genome.fa.s1129.2.7.7.80.10.50.1000.53.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   

This is table  53  of  89  ( 10573 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)
12045058--12045098	19	2.1	20	90	4	66	75	4	0	19	0.98
12049296--12049334	16	2.4	17	91	8	71	33	0	5	61	1.18
12051977--12052029	20	2.6	20	82	8	63	33	15	20	30	1.93
12059099--12059147	18	2.5	20	81	15	59	34	18	20	26	1.95
12064987--12065258	31	8.8	31	85	1	312	23	15	20	40	1.91
12064987--12065258	93	2.9	93	86	2	368	23	15	20	40	1.91
12066002--12066053	22	2.4	22	83	6	61	23	21	30	25	1.99
12070264--12070497	31	7.5	31	90	0	351	21	17	21	39	1.93
12076367--12076444	20	3.8	20	80	6	86	34	25	15	24	1.95
12087269--12087576	126	2.5	124	81	4	314	37	21	27	12	1.90
12087263--12087580	42	7.6	42	73	6	223	38	21	27	12	1.89
12087799--12088175	117	3.2	115	84	4	470	43	7	32	16	1.77
12088635--12088667	16	2.1	16	88	5	50	27	0	18	54	1.44
12090413--12090537	33	3.8	33	75	6	105	35	4	8	51	1.54
12090395--12090544	65	2.3	64	78	13	162	36	6	8	50	1.57
12090597--12090669	32	2.3	32	100	0	146	24	8	16	50	1.72
12094945--12095270	181	1.8	178	80	5	397	35	11	10	42	1.75
12098106--12098165	23	2.7	22	82	12	70	33	21	16	28	1.95
12099567--12099618	19	2.7	19	96	0	95	26	21	30	21	1.98
12099567--12099634	19	3.7	17	90	5	55	26	20	29	23	1.99
12099606--12099814	65	3.2	64	76	9	210	25	19	23	31	1.98
12100089--12100118	14	2.1	14	100	0	60	0	20	0	80	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12100470--12100514	22	2.0	22	100	0	90	35	13	17	33	1.89
12103226--12103385	65	2.5	64	82	6	189	28	18	22	31	1.97
12103397--12103446	20	2.5	20	100	0	100	14	20	32	34	1.92
12111524--12111572	19	2.7	17	84	9	53	26	20	28	24	1.99
12111523--12111730	64	3.3	63	80	8	224	27	18	21	32	1.97
12111543--12111752	64	3.3	64	79	7	219	26	18	22	32	1.97
12112038--12112065	12	2.3	12	100	0	56	0	21	0	78	0.75
12113308--12113340	17	1.9	17	93	0	57	42	24	12	21	1.86
12124923--12124956	13	2.6	13	100	0	68	5	17	0	76	0.98
12124923--12124966	13	3.4	13	90	6	54	4	20	0	75	0.98
12124951--12125014	28	2.3	29	78	13	71	9	15	12	62	1.54
12125048--12125079	9	3.6	9	95	0	55	6	0	12	81	0.87
12127006--12127045	21	1.9	21	89	0	62	35	15	27	22	1.94
12130822--12130867	9	5.1	9	86	0	56	50	0	50	0	1.00
12131145--12131251	56	1.9	56	82	3	135	45	8	11	34	1.70
12131733--12131846	52	2.2	52	82	0	138	39	11	12	36	1.79
12136721--12136792	3	24.3	3	75	13	69	59	0	0	40	0.97
12136710--12136771	14	4.5	14	71	22	51	56	0	0	43	0.99
12136721--12136810	31	2.9	31	81	14	82	60	0	2	37	1.09
12136969--12138244	151	8.4	151	96	0	2304	34	23	20	21	1.97
12136969--12138244	227	5.6	228	96	0	2357	34	23	20	21	1.97
12136969--12138244	378	3.4	379	97	0	2396	34	23	20	21	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12138248--12138568	163	2.0	165	93	1	556	38	12	13	35	1.82
12139083--12139137	22	2.5	22	90	0	92	40	12	10	36	1.79
12142999--12143316	160	2.0	159	98	1	613	30	16	21	32	1.95
12148234--12148274	17	2.4	16	84	11	55	70	0	2	26	0.99
12149004--12149086	38	2.2	39	82	10	100	55	1	2	40	1.21
12150524--12150580	11	4.7	12	78	18	55	56	0	0	43	0.99
12150535--12150603	3	23.3	3	74	14	63	59	0	0	40	0.97
12150524--12150603	21	3.9	22	78	20	93	57	0	0	42	0.98
12150777--12150835	30	1.9	31	89	3	93	40	22	8	28	1.83
12151157--12151196	21	1.9	21	89	0	62	45	12	10	32	1.75
12151417--12151459	2	21.5	2	100	0	86	48	0	0	51	1.00
12155721--12155750	6	5.0	6	95	0	51	46	0	33	20	1.51
12161298--12161549	72	3.5	72	76	8	303	53	8	17	20	1.69
12161281--12161574	146	2.0	147	99	0	581	50	8	17	23	1.72
12164095--12164152	31	1.9	30	89	3	89	31	22	3	43	1.70
12164095--12164173	30	2.6	31	82	6	90	34	22	2	40	1.68
