genome.fa.s9624.2.7.7.80.10.50.1000.17.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: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8249038

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   

This is table  17  of  38  ( 4514 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)
3211209--3211307	41	2.5	40	77	8	119	32	18	14	35	1.90
3212952--3212993	22	1.9	22	85	0	57	38	9	30	21	1.85
3219583--3219631	21	2.3	21	92	0	80	24	4	18	53	1.62
3219965--3220047	41	2.0	41	90	0	130	33	15	18	32	1.92
3230797--3230823	2	13.5	2	100	0	54	0	51	0	48	1.00
3232580--3232681	27	3.7	27	75	12	86	52	0	3	43	1.19
3235371--3235402	14	2.3	14	100	0	64	40	6	46	6	1.54
3236354--3236393	17	2.4	17	91	0	62	40	17	5	37	1.72
3236775--3236809	6	5.8	6	93	0	52	31	45	0	22	1.53
3237299--3237349	16	2.9	17	80	11	59	47	0	0	52	1.00
3240209--3240240	16	2.0	16	93	0	55	53	0	0	46	1.00
3258657--3258927	123	2.2	123	82	6	334	25	20	18	35	1.95
3258728--3258989	123	2.1	123	81	8	302	26	20	17	35	1.95
3258832--3259202	166	2.2	166	83	1	440	23	20	19	35	1.96
3258956--3259283	43	7.8	42	68	11	138	23	20	21	34	1.97
3261504--3261569	24	2.9	23	80	13	73	0	13	4	81	0.83
3261504--3261569	11	6.2	10	75	19	62	0	13	4	81	0.83
3271726--3273645	961	2.0	961	99	0	3795	36	17	14	30	1.91
3274882--3274940	21	2.8	21	81	2	73	22	27	27	23	1.99
3282862--3282898	13	2.8	13	91	0	56	40	18	16	24	1.90
3283682--3283716	3	11.0	3	88	11	52	65	0	2	31	1.07
3283996--3284087	42	2.2	43	84	3	116	33	22	17	26	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3284024--3284131	41	2.7	40	81	7	110	33	19	17	29	1.95
3284590--3284655	22	3.0	22	100	0	132	36	0	13	50	1.42
3284679--3284737	31	1.9	31	92	0	100	44	8	5	42	1.57
3284860--3284950	23	4.0	23	97	0	155	18	21	31	27	1.97
3287891--3287927	19	1.9	19	94	0	65	32	24	16	27	1.96
3287953--3288049	41	2.4	41	85	0	131	32	22	16	27	1.96
3288192--3288239	22	2.2	22	92	0	78	27	45	8	18	1.78
3288606--3288645	14	2.9	14	96	0	71	50	25	15	10	1.74
3288655--3288750	20	4.8	20	85	1	113	13	19	22	43	1.86
3288720--3288757	20	1.9	20	88	0	58	13	13	21	52	1.73
3290656--3290704	20	2.5	20	90	6	73	32	26	22	18	1.97
3290696--3290770	33	2.2	34	90	2	116	45	17	20	17	1.86
3290783--3290850	20	3.4	20	81	0	73	20	20	25	33	1.97
3290837--3290877	20	2.0	20	90	0	64	17	12	21	48	1.79
3291361--3291478	21	5.6	21	72	6	87	22	33	18	24	1.97
3293015--3293065	20	2.5	20	90	0	75	49	21	15	13	1.79
3293028--3293073	20	2.3	20	80	0	56	47	21	19	10	1.80
3293116--3293266	20	7.8	20	82	8	179	24	19	21	35	1.96
3293075--3293218	54	2.7	54	85	2	182	21	18	21	38	1.94
3293437--3293471	18	1.9	18	94	0	61	22	2	20	54	1.58
3296476--3296543	20	3.4	20	93	0	109	25	17	30	26	1.97
3296531--3296606	21	3.7	21	70	10	75	23	15	23	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3296484--3296602	41	2.9	42	83	6	140	25	16	26	31	1.97
3296621--3296667	21	2.2	21	80	0	58	34	19	21	25	1.96
3296701--3296746	19	2.4	19	88	3	65	23	17	28	30	1.97
3296710--3296748	19	2.1	19	95	0	69	23	15	28	33	1.95
3297876--3297915	2	20.0	2	100	0	80	50	0	0	50	1.00
3301096--3301138	21	2.0	21	86	9	59	81	0	9	9	0.88
3303935--3304328	197	2.0	197	100	0	788	38	20	14	26	1.91
3306663--3306687	9	2.8	9	100	0	50	12	52	0	36	1.39
3308101--3308142	21	2.0	20	90	4	66	33	2	16	47	1.60
3311343--3311373	4	7.5	4	92	7	53	74	0	3	22	0.96
3313994--3314370	159	2.4	157	82	6	435	47	7	18	26	1.75
3324753--3324833	42	1.9	42	84	0	108	35	17	17	29	1.93
3334352--3334411	21	2.9	21	76	20	63	48	15	31	5	1.66
3334330--3334411	12	7.6	11	67	22	50	47	13	35	3	1.60
