genome.fa.s9634.2.7.7.80.10.50.1000.15.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

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   

This is table  15  of  78  ( 9351 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)
3288923--3289016	2	47.0	2	70	16	52	42	3	5	48	1.41
3289195--3289266	35	2.1	35	89	0	108	40	11	8	40	1.71
3289207--3289265	16	3.5	16	70	28	50	40	11	8	38	1.72
3289475--3289602	2	66.5	2	72	20	78	46	3	1	48	1.30
3289475--3289602	15	8.9	15	73	14	76	46	3	1	48	1.30
3289476--3289602	54	2.4	53	77	13	127	45	3	1	48	1.30
3299752--3299867	13	8.7	13	69	19	62	39	6	6	47	1.55
3299751--3299893	66	2.2	65	80	10	166	41	7	5	45	1.56
3299836--3299931	15	6.5	15	65	29	55	46	3	5	44	1.41
3299852--3299904	24	2.3	23	78	12	56	47	5	3	43	1.45
3299875--3299942	18	3.6	19	78	13	70	51	1	4	42	1.31
3300236--3300340	56	1.9	56	92	5	180	22	5	11	60	1.52
3300248--3300364	56	2.2	55	86	6	159	25	5	7	60	1.47
3303462--3303500	16	2.4	17	82	4	53	25	5	10	58	1.51
3304828--3304872	20	2.2	21	96	4	83	60	0	11	28	1.31
3313132--3313168	2	18.5	2	100	0	74	51	0	0	48	1.00
3313217--3313404	84	2.2	85	83	5	247	31	17	19	30	1.95
3313217--3313427	84	2.5	84	81	6	241	32	18	19	30	1.95
3318491--3318902	127	3.3	126	83	6	493	27	27	17	27	1.98
3319215--3319261	17	2.7	18	77	16	53	40	0	0	59	0.97
3320763--3320826	28	2.3	27	78	10	65	21	12	6	59	1.55
3322159--3322228	28	2.4	27	81	11	86	28	1	18	51	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3326048--3326123	38	2.0	38	97	0	143	40	5	14	39	1.68
3333183--3333238	28	2.0	28	82	0	67	35	14	14	35	1.86
3333373--3333485	60	1.9	60	90	7	185	34	14	16	34	1.89
3337694--3337745	21	2.5	21	96	0	95	26	21	21	30	1.98
3338471--3338687	31	6.9	31	71	7	161	31	18	19	29	1.96
3338469--3338689	63	3.5	63	88	3	313	31	18	19	30	1.96
3338537--3338691	31	4.9	32	77	9	174	30	18	19	30	1.96
3341695--3341726	15	2.1	15	94	0	55	6	25	15	53	1.65
3343336--3343386	20	2.5	20	87	0	66	11	15	11	60	1.58
3352281--3352335	14	4.2	14	73	17	55	7	9	29	54	1.58
3352280--3352330	24	2.1	24	92	0	84	9	7	29	52	1.62
3352295--3352320	10	2.6	10	100	0	52	7	11	30	50	1.67
3353425--3353475	16	3.3	16	89	5	79	11	9	17	60	1.57
3354867--3354954	10	9.1	10	74	12	85	18	22	30	28	1.97
3354867--3354956	19	4.7	19	87	6	119	17	24	30	27	1.97
3354950--3355007	17	3.4	17	97	0	107	17	43	24	15	1.87
3354997--3355026	7	4.4	7	91	8	53	16	30	30	23	1.96
3354997--3355022	13	2.0	13	100	0	52	15	30	30	23	1.95
3362139--3362207	10	7.1	10	76	12	72	18	23	30	27	1.98
3362139--3362209	19	3.7	19	88	5	90	18	25	29	26	1.98
3362203--3362260	17	3.4	17	92	0	98	18	43	22	15	1.88
3375147--3375256	51	2.2	51	90	1	177	34	17	16	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3384267--3384444	60	3.0	60	81	8	168	44	4	19	31	1.71
3387216--3387259	16	2.8	16	79	3	54	56	0	0	43	0.99
3387214--3387264	23	2.2	22	89	6	75	62	0	0	37	0.95
3387307--3387342	12	3.1	12	88	4	56	47	0	0	52	1.00
3388359--3388843	131	3.8	131	86	4	591	39	16	9	33	1.82
3388603--3388859	120	2.1	120	91	1	417	40	17	9	33	1.82
3390897--3390994	3	32.7	3	92	4	162	64	0	1	34	1.01
3392167--3392227	14	4.4	14	75	6	52	29	18	6	45	1.74
3392176--3392226	15	3.6	14	79	7	59	29	17	5	47	1.71
3392435--3392823	138	2.8	138	87	1	566	31	13	13	42	1.82
3395567--3395620	16	3.4	16	78	14	58	37	0	0	62	0.95
3395567--3395610	23	1.9	23	90	0	70	36	0	0	63	0.95
3396883--3397022	44	3.2	44	100	0	280	25	13	8	52	1.68
3396915--3396988	25	3.2	25	61	28	63	22	13	10	52	1.71
3402013--3402043	14	2.2	14	94	0	53	19	29	6	45	1.75
