genome.fa.s1279.2.7.7.80.10.50.1000.13.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

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   

This is table  13  of  29  ( 3433 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)
2993393--2993792	119	3.3	122	84	4	517	40	15	17	27	1.90
2993843--2994181	137	2.5	139	87	1	459	39	14	18	26	1.90
2994168--2994225	28	2.1	28	96	0	107	24	32	5	37	1.77
2994662--2994701	16	2.5	16	95	0	71	15	40	17	27	1.89
3003720--3003756	9	3.8	10	86	13	51	35	0	16	48	1.46
3003720--3003758	20	2.0	20	94	0	69	35	0	15	48	1.45
3007389--3007432	7	6.3	7	94	0	79	68	0	0	31	0.90
3009060--3009102	18	2.5	17	85	7	61	67	2	4	25	1.22
3008999--3009084	45	1.9	44	81	13	104	60	2	3	33	1.26
3008995--3009114	51	2.4	51	78	12	122	61	3	3	31	1.28
3009459--3009563	37	2.8	37	86	0	147	29	13	14	42	1.83
3010106--3010736	105	6.0	105	91	2	932	21	18	26	33	1.96
3010936--3011011	36	2.1	36	85	4	100	43	14	19	22	1.87
3010913--3011228	104	3.1	103	90	2	467	36	11	20	31	1.88
3011131--3011205	39	1.9	39	83	5	98	37	13	22	26	1.91
3011299--3011466	72	2.3	75	81	9	186	41	13	17	27	1.87
3012614--3013150	183	2.9	183	94	0	959	31	21	20	27	1.98
3017128--3017157	9	3.2	9	95	4	51	80	0	0	20	0.72
3017172--3017311	47	2.9	48	80	13	121	57	1	5	35	1.29
3017303--3017338	18	2.1	18	89	5	56	66	2	5	25	1.27
3017699--3017803	37	2.8	37	86	0	147	29	13	14	42	1.83
3018771--3018815	19	2.4	19	88	0	63	33	33	22	11	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3025895--3025977	22	3.7	22	79	9	87	24	27	26	21	1.99
3025906--3025977	22	3.2	22	82	3	90	22	30	25	22	1.99
3027514--3027559	18	2.5	18	86	10	58	45	19	32	2	1.62
3029364--3029398	17	1.9	19	88	11	56	54	28	0	17	1.43
3040879--3040929	25	2.0	25	96	0	93	25	23	21	29	1.99
3054818--3054887	30	2.3	30	100	0	140	41	17	8	32	1.79
3055689--3055754	31	2.1	31	94	0	114	21	15	34	28	1.93
3056709--3056978	33	7.8	33	78	11	229	24	27	17	30	1.97
3056714--3056865	77	2.0	77	94	0	268	24	30	15	29	1.96
3056785--3056969	99	1.9	99	86	2	264	26	27	17	29	1.97
3056791--3056982	33	5.8	33	85	2	233	25	27	16	30	1.97
3061950--3061982	16	2.1	16	94	0	57	33	9	33	24	1.87
3068748--3068913	27	5.9	27	77	10	172	24	28	16	30	1.97
3068744--3068919	60	3.0	59	76	12	193	24	28	17	30	1.97
3068798--3069083	150	1.9	146	85	5	389	24	30	14	30	1.95
3069011--3069065	27	2.0	27	86	6	76	23	34	14	27	1.94
3069099--3069207	27	3.8	27	76	13	110	29	17	31	22	1.96
3078931--3078974	20	2.2	21	84	8	56	29	2	4	63	1.26
3080315--3080355	18	2.4	16	84	11	55	48	0	7	43	1.30
3081230--3081581	48	7.6	48	80	13	314	16	6	43	32	1.74
3081462--3081581	45	2.7	41	92	5	141	14	5	43	36	1.69
3081102--3081567	231	2.0	229	88	1	691	17	7	44	30	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3081380--3081631	129	2.0	129	80	7	289	17	6	42	33	1.75
3081633--3081704	33	2.2	33	84	0	90	26	9	45	18	1.80
3083305--3083343	17	2.3	17	90	0	60	23	0	5	71	1.05
3083883--3083993	37	2.8	41	66	25	103	52	6	7	34	1.54
3094085--3094136	23	2.3	23	96	0	95	28	7	23	40	1.82
3100730--3100795	24	2.8	24	88	0	105	24	16	25	33	1.96
3104466--3104501	17	2.3	15	90	9	54	69	0	2	27	1.02
3105730--3105828	24	4.4	23	70	17	82	40	6	5	48	1.50
3105730--3105816	42	2.1	41	87	6	122	42	5	4	47	1.48
3105754--3105791	16	2.2	18	90	9	62	39	5	5	50	1.48
3105749--3105792	17	2.4	19	77	11	56	40	6	4	47	1.50
3105800--3105912	37	2.9	36	78	15	120	46	10	3	39	1.56
3105898--3105924	14	1.9	14	100	0	54	40	7	7	44	1.60
3108764--3108821	2	29.0	2	100	0	116	50	0	0	50	1.00
