genome.fa.s8488.2.7.7.80.10.50.1000.12.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: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12876159

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   

This is table  12  of  54  ( 6450 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)
2855272--2855326	10	5.5	10	93	4	85	23	7	0	69	1.14
2857096--2857146	21	2.4	21	96	0	93	33	13	25	27	1.94
2857685--2858023	169	2.0	169	100	0	678	32	12	23	32	1.91
2859838--2859894	7	8.1	7	78	7	62	78	1	17	1	0.91
2861089--2861654	117	4.8	118	81	5	630	40	13	20	25	1.89
2861089--2861678	234	2.5	234	85	2	765	39	14	20	26	1.90
2861089--2861726	117	5.4	118	80	5	519	39	13	20	26	1.90
2862015--2862111	35	2.8	35	81	9	94	35	4	4	56	1.37
2862124--2862156	16	1.9	18	88	11	52	36	0	6	57	1.23
2865854--2865898	19	2.3	20	88	3	65	33	2	8	55	1.43
2876747--2876785	20	2.0	20	89	0	60	33	23	10	33	1.88
2900255--2900405	73	2.1	73	96	0	275	49	1	23	25	1.58
2900404--2900448	23	2.0	22	86	4	63	20	2	42	35	1.64
2907385--2907473	34	2.6	35	80	7	101	43	22	13	20	1.86
2909236--2909281	19	2.4	19	100	0	92	45	15	4	34	1.66
2910250--2910312	29	2.2	29	85	0	90	30	23	6	39	1.80
2910595--2910624	15	2.1	15	93	6	53	70	0	0	30	0.88
2910732--2910797	30	2.2	30	75	2	71	45	9	16	28	1.78
2915924--2915986	21	2.9	22	71	4	65	34	14	12	38	1.84
2916576--2916607	13	2.4	14	94	5	57	28	6	12	53	1.62
2917286--2917324	17	2.4	17	86	4	53	48	23	2	25	1.63
2921917--2922215	85	3.5	85	93	1	485	30	21	16	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2928807--2928971	58	2.8	57	79	8	179	35	6	23	35	1.81
2928807--2928971	29	5.7	29	76	4	152	35	6	23	35	1.81
2935529--2935676	58	2.6	56	81	6	156	38	6	21	33	1.80
2935522--2935676	29	5.4	29	74	6	136	37	6	21	34	1.80
2951596--2951668	3	24.7	3	94	2	130	34	1	0	64	1.02
2951820--2951858	16	2.5	16	95	4	71	7	58	17	15	1.59
2953726--2953768	19	2.3	19	84	8	52	32	4	0	62	1.15
2953740--2953801	22	2.9	22	73	19	60	30	4	1	62	1.25
2964247--2964304	7	8.1	7	81	11	73	84	0	15	0	0.62
2964236--2964301	18	3.7	17	79	16	71	81	0	16	1	0.76
2964236--2964303	23	3.1	21	82	16	84	82	0	16	1	0.75
2964251--2964303	11	4.9	11	81	11	65	84	0	15	0	0.61
2964252--2964303	16	3.2	16	83	5	70	84	0	15	0	0.62
2964236--2964304	27	2.6	27	80	17	81	82	0	15	1	0.74
2964237--2964305	22	3.0	23	80	18	81	81	0	17	1	0.77
2964615--2964659	16	2.8	16	83	10	56	28	8	6	55	1.56
2965440--2965831	83	4.7	83	96	1	734	28	13	21	36	1.92
2965440--2965831	165	2.4	166	96	1	734	28	13	21	36	1.92
2966563--2967237	116	5.9	117	92	3	996	36	12	21	30	1.90
2967553--2967634	3	27.3	3	92	4	139	34	1	0	64	1.01
2967787--2967825	16	2.5	16	95	4	71	7	58	17	15	1.59
2976827--2977190	181	2.0	183	98	1	705	31	21	19	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2986874--2986928	20	2.7	20	82	5	65	34	16	29	20	1.94
2987176--2987243	30	2.4	28	78	9	66	29	5	7	57	1.50
2991430--2991478	21	2.5	19	83	9	55	34	20	14	30	1.92
2999558--2999603	3	16.0	3	82	8	51	58	0	0	41	0.98
2999558--2999599	14	3.0	14	85	0	57	57	0	0	42	0.99
2999558--2999603	20	2.3	20	88	7	67	58	0	0	41	0.98
3000012--3000093	42	2.0	42	92	0	137	31	21	21	24	1.98
3000029--3000094	20	3.2	20	66	16	53	33	21	21	24	1.97
3000102--3001033	177	5.3	176	92	1	1488	31	21	16	30	1.95
3000070--3000387	90	3.6	89	66	13	249	32	22	16	27	1.96
3001026--3001073	21	2.3	21	92	0	78	27	33	12	27	1.92
3002654--3002885	52	4.5	52	82	6	244	24	23	16	35	1.95
3002689--3002882	104	1.9	105	86	5	286	24	22	15	37	1.93
3004356--3004394	20	2.0	20	90	10	62	2	15	0	82	0.79
3004360--3004428	27	2.4	31	83	11	92	4	15	0	79	0.88
