genome.fa.s9175.2.7.7.80.10.50.1000.16.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: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  10629029

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   

This is table  16  of  51  ( 6037 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)
3109297--3109422	55	2.4	51	80	7	135	30	14	21	34	1.93
3119165--3119301	73	1.9	73	90	3	222	31	16	12	40	1.85
3122359--3122401	2	21.5	2	100	0	86	48	0	0	51	1.00
3123081--3123126	2	23.5	2	91	4	76	47	0	2	50	1.13
3123211--3123251	2	20.5	2	100	0	82	51	0	0	48	1.00
3124405--3124463	31	1.9	31	92	0	100	23	20	1	54	1.54
3126074--3126118	21	2.1	21	88	8	65	20	15	35	28	1.93
3126814--3126869	22	2.5	22	94	0	94	3	37	0	58	1.15
3127351--3127432	42	2.0	42	83	9	105	30	19	21	28	1.98
3128296--3128328	12	2.6	13	85	9	50	42	6	0	51	1.26
3141728--3141823	40	2.4	40	84	3	113	31	23	20	23	1.98
3141752--3141858	20	5.3	20	90	0	160	27	28	21	23	1.99
3142041--3142083	22	2.0	22	100	0	86	25	41	13	18	1.88
3142469--3142575	20	5.5	19	83	3	79	14	14	23	47	1.81
3142481--3142537	20	2.9	20	89	2	80	17	21	24	36	1.94
3142480--3142540	19	3.2	19	86	4	86	16	19	22	40	1.90
3142539--3142582	20	2.2	20	87	0	61	13	9	18	59	1.60
3144096--3144142	21	2.2	21	84	0	58	23	17	29	29	1.97
3144303--3144352	18	2.8	18	96	0	91	32	18	6	44	1.74
3144510--3144548	20	2.0	20	89	0	60	46	23	12	17	1.83
3144632--3144727	20	4.8	20	89	0	147	17	17	25	39	1.91
3145227--3145330	21	5.0	21	76	4	104	21	35	19	24	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3145226--3145333	42	2.6	41	79	7	128	21	36	19	23	1.95
3146242--3146303	14	4.3	14	77	6	61	40	0	12	46	1.42
3146402--3146455	20	2.7	20	85	0	72	44	25	18	11	1.83
3146449--3146823	20	20.6	20	79	12	236	23	19	22	34	1.96
3146578--3146642	14	4.6	14	100	0	130	7	21	23	47	1.76
3149174--3149210	14	2.5	15	91	4	58	5	18	21	54	1.64
3149400--3149453	24	2.2	24	93	0	90	40	20	18	20	1.91
3150274--3150360	20	4.3	20	89	0	129	25	20	28	25	1.99
3150275--3150422	20	7.3	20	81	6	127	28	19	25	27	1.99
3150530--3150587	2	29.5	2	96	3	109	50	0	0	50	1.00
3151620--3151688	34	2.1	33	83	2	84	57	1	14	26	1.45
3153189--3153724	270	2.0	270	96	0	991	29	20	15	35	1.93
3154387--3154502	46	2.6	46	74	10	114	32	15	18	32	1.93
3157979--3158097	30	4.0	30	88	0	175	34	14	25	26	1.94
3161417--3161503	30	2.9	30	89	1	131	34	13	26	25	1.93
3161496--3161520	11	2.3	11	100	0	50	60	32	0	8	1.26
3174507--3174536	14	2.2	13	94	5	51	20	6	3	70	1.25
3175954--3176000	22	2.1	22	100	0	94	36	12	17	34	1.87
3191187--3191282	38	2.5	38	87	0	138	25	27	21	26	2.00
3191189--3191250	17	3.4	17	70	23	54	24	32	22	20	1.98
3192843--3193011	84	2.0	84	96	0	311	28	18	8	43	1.79
3194015--3194079	30	2.2	30	81	10	80	32	15	7	44	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3194033--3194105	30	2.4	29	86	8	94	32	16	9	41	1.81
3195256--3195285	2	15.0	2	100	0	60	50	0	0	50	1.00
3214291--3214328	18	2.1	18	100	0	76	18	50	21	10	1.76
3214325--3214506	29	6.3	29	80	9	176	35	4	17	43	1.69
3214325--3214506	57	3.2	57	81	11	210	35	4	17	43	1.69
3221858--3221944	29	3.0	28	78	6	86	35	6	14	42	1.73
3221858--3221969	32	3.8	29	77	10	102	33	6	16	44	1.72
3221902--3221994	32	3.0	31	84	7	109	34	5	15	45	1.69
3227364--3227407	14	3.2	14	80	6	63	45	4	4	45	1.44
3228500--3228558	31	1.9	31	85	0	82	54	10	8	27	1.63
3229044--3229077	14	2.4	14	100	0	68	58	11	0	29	1.33
3230363--3230407	19	2.5	19	82	7	58	55	0	20	24	1.43
3230400--3230737	44	7.9	42	76	7	222	47	7	20	25	1.76
3230488--3230737	86	2.9	86	79	4	227	48	8	19	24	1.75
