genome.fa.s9605.2.7.7.80.10.50.1000.16.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: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9158330

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   

This is table  16  of  35  ( 4090 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)
3455412--3455533	40	3.0	40	81	0	154	38	20	13	27	1.91
3471562--3471631	27	2.6	27	95	2	124	58	12	0	28	1.35
3479880--3479913	18	1.9	17	94	5	59	50	0	26	23	1.50
3483940--3484044	37	2.8	38	82	4	133	41	13	13	31	1.83
3484402--3484444	18	2.5	17	85	7	61	25	4	2	67	1.22
3484569--3484611	23	2.0	22	81	9	52	18	9	0	72	1.11
3484586--3484658	27	2.7	27	73	12	69	16	13	2	67	1.35
3488489--3489025	183	2.9	183	95	0	950	27	21	20	30	1.98
3490166--3490341	72	2.4	75	83	7	209	26	17	13	42	1.86
3490181--3490288	36	3.0	36	75	2	119	26	14	13	44	1.83
3490357--3490509	39	3.6	39	69	21	119	28	22	13	35	1.92
3490412--3490730	105	3.1	104	92	2	518	30	20	12	36	1.89
3490630--3490705	36	2.1	36	90	0	116	22	21	15	40	1.90
3490872--3491535	105	6.3	105	90	2	951	34	26	18	21	1.96
3492078--3492182	37	2.8	37	82	0	129	41	12	14	31	1.82
3492540--3492582	18	2.5	17	85	7	61	25	4	2	67	1.22
3495750--3495781	5	6.4	5	92	0	55	40	0	0	59	0.97
3495744--3495781	15	2.5	15	86	0	58	42	2	0	55	1.14
3506992--3507046	21	2.6	21	73	0	56	27	18	20	34	1.95
3509922--3509973	23	2.3	23	86	0	68	40	19	9	30	1.83
3511521--3511589	28	2.4	28	95	2	120	28	33	11	26	1.91
3512057--3512083	2	13.5	2	100	0	54	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3521613--3521703	45	2.0	45	86	2	128	27	16	26	29	1.97
3521723--3521761	20	2.0	20	94	0	69	23	15	30	30	1.95
3522823--3522866	21	2.1	21	82	0	52	34	18	40	6	1.77
3526027--3526092	19	3.5	19	95	0	114	27	21	30	21	1.98
3526119--3526216	45	2.2	45	83	3	126	32	17	23	26	1.96
3526236--3526273	20	1.9	20	94	0	67	23	15	28	31	1.96
3537227--3537272	23	2.0	23	100	0	92	43	8	17	30	1.79
3542520--3542574	24	2.2	26	83	6	69	78	0	9	12	0.97
3543195--3543285	19	4.8	18	70	17	60	73	0	23	3	0.98
3543194--3543284	38	2.4	38	82	8	107	72	0	24	3	0.99
3543205--3543284	19	4.3	18	76	7	79	73	0	22	3	0.99
3543223--3543312	24	3.6	25	75	15	73	73	3	22	1	1.05
3543205--3543284	6	12.8	6	82	6	79	73	0	22	3	0.99
3543897--3544006	43	2.5	43	84	7	134	27	15	22	34	1.94
3550494--3550555	26	2.4	25	72	2	70	35	9	3	51	1.51
3550662--3550696	18	1.9	17	88	11	52	34	2	11	51	1.53
3551104--3551129	2	13.0	2	100	0	52	50	0	0	50	1.00
3551907--3551972	32	2.1	32	100	0	132	46	12	6	34	1.66
3553340--3553377	2	19.0	2	100	0	76	50	0	0	50	1.00
3553953--3554012	31	1.9	32	86	10	88	26	8	3	61	1.40
3556706--3556757	20	2.6	20	80	17	63	21	26	15	36	1.93
3562995--3563112	49	2.5	45	83	5	137	24	23	7	44	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3563141--3563310	81	2.1	82	82	5	211	28	24	11	36	1.89
3566997--3567076	23	3.6	23	68	13	67	27	23	22	26	2.00
3570906--3570956	21	2.5	20	77	3	57	33	7	3	54	1.47
3577398--3577458	20	2.9	21	87	7	79	18	26	34	21	1.96
3603631--3603714	21	3.9	21	81	7	96	22	28	27	21	1.99
3605278--3605325	18	2.6	17	87	12	69	43	25	31	0	1.55
3609725--3609813	7	12.7	7	83	4	90	41	37	2	19	1.64
3609908--3609954	21	2.2	21	88	0	67	40	34	4	21	1.73
3609915--3609952	14	2.7	14	95	0	67	39	31	5	23	1.77
3611344--3611410	23	2.9	23	84	0	98	34	16	20	28	1.95
3611333--3611407	11	6.6	11	72	11	53	36	16	21	26	1.94
3613246--3613290	23	1.9	23	90	4	72	64	6	17	11	1.46
3613953--3613991	18	2.2	18	90	0	60	23	28	28	20	1.99
3614744--3614783	10	4.0	10	90	0	53	0	22	20	57	1.41