3004354--3004432	10	8.0	10	71	20	51	3	16	0	79	0.87
3011615--3011647	12	2.7	12	95	4	57	21	21	0	57	1.41
3011621--3011658	18	2.1	19	85	5	51	21	26	0	52	1.47
3012434--3012475	3	14.3	3	85	5	59	30	2	2	64	1.19
3016776--3016804	14	2.0	15	93	6	51	62	0	0	37	0.96
3020079--3020130	18	2.8	18	85	5	68	51	0	1	46	1.12
3020093--3020132	17	2.4	17	88	12	57	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3020846--3020882	17	2.1	18	90	5	58	24	21	16	37	1.93
3020943--3021017	17	4.4	17	77	5	71	37	18	5	38	1.74
3034897--3035507	225	2.8	220	82	6	685	31	16	19	32	1.94
3035379--3035481	42	2.5	42	77	3	109	27	21	20	31	1.98
3035536--3035716	36	5.0	36	92	1	272	37	20	18	23	1.94
3035736--3035841	42	2.5	42	87	0	140	28	13	20	37	1.90
3036617--3036664	25	1.9	25	100	0	96	35	31	16	16	1.92
3038476--3038620	55	2.6	55	88	4	211	31	15	26	26	1.96
3040678--3040712	13	2.6	14	86	9	54	42	5	17	34	1.73
3040743--3040781	20	1.9	19	85	10	51	64	10	0	25	1.25
3054547--3054777	72	3.2	72	68	12	218	24	26	22	26	2.00
3055821--3055979	36	4.4	36	89	4	230	37	21	16	24	1.93
3055821--3055998	72	2.5	72	88	0	248	39	19	16	24	1.92
3055821--3055998	36	4.9	36	85	7	209	39	19	16	24	1.92
3056015--3056149	42	3.2	41	81	6	155	29	18	19	32	1.96
3058731--3058875	55	2.6	54	89	4	209	31	15	26	26	1.96
3061411--3061466	20	2.8	20	97	0	103	26	19	28	25	1.99
3065292--3065357	9	7.0	9	71	10	51	16	27	27	28	1.97
3065298--3065355	19	3.0	19	85	7	64	18	27	25	27	1.98
3065292--3065357	29	2.3	28	82	7	71	16	27	27	28	1.97
3065360--3065389	9	3.3	9	95	0	51	26	43	20	10	1.83
3072423--3072521	10	10.3	9	76	12	81	17	28	26	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3072423--3072521	19	5.2	19	77	13	80	17	28	26	28	1.97
3079508--3079564	20	2.8	20	100	0	114	19	24	21	35	1.96
3079664--3079805	54	2.6	54	87	3	196	30	15	26	27	1.96
3080073--3080108	18	1.9	18	88	5	54	25	0	8	66	1.19
3085432--3085472	20	2.0	20	86	9	57	51	0	4	43	1.23
3087485--3087637	81	1.9	81	83	0	198	31	25	11	32	1.91
3087813--3087967	55	2.8	55	85	2	197	29	19	16	35	1.93
3087923--3088783	54	15.9	54	88	1	1197	32	18	16	32	1.93
3088676--3088758	26	3.1	26	63	19	62	33	16	19	30	1.94
3093878--3094024	55	2.7	55	88	1	206	28	19	17	34	1.95
3093929--3094841	54	16.9	54	84	1	965	33	17	16	32	1.92
3097409--3097467	25	2.3	25	82	5	64	81	6	8	3	0.97
3099100--3099147	21	2.3	21	85	0	69	35	22	8	33	1.84
3101758--3101805	20	2.5	19	86	6	62	31	10	31	27	1.90
3102256--3102993	55	13.4	55	90	0	1084	35	10	20	34	1.86
3106993--3107120	62	2.1	62	100	0	256	30	8	22	38	1.84
3108594--3108657	27	2.4	27	100	0	128	31	0	21	46	1.52
3109070--3109095	5	5.2	5	100	0	52	23	57	19	0	1.40
3111708--3111741	2	16.5	2	93	6	59	47	0	2	50	1.16
3116009--3116068	2	30.0	2	100	0	120	50	0	0	50	1.00
3118444--3118485	15	2.8	15	100	0	84	38	0	26	35	1.57
3118632--3118684	21	2.5	21	93	0	97	33	15	18	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3119045--3119133	44	2.0	44	97	0	169	28	11	24	35	1.90
3133136--3133191	21	2.7	21	80	2	69	46	23	10	19	1.81
3133136--3133191	20	2.7	21	80	5	69	46	23	10	19	1.81
3135477--3135509	17	1.9	18	88	11	52	33	9	15	42	1.78
3136580--3136628	19	2.7	17	84	9	53	26	20	28	24	1.99
3136574--3136759	65	2.9	65	81	5	218	26	19	23	30	1.98
3136574--3136809	129	1.8	130	81	8	302	25	19	24	30	1.98
3136600--3136809	65	3.2	64	78	12	223	25	19	24	30	1.98
3137107--3137145	16	2.4	16	91	4	60	41	10	5	43	1.61
3137286--3137334	2	24.5	2	100	0	98	51	0	0	48	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   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54