genome.fa.s8053.2.7.7.80.10.50.1000.16.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: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6772376

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   

This is table  16  of  32  ( 3749 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)
3031354--3031599	105	2.3	108	79	9	272	43	6	4	45	1.50
3031483--3031542	29	2.1	29	84	6	79	45	5	3	46	1.41
3031422--3031567	69	2.1	69	86	6	199	45	7	2	44	1.46
3031609--3031650	2	21.0	2	100	0	84	50	0	0	50	1.00
3032269--3033643	165	8.3	165	78	7	1190	25	19	24	30	1.98
3032270--3033643	84	16.5	82	76	6	1169	25	19	24	30	1.98
3032280--3033643	249	5.5	245	81	5	1233	24	19	24	30	1.98
3032328--3033475	411	2.8	408	84	3	1464	25	20	24	30	1.98
3037612--3037655	21	2.0	22	83	12	56	65	2	0	31	1.05
3039099--3039147	25	2.0	25	88	8	73	44	8	6	40	1.59
3039089--3039454	34	10.3	33	70	18	154	46	5	2	45	1.40
3039163--3039262	29	3.4	28	72	20	78	46	6	4	44	1.47
3039131--3039262	63	2.1	63	87	2	187	44	5	3	46	1.44
3039124--3039338	102	2.1	99	78	15	235	45	4	3	46	1.40
3039193--3039454	75	3.5	73	77	13	227	46	5	2	45	1.39
3039295--3039463	39	4.3	38	82	10	171	46	4	2	46	1.36
3039351--3039488	39	3.6	40	76	11	121	45	5	2	45	1.42
3039171--3039498	149	2.2	144	77	11	328	45	5	3	45	1.42
3039859--3039920	29	2.1	29	85	5	81	22	6	54	16	1.64
3044820--3044847	14	2.0	14	100	0	56	71	0	0	28	0.86
3045433--3045492	28	2.1	28	90	0	93	28	3	10	58	1.46
3049104--3049164	21	2.8	22	82	5	79	21	6	14	57	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3049310--3049474	88	1.9	89	98	1	323	35	12	10	42	1.76
3051312--3051338	14	1.9	14	100	0	54	37	14	7	40	1.74
3052883--3052951	23	3.0	23	80	0	84	31	24	24	18	1.98
3055479--3055567	25	3.5	25	78	18	78	32	3	2	61	1.24
3055504--3055582	29	2.9	27	80	19	78	35	1	1	62	1.12
3055527--3055585	29	2.2	26	90	9	91	35	1	0	62	1.05
3055629--3055731	29	3.4	28	82	15	109	51	0	6	40	1.35
3056979--3057054	33	2.3	33	77	2	82	44	3	22	28	1.70
3057120--3057235	60	1.9	60	89	0	178	32	17	13	36	1.89
3062923--3062982	3	19.7	3	93	3	102	66	0	1	31	1.01
3064986--3065028	21	2.0	22	86	4	61	30	32	18	18	1.95
3072188--3072226	20	2.0	20	94	0	69	20	33	33	12	1.91
3075085--3075182	29	3.3	29	77	9	101	39	13	10	36	1.78
3075131--3075189	30	2.0	30	81	18	70	40	8	8	42	1.66
3075756--3075795	21	1.9	21	85	10	55	40	7	2	50	1.44
3078779--3078805	13	2.1	13	100	0	54	37	18	7	37	1.79
3085907--3085954	19	2.5	20	82	6	62	33	14	6	45	1.70
3097474--3097509	18	2.0	18	94	0	63	47	5	8	38	1.57
3098669--3098717	21	2.2	22	82	13	57	48	4	6	40	1.47
3098863--3098922	4	15.0	4	89	0	84	31	25	18	25	1.97
3098863--3098922	16	3.8	16	95	0	111	31	25	18	25	1.97
3098923--3098985	2	31.5	2	96	0	117	0	0	47	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3101811--3101871	16	3.8	16	88	0	95	54	21	14	9	1.69
3110126--3110182	6	9.3	6	76	16	55	80	0	17	1	0.79
3110128--3110166	13	2.7	14	81	18	53	82	0	15	2	0.79
3110130--3110187	19	3.0	18	76	18	55	75	0	20	3	0.94
3111874--3111925	2	27.5	2	86	11	74	48	1	0	50	1.12
3113031--3113094	17	3.9	16	74	12	51	26	3	0	70	1.02
3113020--3113084	30	2.2	29	81	15	71	27	1	0	70	0.96
3113152--3113177	5	5.2	5	100	0	52	19	0	0	80	0.71
3113203--3113262	14	4.1	14	71	14	50	38	3	0	58	1.15
3114797--3114851	16	3.2	17	79	20	62	58	0	0	41	0.98
3114797--3114851	19	3.2	17	80	16	69	58	0	0	41	0.98
3114828--3114915	23	3.9	23	76	7	92	56	1	2	39	1.19
3115762--3115793	14	2.1	16	88	11	50	40	0	0	59	0.97
3119899--3119932	14	2.4	14	86	13	52	82	0	0	17	0.67
