genome.fa.s8527.2.7.7.80.10.50.1000.18.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: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9057482

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  18  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)
4307486--4307530	21	2.1	21	87	0	63	31	28	24	15	1.96
4309236--4309276	13	3.5	13	75	25	54	21	26	26	24	2.00
4309224--4309289	22	3.0	22	97	0	123	21	27	27	24	1.99
4312368--4312412	21	2.1	21	87	0	63	31	28	24	15	1.96
4314118--4314158	13	3.5	13	75	25	54	21	26	26	24	2.00
4314106--4314171	22	3.0	22	97	0	123	21	27	27	24	1.99
4315223--4315302	37	2.2	38	84	4	101	22	16	15	46	1.84
4325528--4325559	2	16.0	2	100	0	64	50	0	50	0	1.00
4325620--4325647	4	7.0	4	100	0	56	75	0	0	25	0.81
4326372--4326402	16	1.9	16	100	0	62	51	19	9	19	1.74
4335089--4335191	36	2.8	37	80	2	118	43	11	14	30	1.81
4335549--4335591	18	2.5	17	85	7	61	25	4	2	67	1.22
4336092--4336145	2	27.0	2	96	0	99	48	0	0	51	1.00
4340332--4340861	183	2.9	183	96	0	954	27	20	21	30	1.98
4342001--4342114	36	3.2	35	71	9	104	25	16	13	44	1.84
4341985--4342160	72	2.4	74	83	7	207	26	18	12	42	1.86
4342176--4342318	39	3.4	39	66	23	99	27	21	13	37	1.91
4342231--4342549	105	3.1	104	90	2	491	31	19	11	37	1.88
4342449--4342524	36	2.1	36	90	0	116	22	21	15	40	1.90
4342724--4343248	105	5.0	104	88	3	761	34	26	17	21	1.95
4343791--4343895	37	2.8	37	85	0	138	41	14	14	29	1.85
4344236--4344282	18	2.8	17	84	9	62	25	4	2	68	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4344452--4344590	58	2.4	57	76	16	128	30	5	1	61	1.28
4344543--4344598	21	2.7	20	75	8	58	25	3	0	71	1.02
4344786--4344822	2	18.5	2	94	0	65	45	0	0	54	1.00
4348942--4349014	6	12.2	6	97	0	137	32	49	16	1	1.54
4349012--4349050	5	7.8	5	91	0	51	23	33	41	2	1.68
4354914--4354998	6	14.2	6	97	0	161	32	49	16	1	1.53
4354996--4355039	5	8.8	5	97	0	70	25	34	40	0	1.56
4357000--4357042	22	2.0	21	86	8	61	25	0	0	74	0.82
4357071--4357105	18	1.9	18	94	0	61	22	31	28	17	1.96
4357223--4357268	19	2.4	19	88	0	65	21	19	21	36	1.95
4357325--4357469	48	2.9	48	83	10	143	17	31	28	22	1.97
4357347--4357474	50	2.6	50	86	7	163	17	29	31	21	1.96
4361053--4361139	35	2.5	34	80	12	97	55	10	8	26	1.61
4361346--4361388	21	2.0	21	90	0	68	13	27	18	39	1.89
4361725--4361764	18	2.2	18	90	0	62	20	17	32	30	1.95
4363275--4363488	111	1.9	111	92	1	358	44	10	7	36	1.68
4365987--4366033	3	15.7	3	95	0	85	29	0	0	70	0.88
4368124--4368157	15	2.2	16	89	5	52	14	2	5	76	1.09
4379386--4379431	23	2.0	23	100	0	92	78	0	17	4	0.91
4381355--4381399	21	2.1	21	87	0	63	31	28	24	15	1.96
4382201--4382325	31	4.0	31	90	6	191	20	19	23	37	1.94
4385383--4385416	15	2.2	16	89	5	52	14	2	5	76	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4387173--4387232	21	3.0	20	78	7	68	38	3	8	50	1.49
4390448--4390488	21	2.0	21	85	4	57	39	0	4	56	1.21
4390482--4390631	76	2.0	76	98	0	291	40	10	2	46	1.53
4391088--4391156	21	3.3	21	85	2	77	44	21	10	23	1.82
4391145--4391213	20	3.5	20	75	16	72	31	21	10	36	1.87
4391321--4391370	22	2.3	22	85	0	64	14	38	18	30	1.89
4391733--4391807	34	2.2	34	90	6	118	49	22	12	16	1.78
4392051--4392098	20	2.4	20	82	6	62	31	6	22	39	1.79
4392120--4392182	20	3.2	20	77	8	83	47	9	20	22	1.78
4392166--4392350	22	9.1	20	73	11	76	29	13	24	32	1.93
4392087--4392199	40	2.8	40	80	0	136	41	10	20	27	1.85
4392167--4392246	22	3.7	22	88	6	112	32	13	23	30	1.93
4396486--4396536	19	2.9	18	80	8	52	41	0	1	56	1.10
4409541--4409717	85	2.1	85	91	2	284	32	19	24	23	1.98
