genome.fa.s8488.2.7.7.80.10.50.1000.15.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  15  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)
3553427--3553485	21	2.8	21	84	0	82	23	3	23	49	1.65
3553667--3553782	44	2.6	44	82	6	128	37	16	15	31	1.90
3553687--3553793	44	2.4	44	82	4	126	36	14	15	32	1.89
3553700--3553814	44	2.6	43	83	5	140	39	15	14	30	1.88
3557863--3558005	21	6.8	21	82	10	177	37	21	20	20	1.94
3557863--3558005	63	2.3	61	90	4	223	37	21	20	20	1.94
3558847--3558881	2	17.5	2	100	0	70	51	0	0	48	1.00
3560791--3560847	14	4.1	14	88	0	78	28	49	21	1	1.59
3560785--3560856	14	5.3	14	79	9	69	31	48	18	1	1.56
3561435--3561477	19	2.3	19	81	18	54	65	0	18	16	1.28
3570041--3570085	17	2.6	18	78	7	56	55	0	0	44	0.99
3570788--3570823	16	2.2	17	95	5	65	16	0	0	83	0.65
3572147--3572193	18	2.7	18	90	3	69	27	29	8	34	1.87
3572744--3572849	3	35.0	3	81	9	126	32	0	0	66	0.98
3574351--3574413	2	32.5	2	90	6	103	47	0	1	50	1.10
3576598--3576916	159	2.0	159	98	1	622	27	11	19	40	1.87
3582169--3583392	257	4.7	257	83	3	1422	33	14	16	35	1.90
3583073--3583166	42	2.3	41	87	5	136	24	22	22	30	1.99
3582173--3583370	518	2.3	514	82	5	1455	33	14	16	34	1.90
3583512--3583556	3	14.7	3	81	4	54	37	0	0	62	0.96
3583513--3583564	9	5.7	9	81	4	59	38	1	0	59	1.08
3592924--3592958	17	2.1	17	94	0	61	14	0	22	62	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3595698--3595739	20	2.2	19	87	12	59	57	7	0	35	1.26
3595681--3595739	19	3.2	19	79	15	61	55	10	0	33	1.33
3599879--3599928	19	2.6	19	81	12	66	76	2	4	18	1.04
3600390--3600419	12	2.5	12	88	0	51	66	0	26	6	1.16
3600495--3600549	21	2.8	20	75	10	51	54	14	1	29	1.50
3600559--3600735	76	2.3	76	85	5	225	57	9	2	30	1.43
3602591--3602639	21	2.3	21	86	6	73	81	4	2	12	0.91
3602589--3602637	15	3.3	15	79	0	62	83	4	2	10	0.85
3606395--3606428	15	2.3	15	89	0	50	5	20	23	50	1.70
3608073--3608121	24	2.0	25	84	7	66	71	0	4	24	1.03
3608177--3608217	21	1.9	22	90	5	66	75	0	4	19	0.98
3608868--3609031	76	2.2	76	87	3	233	57	10	2	28	1.45
3612162--3612206	24	2.0	22	83	16	56	37	15	6	40	1.74
3632407--3632592	76	2.4	76	94	0	318	25	2	13	58	1.48
3633235--3633274	18	2.2	18	86	0	53	25	7	0	67	1.16
3641317--3641399	24	3.5	24	83	0	112	20	10	16	51	1.74
3641317--3641399	12	6.9	12	70	15	55	20	10	16	51	1.74
3641303--3641399	48	2.0	48	87	0	140	19	12	16	51	1.76
3641574--3641633	2	30.0	2	100	0	120	50	0	0	50	1.00
3643207--3643249	11	3.8	12	82	11	56	13	6	0	79	0.93
3643258--3643300	20	2.2	20	87	8	61	20	4	0	74	1.00
3643258--3643300	15	2.9	14	89	6	59	20	4	0	74	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3643258--3643300	5	8.6	5	80	10	52	20	4	0	74	1.00
3645204--3645335	44	3.3	42	66	28	106	25	2	12	59	1.44
3645188--3645415	76	3.0	76	92	1	379	27	2	12	57	1.46
3646013--3646059	17	2.6	18	90	10	78	23	6	2	68	1.24
3646931--3646962	15	2.1	15	94	0	55	18	28	3	50	1.62
3653608--3653777	76	2.2	76	97	0	322	25	1	12	60	1.40
3654388--3654434	17	2.6	18	90	10	78	23	6	2	68	1.24
3655303--3655334	15	2.1	15	94	0	55	18	28	3	50	1.62
3669441--3669477	18	2.1	18	85	14	51	32	13	10	43	1.79
3675095--3675131	18	2.1	18	85	14	51	32	13	10	43	1.79
3681914--3681958	20	2.2	20	96	0	81	35	13	24	26	1.92
3684899--3684949	14	3.6	14	92	5	68	21	11	27	39	1.88
3689753--3690396	39	16.6	39	87	1	819	34	15	14	35	1.89