3334330--3334410	33	2.5	33	80	8	85	46	13	35	3	1.61
3334379--3334431	21	2.5	21	87	6	72	50	16	30	1	1.56
3334813--3334912	43	2.3	43	86	6	132	33	19	21	27	1.97
3340345--3340787	222	2.0	221	99	0	877	34	20	13	31	1.91
3342583--3342613	16	1.9	16	100	0	62	38	6	19	35	1.77
3345688--3345738	20	2.4	22	83	6	61	31	11	29	27	1.92
3351393--3351502	23	4.8	23	79	0	76	21	19	23	35	1.96
3351393--3351482	46	2.0	46	84	0	117	21	22	23	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3358372--3358422	23	2.2	23	89	0	75	15	25	27	31	1.96
3358830--3358860	16	1.9	16	100	0	62	35	19	12	32	1.90
3360260--3360363	53	2.0	53	86	0	145	51	16	9	22	1.72
3360309--3360440	64	2.0	65	85	1	176	53	18	6	21	1.68
3360818--3360861	20	2.1	21	83	4	54	54	4	6	34	1.47
3360995--3361289	81	3.5	80	72	11	223	36	12	12	38	1.81
3360981--3361337	171	2.1	170	83	7	454	39	11	12	36	1.80
3361400--3361439	21	1.9	21	84	0	53	37	15	5	42	1.68
3361129--3362814	234	7.1	232	85	7	2114	40	12	11	35	1.79
3361129--3362814	469	3.6	468	86	7	2275	40	12	11	35	1.79
3361839--3361894	22	2.5	22	88	0	85	51	10	7	30	1.63
3361893--3361932	21	1.9	21	84	0	53	37	15	5	42	1.68
3362728--3362773	21	2.1	21	88	4	65	52	2	10	34	1.49
3364086--3364183	34	2.9	33	76	15	101	46	5	4	43	1.44
3364130--3364252	63	2.0	63	87	6	178	44	4	5	44	1.49
3366947--3366979	3	11.0	3	100	0	66	33	0	33	33	1.58
3381428--3381715	143	2.0	144	98	1	560	47	6	16	29	1.71
3382107--3382183	36	2.1	36	95	0	136	59	2	9	28	1.41
3382220--3382287	11	6.1	11	72	16	59	61	4	0	33	1.16
3383231--3383292	21	3.3	20	66	29	55	50	12	1	35	1.51
3385818--3385859	13	3.5	13	81	18	63	16	47	21	14	1.82
3385867--3385972	29	3.7	29	89	1	160	32	5	23	38	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3386698--3386818	24	5.0	24	78	0	134	27	15	17	39	1.90
3386698--3386818	48	2.5	48	93	0	206	27	15	17	39	1.90
3395142--3395166	13	1.9	13	100	0	50	16	48	20	16	1.82
3395179--3395265	29	3.0	29	96	0	156	28	5	26	39	1.79
3395179--3395305	58	2.2	58	81	5	141	29	4	22	43	1.73
3395270--3395332	29	2.2	29	80	8	76	38	1	14	46	1.54
3395274--3395338	28	2.3	28	80	15	71	38	3	15	43	1.62
3396027--3396147	24	5.0	24	78	0	134	25	16	18	39	1.91
3396027--3396147	48	2.5	48	95	0	215	25	16	18	39	1.91
3397087--3397139	6	8.8	6	97	0	97	0	64	0	35	0.94
3400522--3400561	14	2.9	14	85	10	55	62	0	0	37	0.95
3404932--3405010	23	3.4	23	85	0	86	17	46	17	17	1.84
3405783--3405879	49	2.0	48	97	2	185	38	14	14	32	1.86
3407457--3407493	20	2.0	20	89	10	60	35	16	13	35	1.88
3430353--3430393	14	2.8	15	85	7	57	24	34	19	21	1.97
3432859--3432991	24	5.5	24	81	3	142	40	19	12	27	1.88
3432855--3433009	72	2.2	72	78	2	168	44	18	11	25	1.83
3439293--3439333	21	2.0	21	100	0	82	24	17	19	39	1.92
3441639--3441758	2	62.0	2	70	18	85	49	3	0	46	1.24
3441723--3441761	11	3.5	11	86	10	53	46	0	0	53	1.00
3441639--3441761	13	10.0	13	73	21	79	48	3	0	47	1.23
3442110--3442160	4	12.8	4	82	0	66	25	7	23	43	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3442110--3442160	8	6.4	8	97	0	84	25	7	23	43	1.81
3442387--3442428	2	21.0	2	100	0	84	50	0	0	50	1.00
3442426--3442530	49	2.1	49	82	3	122	48	11	7	32	1.67
3442858--3442900	13	3.1	14	86	10	61	39	2	0	58	1.11
3442929--3442983	19	2.9	19	86	10	85	50	5	0	43	1.25
3442929--3442971	2	21.5	2	83	9	52	51	4	0	44	1.22
3443010--3443102	7	13.3	7	77	0	87	49	32	0	18	1.48
3443010--3443102	21	4.4	21	77	0	105	49	32	0	18	1.48
3442393--3443426	536	1.9	539	87	4	1501	42	12	9	35	1.74
3443392--3443445	22	2.3	24	84	9	67	35	1	3	59	1.26

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