3230401--3230785	130	3.0	127	81	6	386	47	7	19	25	1.75
3230533--3230780	86	2.9	87	79	7	226	50	6	17	25	1.70
3231140--3231205	23	2.9	23	90	2	107	12	15	15	57	1.65
3231140--3231229	23	4.0	22	82	13	105	13	16	13	56	1.67
3232601--3232646	24	2.0	23	87	12	67	76	2	2	19	1.00
3232621--3232658	16	2.4	16	86	8	51	76	5	2	15	1.08
3232849--3232901	21	2.6	20	82	11	72	62	11	3	22	1.45
3242923--3243404	137	3.5	137	86	3	569	26	18	14	39	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3244045--3244081	18	2.1	18	94	0	65	59	5	8	27	1.48
3244441--3244492	4	13.5	4	82	11	56	0	17	0	82	0.66
3244427--3244488	12	5.5	11	77	12	63	4	14	0	80	0.87
3244449--3244495	11	4.6	10	79	12	51	0	17	0	82	0.66
3244441--3244492	12	4.5	12	83	9	72	0	17	0	82	0.66
3255269--3255300	2	16.0	2	100	0	64	50	0	0	50	1.00
3263168--3263209	21	2.1	19	86	8	57	9	2	4	83	0.88
3270183--3270400	59	3.7	60	79	10	218	18	25	26	29	1.98
3271436--3271467	17	1.9	17	93	6	57	15	6	12	65	1.44
3272313--3272374	32	2.0	31	87	3	88	27	14	17	40	1.89
3272344--3272447	55	1.9	55	89	0	163	30	22	16	30	1.95
3274042--3274104	27	2.3	27	100	0	126	23	26	22	26	2.00
3277166--3277224	28	2.1	28	100	0	118	32	25	10	32	1.89
3280861--3280902	16	2.5	17	80	3	50	23	7	9	59	1.53
3283878--3283931	28	2.0	27	88	3	81	35	5	0	59	1.21
3291424--3291463	21	1.9	21	85	10	55	35	10	2	52	1.48
3293303--3293359	21	2.7	21	97	0	105	15	31	31	21	1.94
3302115--3302172	22	2.6	22	94	0	98	32	18	13	34	1.91
3302611--3302776	73	2.3	73	96	0	305	30	18	19	31	1.96
3302686--3303137	114	4.0	112	77	12	413	38	15	18	28	1.91
3303345--3303443	3	32.7	3	82	13	96	38	0	0	61	0.96
3303350--3303439	28	3.3	27	80	9	94	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3303345--3303443	25	4.0	25	82	5	112	38	0	0	61	0.96
3304729--3304788	32	1.9	32	83	10	79	33	5	5	56	1.42
3304822--3304864	14	3.2	13	80	9	50	25	2	2	69	1.12
3304809--3304864	17	3.3	17	73	14	53	28	1	1	67	1.10
3306220--3306315	43	2.3	42	77	10	106	48	7	4	39	1.50
3311080--3311122	18	2.4	18	85	11	54	51	4	0	44	1.22
3311658--3311686	14	2.0	15	93	6	51	68	0	0	31	0.89
3313777--3313808	12	2.7	12	100	0	64	25	0	21	53	1.46
3322074--3322130	3	18.0	3	82	10	69	63	0	0	36	0.95
3322074--3322130	13	4.7	13	79	14	68	63	0	0	36	0.95
3322074--3322130	16	3.6	15	83	9	69	63	0	0	36	0.95
3323158--3323209	21	2.5	21	96	0	95	34	21	17	26	1.95
3326261--3326363	51	2.0	51	100	0	206	34	35	7	21	1.82
3326550--3326586	17	2.2	17	100	0	74	29	13	18	37	1.90
3327790--3327864	3	25.7	3	91	5	127	32	0	1	66	1.00
3330122--3330243	42	3.0	41	78	4	120	24	19	23	31	1.98
3330382--3330483	42	2.5	40	82	9	116	23	21	21	33	1.97
3330378--3330483	41	2.6	41	82	8	126	24	20	21	33	1.97
3330423--3330885	218	2.1	215	85	5	603	32	16	17	33	1.92
3330874--3330953	42	1.9	41	92	2	133	22	18	20	38	1.93
3332598--3334780	754	2.9	752	90	2	3425	33	14	12	39	1.84
3334095--3335461	685	2.0	682	92	2	2251	34	13	11	40	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3339761--3339800	20	2.0	20	100	0	80	35	20	20	25	1.96
3346274--3346815	269	2.0	269	99	0	1075	34	9	20	34	1.86
3347395--3347446	21	2.4	22	81	18	65	28	17	25	28	1.97
3358259--3358298	21	2.0	21	95	5	73	25	25	10	40	1.86
3359663--3359969	48	6.3	48	86	3	389	32	0	38	28	1.60
3359675--3359965	4	72.8	4	80	0	303	31	0	39	29	1.60
3360764--3360849	43	2.0	43	86	4	120	29	6	22	41	1.79
3367601--3367708	54	2.0	54	88	0	162	38	13	22	25	1.91
3368075--3368128	21	2.6	20	91	5	81	35	18	11	35	1.86
3368484--3368936	113	3.9	113	82	6	486	38	15	19	27	1.91

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