genome.fa.s8087.2.7.7.80.10.50.1000.19.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: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8279816

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   

This is table  19  of  37  ( 4336 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)
4288620--4288668	22	2.3	21	80	10	55	24	14	40	20	1.89
4288627--4288670	22	2.0	22	90	0	70	20	15	43	20	1.88
4288837--4289015	41	4.4	41	78	2	164	24	16	24	35	1.95
4288857--4288970	20	5.7	20	78	6	104	23	16	27	32	1.96
4288911--4289028	41	2.9	41	84	5	150	22	19	22	36	1.95
4288965--4289052	20	4.3	20	71	9	70	25	19	17	38	1.92
4289042--4289094	21	2.5	20	79	8	70	33	18	26	20	1.96
4293370--4293398	5	5.8	5	100	0	58	79	20	0	0	0.74
4293932--4293968	19	1.9	19	94	0	65	35	8	21	35	1.83
4293945--4294093	74	2.0	74	100	0	298	44	8	14	32	1.75
4298438--4298474	19	1.9	19	94	0	65	35	8	21	35	1.83
4298451--4298599	74	2.0	74	100	0	298	44	8	14	32	1.75
4299380--4299425	21	2.2	21	88	7	67	73	2	6	17	1.14
4299380--4299438	10	5.7	10	76	7	55	71	3	5	20	1.20
4299962--4300016	19	2.8	19	81	8	58	21	5	3	69	1.25
4299962--4300017	10	5.7	10	78	4	60	23	5	3	67	1.27
4304614--4304659	20	2.2	21	84	7	58	54	2	2	41	1.25
4304974--4305004	2	16.0	2	93	6	55	51	0	0	48	1.00
4311943--4312002	31	1.9	31	86	0	84	30	6	5	58	1.45
4312802--4312832	16	1.9	16	93	0	53	32	3	0	64	1.09
4318629--4318669	9	5.0	8	83	16	57	60	0	0	39	0.96
4318605--4318669	33	2.0	33	84	6	87	60	1	0	38	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4318628--4318680	17	3.2	16	86	7	70	60	0	0	39	0.97
4318611--4318679	26	2.6	26	75	15	70	62	1	0	36	1.04
4323115--4323248	29	4.6	29	98	0	259	19	45	27	7	1.77
4323263--4323372	30	3.7	30	87	0	175	22	47	19	10	1.80
4324020--4324063	21	2.1	21	91	0	70	29	0	15	54	1.42
4324040--4324093	28	1.9	28	96	0	99	29	0	12	57	1.36
4327161--4327511	60	5.8	60	93	2	607	39	0	13	45	1.50
4327518--4327551	7	4.9	7	100	0	68	55	14	14	14	1.69
4327547--4327684	26	5.5	26	73	17	96	44	2	10	42	1.50
4327547--4327765	98	2.2	98	96	1	404	43	1	10	44	1.48
4327618--4327765	26	5.9	26	73	12	121	43	2	9	45	1.48
4327907--4327971	14	5.2	13	75	17	50	38	7	7	46	1.61
4327918--4327951	11	3.2	11	83	8	52	38	8	5	47	1.59
4327918--4327961	21	2.1	21	86	0	61	40	9	4	45	1.56
4327956--4327988	17	1.9	17	100	0	66	36	6	9	48	1.60
4330137--4330167	15	2.1	14	94	5	53	54	6	0	38	1.26
4330142--4330188	16	3.0	16	84	9	53	59	10	0	29	1.31
4330224--4330305	34	2.5	34	84	9	100	48	12	0	39	1.41
4330346--4330437	45	2.0	48	83	12	120	46	11	0	41	1.41
4330346--4330450	47	2.2	48	81	13	119	47	12	0	40	1.41
4330418--4330506	41	2.2	40	78	8	90	46	10	1	42	1.45
4330542--4330580	16	2.3	18	86	8	55	56	5	0	38	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4330609--4330643	12	2.9	12	100	0	70	0	40	0	60	0.97
4330804--4330911	50	2.2	50	91	4	177	22	19	37	20	1.94
4330928--4330954	13	2.1	13	100	0	54	29	7	55	7	1.55
4330959--4331053	29	3.3	29	95	0	163	23	32	30	13	1.93
4331040--4331111	32	2.2	32	87	0	108	9	30	29	30	1.89
4331126--4331163	19	2.0	19	100	0	76	10	21	36	31	1.87
4342894--4342936	20	2.3	18	84	8	50	62	11	4	20	1.46
4346519--4346585	29	2.3	29	92	2	107	41	19	1	37	1.61
4349042--4349089	23	2.1	23	100	0	96	33	8	4	54	1.50
4356039--4356086	19	2.5	19	82	3	51	35	27	12	25	1.92
4356101--4356215	21	5.6	21	80	6	103	38	25	15	20	1.92
4356384--4356462	36	2.3	35	88	4	115	29	16	39	15	1.89
4357238--4357340	20	5.2	20	78	2	100	20	18	23	37	1.94
4357238--4357340	39	2.6	40	79	3	109	20	18	23	37	1.94