3404739--3404798	29	2.0	31	90	6	97	36	6	15	41	1.73
3404996--3405037	21	2.0	21	95	0	75	23	21	28	26	1.99
3405324--3405393	34	2.1	32	89	5	104	31	15	31	21	1.95
3405900--3405934	17	2.1	17	88	0	52	71	11	2	14	1.25
3408697--3408744	20	2.4	20	85	0	60	35	16	10	37	1.83
3413939--3414083	47	3.1	47	64	20	115	24	18	19	37	1.94
3413902--3414081	91	2.0	91	94	0	315	23	18	18	38	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3414332--3414401	35	2.0	35	91	0	113	32	11	20	35	1.88
3424287--3424339	23	2.3	23	83	6	72	32	1	3	62	1.24
3425228--3425476	109	2.3	108	81	12	269	22	14	17	46	1.84
3425266--3425476	109	1.9	107	83	11	270	21	13	17	46	1.83
3426506--3426566	22	2.7	23	97	2	115	44	11	4	39	1.62
3426552--3426837	131	2.2	131	91	1	457	33	11	16	39	1.84
3427629--3427687	31	2.0	29	83	12	75	50	0	1	47	1.11
3427652--3427873	116	1.9	113	82	4	268	44	8	8	38	1.65
3429295--3429364	3	24.0	3	77	11	74	58	0	0	41	0.98
3429284--3429364	18	4.3	18	82	14	94	56	0	0	43	0.99
3429517--3430381	76	11.4	76	95	0	1525	35	21	19	24	1.96
3431447--3431601	54	3.0	50	83	5	150	26	25	14	34	1.94
3437926--3437967	7	6.0	7	78	10	50	54	14	16	14	1.71
3439457--3439487	16	1.9	16	93	0	53	67	0	0	32	0.91
3439433--3439509	24	3.4	22	76	20	79	64	2	3	28	1.24
3439478--3439531	28	2.0	27	85	3	72	59	1	5	33	1.31
3439999--3440057	31	2.0	29	83	12	75	50	0	1	47	1.11
3440341--3440400	3	20.3	3	86	3	86	70	0	1	28	0.97
3441693--3441762	3	24.0	3	77	11	74	58	0	0	41	0.98
3441682--3441762	18	4.3	18	82	14	94	56	0	0	43	0.99
3445597--3445655	23	2.6	23	94	0	100	25	27	28	18	1.98
3446152--3446185	2	17.0	2	100	0	68	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3447355--3447485	63	2.1	62	80	8	140	25	24	20	29	1.99
3449437--3449475	20	2.0	20	89	0	60	41	33	5	20	1.74
3450746--3450897	2	76.0	2	100	0	304	50	50	0	0	1.00
3451364--3451388	3	8.3	3	100	0	50	68	32	0	0	0.90
3454281--3454306	13	2.0	13	100	0	52	46	7	7	38	1.61
3453838--3454764	465	2.0	465	99	0	1836	36	17	11	34	1.85
3457474--3457780	30	10.2	30	72	15	177	52	0	7	39	1.35
3457474--3457826	59	5.9	59	71	11	213	52	1	7	38	1.37
3457543--3457597	25	2.2	26	83	3	67	50	1	7	40	1.40
3457450--3457645	93	2.1	94	82	10	235	52	1	5	41	1.30
3457474--3457780	89	3.4	86	73	12	235	52	0	7	39	1.35
3462545--3462605	16	3.9	16	76	4	70	55	1	1	40	1.19
3462545--3462617	11	6.8	11	72	12	53	52	2	1	43	1.24
3462943--3462977	7	5.0	7	89	0	52	31	0	2	65	1.07
3472253--3472295	20	2.2	20	86	0	59	32	23	13	30	1.93
3476115--3476173	19	2.8	21	80	15	77	28	18	25	27	1.98
3479249--3479287	18	2.1	19	90	4	62	64	5	5	25	1.35
3485391--3485909	264	2.0	264	85	1	700	29	11	32	26	1.91
3491965--3492031	32	2.1	32	100	0	134	8	38	13	38	1.76
3492425--3492472	23	2.1	23	92	0	78	35	8	18	37	1.81
3492494--3493190	198	3.5	199	82	7	819	31	15	14	38	1.88
3495266--3495339	18	4.1	18	87	6	114	6	36	1	55	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3495524--3495623	33	3.0	33	95	0	182	25	48	0	27	1.52
3495660--3495701	21	2.0	21	90	0	66	14	26	11	47	1.78
3495782--3495813	15	2.1	15	94	0	55	12	56	9	21	1.64
3498108--3498960	182	4.7	182	91	2	1288	27	16	15	40	1.88
3498108--3498960	363	2.4	362	89	3	1322	27	16	15	40	1.88
3501583--3501619	18	2.1	18	90	10	58	32	2	5	59	1.34
3504626--3504821	55	3.5	55	82	4	209	31	23	15	29	1.95
3504733--3505129	51	7.9	51	87	6	553	26	28	15	28	1.96
3506452--3506575	16	7.8	16	72	21	86	6	20	0	71	1.13
3506452--3506573	8	14.4	8	67	28	51	6	20	0	72	1.12

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