genome.fa.s8959.2.7.7.80.10.50.1000.16.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: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4521124

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   

This is table  16  of  21  ( 2431 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)
3168714--3168741	8	3.5	8	100	0	56	10	0	0	89	0.49
3170345--3170374	15	2.0	15	100	0	60	40	26	26	6	1.81
3174526--3174558	15	2.2	15	94	0	57	60	15	18	6	1.54
3174861--3174937	3	26.0	3	81	2	93	31	1	0	67	0.99
3176148--3176206	20	3.0	20	79	13	61	30	3	3	62	1.28
3177145--3177198	19	2.8	19	86	8	74	33	0	1	64	1.04
3177147--3177173	14	1.9	14	100	0	54	33	0	0	66	0.92
3178737--3178801	33	1.9	34	90	3	105	23	12	6	58	1.56
3181121--3181279	84	1.8	84	85	8	219	33	20	14	31	1.93
3183207--3183423	114	1.9	114	90	0	344	33	16	20	29	1.95
3184904--3185059	54	2.9	54	90	1	233	37	16	24	22	1.93
3185426--3185480	22	2.5	22	85	5	76	36	12	14	36	1.84
3185880--3186208	113	2.9	111	88	3	480	38	14	19	27	1.91
3186318--3186497	79	2.3	81	87	4	251	38	16	17	27	1.90
3186652--3186717	3	22.0	3	81	6	80	28	1	0	69	0.97
3186662--3186726	21	3.0	21	88	4	94	29	3	0	67	1.05
3187936--3187988	20	2.7	20	78	18	58	26	3	1	67	1.17
3188009--3188039	11	2.8	11	95	0	53	19	6	6	67	1.35
3190152--3190316	76	2.2	75	85	3	224	30	3	10	56	1.48
3190965--3191013	22	2.2	23	88	3	73	20	4	0	75	0.96
3196030--3196062	16	2.1	16	88	11	50	51	0	6	42	1.26
3196042--3196096	28	2.0	28	86	13	78	52	3	1	41	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3196040--3196108	29	2.4	29	81	11	81	56	2	1	39	1.23
3196109--3196163	28	2.0	28	89	7	85	41	9	3	45	1.53
3196149--3196220	2	38.0	2	74	20	66	45	1	1	51	1.18
3196100--3196161	28	2.3	26	76	15	63	43	8	3	45	1.49
3202474--3202600	62	2.0	63	98	1	247	42	1	19	36	1.61
3204432--3204488	29	1.9	30	85	3	80	24	15	26	33	1.95
3207868--3207943	21	3.6	20	80	16	82	32	17	25	25	1.96
3209964--3210039	21	3.6	20	80	16	82	32	15	25	26	1.95
3210444--3210503	18	3.2	20	77	13	58	30	6	18	45	1.75
3211454--3211541	32	2.9	29	80	8	86	27	17	21	34	1.95
3211487--3211546	30	2.0	30	90	0	93	26	13	25	35	1.93
3212404--3212443	20	2.0	20	100	0	80	50	5	15	30	1.65
3212461--3212502	22	2.0	22	90	4	68	57	9	0	33	1.31
3219551--3219728	90	2.0	90	93	0	302	37	10	6	45	1.64
3224814--3224884	28	2.6	27	82	8	83	40	4	1	53	1.29
3224934--3224976	10	4.4	9	82	11	50	74	0	6	18	1.04
3224994--3225052	14	3.9	16	74	14	54	61	1	1	35	1.16
3225014--3225081	28	2.4	27	84	15	86	57	4	1	36	1.28
3225130--3225208	22	3.5	22	79	5	88	48	7	1	43	1.39
3225203--3225268	10	6.4	11	71	18	61	45	1	0	53	1.09
3225226--3225265	16	2.5	15	84	11	53	42	2	0	55	1.13
3226027--3226088	29	2.1	29	90	0	97	37	6	17	38	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3226597--3226709	51	2.2	50	84	1	145	15	33	31	19	1.93
3226844--3226884	10	4.1	10	84	12	57	31	29	0	39	1.57
3227008--3227228	110	2.0	111	91	0	363	36	8	9	46	1.65
3229245--3229317	25	3.0	24	68	24	62	26	6	4	63	1.38
3231733--3231788	27	2.1	27	93	6	96	42	3	46	7	1.48
3234774--3234846	15	4.6	15	70	21	51	67	0	2	30	1.05
3237513--3237547	7	5.3	7	93	6	56	77	0	0	22	0.78
3237504--3237572	4	19.0	4	77	19	62	75	4	0	20	0.97
3237512--3237593	16	5.4	16	72	16	52	73	3	1	21	1.06
3237686--3237791	41	2.7	41	95	4	191	47	6	1	44	1.40
3237770--3237805	2	18.5	2	94	5	65	47	0	0	52	1.00
3238246--3238725	200	2.4	202	81	5	562	27	21	20	29	1.98
3240038--3240120	39	2.1	39	90	0	130	30	15	30	24	1.96
3240076--3240398	44	7.3	44	87	0	421	30	20	26	22	1.98