12165472--12165498	2	13.5	2	100	0	54	51	0	0	48	1.00
12167400--12167465	34	1.9	34	85	11	91	43	3	4	48	1.38
12170289--12170335	23	2.0	23	100	0	94	57	4	12	25	1.54
12180072--12180186	55	2.1	54	96	3	221	33	14	11	40	1.82
12180085--12180177	27	3.4	27	66	10	80	26	16	12	44	1.84
12182507--12182556	13	3.1	17	70	24	54	24	18	14	44	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12183838--12183896	24	2.5	24	85	0	73	28	32	15	23	1.95
12185195--12185263	21	3.2	21	84	15	88	28	0	31	39	1.57
12185206--12185269	21	3.0	21	95	0	119	31	0	29	39	1.57
12185883--12185962	24	3.4	24	82	1	99	25	21	22	31	1.98
12207525--12208306	404	1.9	404	98	0	1512	40	13	17	28	1.88
12215248--12215281	14	2.3	15	85	10	52	23	0	17	58	1.38
12217275--12217340	18	3.8	17	75	11	62	27	18	13	40	1.88
12219486--12219530	18	2.4	19	85	3	56	44	31	2	22	1.65
12219500--12219573	26	2.8	26	93	0	121	47	32	0	20	1.50
12226170--12226248	23	3.7	23	86	9	114	18	20	29	31	1.97
12227531--12227584	2	27.0	2	100	0	108	50	0	0	50	1.00
12228133--12228162	16	1.9	15	93	6	51	66	0	13	20	1.24
12229361--12229408	21	2.3	21	96	0	87	27	14	20	37	1.92
12229361--12229415	21	2.6	21	83	16	78	27	18	18	36	1.94
12233930--12233969	21	1.9	21	89	0	62	52	5	2	40	1.37
12235239--12235272	16	2.1	16	88	0	50	52	0	2	44	1.16
12235144--12235312	93	1.9	90	80	8	202	47	1	4	46	1.31
12235446--12235546	29	3.4	29	68	21	84	48	0	0	49	1.14
12235440--12235558	59	2.0	58	81	12	136	49	0	1	47	1.17
12235521--12235563	22	2.0	22	81	9	52	55	0	2	41	1.12
12240419--12240460	21	2.0	22	90	4	68	26	23	26	23	2.00
12241815--12241896	40	2.0	40	97	0	155	40	4	31	23	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12244741--12245383	14	45.9	14	98	0	1007	20	0	22	57	1.41
12246000--12246044	22	2.0	22	86	0	63	35	20	20	24	1.96
12259142--12259832	344	2.0	344	98	0	1328	33	12	13	39	1.83
12260719--12261303	27	22.3	26	65	22	103	50	3	4	41	1.39
12260720--12261329	20	30.8	19	67	20	197	50	3	4	41	1.40
12260725--12260872	11	14.5	11	67	20	72	51	3	2	42	1.32
12260977--12261031	11	5.3	11	73	18	55	49	1	1	47	1.23
12261054--12261327	82	3.4	80	75	16	244	54	2	4	37	1.35
12261135--12261285	13	11.9	13	71	24	76	55	1	4	37	1.32
12261100--12261446	130	2.6	129	75	16	291	54	2	6	36	1.40
12261213--12261478	59	4.4	59	72	19	180	54	2	6	36	1.37
12261299--12261347	19	2.5	19	86	3	62	46	2	12	38	1.53
12260716--12261327	2	313.0	2	64	21	178	50	3	4	41	1.40
12261385--12261482	13	6.8	14	69	26	71	58	1	5	35	1.27
12261377--12261482	7	14.7	7	73	11	72	58	0	4	35	1.25
12261204--12261482	42	6.2	44	71	18	141	54	2	6	36	1.37
12262076--12262109	17	2.0	17	94	0	59	47	17	14	20	1.83
12262719--12262776	16	3.7	16	75	11	57	44	13	17	24	1.85
12263535--12263582	24	2.1	23	84	7	62	52	0	10	37	1.36
12267312--12267369	24	2.5	24	82	2	73	12	18	20	48	1.80
12277019--12277162	47	3.1	47	82	3	175	24	21	11	43	1.85
12285140--12285170	8	3.9	8	100	0	62	77	0	22	0	0.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12286333--12286404	17	4.2	16	75	12	63	37	12	11	38	1.79
12292230--12292341	48	2.4	47	84	4	145	33	22	21	22	1.97
12292243--12292341	47	2.1	48	86	1	137	35	23	19	22	1.96
12298406--12298447	17	2.5	17	77	14	50	16	23	2	57	1.51
12300927--12301005	39	2.0	40	82	7	99	22	13	44	18	1.86
12300980--12301023	20	2.2	20	95	0	79	25	15	43	15	1.87
12301083--12301173	33	2.8	33	73	17	100	16	20	29	32	1.95
12301377--12301402	13	2.0	13	100	0	52	23	0	23	53	1.46
12303795--12304263	14	34.4	14	67	18	161	47	3	6	42	1.44
12303795--12304089	42	6.8	42	81	7	322	48	2	6	42	1.44

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   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89