genome.fa.s7823.2.7.7.80.10.50.1000.18.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: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6287495

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   

This is table  18  of  33  ( 3920 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)
3414818--3414872	24	2.3	24	90	0	83	14	9	20	56	1.65
3416379--3416453	10	7.7	10	68	21	52	9	10	21	58	1.59
3416385--3416449	16	4.1	16	91	0	112	7	10	23	58	1.57
3416519--3416550	16	2.0	16	100	0	64	6	12	25	56	1.59
3417058--3417546	181	2.7	177	77	6	475	41	10	12	36	1.76
3421025--3421090	20	3.2	20	76	4	69	46	3	6	43	1.43
3422369--3422411	21	2.1	20	86	4	59	11	23	41	23	1.87
3422686--3422847	82	2.0	82	98	0	315	35	16	7	41	1.76
3423130--3423176	17	2.8	16	81	15	51	57	17	4	21	1.56
3425006--3425087	23	3.7	23	85	3	96	20	25	30	23	1.99
3428922--3428962	21	1.9	22	90	5	66	29	4	7	58	1.46
3433128--3433166	14	2.7	14	88	4	51	61	2	0	35	1.10
3433146--3433197	16	3.3	15	78	10	50	73	5	1	19	1.14
3433154--3433197	16	2.7	16	86	10	54	72	6	2	18	1.17
3433239--3433353	51	2.2	51	79	11	119	56	8	13	20	1.64
3434086--3434139	2	27.0	2	100	0	108	50	0	0	50	1.00
3444388--3445045	323	2.0	322	87	5	940	44	4	7	43	1.52
3445736--3445768	6	5.5	6	96	0	57	18	3	36	42	1.66
3449478--3449621	3	48.0	3	82	0	180	39	2	0	58	1.10
3449734--3449778	16	2.8	16	96	0	81	11	55	20	13	1.68
3450979--3451018	12	3.1	13	82	10	55	40	0	0	60	0.97
3462297--3462325	9	3.3	9	90	9	51	82	0	17	0	0.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3462297--3462338	8	5.2	8	85	8	59	83	0	16	0	0.65
3462297--3462332	16	2.2	17	95	5	65	83	0	16	0	0.65
3463150--3463568	83	5.1	81	90	4	642	28	13	21	36	1.91
3464354--3465482	113	10.0	113	93	0	1767	36	14	19	29	1.92
3465814--3465933	3	40.0	3	82	0	150	40	1	0	58	1.08
3466044--3466084	16	2.6	16	100	0	82	7	56	19	17	1.64
3467528--3467552	12	2.1	12	100	0	50	24	0	8	68	1.16
3469071--3469117	19	2.4	20	85	3	60	34	25	10	29	1.90
3470538--3470666	41	3.2	40	80	4	143	31	20	14	33	1.93
3470532--3470701	81	2.1	83	81	6	195	28	19	15	36	1.93
3473621--3473661	13	3.1	14	86	10	59	0	24	29	46	1.53
3474124--3474176	27	2.1	24	82	10	61	58	0	0	41	0.98
3474137--3474191	18	3.1	19	82	7	64	63	0	0	36	0.95
3474137--3474176	3	13.7	3	89	5	55	62	0	0	37	0.95
3480622--3481030	210	2.0	209	99	0	809	36	21	17	24	1.94
3482615--3482688	2	37.0	2	100	0	148	0	50	0	50	1.00
3483273--3483313	22	1.9	21	90	5	64	68	0	0	31	0.90
3487050--3487305	20	12.6	20	79	9	234	38	25	18	17	1.93
3487091--3487281	40	4.7	40	90	0	265	37	24	19	18	1.94
3487862--3487902	20	2.0	20	95	0	73	56	17	14	12	1.68
3487884--3487976	33	2.8	33	86	1	114	45	23	19	11	1.83
3487981--3488098	33	3.4	33	83	9	146	12	22	20	44	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3488034--3488089	20	2.8	20	84	10	87	14	25	21	39	1.91
3489711--3490090	94	4.1	94	96	1	665	21	12	18	47	1.82
3490178--3490237	17	3.6	17	81	14	63	46	21	20	11	1.82
3490211--3490250	14	2.9	14	88	0	62	47	25	17	10	1.78
3490300--3490346	20	2.3	20	88	0	67	21	19	23	36	1.95
3490830--3490928	21	4.7	21	71	3	74	23	34	19	23	1.97
3490827--3490937	42	2.6	42	80	5	118	21	36	18	23	1.94
3492292--3492327	14	2.6	14	90	0	54	30	0	22	47	1.52
3492429--3492557	33	3.8	33	94	2	213	41	19	24	14	1.89
3492566--3492710	19	7.8	19	85	9	210	15	20	16	46	1.83
3492566--3492763	57	3.6	54	82	9	215	16	22	18	43	1.88
3492715--3492808	20	4.7	20	89	2	145	19	22	24	34	1.97
3495207--3495260	24	2.2	24	90	0	81	40	20	16	22	1.91
3496113--3496532	20	20.9	19	72	15	181	23	18	25	33	1.96
