genome.fa.s8488.2.7.7.80.10.50.1000.13.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: 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  13  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)
3145195--3145383	65	2.9	63	76	14	163	25	17	23	32	1.96
3146536--3146595	9	6.7	9	77	7	59	26	31	30	11	1.92
3146536--3146595	18	3.3	18	76	0	66	26	31	30	11	1.92
3146575--3146632	22	2.7	21	81	10	64	20	32	31	15	1.94
3148984--3149014	11	2.7	11	95	5	53	80	0	16	3	0.83
3149158--3149203	2	23.0	2	100	0	92	50	0	0	50	1.00
3150266--3150290	12	2.1	12	100	0	50	60	0	0	40	0.97
3150986--3151037	26	2.0	26	100	0	104	46	7	11	34	1.69
3155056--3155097	21	2.0	21	85	0	57	28	19	16	35	1.93
3162106--3162138	12	2.8	12	100	0	66	69	0	24	6	1.10
3163390--3163808	111	3.8	111	88	2	592	31	25	15	27	1.96
3163940--3163979	3	12.7	3	84	10	53	32	0	5	62	1.17
3165470--3165531	2	31.0	2	100	0	124	50	0	0	50	1.00
3165694--3165731	2	19.0	2	88	0	58	52	2	0	44	1.14
3169582--3169648	30	2.2	30	81	0	80	25	38	22	13	1.90
3180742--3180785	21	2.1	21	86	0	61	25	18	27	29	1.98
3180835--3180892	25	2.3	25	100	0	116	29	20	15	34	1.94
3183092--3183141	24	2.1	24	85	7	66	60	16	2	22	1.46
3190984--3191423	210	2.1	211	89	1	668	33	22	20	24	1.97
3190984--3191423	106	4.2	105	88	2	607	33	22	20	24	1.97
3191909--3191980	35	2.1	35	100	0	144	40	11	20	27	1.87
3192353--3192392	18	2.3	18	83	8	57	25	5	2	67	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3192450--3192474	2	12.5	2	100	0	50	48	0	0	52	1.00
3192799--3192875	41	1.9	39	86	5	109	16	25	6	50	1.69
3193043--3193084	9	4.7	9	78	21	52	16	4	0	78	0.91
3193011--3193119	18	6.2	17	73	16	73	15	11	0	72	1.17
3193035--3193080	22	2.1	22	84	8	58	17	6	0	76	1.00
3194444--3194561	44	2.8	42	74	5	103	41	16	11	30	1.84
3194721--3194887	83	2.0	81	94	2	289	26	17	18	37	1.93
3194762--3194895	41	3.3	41	69	15	132	25	17	19	37	1.94
3196972--3197030	29	2.0	29	96	0	109	20	13	18	47	1.82
3201909--3201950	17	2.5	17	84	3	59	66	2	4	26	1.23
3202939--3203525	105	5.7	103	87	5	802	22	18	25	33	1.97
3202939--3203525	204	2.9	205	89	3	864	22	18	25	33	1.97
3202939--3203991	293	3.4	302	85	9	1193	21	18	26	33	1.97
3203136--3203930	188	4.0	191	86	9	976	21	18	26	33	1.96
3203528--3203960	105	4.1	106	94	0	717	21	18	26	33	1.96
3203528--3203991	212	2.2	211	90	3	725	21	18	26	33	1.96
3204700--3204858	67	2.4	67	89	4	241	36	11	20	32	1.88
3204733--3205005	36	7.9	35	70	17	196	36	13	21	28	1.91
3204733--3204988	103	2.5	101	82	4	309	36	12	21	28	1.91
3205443--3205478	18	2.0	18	88	0	54	41	30	8	19	1.81
3205892--3205961	22	3.2	22	83	4	97	28	12	22	35	1.91
3205895--3205960	21	3.1	21	82	4	87	27	12	24	36	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3205924--3205968	22	2.0	22	82	0	54	33	11	22	33	1.89
3206595--3206668	23	3.2	22	72	14	60	1	13	8	77	1.06
3206615--3206684	8	9.1	7	77	20	61	0	15	7	77	0.98
3206609--3206663	16	3.4	17	78	7	53	0	16	9	74	1.06
3206640--3206690	15	3.2	16	79	17	54	0	13	7	78	0.96
3208667--3208705	16	2.4	17	95	4	71	17	20	17	43	1.88
3210214--3210265	15	3.3	16	77	20	56	67	5	1	25	1.23
3216062--3216098	14	2.6	15	83	8	51	59	0	0	40	0.97
3216086--3216324	123	1.9	123	85	9	326	38	11	7	42	1.70
3217049--3217077	13	2.1	14	93	6	51	44	0	13	41	1.44
3222591--3222995	201	2.0	203	98	1	787	30	21	17	31	1.96
3223781--3223805	2	12.5	2	100	0	50	0	48	0	52	1.00
3229030--3229065	16	2.2	16	95	0	63	80	0	0	19	0.71
3229465--3229503	18	2.2	18	100	0	78	20	25	25	28	1.99
3231061--3231142	41	2.0	41	97	0	155	41	15	17	25	1.89
