genome.fa.s9001.2.7.7.80.10.50.1000.21.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: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4740655

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   

This is table  21  of  24  ( 2777 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)
4228518--4228557	15	2.6	16	88	4	55	0	10	2	87	0.63
4233341--4233374	12	2.9	12	86	4	52	50	8	11	29	1.69
4233777--4233815	18	2.2	18	90	0	60	56	15	0	28	1.40
4242222--4242256	13	2.7	13	100	0	70	62	0	37	0	0.95
4250980--4251017	18	2.1	18	90	0	58	36	26	34	2	1.71
4254630--4254680	24	2.0	25	88	11	77	54	27	9	7	1.60
4254639--4254689	20	2.8	17	75	18	57	60	23	9	5	1.50
4256009--4256033	13	1.9	13	100	0	50	36	16	24	24	1.94
4267687--4267843	79	2.0	78	97	1	296	38	5	16	39	1.73
4267925--4267967	21	2.0	21	100	0	86	23	32	20	23	1.98
4267957--4267991	11	3.2	11	95	0	61	22	28	20	28	1.98
4276658--4276697	21	1.9	21	89	0	62	25	40	25	10	1.86
4281491--4281521	14	2.2	14	100	0	62	25	19	25	29	1.99
4284547--4284612	34	2.0	34	90	3	107	22	15	25	36	1.93
4295093--4295152	31	1.9	31	86	6	86	40	3	5	51	1.40
4295093--4295161	31	2.3	30	82	12	79	37	2	4	55	1.35
4295336--4295402	23	2.8	24	75	13	66	49	0	2	47	1.16
4296184--4296217	9	3.7	9	84	7	50	82	0	0	17	0.67
4297424--4297464	21	2.1	21	86	13	61	73	2	0	24	0.96
4299782--4299850	30	2.3	30	97	0	129	23	28	11	36	1.90
4306130--4306167	20	1.9	20	94	0	67	42	2	5	50	1.39
4306124--4306168	19	2.3	20	85	7	67	44	2	4	48	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4306319--4306389	35	2.0	35	81	13	83	40	7	9	42	1.65
4306343--4306424	23	3.5	23	69	9	67	43	6	8	41	1.60
4306366--4306399	12	2.8	12	100	0	68	41	8	8	41	1.67
4306330--4306434	47	2.2	45	88	6	147	41	7	8	41	1.64
4306378--4306456	35	2.3	35	91	4	133	44	5	10	40	1.60
4306425--4306481	23	2.4	24	88	2	89	40	3	14	42	1.62
4306390--4306517	61	2.2	58	85	7	168	42	3	11	41	1.60
4306448--4306521	38	1.9	39	88	2	114	43	4	12	40	1.61
4306453--4306554	39	2.6	39	81	7	102	47	3	9	39	1.55
4306608--4306656	22	2.2	22	81	0	62	42	2	12	42	1.53
4306677--4306739	19	3.3	19	77	18	67	28	0	3	68	1.05
4306674--4306744	12	5.6	13	73	17	69	28	0	2	69	1.03
4310891--4310928	12	3.2	12	88	0	58	10	15	47	26	1.78
4310894--4310945	24	2.2	24	85	0	68	15	13	44	26	1.84
4311051--4311099	13	3.8	13	89	2	73	14	14	55	16	1.70
4311305--4311367	32	2.0	32	87	6	92	28	1	3	66	1.16
4311327--4311389	24	2.8	22	73	7	54	25	3	3	68	1.19
4311341--4311415	22	3.5	22	71	12	66	29	5	5	60	1.41
4311332--4311402	22	3.1	23	74	10	65	26	4	5	63	1.35
4311342--4311785	87	5.1	86	74	12	288	28	13	5	52	1.61
4311379--4311808	130	3.3	129	75	9	345	28	14	5	52	1.64
4311627--4311743	48	2.6	48	80	15	133	27	16	3	52	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4311360--4311785	43	9.8	43	74	10	287	28	13	5	52	1.62
4312271--4312358	15	5.5	15	79	18	97	44	0	1	54	1.07
4312338--4312691	32	12.4	32	72	21	290	35	0	11	52	1.38
4312361--4312403	22	2.0	22	100	0	86	34	0	13	51	1.42
4312338--4312489	54	2.8	54	97	0	295	36	0	11	52	1.37
4312383--4312723	86	4.0	86	84	10	482	35	0	12	52	1.38
4312469--4312723	54	4.6	54	73	11	244	34	0	12	52	1.39
4312532--4312585	14	3.6	14	72	18	54	37	0	5	57	1.22
4312671--4312713	22	2.0	22	100	0	86	34	0	13	51	1.42
4312738--4312796	31	1.9	31	89	0	91	44	10	5	40	1.60
4313542--4313882	157	2.2	154	87	2	477	26	17	7	49	1.72
4313563--4313946	157	2.5	156	83	5	395	28	17	7	47	1.73
4317855--4318106	43	5.9	43	85	2	346	33	17	25	24	1.96
4317854--4318105	85	3.0	85	88	1	353	33	17	25	23	1.96
