genome.fa.s190.2.7.7.80.10.50.1000.15.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: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  14308945

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   55   56   57   58   59   60   61   62   

This is table  15  of  62  ( 7381 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)
3464833--3464894	21	3.0	20	73	17	63	37	17	22	22	1.94
3466830--3466954	63	2.0	63	90	0	196	44	18	21	16	1.87
3469103--3469144	21	2.0	21	86	4	59	71	2	2	23	1.10
3469146--3469230	37	2.2	39	77	8	95	69	3	12	14	1.32
3471101--3472241	106	11.0	106	93	3	1848	22	18	25	33	1.96
3471914--3472069	43	3.4	43	69	13	141	21	18	25	34	1.96
3471878--3472241	94	3.7	94	89	8	566	23	17	25	33	1.96
3475756--3475798	11	4.0	11	82	14	54	72	0	2	25	0.97
3475810--3475894	37	2.2	39	77	8	95	69	3	12	14	1.32
3477935--3478058	61	2.0	61	92	0	203	27	15	16	40	1.89
3491689--3491808	42	2.9	42	94	0	213	17	17	20	45	1.86
3491997--3492040	22	2.0	23	86	4	63	45	0	0	54	0.99
3491989--3492112	36	3.7	34	78	16	109	45	0	0	54	1.05
3492063--3492133	27	2.7	26	83	16	85	40	0	0	59	0.98
3492071--3492141	35	2.0	36	83	8	92	45	0	0	54	0.99
3492082--3492141	18	3.3	18	75	15	52	43	0	0	56	0.99
3492067--3492140	10	8.0	10	72	22	56	43	0	0	56	0.99
3492136--3492180	23	2.0	23	86	0	63	53	2	2	42	1.25
3492235--3492294	27	2.1	28	82	11	70	58	3	0	38	1.15
3492445--3492472	14	2.0	14	100	0	56	42	14	14	28	1.84
3492503--3492566	15	4.3	15	80	11	78	37	15	6	40	1.73
3492488--3492573	30	2.9	30	86	5	104	33	16	5	44	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3492488--3492574	15	5.9	15	78	8	70	33	16	5	44	1.71
3492785--3492809	2	12.5	2	100	0	50	48	0	0	52	1.00
3496349--3496392	21	2.1	21	86	0	61	34	15	40	9	1.79
3497391--3497429	13	3.1	13	88	3	53	48	2	7	41	1.45
3497964--3498026	24	2.6	24	94	0	90	33	20	26	19	1.96
3502032--3502070	15	2.6	15	95	0	69	20	33	10	35	1.86
3503831--3503996	91	1.8	91	85	5	237	29	15	25	29	1.96
3515330--3515383	26	2.1	26	86	3	74	64	0	0	35	0.94
3527246--3527275	16	1.9	16	93	6	53	53	23	10	13	1.69
3527365--3527457	3	31.0	3	100	0	186	33	33	0	33	1.58
3528365--3528574	65	3.3	63	80	12	214	30	24	19	25	1.98
3534364--3534444	24	3.5	24	73	20	84	22	23	23	30	1.99
3534365--3534467	44	2.3	44	85	9	147	22	25	22	30	1.99
3535967--3536010	21	2.1	21	82	0	52	9	43	15	31	1.79
3537043--3537252	65	3.2	64	78	9	221	30	24	18	26	1.98
3537224--3537272	19	2.6	19	84	9	57	24	28	20	26	1.99
3537093--3537272	65	2.8	63	81	9	168	29	24	18	27	1.98
3541623--3541652	15	2.0	15	100	0	60	40	33	13	13	1.83
3543368--3543407	19	2.1	19	86	9	55	35	5	12	47	1.63
3547776--3548093	167	1.9	167	86	6	457	34	12	20	32	1.90
3561188--3561244	2	28.5	2	100	0	114	49	0	0	50	1.00
3561956--3562008	21	2.6	20	80	11	54	56	1	3	37	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3567973--3567997	12	2.1	12	100	0	50	68	0	0	32	0.90
3568627--3568731	51	2.1	51	96	0	192	30	23	16	29	1.96
3581476--3581508	2	16.0	2	93	6	57	48	3	0	48	1.17
3582207--3582267	28	2.1	29	90	3	97	36	3	1	59	1.24
3582244--3582321	30	2.7	29	76	7	77	43	5	3	47	1.43
3582416--3582489	38	1.9	38	91	5	123	48	14	2	33	1.58
3590611--3590642	15	2.1	15	100	0	64	9	0	56	34	1.32
3591483--3591539	28	2.0	28	100	0	114	33	7	7	52	1.55
3600427--3600474	20	2.4	20	89	0	78	25	27	22	25	2.00
3602445--3602573	58	2.2	58	81	13	140	34	10	12	43	1.76
3606103--3606260	83	1.9	83	89	2	246	39	3	12	43	1.61
3609408--3609597	105	1.8	103	80	4	229	35	17	14	32	1.90
3620179--3620213	15	2.3	15	85	0	52	71	2	0	25	1.00
3620357--3620410	20	2.7	20	82	0	63	35	9	0	55	1.32