3620239--3620429	21	9.2	21	75	13	155	31	23	20	24	1.98
3620254--3620405	41	3.7	41	76	10	166	32	21	20	25	1.97
3620240--3620429	83	2.3	83	92	0	317	31	23	20	24	1.98
3620414--3620495	41	2.0	41	97	0	137	25	21	18	34	1.96
3620419--3620488	20	3.5	20	78	18	90	22	22	18	35	1.95
3620376--3620581	21	9.9	21	78	14	119	25	19	23	31	1.98
3620438--3620595	21	7.6	21	84	9	198	23	19	25	31	1.98
3620905--3620981	38	2.0	38	97	0	145	40	12	9	37	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3630205--3630264	21	2.9	21	84	0	93	8	30	40	21	1.83
3630507--3630626	32	3.8	31	78	6	109	15	13	35	35	1.87
3630616--3630755	46	3.1	46	82	5	144	17	10	28	43	1.82
3631073--3631109	4	9.2	4	100	0	74	75	0	0	24	0.80
3631222--3631330	16	6.8	16	67	10	60	9	13	27	49	1.72
3631819--3631857	15	2.6	15	91	0	69	38	33	0	28	1.57
3632644--3632806	90	1.8	89	95	1	299	35	11	8	44	1.70
3639440--3639612	90	1.9	89	91	1	283	38	9	8	43	1.68
3643268--3643311	18	2.4	18	96	0	79	43	2	0	54	1.12
3645610--3645676	18	3.8	18	72	16	59	31	11	11	44	1.78
3652441--3652496	18	3.2	17	82	5	67	32	8	10	48	1.69
3652434--3652489	18	3.2	17	82	5	67	32	10	8	48	1.69
3652434--3652531	35	2.8	35	82	3	108	32	9	10	47	1.69
3652434--3652531	18	5.6	18	69	12	60	32	9	10	47	1.69
3652633--3652662	7	4.3	7	91	0	51	30	13	10	46	1.75
3672210--3672261	25	2.1	25	85	3	70	59	21	7	11	1.56
3672797--3672840	23	2.0	23	81	4	54	36	20	18	25	1.95
3673968--3674110	65	2.2	65	92	0	232	33	18	11	36	1.87
3683273--3683547	46	6.0	46	87	3	347	23	20	12	43	1.85
3683440--3683518	26	3.3	26	67	20	80	20	21	13	44	1.86
3683415--3683538	20	5.6	20	65	20	59	21	24	12	41	1.88
3692921--3693086	90	1.9	89	96	1	305	38	10	6	44	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3699637--3699809	90	1.9	89	94	1	301	38	10	5	45	1.62
3699771--3699840	22	3.3	21	74	16	63	48	1	4	45	1.30
3703603--3703654	20	2.5	21	87	9	72	26	21	19	32	1.97
3704929--3704996	30	2.3	29	87	7	93	22	17	17	42	1.89
3706212--3706263	25	2.1	25	82	3	61	55	23	7	13	1.63
3708794--3708889	3	31.3	3	81	4	75	30	1	8	60	1.33
3709802--3709876	30	2.5	29	81	12	82	18	12	12	57	1.65
3709851--3709907	30	1.9	30	82	13	73	22	14	7	56	1.62
3715045--3715173	43	3.0	43	81	2	143	29	29	18	22	1.97
3714788--3715501	335	2.1	338	87	3	1026	33	23	18	24	1.97
3715380--3715494	43	2.7	43	83	4	151	33	30	17	19	1.95
3715317--3715810	206	2.4	210	88	3	723	32	26	18	22	1.97
3715586--3715708	43	2.9	43	83	0	156	30	29	17	22	1.96
3715809--3715880	37	1.9	37	86	5	101	27	18	13	40	1.88
3716083--3716411	46	7.6	44	69	14	177	24	30	17	27	1.97
3715998--3716543	129	4.2	129	85	1	673	25	30	17	26	1.97
3716700--3716831	3	43.3	3	81	3	147	31	0	4	64	1.14
3717693--3717766	30	2.5	29	76	8	69	17	12	13	56	1.66
3721324--3721363	21	1.9	21	89	0	62	30	7	7	55	1.56
3732014--3732063	20	2.5	20	96	0	91	24	32	14	30	1.94
3737710--3737748	17	2.3	17	86	8	53	43	7	7	41	1.62
3742112--3742157	21	2.2	20	84	3	56	34	21	4	39	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3744387--3744469	20	4.0	21	76	7	82	34	25	19	20	1.96
3747538--3747609	35	2.1	35	89	5	110	33	9	27	29	1.89
3765391--3765425	9	3.8	9	85	7	52	22	51	20	5	1.68
3765385--3765430	5	9.6	5	76	9	51	23	52	19	4	1.64
3765385--3765430	19	2.4	19	96	0	83	23	52	19	4	1.64
3765404--3765432	14	2.1	14	100	0	58	20	48	24	6	1.74
3768614--3768655	15	2.7	15	86	13	59	61	0	28	9	1.27
3773559--3773598	19	2.0	20	86	13	57	67	0	10	22	1.20
3774011--3774062	19	2.6	21	84	6	72	44	7	13	34	1.72
3777955--3778006	19	2.6	21	90	6	81	46	5	13	34	1.67

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