3231278--3231364	2	43.5	2	100	0	174	0	49	0	50	1.00
3231364--3231390	2	13.5	2	100	0	54	48	0	0	51	1.00
3233505--3233640	41	3.3	41	94	0	236	20	19	23	36	1.95
3233568--3233701	61	2.2	61	98	0	259	16	21	23	38	1.92
3233501--3233681	82	2.2	82	82	2	211	21	19	23	35	1.96
3233714--3233761	19	2.5	19	89	0	69	20	16	16	45	1.85
3233752--3233825	22	3.4	22	73	3	78	21	16	22	39	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3233733--3233825	43	2.2	41	84	3	123	21	16	21	40	1.91
3234866--3234892	6	4.5	6	100	0	54	0	14	51	33	1.43
3235013--3235065	20	2.7	20	93	0	88	45	20	22	11	1.83
3241159--3241332	93	1.9	94	95	1	314	40	18	6	34	1.76
3242030--3242059	5	6.0	5	100	0	60	60	0	0	40	0.97
3246033--3246125	46	2.0	48	89	8	147	22	12	16	48	1.80
3246152--3246330	54	3.4	54	83	2	200	30	17	19	32	1.95
3252921--3253015	48	2.0	48	85	4	129	23	11	17	47	1.80
3253037--3253187	54	2.8	54	82	5	164	29	17	17	35	1.93
3253035--3253220	54	3.5	53	73	12	146	29	18	17	34	1.94
3259389--3260067	81	8.4	81	88	1	905	28	24	11	35	1.90
3260037--3260629	68	8.7	68	91	0	936	29	24	14	31	1.95
3260833--3260990	55	2.9	55	83	11	207	31	18	12	37	1.88
3261343--3261392	19	2.4	21	87	9	68	32	20	14	34	1.92
3265524--3266090	243	2.3	242	88	3	825	28	25	11	35	1.90
3265554--3266090	81	6.6	81	88	1	736	28	25	11	34	1.90
3266040--3266554	68	7.6	68	86	1	656	30	20	14	33	1.93
3266732--3266891	55	2.9	55	87	2	232	31	19	13	35	1.91
3274073--3274224	53	2.9	53	80	6	148	32	14	17	35	1.90
3278398--3278432	17	2.1	17	100	0	70	45	5	25	22	1.74
3279447--3279490	21	2.1	21	83	8	54	38	0	2	59	1.10
3279481--3279525	20	2.1	22	84	15	60	42	4	0	53	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3280652--3280678	13	2.1	13	100	0	54	37	14	7	40	1.74
3284606--3284767	81	2.0	81	100	0	324	29	17	13	39	1.88
3285814--3285909	48	2.0	48	97	0	183	27	14	17	40	1.89
3294704--3294748	22	2.0	22	83	8	56	64	2	8	24	1.34
3294773--3294810	11	3.5	11	85	0	58	65	5	10	18	1.41
3294767--3294810	22	2.0	22	90	0	70	63	4	11	20	1.44
3300476--3300505	4	7.2	4	92	7	51	73	0	0	26	0.84
3300472--3300505	17	2.0	17	94	0	59	73	0	0	26	0.83
3301114--3301273	85	1.9	85	92	2	268	56	11	2	28	1.48
3317707--3317804	2	50.0	2	88	4	146	46	2	1	50	1.19
3317981--3318360	81	4.7	80	88	2	483	29	22	12	35	1.91
3317980--3318360	161	2.4	162	86	2	534	29	22	12	35	1.91
3318354--3318701	68	5.1	68	90	0	527	30	24	16	29	1.96
3321125--3321233	54	2.0	54	100	0	218	26	29	9	34	1.87
3322764--3322847	42	2.0	42	97	0	159	36	28	5	28	1.81
3323735--3324104	81	4.6	81	87	2	478	29	21	12	36	1.90
3324097--3324377	68	4.2	68	86	8	398	29	25	15	29	1.96
3324118--3324367	60	3.9	61	83	12	295	30	25	14	30	1.94
3324097--3324377	128	2.1	132	86	6	390	29	25	15	29	1.96
3324627--3324740	59	2.0	57	89	3	174	35	17	12	34	1.87
3325064--3325287	95	2.4	96	78	4	231	26	22	15	35	1.94
3327603--3327645	18	2.4	18	88	0	59	41	25	0	32	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3327841--3327963	31	4.0	31	88	3	185	39	18	17	24	1.92
3336156--3336261	10	10.6	10	75	8	81	80	0	15	3	0.91
3336186--3336259	5	14.0	5	77	13	51	81	0	17	1	0.77
3336177--3336261	25	3.5	24	75	17	70	80	1	16	2	0.89
3336156--3336261	30	3.6	28	83	10	106	80	0	15	3	0.91
3336192--3336251	17	3.7	15	81	18	68	81	0	18	0	0.69
3336187--3336261	39	2.0	39	86	5	109	82	0	16	1	0.73
3336187--3336250	23	2.8	23	75	15	53	81	0	18	0	0.70
3342774--3342809	18	2.1	18	94	5	65	38	16	16	27	1.90
3343490--3343591	31	3.1	31	69	17	96	27	30	13	28	1.94

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