3248390--3248483	36	2.5	38	79	10	104	61	0	9	28	1.27
3249746--3249802	4	14.8	4	78	14	66	75	1	0	22	0.90
3249746--3249802	27	2.3	23	88	11	78	75	1	0	22	0.90
3249847--3250087	65	3.7	65	82	9	265	43	4	2	48	1.38
3249880--3249940	29	2.1	30	84	6	81	40	6	6	45	1.56
3249913--3249999	41	2.2	39	91	6	140	43	5	2	48	1.39
3249968--3250030	26	2.3	28	81	10	94	44	4	0	50	1.23
3250044--3250100	9	6.0	9	74	11	51	42	0	1	56	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3254025--3254140	60	2.0	58	86	3	160	25	21	25	26	2.00
3254753--3254786	7	4.9	7	100	0	68	29	26	29	14	1.95
3264622--3264694	27	2.7	29	77	12	82	17	12	21	47	1.80
3273139--3273186	18	2.7	19	76	23	59	64	0	29	6	1.18
3283917--3283965	22	2.2	22	89	7	73	16	6	4	73	1.19
3284765--3284805	13	3.2	13	86	3	57	12	26	24	36	1.91
3289349--3289428	30	3.1	25	72	19	74	40	0	5	55	1.22
3294063--3294167	41	2.6	41	77	3	97	38	19	18	24	1.93
3294284--3294432	42	3.5	42	83	3	174	28	18	23	30	1.97
3298278--3298628	43	8.2	42	85	2	425	23	23	21	32	1.98
3298278--3298628	85	4.1	85	84	3	420	23	23	21	32	1.98
3310773--3311264	245	2.0	245	98	0	957	34	9	19	37	1.84
3313261--3313308	3	16.0	3	82	0	60	68	2	2	27	1.11
3313261--3313309	18	2.7	18	87	0	71	67	2	4	26	1.19
3313882--3313906	9	2.8	9	100	0	50	12	0	0	88	0.53
3315107--3315133	2	13.5	2	100	0	54	51	0	0	48	1.00
3316155--3316227	36	2.0	37	91	2	121	39	24	15	20	1.91
3320665--3321076	208	2.0	212	91	2	679	39	14	24	21	1.91
3324033--3324144	32	3.6	32	74	22	112	42	1	8	47	1.43
3324294--3324383	33	2.6	34	75	16	96	46	1	7	44	1.39
3324380--3324447	32	2.2	31	84	7	84	17	4	0	77	0.92
3328007--3328304	149	2.0	149	97	2	564	30	17	11	41	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3329995--3330720	81	9.0	81	86	3	885	35	10	20	33	1.87
3329989--3330713	240	3.0	240	84	3	949	35	10	19	33	1.87
3329995--3330720	159	4.5	159	85	3	834	35	10	20	33	1.87
3329995--3330749	321	2.4	321	82	5	796	35	11	20	33	1.88
3335526--3336342	81	10.1	81	90	0	1195	35	11	21	32	1.89
3336972--3336999	2	14.0	2	100	0	56	50	0	0	50	1.00
3340841--3340902	27	2.3	27	83	5	72	37	25	14	22	1.92
3342915--3342953	20	2.0	20	89	0	60	38	12	10	38	1.78
3344436--3344483	20	2.4	21	86	10	66	52	2	12	33	1.51
3351359--3351401	21	2.1	20	82	4	50	39	16	20	23	1.92
3353503--3353553	25	1.9	27	84	11	70	37	5	15	41	1.72
3357887--3357911	12	2.1	12	100	0	50	24	16	24	36	1.94
3358843--3358897	28	2.0	28	96	0	101	32	9	10	47	1.70
3358857--3358913	28	2.1	28	83	6	73	38	8	10	42	1.71
3359914--3359964	10	5.1	10	76	9	50	62	0	3	33	1.13
3359937--3359970	7	4.9	7	89	10	52	73	0	0	26	0.83
3359945--3359971	13	2.1	13	100	0	54	77	0	0	22	0.76
3361978--3362011	15	2.2	16	94	5	61	35	11	41	11	1.78
3362744--3362818	23	3.3	23	86	0	96	38	30	13	17	1.88
3376554--3376603	19	2.6	19	75	15	57	16	8	20	56	1.65
3379598--3379656	15	3.8	15	81	4	55	5	8	11	74	1.20
3379893--3380118	113	2.0	111	93	5	384	38	6	22	32	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3381539--3381618	32	2.5	32	83	4	99	27	21	16	35	1.94
3391264--3391380	56	2.1	56	86	0	162	40	15	10	34	1.81
3394302--3394326	2	12.5	2	100	0	50	48	0	0	52	1.00
3394421--3394457	2	19.0	2	94	5	67	48	0	0	51	1.00
3394616--3394647	16	1.9	17	93	6	57	25	18	0	56	1.42
3404053--3404103	21	2.4	21	93	0	84	23	17	27	31	1.97
3404262--3404382	64	1.9	64	84	3	163	33	17	15	33	1.91
3406424--3406451	2	14.0	2	100	0	56	50	0	0	50	1.00
3406510--3406541	10	3.2	10	95	0	55	6	0	43	50	1.27
3406577--3406608	2	16.0	2	100	0	64	50	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21