4317860--4318106	128	1.9	129	88	4	374	32	17	25	24	1.96
4318241--4318301	21	2.9	21	92	0	104	50	21	8	19	1.73
4322148--4322262	42	2.7	43	79	9	130	27	14	22	34	1.94
4322290--4322600	41	7.6	41	72	11	201	30	18	19	31	1.96
4322254--4322531	82	3.4	78	72	13	220	31	18	19	30	1.96
4322307--4322600	123	2.4	122	76	11	296	31	19	19	29	1.96
4322171--4322590	164	2.6	164	86	4	560	30	17	20	32	1.96
4331767--4331816	22	2.3	22	92	0	91	34	24	18	24	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4332239--4332276	16	2.3	17	86	4	51	47	2	7	42	1.46
4334568--4334597	11	2.7	11	94	0	51	30	0	40	30	1.57
4336714--4336756	11	3.7	11	79	11	50	32	0	34	32	1.58
4338479--4338563	18	4.7	18	79	0	98	41	21	16	21	1.90
4338474--4338563	36	2.5	36	96	0	162	40	21	15	23	1.91
4343391--4343450	29	2.2	25	85	11	75	35	1	3	60	1.23
4343636--4343684	19	2.5	20	77	6	57	44	2	0	53	1.12
4343680--4343714	17	2.1	17	94	0	61	34	8	0	57	1.29
4344501--4344550	20	2.5	20	93	0	82	34	20	16	30	1.94
4357904--4357992	29	3.1	29	100	0	178	13	31	37	17	1.89
4358082--4358261	15	11.1	15	72	17	137	21	7	53	17	1.69
4358069--4358195	65	1.9	66	95	3	229	23	9	50	16	1.74
4358084--4358260	82	2.2	83	84	4	234	21	7	53	17	1.69
4358147--4358271	51	2.5	51	93	5	213	20	7	54	18	1.66
4358312--4358375	32	2.0	32	100	0	128	21	25	21	31	1.98
4358683--4358731	21	2.3	21	82	3	62	32	0	16	51	1.45
4358708--4358770	28	2.2	30	88	5	94	33	0	11	55	1.35
4359256--4359313	16	3.4	16	73	17	53	37	0	12	50	1.40
4359574--4359632	26	2.3	25	75	18	66	47	8	3	40	1.51
4362511--4362980	26	19.0	26	76	16	351	42	2	10	44	1.51
4362456--4362677	97	2.3	98	94	0	383	44	2	9	43	1.51
4362634--4362993	98	3.7	98	95	1	605	42	2	10	45	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4362511--4362893	124	3.1	120	85	7	447	43	2	9	43	1.51
4362843--4362888	12	3.7	12	77	11	56	47	4	6	41	1.49
4362931--4362978	14	3.6	14	77	11	55	39	4	6	50	1.47
4363052--4363084	17	1.9	17	93	0	57	36	6	12	45	1.66
4365447--4365537	45	2.0	47	87	8	134	46	13	0	40	1.43
4365468--4365606	41	3.3	40	76	14	111	46	12	0	40	1.46
4365770--4365801	17	1.9	16	93	6	55	0	37	0	62	0.95
4365743--4365800	4	14.0	4	75	7	53	1	34	0	63	1.04
4365743--4365800	25	2.3	25	96	0	107	1	34	0	63	1.04
4365862--4365913	25	2.1	25	92	0	86	28	32	9	28	1.89
4366024--4366083	23	2.6	23	97	0	111	23	8	45	23	1.80
4366089--4366197	29	3.8	29	93	2	175	22	30	31	16	1.96
4366205--4366242	19	2.0	19	100	0	76	21	42	15	21	1.89
4366305--4366415	55	2.0	55	100	0	222	16	34	21	27	1.95
4366224--4366499	139	2.0	139	100	0	552	17	32	25	24	1.96
4366312--4366397	27	3.1	27	62	15	68	16	37	22	24	1.93
4366370--4366501	41	3.2	41	66	19	119	16	31	28	23	1.96
4367825--4367863	18	2.2	18	95	0	69	61	0	17	20	1.34
4369183--4369282	25	4.0	25	77	2	103	34	20	21	25	1.97
4369617--4369660	11	3.8	11	85	11	61	56	11	0	31	1.35
4370236--4370280	2	22.5	2	95	0	81	51	0	0	48	1.00
4372701--4372735	18	1.9	18	100	0	70	45	5	11	37	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4373790--4373824	15	2.4	15	90	4	54	11	20	14	54	1.70
4373770--4373820	26	2.0	26	84	0	66	11	17	13	56	1.66
4375185--4375229	21	2.1	21	87	0	63	31	28	24	15	1.96
4375765--4375804	2	20.0	2	100	0	80	50	0	0	50	1.00
4376244--4376355	31	3.6	31	93	0	188	19	20	22	37	1.94
4379384--4379428	21	2.1	21	87	0	63	31	28	24	15	1.96
4379961--4379992	2	16.0	2	100	0	64	50	0	0	50	1.00
4380432--4380541	31	3.5	31	86	3	150	20	19	20	40	1.92
4380432--4380556	31	4.0	31	82	8	148	21	18	21	38	1.93
4380432--4380553	62	2.0	62	85	6	167	22	18	21	38	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