genome.fa.s7782.2.7.7.80.10.50.1000.16.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: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  3900615

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

This is table  16  of  19  ( 2174 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)
3261433--3261544	37	3.0	36	93	5	188	30	14	14	41	1.85
3272578--3272627	11	4.5	11	76	0	55	50	30	0	20	1.49
3272578--3272628	22	2.3	22	96	0	93	49	31	0	19	1.49
3273108--3273157	23	2.2	23	100	0	100	22	16	0	62	1.33
3273115--3273155	13	3.4	13	74	19	52	21	14	0	63	1.30
3274128--3274166	5	7.2	5	86	13	51	58	0	2	38	1.12
3274128--3274167	17	2.4	16	87	4	62	60	0	2	37	1.11
3287556--3287604	19	2.6	19	100	0	98	20	16	32	30	1.94
3289819--3289857	13	3.1	13	85	3	53	51	2	10	35	1.50
3298776--3298874	22	4.5	22	96	0	180	15	27	30	27	1.96
3303815--3303847	17	1.9	18	88	11	52	84	0	9	6	0.76
3305049--3305173	37	3.4	37	84	3	146	42	16	18	22	1.89
3305218--3305616	55	7.6	52	76	14	319	32	18	21	27	1.97
3305200--3305673	206	2.2	210	79	12	508	32	18	21	27	1.97
3305466--3305676	106	2.0	107	85	7	286	33	17	22	27	1.96
3305477--3305707	106	2.1	108	82	5	281	32	18	20	27	1.96
3305935--3306496	293	1.9	286	92	7	947	36	13	13	36	1.84
3311082--3311119	20	1.9	20	88	0	58	13	26	39	21	1.89
3314883--3314922	21	1.9	21	85	10	55	35	10	2	52	1.48
3320057--3320095	17	2.3	17	86	0	51	71	2	0	25	0.98
3327279--3327331	21	2.5	21	87	6	72	30	28	20	20	1.98
3327343--3327586	21	11.8	21	75	14	231	20	20	24	34	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3327327--3327495	42	4.1	42	88	6	267	20	20	24	34	1.96
3327335--3327507	81	2.1	82	94	1	303	20	20	24	33	1.97
3327327--3327558	63	3.8	61	84	8	276	20	20	25	34	1.96
3327386--3327586	105	1.9	102	93	3	348	20	19	25	33	1.97
3327720--3327915	21	9.4	20	62	24	50	38	20	18	22	1.93
3327823--3327940	21	5.7	21	69	11	91	37	22	20	19	1.94
3327713--3327934	42	5.3	42	91	1	349	37	20	18	22	1.94
3327928--3327979	20	2.6	20	93	0	95	40	17	19	23	1.91
3327975--3328063	21	4.2	21	97	0	169	19	17	33	29	1.95
3332693--3332730	3	12.3	3	88	5	58	65	0	0	34	0.93
3332989--3333331	131	2.6	130	83	2	409	25	17	29	27	1.97
3333350--3333521	36	5.2	36	65	25	117	40	16	19	23	1.90
3333333--3333607	65	4.2	65	89	0	415	40	15	20	24	1.91
3333435--3333607	29	5.5	29	66	22	89	39	13	21	24	1.90
3333734--3333838	38	2.8	37	82	5	131	38	11	18	32	1.86
3333734--3333883	37	4.1	36	79	7	133	38	13	18	30	1.89
3335046--3335090	22	2.0	23	86	4	65	6	11	6	75	1.18
3346868--3346906	15	2.6	15	87	0	60	23	15	2	58	1.49
3347306--3347374	3	23.3	3	80	11	72	34	2	0	62	1.10
3352597--3352658	8	7.6	8	77	15	56	80	0	19	0	0.71
3352596--3352643	11	4.4	11	84	7	62	81	0	18	0	0.70
3355121--3355800	113	6.2	112	83	6	800	28	24	16	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3355121--3355800	224	3.1	221	84	5	823	28	24	16	30	1.96
3356111--3356183	3	24.7	3	81	10	80	32	1	0	65	1.01
3356097--3356183	26	3.4	25	82	4	84	33	2	1	63	1.15
3360741--3360816	38	2.0	38	89	0	116	36	23	13	26	1.91
3360794--3360948	46	3.4	45	78	9	161	32	28	14	23	1.95
3363327--3363395	3	22.3	3	77	11	68	62	1	2	33	1.19
3363332--3363395	28	2.3	28	86	10	103	62	0	3	34	1.11
3363326--3363408	28	3.1	26	79	17	89	62	1	3	32	1.20
3363339--3363408	31	2.4	28	79	15	79	62	0	4	32	1.14
3363748--3363854	42	2.6	41	76	8	126	30	22	21	25	1.99
3363552--3364948	261	5.4	261	85	3	1855	33	16	16	33	1.91
3364786--3364887	42	2.5	41	83	3	132	34	21	21	22	1.97
3363552--3364948	512	2.7	509	86	3	1917	33	16	16	33	1.91
3365922--3366003	40	2.0	40	83	0	101	18	13	17	51	1.77
