genome.fa.s8488.2.7.7.80.10.50.1000.18.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: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12876159

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   

This is table  18  of  54  ( 6450 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)
4390266--4390330	21	3.1	21	93	0	103	16	30	10	41	1.83
4392353--4392405	24	2.2	24	83	6	63	26	7	13	52	1.66
4392542--4392584	20	2.3	18	85	14	61	20	16	11	51	1.75
4392547--4392593	20	2.4	19	82	10	67	19	17	10	53	1.72
4392514--4392986	181	2.6	181	88	1	687	27	16	13	42	1.85
4393566--4393590	11	2.3	11	100	0	50	36	24	8	32	1.84
4394948--4394984	19	2.0	18	94	5	65	62	10	0	27	1.28
4395017--4395080	23	2.8	23	77	11	60	25	25	18	31	1.98
4395247--4395276	12	2.6	11	90	10	51	66	20	0	13	1.24
4403431--4403484	22	2.6	21	76	5	56	61	22	5	11	1.50
4403431--4403480	21	2.3	22	82	3	57	62	22	4	12	1.46
4403509--4403580	21	3.4	21	77	9	74	61	22	6	9	1.51
4403441--4403556	21	5.5	21	71	11	67	59	22	6	11	1.55
4403990--4404044	25	2.3	23	82	17	67	29	0	3	67	1.08
4403991--4404041	24	2.1	25	86	13	72	27	0	3	68	1.07
4404706--4404779	39	1.9	38	81	10	89	54	27	1	17	1.51
4413785--4413943	77	2.0	79	86	4	225	44	4	11	40	1.60
4415331--4415402	20	3.5	21	71	7	58	26	29	18	26	1.98
4419565--4419600	18	2.0	18	88	0	54	30	36	13	19	1.91
4420113--4420192	42	1.9	42	97	0	151	37	12	20	30	1.89
4428946--4429017	17	4.2	17	75	10	67	36	9	13	40	1.78
4432188--4432230	16	2.8	16	89	3	70	32	34	11	20	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4444578--4444602	2	12.5	2	100	0	50	48	0	0	52	1.00
4446121--4446146	13	2.0	13	100	0	52	30	0	0	69	0.89
4446104--4446171	16	4.1	16	70	21	50	32	0	2	64	1.08
4457269--4457484	107	2.0	107	99	0	423	29	12	24	33	1.93
4465149--4465200	23	2.3	23	93	0	86	36	36	17	9	1.82
4477394--4477453	11	5.4	11	86	4	84	18	8	0	73	1.08
4477394--4477442	6	8.5	6	80	8	57	20	8	0	71	1.11
4477395--4477453	22	2.6	23	94	2	102	18	8	0	72	1.09
4477803--4477877	39	1.9	39	81	10	91	25	28	0	46	1.53
4503816--4503893	35	2.2	35	90	0	138	21	12	23	42	1.87
4503826--4503908	35	2.4	35	85	4	96	20	14	25	39	1.90
4503993--4504042	25	2.0	25	100	0	100	44	8	16	32	1.76
4515941--4515966	2	13.0	2	100	0	52	50	0	0	50	1.00
4518620--4518751	66	2.0	67	81	1	158	38	21	19	20	1.93
4520013--4520050	16	2.4	16	90	0	58	50	2	7	39	1.46
4533975--4534011	17	2.2	17	100	0	74	48	10	5	35	1.61
4534952--4535017	30	2.2	30	81	10	73	27	24	3	45	1.68
4540335--4540508	86	2.0	86	100	0	348	33	10	17	38	1.84
4540665--4540715	24	2.1	24	100	0	102	15	33	31	19	1.93
4542338--4542378	2	20.5	2	100	0	82	51	0	0	48	1.00
4545041--4545109	9	7.3	9	80	8	75	14	27	30	27	1.95
4545041--4545107	19	3.5	19	86	11	93	14	25	31	28	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4545106--4545146	5	7.8	5	84	10	55	19	53	21	4	1.63
4545105--4545153	22	2.2	22	100	0	98	18	48	22	10	1.77
4552327--4552385	20	2.9	21	85	7	86	18	27	23	30	1.98
4552348--4552417	10	7.3	10	69	24	53	15	28	28	27	1.96
4552328--4552392	30	2.2	29	86	13	89	16	27	26	29	1.97
4552348--4552415	19	3.5	20	86	9	81	16	26	29	27	1.97
4552413--4552451	17	2.3	17	100	0	78	17	46	23	12	1.83
4552441--4552471	7	4.4	7	100	0	62	16	29	29	25	1.96
4554297--4554549	126	2.0	128	97	2	485	35	6	22	35	1.80
4555401--4555538	54	2.6	54	85	0	186	36	21	18	23	1.94
4562889--4563159	135	2.0	135	97	0	506	33	19	5	41	1.74
4563639--4563792	54	2.9	54	83	1	184	33	20	18	27	1.96
4564545--4564576	15	2.1	15	94	0	55	40	6	9	43	1.62
4564558--4564701	17	8.5	17	69	19	86	36	5	6	50	1.53