3109534--3109575	20	2.2	20	91	4	68	38	0	2	59	1.10
3115269--3115330	26	2.6	25	80	16	69	27	12	9	50	1.72
3116203--3116346	73	2.0	74	98	1	281	56	17	5	20	1.60
3116607--3116640	2	17.0	2	100	0	68	50	0	0	50	1.00
3117769--3117810	4	10.8	4	89	5	50	16	0	7	76	1.00
3117766--3117803	20	1.9	20	94	0	67	13	0	10	76	1.02
3120862--3120903	7	6.0	7	81	8	50	14	16	14	54	1.71
3120862--3120903	15	3.0	14	83	10	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)
3123658--3123747	9	9.9	9	73	11	76	80	0	17	2	0.82
3123658--3123747	17	5.5	16	71	17	69	80	0	17	2	0.82
3123659--3123721	10	6.4	10	80	8	67	84	0	14	1	0.71
3123668--3123746	25	3.2	24	81	15	81	79	0	18	1	0.80
3123668--3123761	8	11.6	8	77	13	77	78	0	20	1	0.81
3123681--3123761	34	2.4	34	85	8	103	76	0	22	1	0.86
3123679--3123761	26	3.2	25	84	5	103	77	0	21	1	0.84
3123681--3123761	17	4.8	17	78	13	78	76	0	22	1	0.86
3125921--3126148	114	2.0	114	99	0	447	32	15	21	31	1.94
3128684--3128735	22	2.4	22	86	0	68	38	5	13	42	1.68
3129415--3129798	76	5.1	76	96	0	696	23	20	21	34	1.97
3129808--3130223	113	3.7	114	87	2	597	38	13	19	28	1.89
3130555--3130598	3	15.0	3	81	13	56	31	0	2	65	1.05
3130551--3130598	13	3.8	13	80	20	57	31	0	2	66	1.03
3130552--3130598	16	3.0	16	87	3	69	31	0	2	65	1.04
3131942--3132010	3	23.3	3	76	14	63	27	2	1	68	1.13
3132086--3132307	117	1.9	118	81	10	274	38	11	7	42	1.69
3133189--3133221	13	2.4	14	85	5	50	69	18	0	12	1.18
3138804--3138842	20	1.9	21	89	5	62	53	2	28	15	1.55
3139710--3139848	70	2.0	68	92	2	233	43	11	11	33	1.77
3146235--3146282	14	3.5	14	82	2	53	18	12	22	45	1.83
3147769--3147794	3	8.7	3	100	0	52	69	0	0	30	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3163985--3164326	171	2.0	170	81	5	395	27	31	11	29	1.92
3165698--3166085	142	2.7	144	80	6	418	30	18	12	38	1.88
3180464--3180510	24	2.0	24	83	8	60	57	14	2	25	1.49
3187835--3187883	24	2.0	24	100	0	98	40	18	16	24	1.90
3190698--3190744	24	2.0	24	83	8	60	59	14	0	25	1.36
3199768--3199800	16	2.1	16	88	11	50	39	0	0	60	0.97
3199806--3199839	17	2.0	17	88	11	52	29	5	0	64	1.17
3199853--3199894	2	21.0	2	100	0	84	50	0	0	50	1.00
3200072--3200126	27	2.0	27	89	0	83	47	0	0	52	1.00
3209337--3209439	54	1.9	53	84	5	136	36	15	21	26	1.93
3210339--3210975	113	5.7	113	93	0	985	38	14	18	28	1.90
3212418--3212450	16	2.1	16	88	11	50	39	0	0	60	0.97
3212714--3212768	27	2.0	27	86	6	76	47	0	1	50	1.11
3220843--3221028	18	11.0	16	77	18	125	36	3	4	56	1.35
3220875--3220956	10	8.4	10	71	20	59	40	1	2	56	1.20
3220865--3220975	57	2.0	56	87	8	163	39	0	4	54	1.27
3220860--3220974	28	4.1	28	82	10	146	38	0	4	56	1.25
3230552--3230585	17	2.0	17	94	0	59	23	29	14	32	1.94
3231891--3231930	19	2.1	19	90	0	62	30	20	32	17	1.95
3232672--3232703	2	16.5	2	93	6	57	50	0	0	50	1.00
3235192--3235216	13	1.9	13	100	0	50	40	20	24	16	1.91
3245890--3245937	20	2.5	19	83	12	62	22	6	6	64	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3245890--3245938	19	2.6	18	83	9	53	24	6	6	63	1.41
3259323--3259443	59	2.1	59	91	0	197	33	24	18	23	1.97
3263798--3263918	59	2.1	59	93	0	206	33	22	18	26	1.97
3264821--3264886	27	2.4	27	94	2	114	25	13	15	45	1.83
3270900--3270930	16	2.0	15	93	6	53	58	6	0	35	1.24
3276578--3276734	78	2.0	78	94	0	278	35	5	14	45	1.68
3276753--3276819	31	2.1	32	83	8	84	38	4	5	50	1.47
3278918--3278966	17	2.6	19	81	18	59	61	8	2	28	1.36
3281166--3281213	20	2.5	19	77	9	53	41	0	2	56	1.11
3283308--3283368	31	2.0	31	90	0	95	21	44	16	18	1.87

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