3367657--3367705	19	2.7	17	84	9	53	26	18	30	24	1.98
3367657--3367835	64	2.8	62	76	10	182	26	15	27	30	1.96
3376342--3376390	19	2.7	17	84	9	53	26	18	30	24	1.98
3376342--3376520	64	2.8	62	80	10	200	26	17	26	29	1.97
3376359--3376550	64	3.0	61	77	10	179	28	16	25	29	1.97
3376857--3376954	29	3.4	28	74	13	74	10	14	1	74	1.12
3381304--3381339	12	3.0	12	87	0	54	58	13	5	22	1.56
3383937--3383970	17	1.9	18	88	5	52	52	8	23	14	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3385080--3385127	3	15.7	3	83	12	62	66	0	0	33	0.92
3385170--3385443	46	5.9	46	75	1	197	33	30	13	22	1.93
3385463--3385529	35	1.9	35	84	6	91	22	26	19	31	1.98
3385738--3385809	32	2.2	32	95	0	126	26	9	23	40	1.85
3387352--3387399	12	3.9	12	78	13	53	20	4	4	70	1.21
3387352--3387399	25	2.0	25	92	8	82	20	4	4	70	1.21
3389426--3389464	20	1.9	20	89	5	60	69	0	12	17	1.19
3403747--3403787	21	1.9	21	85	5	55	24	36	24	14	1.93
3404114--3404157	23	2.0	23	83	12	58	36	4	11	47	1.60
3404901--3404940	21	1.9	21	89	0	62	37	35	0	27	1.57
3405840--3405869	12	2.5	12	88	0	51	26	26	46	0	1.53
3406169--3406242	23	3.2	23	77	17	64	16	1	27	55	1.49
3406792--3406835	23	2.0	23	81	4	54	50	11	2	36	1.51
3406874--3406948	21	3.6	21	75	10	91	18	45	17	18	1.86
3406873--3406957	41	2.1	41	100	0	170	21	41	16	21	1.90
3408167--3408249	42	2.0	42	97	0	157	25	16	16	40	1.90
3416759--3417048	84	3.5	82	80	5	287	33	17	18	31	1.94
3421325--3421737	43	9.7	42	85	4	481	25	20	19	33	1.97
3421325--3421737	85	4.8	84	86	2	524	25	20	19	33	1.97
3421325--3421737	128	3.2	127	86	2	542	25	20	19	33	1.97
3422017--3422111	42	2.3	42	88	0	136	31	15	24	28	1.96
3423180--3423338	52	3.1	52	98	0	309	32	7	16	43	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3426228--3426284	26	2.2	26	96	0	105	21	10	17	50	1.75
3426404--3426541	43	3.2	43	86	0	195	22	21	21	34	1.97
3426711--3426814	43	2.4	44	82	6	124	31	25	17	25	1.97
3426859--3426895	15	2.7	14	84	15	51	8	24	32	35	1.85
3427006--3427112	43	2.5	43	87	0	160	28	19	19	32	1.96
3428674--3428731	28	2.1	28	90	6	91	10	32	51	5	1.58
3431151--3431189	18	2.2	18	85	0	51	53	0	2	43	1.14
3434207--3434271	28	2.3	28	78	10	69	40	7	7	44	1.62
3434214--3434281	27	2.5	27	75	13	68	38	5	13	42	1.68
3434716--3434798	43	1.9	43	82	4	105	32	14	24	28	1.94
3436935--3436966	2	16.0	2	100	0	64	50	0	0	50	1.00
3438328--3438365	20	1.9	20	88	0	58	39	23	10	26	1.87
3438802--3438939	44	3.1	44	100	0	276	20	14	18	47	1.83
3440609--3440636	14	2.0	14	100	0	56	50	0	21	28	1.49
3441536--3441587	27	2.0	26	88	3	77	26	28	19	25	1.98
3447897--3447950	27	2.0	27	89	3	83	29	29	16	24	1.97
3451423--3451469	22	2.1	22	81	14	53	70	2	12	14	1.26
3452649--3452706	18	3.4	16	77	17	64	68	3	0	27	1.05
3452773--3452881	28	4.0	28	87	11	163	45	8	2	43	1.48
3452866--3452948	36	2.3	36	79	6	87	42	7	4	45	1.53
3453736--3453868	41	3.5	41	70	17	140	24	15	23	37	1.93
3453674--3453903	73	3.2	73	85	3	297	24	14	24	35	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3457801--3457856	20	2.8	20	86	5	78	17	28	33	19	1.95
3461300--3461358	20	3.0	20	87	2	84	16	28	33	20	1.95
3461284--3461354	20	3.9	19	74	18	71	18	28	33	19	1.95
3464839--3464889	19	3.0	17	76	23	54	19	27	35	17	1.94
3469729--3469766	15	2.4	16	86	4	51	36	2	7	52	1.45
3470644--3470677	2	16.5	2	93	6	59	47	0	2	50	1.16
3477438--3477472	16	2.2	16	89	0	52	57	11	2	28	1.48
3483128--3483167	20	2.0	20	100	0	80	45	10	20	25	1.81
3494939--3494963	5	5.0	5	100	0	50	80	0	0	20	0.72
3508837--3508934	35	2.8	35	93	0	169	44	18	17	19	1.87

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