3120274--3120304	15	2.1	15	93	0	53	54	0	0	45	0.99
3120393--3120417	11	2.3	11	100	0	50	64	0	0	36	0.94
3126082--3126123	21	2.0	21	86	9	59	26	40	0	33	1.56
3126930--3126972	5	9.0	5	80	10	54	58	0	2	39	1.11
3126930--3126972	14	3.0	15	83	10	54	58	0	2	39	1.11
3132948--3132982	18	2.1	18	89	10	56	60	5	17	17	1.55
3134085--3134116	17	2.0	17	88	11	50	28	6	31	34	1.82
3135257--3135332	22	3.4	22	75	7	71	27	14	23	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3150467--3150493	14	1.9	14	100	0	54	25	0	44	29	1.54
3156355--3156435	6	12.5	6	73	17	56	79	3	4	12	1.03
3156346--3156435	19	4.7	19	72	6	74	80	3	4	12	0.99
3156346--3156435	40	2.2	42	76	7	96	80	3	4	12	0.99
3156346--3156398	22	2.4	22	81	12	65	84	3	0	11	0.73
3156385--3156448	21	3.3	20	66	29	57	75	3	9	12	1.16
3156456--3156622	3	56.7	3	68	18	68	67	1	2	28	1.14
3157767--3157801	15	2.4	14	90	9	52	74	0	2	22	0.95
3157761--3157799	18	2.0	20	90	9	64	74	0	5	20	1.01
3157827--3157856	2	15.5	2	93	6	53	46	0	0	53	1.00
3157799--3157887	46	1.9	46	86	8	128	48	4	1	46	1.30
3157836--3158053	38	5.7	37	70	15	124	50	8	2	39	1.45
3157834--3158009	40	4.5	39	68	17	105	49	7	2	40	1.45
3157947--3158045	40	2.5	40	88	3	148	47	10	2	40	1.49
3158791--3158850	17	3.4	17	81	6	57	30	3	6	60	1.39
3159753--3159800	12	4.1	12	78	5	53	31	52	2	14	1.54
3163060--3163508	229	2.0	227	94	1	783	45	7	7	39	1.61
3163574--3163619	20	2.3	19	89	10	74	54	10	17	17	1.70
3163741--3163787	20	2.4	19	89	10	76	55	10	17	17	1.69
3163745--3163792	20	2.6	18	84	15	62	56	10	14	18	1.66
3166020--3166084	21	3.1	21	80	6	69	40	15	29	15	1.88
3166118--3166183	33	2.0	33	90	0	105	28	0	48	22	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3167975--3168023	19	2.6	19	93	0	80	30	0	10	59	1.31
3167975--3168035	19	3.3	19	86	2	70	32	0	11	55	1.36
3168142--3169703	198	7.9	198	98	0	3049	36	16	16	30	1.91
3168142--3169703	593	2.6	593	98	0	3054	36	16	16	30	1.91
3168142--3169703	395	3.9	395	99	0	3061	36	16	16	30	1.91
3171177--3171251	3	25.0	3	79	0	78	34	5	34	25	1.79
3172448--3173141	183	3.8	183	96	1	1250	36	14	16	33	1.89
3173137--3173179	22	1.9	23	95	4	79	30	9	13	46	1.75
3176306--3176369	23	2.8	23	87	0	92	35	6	20	37	1.78
3176306--3176378	23	3.2	23	82	7	85	34	5	20	39	1.76
3176524--3176590	30	2.2	30	82	10	75	52	4	0	43	1.21
3176735--3176798	23	2.8	23	87	0	92	35	6	20	37	1.78
3176735--3176807	23	3.2	23	82	7	85	34	5	20	39	1.76
3176208--3177043	429	1.9	429	98	0	1604	39	8	12	39	1.73
3177075--3177125	25	2.0	25	92	0	84	33	7	19	39	1.81
3177374--3177410	18	2.1	18	89	0	56	32	5	10	51	1.60
3177366--3177412	24	2.0	24	86	0	67	34	4	14	46	1.64
3177669--3177794	39	3.2	39	97	0	234	48	20	13	17	1.81
3178199--3178262	23	2.8	23	85	0	83	35	7	20	35	1.82
3178220--3178271	23	2.3	23	90	6	79	34	1	19	44	1.62
3181823--3181871	21	2.3	21	82	0	62	12	10	67	10	1.43
3181847--3181871	9	2.8	9	100	0	50	12	12	68	8	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3185302--3185581	75	3.8	74	85	3	366	41	13	11	33	1.81
3185302--3185581	148	1.9	148	86	2	402	41	13	11	33	1.81
3185662--3185893	112	2.1	112	94	0	410	46	12	12	28	1.78
3186843--3186884	20	2.2	19	87	8	59	47	0	4	47	1.23
3191743--3191775	17	1.9	17	88	11	50	72	0	3	24	0.98
3195364--3195397	16	2.1	16	88	0	50	50	0	2	47	1.16
3195439--3195472	16	2.0	18	88	11	54	26	2	5	64	1.30
3195941--3196188	130	1.9	130	92	0	415	35	12	15	36	1.86
3196585--3196660	35	2.2	35	92	0	125	35	1	23	39	1.63
3197594--3197620	2	13.5	2	100	0	54	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