3496309--3496509	40	5.0	40	88	3	271	18	18	26	36	1.94
3497514--3497597	32	2.6	32	88	0	114	20	13	27	39	1.89
3497525--3497665	64	2.2	64	75	14	146	22	14	25	37	1.92
3497893--3497952	30	2.0	30	93	0	102	31	1	13	53	1.50
3500678--3500745	29	2.3	29	82	7	84	42	5	20	30	1.76
3505053--3505090	15	2.5	15	95	0	67	26	7	21	44	1.79
3505697--3505740	22	2.0	22	100	0	88	18	13	22	45	1.84
3505670--3505722	16	3.3	16	86	0	70	15	15	26	43	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3505672--3505746	16	4.3	16	73	18	60	13	14	28	44	1.83
3505683--3505762	38	2.1	38	85	0	106	12	13	26	47	1.79
3505700--3505750	22	2.3	22	90	6	77	15	13	25	45	1.83
3505920--3505975	18	3.2	17	80	7	51	51	0	3	44	1.18
3507493--3507534	6	6.8	6	91	2	57	61	0	23	14	1.32
3508360--3508405	21	2.1	22	88	4	67	45	6	4	43	1.49
3508360--3508413	21	2.6	21	85	5	56	46	7	3	42	1.49
3509077--3509111	12	2.9	12	82	0	52	45	31	11	11	1.76
3509782--3509903	6	19.8	6	70	12	52	19	4	2	72	1.14
3509994--3510025	5	6.6	5	92	7	57	18	0	0	81	0.70
3511311--3511365	24	2.3	24	96	0	101	32	27	18	21	1.96
3512198--3512443	95	2.7	94	83	10	291	30	17	19	31	1.95
3513633--3513749	36	3.2	36	92	1	180	31	18	10	39	1.85
3513784--3514017	36	6.9	36	72	15	192	27	19	9	42	1.83
3513833--3514242	65	6.2	63	72	16	303	28	19	9	42	1.82
3514031--3514151	36	3.5	35	79	7	131	28	19	10	42	1.84
3514090--3514145	15	3.5	15	71	21	51	19	21	12	46	1.83
3514080--3514147	33	2.1	32	94	2	118	23	19	11	45	1.83
3513642--3514199	134	4.1	133	91	1	882	27	19	10	42	1.83
3514116--3514246	67	2.0	65	88	5	192	29	20	9	40	1.83
3515112--3515160	23	2.1	24	85	11	66	44	26	14	14	1.83
3515934--3515979	3	15.3	3	90	0	74	32	4	0	63	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3515972--3516014	17	2.5	17	80	3	50	23	2	2	72	1.08
3516121--3516176	18	3.2	17	81	18	55	17	8	1	71	1.21
3516127--3516177	18	2.9	18	81	18	56	17	11	1	68	1.29
3517068--3517130	30	2.1	30	88	11	94	50	6	14	28	1.67
3522623--3523004	186	2.0	191	96	3	720	29	8	24	36	1.86
3522910--3523167	49	5.3	49	84	3	317	23	14	22	39	1.91
3522922--3523154	98	2.4	96	90	2	360	23	13	23	39	1.90
3522922--3523198	98	2.8	96	83	7	274	24	13	23	38	1.91
3523305--3523386	30	2.7	30	77	7	87	46	7	20	25	1.76
3524355--3524461	22	4.9	22	76	8	67	39	20	14	25	1.91
3533747--3533771	3	8.3	3	100	0	50	36	0	32	32	1.58
3534694--3534769	17	4.9	15	72	15	57	50	0	1	48	1.09
3534708--3534769	26	2.4	27	76	17	69	51	0	0	48	1.00
3534627--3535195	277	2.0	290	89	9	904	46	1	3	49	1.25
3534929--3534979	23	2.2	23	82	0	57	45	1	1	50	1.24
3534967--3535061	19	5.0	19	71	19	65	48	1	2	48	1.20
3535617--3535672	12	4.8	12	79	16	64	55	1	0	42	1.10
3535616--3535669	23	2.3	23	84	9	74	53	1	0	44	1.11
3535736--3535823	28	3.1	29	71	12	67	46	0	2	51	1.13
3535757--3535821	27	2.3	26	87	10	85	47	0	1	50	1.10
3535936--3536013	26	3.0	25	77	5	84	51	0	0	48	1.00
3536142--3536211	20	3.5	20	88	3	106	37	12	8	41	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3536144--3536204	19	3.2	19	90	2	95	36	13	8	42	1.74
3536194--3536236	14	2.9	15	75	6	52	30	18	6	44	1.76
3536860--3536973	39	2.9	39	75	8	117	33	14	1	50	1.52
3543434--3543491	28	2.1	28	96	0	107	41	10	15	32	1.81
3544889--3545030	38	3.7	38	81	4	160	41	14	16	26	1.88
3545371--3545442	21	3.5	21	70	14	78	40	15	5	38	1.70
3546318--3546376	20	3.0	20	82	0	73	23	10	6	59	1.54
3546818--3546842	6	4.2	6	100	0	50	48	20	16	16	1.82
3555275--3555333	21	2.8	21	73	0	55	37	25	18	18	1.94
3555205--3555398	92	2.1	92	80	9	209	37	21	15	25	1.93

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