4359345--4359450	19	5.8	19	75	15	91	11	16	24	47	1.80
4359879--4360001	21	5.9	21	73	6	106	19	34	19	26	1.96
4359903--4360014	42	2.7	42	84	0	134	22	34	18	24	1.96
4359878--4360014	21	6.5	21	72	6	71	21	35	18	24	1.96
4361391--4361452	14	4.3	14	79	6	70	37	0	16	46	1.47
4361393--4361447	29	1.9	29	85	3	76	34	0	18	47	1.49
4361551--4361604	20	2.7	20	82	5	65	42	29	18	9	1.81
4361607--4361844	74	3.2	73	74	7	228	25	17	22	34	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4361688--4361843	54	2.9	54	97	0	285	24	16	24	35	1.95
4361598--4361844	20	13.3	20	72	15	190	25	17	22	34	1.96
4361822--4362104	140	2.0	140	95	0	512	44	15	12	27	1.83
4362162--4362196	18	1.9	18	94	0	61	20	2	22	54	1.58
4364445--4364498	24	2.2	24	90	0	81	40	20	16	22	1.91
4371697--4371735	17	2.3	17	90	0	60	64	5	0	30	1.15
4372324--4372393	33	2.2	34	80	12	85	42	0	1	55	1.08
4373494--4373535	19	2.1	19	86	8	57	50	0	2	47	1.14
4373506--4373547	18	2.3	19	91	4	68	50	0	2	47	1.14
4374179--4374248	21	3.3	21	80	11	81	18	27	24	30	1.98
4374756--4374827	34	2.1	35	92	2	119	50	6	6	36	1.57
4374930--4374959	14	2.1	14	100	0	60	60	13	0	26	1.34
4375260--4375295	14	2.6	14	90	0	54	75	0	2	22	0.94
4381331--4381400	36	2.0	35	88	8	106	22	11	15	50	1.76
4385852--4385896	23	2.0	23	86	0	63	26	28	24	20	1.99
4385875--4386178	149	2.0	149	97	0	572	36	20	16	27	1.93
4392819--4393122	149	2.0	149	96	0	563	36	20	16	27	1.93
4397023--4397082	31	1.9	31	86	0	84	26	3	16	53	1.59
4400335--4400454	31	3.7	31	76	15	109	37	16	22	23	1.94
4415619--4415656	20	1.9	20	88	0	58	52	2	7	36	1.45
4419490--4419552	19	3.1	20	80	13	67	47	17	26	7	1.75
4419836--4419867	12	2.6	12	95	5	55	59	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4430261--4430313	23	2.3	23	90	0	88	24	26	30	18	1.98
4431342--4431482	64	2.2	64	83	5	169	29	19	17	34	1.94
4436321--4436384	23	2.8	23	87	0	92	28	26	26	18	1.98
4436400--4436617	103	2.1	103	96	0	400	36	23	13	26	1.92
4437355--4437575	64	3.5	64	83	7	245	27	19	19	33	1.96
4449222--4449277	23	2.5	23	80	11	55	67	3	5	23	1.27
4449731--4449757	5	5.4	5	100	0	54	62	0	0	37	0.95
4451637--4451675	2	19.5	2	100	0	78	51	0	0	48	1.00
4451828--4451858	15	2.1	15	93	0	53	54	0	0	45	0.99
4452591--4452634	19	2.3	19	100	0	88	50	20	4	25	1.67
4458495--4458623	50	2.6	49	81	6	134	20	31	29	18	1.96
4464665--4464703	20	2.0	19	90	5	60	43	0	23	33	1.54
4464815--4464941	51	2.5	51	87	1	166	18	29	33	17	1.94
4466050--4466090	2	20.5	2	100	0	82	51	0	0	48	1.00
4466205--4466237	2	16.5	2	100	0	66	51	0	0	48	1.00
4490607--4490643	19	1.9	19	94	0	65	37	0	29	32	1.58
4491685--4491816	59	2.2	59	87	2	185	26	24	7	41	1.81
4492648--4492807	65	2.5	64	83	5	205	46	7	10	35	1.67
4492980--4493010	16	1.9	16	93	0	53	48	0	3	48	1.17
4493518--4493567	23	2.2	23	81	0	55	40	4	4	52	1.39
4503339--4503534	24	8.1	24	80	5	189	23	0	28	46	1.56
4503712--4503764	24	2.2	24	83	6	63	26	1	22	49	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4503817--4503997	28	6.8	27	73	14	130	52	11	8	27	1.66
4503846--4503937	26	3.5	26	82	11	91	52	7	9	30	1.62
4505502--4505546	18	2.6	17	80	10	56	24	4	24	46	1.71
4506039--4506223	96	1.9	96	89	4	284	29	19	18	32	1.96
4506038--4506209	32	5.4	32	90	2	256	29	19	19	31	1.96
4508684--4508720	14	2.6	14	100	0	74	35	13	16	35	1.88
4509986--4510019	8	4.2	8	84	0	50	32	0	38	29	1.58
4509990--4510020	16	1.9	16	100	0	62	35	0	38	25	1.56
4510113--4510505	170	2.3	170	81	3	434	29	18	19	32	1.96
4510227--4510635	170	2.4	170	80	5	418	29	18	18	33	1.95

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