genome.fa.s8138.2.7.7.80.10.50.1000.16.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: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  3838456

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   

This is table  16  of  18  ( 2117 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)
3258605--3258641	18	2.1	18	100	0	74	27	24	10	37	1.88
3259981--3260052	29	2.5	28	78	10	83	55	6	19	18	1.64
3264428--3264486	20	2.9	21	78	14	77	23	1	0	74	0.91
3264441--3264491	19	2.8	18	79	5	66	21	1	0	76	0.88
3264398--3264485	27	3.4	27	69	22	82	25	3	0	71	1.01
3270070--3270243	65	2.8	65	88	4	250	36	19	16	27	1.93
3270208--3270424	66	3.4	65	68	27	194	35	24	13	26	1.92
3270500--3270716	85	2.5	85	81	3	247	35	19	20	24	1.96
3271733--3271816	21	4.1	21	90	4	136	19	40	27	13	1.88
3271733--3271816	41	2.1	40	93	2	141	19	40	27	13	1.88
3272866--3272896	15	2.0	16	93	6	55	32	6	3	58	1.40
3273128--3273182	23	2.4	24	79	14	62	25	1	0	72	0.94
3273239--3273264	3	8.7	3	100	0	52	30	0	0	69	0.89
3273384--3273413	6	5.0	6	100	0	60	33	0	0	66	0.92
3273378--3273413	18	2.0	18	88	0	54	33	2	2	61	1.25
3275913--3275955	3	15.3	3	81	13	56	32	0	0	67	0.91
3275911--3275960	22	2.2	23	85	7	75	34	0	0	66	0.92
3276402--3276431	16	1.9	16	93	6	53	80	3	16	0	0.85
3277497--3277732	119	2.0	116	82	5	287	36	7	8	46	1.64
3277697--3277753	29	2.0	29	82	6	71	45	1	0	52	1.11
3277725--3277814	47	1.9	47	81	4	110	46	2	2	48	1.26
3279749--3279790	7	6.0	7	81	8	50	14	16	14	54	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3279749--3279790	15	3.0	14	83	10	50	14	16	14	54	1.71
3279849--3279896	12	3.8	12	81	10	60	22	12	8	56	1.63
3279850--3279908	26	2.3	26	84	0	82	22	11	6	59	1.56
3279848--3279902	12	4.4	12	75	8	56	21	10	7	60	1.55
3279850--3279908	12	4.5	14	79	12	54	22	11	6	59	1.56
3283972--3284180	114	1.8	114	92	0	355	32	15	20	31	1.94
3285342--3285512	76	2.3	74	82	5	202	28	14	24	32	1.94
3286035--3286141	54	2.0	54	81	7	128	35	12	21	30	1.90
3286513--3286634	22	5.6	22	93	1	201	31	14	13	39	1.86
3287308--3287491	76	2.4	76	90	5	273	25	20	20	34	1.96
3287500--3288368	112	7.7	112	94	1	1415	37	13	19	28	1.90
3288703--3288745	3	15.3	3	81	13	56	32	0	0	67	0.91
3288701--3288750	22	2.2	23	85	7	75	34	0	0	66	0.92
3288806--3288839	14	2.4	14	90	5	50	38	41	17	2	1.65
3290169--3290231	22	3.0	21	74	19	60	49	0	0	50	1.00
3290171--3290231	20	2.8	21	78	11	61	49	0	0	50	1.00
3290254--3290487	119	2.0	116	83	5	292	38	7	8	46	1.62
3290452--3290508	29	2.0	29	82	6	71	45	1	0	52	1.11
3290480--3290570	47	1.9	47	82	4	112	43	2	5	48	1.38
3295856--3295915	30	2.0	30	96	0	111	30	5	20	45	1.72
3296096--3296171	21	3.7	21	89	1	118	19	34	17	28	1.94
3297466--3297514	19	2.5	19	80	6	53	51	6	14	28	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3298785--3298844	30	2.0	30	96	0	111	30	5	20	45	1.72
3299043--3299160	8	17.1	8	64	29	67	21	38	14	26	1.91
3299025--3299160	20	6.7	20	93	0	218	20	36	15	27	1.93
3299526--3299595	34	2.1	32	84	5	86	31	15	28	24	1.96
3301967--3302134	47	3.6	47	84	2	221	30	12	20	36	1.90
3301963--3302134	46	3.7	46	82	2	191	30	12	20	36	1.89
3301963--3302134	94	1.8	93	88	1	263	30	12	20	36	1.89
3304652--3304694	6	7.2	6	82	10	52	16	13	16	53	1.73
3308719--3308782	20	3.0	21	74	17	78	25	17	25	32	1.96
3308712--3308774	20	3.0	20	74	17	74	23	22	23	30	1.99
3308717--3309103	42	8.8	42	68	18	155	28	17	22	31	1.97
3308620--3308926	122	2.4	126	86	7	406	28	18	23	29	1.98
3308834--3308858	13	1.9	13	100	0	50	32	24	20	24	1.98
3308713--3309087	177	2.1	177	92	2	619	28	18	23	30	1.97