4413166--4413221	23	2.4	23	87	0	85	39	14	17	28	1.89
4414700--4414762	23	2.8	22	81	9	65	53	12	23	9	1.67
4414711--4414762	23	2.2	23	86	3	68	57	9	23	9	1.60
4417888--4417921	16	2.1	16	88	0	50	32	11	26	29	1.92
4423180--4423209	16	1.9	16	93	6	53	33	10	13	43	1.77
4426597--4426874	128	2.2	128	96	0	511	30	23	24	21	1.99
4426952--4426992	8	5.2	8	82	5	57	36	29	0	34	1.58
4433859--4435165	105	12.4	105	93	0	2159	24	18	24	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4439001--4439060	27	2.2	27	82	11	70	73	3	1	21	1.07
4439052--4439098	25	1.9	24	82	4	58	72	2	6	19	1.17
4445444--4445477	17	2.0	17	100	0	68	23	11	35	29	1.90
4452802--4452852	23	2.2	23	78	0	57	35	7	23	33	1.84
4457611--4457652	20	2.1	20	90	0	66	30	23	7	38	1.82
4459775--4459799	5	5.0	5	100	0	50	80	0	20	0	0.72
4464418--4464521	23	4.5	23	92	0	127	19	27	26	25	1.99
4465192--4465262	32	2.2	32	97	0	133	35	2	12	49	1.56
4466086--4466274	94	2.0	94	96	0	351	40	19	17	23	1.91
4479826--4479877	20	2.8	18	82	5	59	32	25	21	21	1.98
4480246--4480278	16	2.1	16	100	0	66	57	6	6	30	1.47
4481401--4481444	21	2.1	21	83	8	54	9	34	15	40	1.79
4485044--4485570	41	12.9	40	75	6	287	33	18	19	28	1.95
4485032--4485549	82	6.3	81	80	5	460	33	18	19	28	1.96
4486859--4486908	18	2.8	18	100	0	100	30	4	16	50	1.63
4493005--4493040	2	18.0	2	100	0	72	50	0	0	50	1.00
4493771--4493889	63	1.9	62	86	5	168	30	17	21	31	1.96
4493767--4493890	31	3.9	32	73	11	112	29	17	20	31	1.96
4493771--4493889	62	1.9	63	86	5	170	30	17	21	31	1.96
4494609--4494655	18	2.5	19	93	6	78	25	19	31	23	1.98
4502197--4502224	8	3.5	8	100	0	56	89	0	10	0	0.49
4503122--4503217	31	3.1	31	90	3	149	23	12	14	48	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4509707--4509759	26	2.0	26	92	0	88	37	7	26	28	1.83
4511110--4511152	13	3.3	13	83	0	59	44	11	11	32	1.77
4513042--4513151	45	2.4	45	90	0	175	18	16	18	47	1.83
4513108--4513175	30	2.5	27	84	13	70	14	19	20	45	1.85
4513108--4513166	30	2.0	30	93	0	100	11	20	23	44	1.85
4513044--4513154	15	7.4	15	70	11	84	18	16	18	47	1.83
4513092--4513220	69	1.9	69	83	0	168	18	17	18	44	1.86
4514396--4514462	24	2.8	24	95	0	125	20	11	35	31	1.89
4514476--4514664	64	3.0	63	91	3	306	30	13	28	27	1.94
4514523--4514639	33	3.6	33	75	14	134	31	15	25	27	1.96
4514493--4514606	31	3.6	30	72	14	95	30	11	30	27	1.91
4514557--4514672	31	3.7	31	70	15	96	29	12	31	26	1.93
4518043--4518075	3	11.0	3	100	0	66	66	0	0	33	0.92
4519083--4519135	17	3.5	16	71	28	53	52	3	1	41	1.30
4519071--4519138	28	2.4	28	97	0	127	54	2	1	41	1.24
4533031--4533077	24	2.0	24	95	0	85	48	8	17	25	1.74
4533036--4533094	24	2.5	24	82	0	73	52	8	15	23	1.70
4538965--4539174	75	2.8	77	84	3	273	24	31	23	20	1.98
4546960--4547010	9	6.2	8	76	19	52	13	0	27	58	1.36
4546962--4547005	17	2.6	17	85	7	63	13	0	29	56	1.38
4547579--4547783	75	2.7	76	88	2	288	24	31	23	20	1.98
4555375--4555450	35	2.2	35	90	0	116	38	25	1	35	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4555847--4556094	130	1.9	130	90	0	397	36	14	12	35	1.85
4556021--4556067	23	2.1	21	88	7	67	36	12	14	36	1.85
4555861--4556125	130	2.0	129	79	4	282	39	13	13	33	1.83
4556422--4556484	28	2.3	27	78	8	63	42	1	4	50	1.32
4556566--4556599	16	2.0	18	88	11	54	64	5	2	26	1.30
4558184--4558248	19	3.4	19	75	16	62	26	33	15	24	1.95
4571347--4571385	2	19.5	2	100	0	78	51	0	0	48	1.00
4576373--4576442	3	23.0	3	85	2	86	60	1	0	38	1.06
4576364--4576442	18	4.2	18	78	15	81	58	1	0	40	1.06
4576598--4577361	76	10.0	76	98	0	1440	34	21	21	21	1.96

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