345793	12	2.5	12	94	5	51	68	6	17	6	1.34
5357916--5357949	15	2.3	15	94	0	59	47	2	5	44	1.42
5359098--5359133	6	5.8	6	87	6	54	61	2	0	36	1.11
5359098--5359133	13	2.9	12	84	8	54	61	2	0	36	1.11
5361676--5361764	23	3.9	23	93	0	151	35	21	20	22	1.96
5367776--5367802	13	2.1	13	100	0	54	25	7	22	44	1.79
5372324--5372362	18	2.2	17	90	4	60	33	0	0	66	0.92
5373541--5373592	24	2.2	24	82	0	59	48	21	9	21	1.78
5373557--5373702	24	6.1	24	86	6	172	39	19	15	25	1.91
5373637--5373706	12	5.8	12	69	29	51	40	18	15	25	1.90
5373571--5373719	48	3.1	46	77	12	131	41	18	14	25	1.88
5377269--5377329	9	6.9	8	77	18	59	16	1	1	80	0.88
5377290--5377324	10	3.4	10	84	7	52	14	2	0	82	0.77
5377274--5377387	20	5.7	20	68	17	58	15	6	2	75	1.11
5377358--5377420	26	2.4	27	80	15	87	20	9	0	69	1.15
5380974--5381177	36	5.6	36	89	3	302	26	21	12	40	1.88
5380974--5381343	72	5.2	72	82	7	434	25	20	13	40	1.89
5381056--5381305	138	1.8	137	89	2	394	26	20	13	40	1.89
5381185--5381343	37	4.4	36	87	6	232	24	20	15	40	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5381185--5381343	73	2.2	73	91	1	257	24	20	15	40	1.90
5381329--5381451	36	3.5	35	88	7	171	43	17	8	30	1.77
5381955--5382062	37	2.9	37	94	0	180	39	12	12	35	1.81
5382667--5382813	4	36.8	4	68	21	51	23	2	1	72	1.06
5382639--5382722	37	2.2	38	85	10	111	27	2	3	66	1.20
5382656--5382769	43	2.5	44	75	9	115	26	2	2	68	1.16
5382690--5382785	20	4.8	19	72	16	61	21	2	2	73	1.03
5382624--5382814	81	2.4	80	80	6	192	25	2	2	69	1.12
5382770--5382797	11	2.5	11	100	0	56	7	7	0	85	0.73
5388517--5388668	76	2.0	76	94	0	268	37	11	25	25	1.90
5394418--5394592	88	2.0	87	96	3	325	45	16	12	25	1.82
5395299--5395467	60	2.8	58	80	6	178	34	20	5	39	1.77
5396865--5396921	25	2.3	25	93	3	98	45	10	12	31	1.76
5397088--5397146	25	2.4	25	94	0	100	45	10	11	32	1.74
5396754--5397203	225	2.0	223	96	2	841	29	16	14	40	1.87
5399955--5400055	47	2.1	50	87	5	145	27	10	18	42	1.84
5409724--5409799	24	3.3	24	70	26	65	73	1	17	7	1.13
5409723--5409854	17	7.9	16	66	25	53	71	1	19	6	1.16
5409783--5409839	21	2.8	21	77	15	66	66	1	24	7	1.26
5409724--5409851	27	5.1	24	68	23	68	71	1	20	6	1.15
5411180--5411951	102	7.3	108	87	5	589	29	16	26	28	1.97
5411172--5411788	51	11.9	51	91	3	880	29	15	27	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5411800--5411955	55	2.8	55	96	0	276	28	19	25	27	1.98
5411632--5411951	166	1.9	166	80	7	373	28	16	23	31	1.96
5411180--5411955	51	14.7	52	88	6	250	29	16	26	28	1.97
5414528--5414571	2	22.0	2	100	0	88	50	0	0	50	1.00
5420497--5420524	5	5.6	5	100	0	56	78	0	0	21	0.75
5423480--5423555	36	2.1	36	90	0	116	25	21	21	32	1.97
5423666--5423712	23	2.0	23	100	0	94	23	21	34	21	1.97
5426487--5426529	16	2.7	16	88	0	68	37	6	18	37	1.78
5428946--5429044	21	4.8	20	75	6	81	37	23	18	21	1.94
5429011--5429165	40	3.8	40	82	4	186	37	26	18	18	1.93

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