3630261--3630295	17	2.1	17	100	0	70	17	11	28	42	1.83
3634555--3634588	16	2.2	16	89	5	52	41	5	0	52	1.25
3634652--3634711	13	4.7	12	76	10	57	71	1	3	23	1.10
3634656--3634706	27	1.9	26	84	4	66	70	1	3	23	1.14
3635735--3635803	23	3.0	23	80	0	93	30	24	26	18	1.98
3636193--3636223	2	15.5	2	100	0	62	48	0	0	51	1.00
3637405--3637565	64	2.5	63	82	6	180	24	25	18	32	1.97
3641959--3642041	29	2.9	29	90	0	121	21	40	22	14	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3642332--3642393	23	2.7	23	94	2	106	58	1	40	0	1.08
3642449--3642556	39	2.5	42	75	23	118	32	3	15	48	1.63
3642446--3642553	38	2.8	38	83	12	132	35	3	15	45	1.64
3642911--3642950	21	1.9	21	94	0	71	30	0	12	57	1.36
3642515--3643189	371	1.8	363	83	9	889	40	1	11	46	1.49
3643137--3643226	30	3.1	30	85	9	116	43	0	10	46	1.37
3643203--3643241	11	3.5	11	80	13	53	48	0	12	38	1.42
3643200--3643248	22	2.2	22	100	0	98	46	0	14	38	1.44
3645549--3645669	59	2.1	56	90	4	188	49	6	4	39	1.48
3645754--3646083	11	27.2	11	72	20	225	46	9	0	43	1.41
3645754--3646083	72	4.5	72	79	14	333	46	9	0	43	1.41
3645754--3646052	98	3.1	95	81	12	331	46	8	1	43	1.41
3645754--3646036	61	4.7	58	77	13	225	46	8	1	43	1.41
3646122--3646245	52	2.4	51	89	5	180	46	12	0	40	1.42
3651192--3651218	3	9.0	3	100	0	54	66	33	0	0	0.92
3652133--3652176	23	1.9	23	95	0	79	29	27	20	22	1.99
3653017--3653086	21	3.5	20	72	16	72	55	1	14	28	1.48
3653017--3653091	40	1.9	38	92	7	125	56	1	16	26	1.48
3653029--3653093	21	3.2	20	68	23	55	53	1	21	23	1.54
3658499--3658543	18	2.5	17	86	13	56	71	0	6	22	1.09
3660256--3660288	13	2.4	14	90	5	50	63	0	0	36	0.95
3666640--3666766	44	2.9	44	98	0	245	37	14	11	36	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3668055--3668105	2	26.0	2	96	4	95	50	0	0	49	1.00
3671162--3671222	21	2.9	21	71	9	61	26	39	19	14	1.90
3674478--3674556	39	2.0	39	87	0	113	36	3	11	48	1.57
3691916--3691957	16	2.6	16	92	0	75	16	7	50	26	1.71
3692374--3692423	17	3.1	17	68	26	54	20	6	22	52	1.68
3693397--3693428	16	2.0	16	93	0	55	50	21	12	15	1.77
3693777--3693930	65	2.4	65	87	2	211	27	21	19	31	1.97
3696352--3696511	65	2.5	65	86	5	218	28	18	23	30	1.98
3696481--3696585	45	2.3	45	98	0	201	28	16	20	34	1.94
3699127--3699206	23	3.6	22	76	5	90	23	23	26	26	2.00
3703015--3703054	21	1.9	21	85	10	55	35	10	2	52	1.48
3704996--3705205	65	3.2	64	79	8	210	28	18	22	30	1.97
3707030--3707090	19	3.2	19	92	0	104	55	8	14	21	1.65
3708729--3708768	17	2.4	17	95	0	71	22	27	12	37	1.90
3709512--3709611	44	2.3	43	89	5	148	29	25	21	25	1.99
3709535--3709607	23	3.3	22	71	7	67	27	24	20	27	1.99
3710082--3710144	12	5.0	13	92	7	112	39	12	0	47	1.42
3710082--3710144	25	2.5	25	100	0	126	39	12	0	47	1.42
3712235--3712388	65	2.4	65	85	4	195	27	21	19	31	1.97
3719094--3719181	10	8.1	10	74	16	68	7	12	20	59	1.58
3719133--3719179	20	2.3	20	92	0	76	2	12	25	59	1.45
3719838--3719947	43	2.6	43	85	0	148	32	20	22	24	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3719981--3720089	41	2.6	41	80	8	121	36	20	19	23	1.95
3719958--3720143	42	4.4	43	79	4	200	36	17	20	24	1.94
3723787--3723822	15	2.4	15	85	0	54	44	0	22	33	1.53
3724197--3724289	30	3.1	30	89	1	134	20	20	25	33	1.97
3728881--3728916	15	2.4	15	85	0	54	44	0	22	33	1.53
3729291--3729383	30	3.1	30	87	1	134	20	19	26	33	1.96
3731576--3731699	43	2.9	43	80	8	103	33	11	16	37	1.85
3731588--3731709	41	2.9	41	80	7	113	31	12	20	36	1.90
3734241--3734296	21	2.7	20	86	5	67	33	21	10	33	1.88
3734169--3734331	20	8.0	21	72	11	72	31	25	12	30	1.92

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   55   56   57   58   59   60   61   62