3309166--3309236	37	1.9	37	94	0	124	39	25	16	18	1.91
3317052--3317098	15	3.2	14	85	8	58	36	0	2	61	1.08
3317839--3317882	13	3.5	13	84	12	65	20	50	15	13	1.78
3317906--3317987	35	2.3	35	89	2	119	52	0	0	47	1.00
3318002--3318027	12	2.2	12	100	0	52	23	50	19	7	1.73
3319262--3319301	21	1.9	21	84	0	53	42	0	2	55	1.13
3319266--3319326	24	2.5	25	78	10	63	40	0	3	55	1.16
3320294--3320351	17	3.5	17	88	2	82	44	1	10	43	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3320368--3320480	39	3.2	39	61	23	102	52	2	4	40	1.36
3320355--3320508	68	2.3	68	97	1	292	47	3	6	42	1.45
3320522--3320582	7	8.4	7	74	18	54	31	0	4	63	1.15
3320517--3320587	24	3.1	24	78	21	89	30	0	7	61	1.22
3320535--3320582	19	2.4	20	89	6	71	31	0	6	62	1.20
3320574--3322272	5	340.8	5	99	0	3331	19	0	19	60	1.37
3323393--3323436	19	2.4	17	82	14	52	27	0	4	68	1.09
3327354--3327386	15	2.2	15	100	0	66	27	18	6	48	1.71
3328143--3328213	23	3.1	23	79	2	90	36	22	23	16	1.94
3335543--3335643	15	6.8	14	70	15	69	29	0	2	66	1.13
3335613--3335640	5	5.6	5	100	0	56	35	0	0	64	0.94
3337797--3337896	51	2.0	51	91	0	164	30	21	21	28	1.98
3339276--3339313	17	2.4	17	91	8	62	42	0	0	57	0.98
3340826--3340995	60	2.8	59	84	5	225	34	23	3	38	1.72
3341189--3341303	60	1.9	60	85	3	160	46	4	13	34	1.63
3346443--3346506	10	6.7	9	73	19	58	59	6	3	31	1.38
3347511--3347541	2	15.5	2	100	0	62	48	0	0	51	1.00
3350962--3351036	2	37.5	2	100	0	150	50	0	0	49	1.00
3352627--3354424	224	8.0	225	92	0	2996	36	27	14	22	1.92
3352627--3354420	449	4.0	449	95	0	3184	36	27	14	22	1.92
3355315--3355374	22	2.7	22	79	5	59	46	0	0	53	1.00
3359665--3359784	35	3.3	37	88	6	174	32	5	18	44	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3364237--3364314	37	2.1	37	88	2	113	37	3	17	41	1.68
3364204--3364316	36	3.2	36	80	9	108	35	6	18	39	1.76
3366172--3366272	35	2.8	36	90	6	159	32	5	17	43	1.73
3370768--3370831	21	3.4	20	66	29	59	31	4	18	45	1.70
3370766--3370877	35	3.1	36	90	3	172	32	4	20	42	1.72
3370854--3371055	101	2.0	101	99	0	395	31	8	18	41	1.81
3373715--3373752	20	1.9	20	88	0	58	21	26	10	42	1.85
3377489--3377534	23	2.0	23	83	8	58	39	13	8	39	1.75
3383214--3383254	20	2.0	21	95	4	75	19	39	19	21	1.93
3387065--3387099	15	2.3	15	95	0	61	54	5	31	8	1.54
3389534--3389572	13	2.9	13	96	3	69	33	12	7	46	1.71
3391601--3391641	20	2.0	21	95	4	75	19	39	19	21	1.93
3391674--3391714	20	2.0	20	100	0	82	19	36	19	24	1.95
3396935--3396981	22	2.1	22	100	0	94	38	8	19	34	1.82
3397351--3397395	12	3.8	12	87	0	72	46	2	0	51	1.13
3397343--3397399	24	2.3	25	96	3	107	38	5	0	56	1.22
3406023--3406086	2	32.0	2	100	0	128	50	0	0	50	1.00
3412224--3412782	103	5.5	103	86	4	715	38	9	15	35	1.80
3412224--3412781	202	2.7	202	88	2	769	38	9	15	36	1.80
3412224--3412929	305	2.4	305	81	8	784	39	9	15	35	1.79
3412703--3412861	79	2.0	79	91	0	255	42	7	12	37	1.71
3417744--3417883	56	2.4	59	79	7	160	33	13	24	28	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3417911--3418026	42	2.8	42	74	5	112	34	20	19	25	1.96
3426018--3426086	32	2.1	32	83	5	84	30	23	20	26	1.98
3427286--3427329	18	2.4	18	96	0	79	25	22	15	36	1.94
3432207--3432264	23	2.6	23	86	2	82	32	29	22	15	1.95
3432663--3432726	23	2.8	23	80	0	74	35	26	21	15	1.94
3443085--3443250	39	4.3	39	79	3	154	35	21	24	18	1.96
3443085--3443233	78	1.9	78	80	2	174	35	21	24	18	1.95
3453026--3453087	27	2.3	27	97	0	115	37	4	12	45	1.64
3454390--3454429	21	2.0	21	85	5	55	27	37	25	10	1.88
3460835--3460876	21	2.0	21	85	0	57	30	19	19	30	1.96

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18