4564548--4564646	35	2.9	34	80	8	103	38	3	9	49	1.50
4564752--4564888	40	3.5	38	78	14	143	41	5	2	50	1.39
4564773--4564827	17	3.3	17	76	19	53	38	7	3	50	1.48
4564782--4564917	13	10.1	14	69	21	69	40	5	4	50	1.45
4564714--4564894	79	2.3	79	89	1	272	42	6	2	48	1.44
4564714--4564932	79	2.7	78	83	8	244	41	5	4	48	1.46
4564960--4564992	9	3.8	9	88	8	50	36	6	0	57	1.23
4565121--4565173	21	2.6	21	82	8	56	45	5	1	47	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4574727--4574759	13	2.4	14	90	5	50	15	24	48	12	1.78
4584581--4584742	3	53.7	3	86	6	229	33	1	0	64	1.04
4585237--4585266	14	2.1	15	93	6	53	76	6	16	0	0.99
4585231--4585268	18	2.0	20	90	10	62	73	7	18	0	1.06
4586178--4586218	20	2.0	21	85	4	57	41	2	2	53	1.27
4597558--4597607	8	6.0	8	82	15	57	86	0	14	0	0.58
4597566--4597607	7	6.3	7	88	5	61	88	0	11	0	0.53
4597561--4597599	11	3.4	11	92	7	60	87	0	12	0	0.55
4597561--4597607	18	2.6	18	83	16	69	87	0	12	0	0.55
4597917--4597961	16	2.8	16	83	10	56	28	8	6	55	1.56
4598762--4598974	52	4.1	52	100	0	426	25	15	23	36	1.94
4599001--4599161	52	3.1	52	97	0	304	25	14	23	36	1.93
4598866--4599109	135	1.8	135	99	0	479	27	14	22	35	1.94
4598814--4599226	187	2.2	185	96	1	765	26	14	23	36	1.92
4599964--4600485	113	4.6	113	95	0	897	35	15	19	29	1.92
4600803--4600972	3	56.7	3	92	0	286	32	1	0	65	1.03
4601461--4601499	19	1.9	19	90	10	60	74	7	17	0	1.05
4601467--4601498	15	2.1	16	94	5	57	78	6	15	0	0.95
4601461--4601504	21	2.1	21	87	8	63	72	9	15	2	1.19
4602400--4602440	20	2.0	21	85	4	57	41	2	2	53	1.27
4606776--4606838	30	2.1	30	82	8	76	46	7	19	26	1.77
4609855--4609903	25	2.0	25	91	0	80	44	16	26	12	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4621241--4621283	21	2.2	19	87	8	59	9	11	0	79	0.95
4622189--4622227	4	10.0	4	83	5	53	69	0	0	30	0.89
4622190--4622285	15	6.3	15	88	9	83	67	0	0	32	0.91
4622190--4622230	8	5.2	8	91	5	66	68	0	0	31	0.90
4622202--4622292	3	32.3	3	80	12	113	67	0	0	32	0.91
4622413--4622496	5	15.8	5	73	18	64	75	0	3	21	0.96
4622413--4622476	8	8.1	8	74	19	55	78	0	1	20	0.84
4624497--4624546	21	2.4	20	81	15	57	26	12	22	40	1.88
4625410--4625556	68	2.2	66	82	10	185	11	20	9	58	1.60
4631282--4631786	250	2.0	249	92	1	841	26	20	18	34	1.96
4633778--4633802	13	1.9	13	100	0	50	40	8	8	44	1.63
4636251--4636291	21	1.9	21	90	5	64	17	24	34	24	1.96
4643776--4643818	21	2.0	21	81	0	50	20	25	4	48	1.69
4646611--4646651	22	1.9	22	90	5	66	58	0	17	24	1.38
4651204--4651238	17	2.1	17	100	0	70	42	11	22	22	1.85
4654509--4654768	130	2.0	128	92	2	432	43	19	18	19	1.89
4662491--4662517	11	2.5	11	100	0	54	18	11	14	55	1.68
4672973--4673049	31	2.5	31	78	6	84	16	27	28	27	1.97
4679951--4679995	21	2.1	21	83	0	54	22	24	22	31	1.99
4681148--4681206	26	2.3	26	96	0	109	47	27	10	15	1.77
4690936--4690961	2	13.0	2	100	0	52	50	0	0	50	1.00
4691069--4691120	20	2.4	22	81	9	63	42	11	15	30	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4691734--4691791	27	2.0	27	83	9	71	44	1	0	53	1.10
4691734--4691793	28	2.2	27	85	8	77	45	1	0	53	1.10
4691894--4691958	27	2.4	27	85	10	80	53	3	1	41	1.25
4692010--4692063	22	2.5	22	96	0	99	37	3	0	59	1.15
4693053--4693211	79	2.0	79	100	0	318	32	10	20	37	1.86
4693240--4693332	46	2.0	46	100	0	186	23	12	26	36	1.91
4693793--4693831	16	2.4	17	82	8	53	25	2	0	71	0.98
4695406--4695444	19	2.1	19	90	0	60	51	0	20	28	1.48
4696532--4696556	2	12.5	2	100	0	50	48	0	0	52	1.00
4696585--4696623	2	19.5	2	100	0	78	48	0	0	51	1.00

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