3689951--3690055	19	5.4	19	63	20	56	26	20	17	36	1.94
3690142--3690206	20	3.2	21	68	12	64	30	13	20	35	1.91
3693174--3693198	13	1.9	13	100	0	50	80	0	8	12	0.92
3693532--3693580	24	2.0	25	88	4	73	46	0	0	53	1.00
3694486--3694535	21	2.4	21	93	0	82	4	18	18	60	1.52
3698130--3698155	6	4.3	6	100	0	52	15	15	15	53	1.73
3703493--3703650	54	2.9	56	78	9	191	31	10	15	41	1.82
3703713--3704292	230	2.5	230	88	2	840	30	17	17	34	1.93
3704243--3704316	21	3.6	21	72	3	78	29	20	20	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3704228--3704334	41	2.6	41	82	5	135	27	22	18	31	1.97
3704737--3705146	207	2.0	207	100	0	820	29	28	13	29	1.94
3705468--3705545	39	2.0	38	80	11	88	42	23	6	28	1.78
3708640--3708703	31	2.1	31	87	0	92	20	45	18	15	1.86
3708658--3708697	18	2.2	18	86	0	53	20	47	17	15	1.83
3708644--3708703	13	4.2	13	73	19	57	20	43	20	16	1.88
3708715--3708742	10	2.8	10	100	0	56	21	28	21	28	1.99
3709928--3710015	24	3.6	25	92	3	119	37	22	18	21	1.94
3712505--3712550	18	2.6	18	85	0	65	15	21	45	17	1.85
3722674--3722765	12	7.8	12	73	16	66	18	15	18	47	1.82
3722660--3722767	47	2.3	48	81	12	125	19	15	17	47	1.83
3722660--3722769	24	4.6	24	77	8	102	20	15	17	47	1.83
3728046--3728070	1	25.0	1	100	0	50	0	0	0	100	0.00
3729157--3729215	30	1.9	31	82	3	75	5	38	1	54	1.33
3730308--3730344	2	18.5	2	100	0	74	48	0	0	51	1.00
3730258--3730314	26	2.1	28	87	6	82	40	0	0	59	0.97
3730465--3730582	57	2.1	57	80	12	136	47	4	8	39	1.53
3731409--3731448	14	3.0	14	85	7	57	40	10	0	50	1.36
3749371--3749428	23	2.6	22	91	2	89	24	29	27	18	1.98
3750874--3750908	18	1.9	18	88	0	52	42	34	20	2	1.66
3751544--3751575	16	2.0	16	100	0	64	37	0	25	37	1.56
3752115--3752156	17	2.5	17	92	0	66	73	11	7	7	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3754509--3754555	9	5.6	8	78	16	51	85	0	0	14	0.61
3754508--3754549	9	4.6	9	85	14	59	85	0	0	14	0.59
3754514--3754560	19	2.4	20	89	3	78	85	0	0	14	0.61
3754508--3754560	12	4.9	11	81	13	58	84	0	0	15	0.61
3755225--3755280	2	28.0	2	100	0	112	50	0	50	0	1.00
3756052--3756081	15	2.0	15	93	0	51	70	0	3	26	1.03
3756254--3756909	134	4.9	133	82	3	719	30	15	21	32	1.94
3766875--3766928	3	18.0	3	100	0	108	66	0	0	33	0.92
3767383--3767446	9	6.8	10	80	16	59	37	1	1	59	1.16
3767396--3767446	3	17.0	3	88	8	68	35	1	1	60	1.19
3767383--3767446	21	3.0	22	77	20	66	37	1	1	59	1.16
3770365--3770404	20	2.0	20	90	0	62	17	22	22	37	1.94
3774192--3774225	15	2.3	15	89	0	50	20	29	29	20	1.98
3779312--3779349	19	2.0	19	100	0	76	31	5	36	26	1.79
3781874--3781902	11	2.6	11	100	0	58	93	6	0	0	0.36
3782187--3782399	51	4.1	51	78	4	205	18	12	12	56	1.66
3786549--3786648	23	4.2	23	73	18	80	76	1	16	7	1.06
3786568--3786666	40	2.4	39	74	11	92	76	0	17	6	0.97
3786601--3786682	18	4.3	19	77	16	73	75	0	19	4	0.98
3786568--3786710	65	2.2	67	81	8	168	75	0	16	7	1.06
3786568--3786712	66	2.2	66	82	7	170	75	0	16	7	1.07
3786570--3786665	17	5.2	18	76	14	72	76	0	17	6	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3786588--3786677	35	2.7	32	72	23	62	75	0	18	5	0.99
3788977--3789071	35	2.7	35	83	3	118	16	13	22	47	1.82
3789546--3789722	91	1.9	92	90	3	286	37	14	22	25	1.92
3789777--3789960	91	2.0	91	90	0	287	37	15	21	26	1.92
3789546--3790099	230	2.4	230	89	0	822	36	16	20	26	1.94
3789868--3790376	139	3.7	139	89	2	772	36	16	20	26	1.94
3791889--3792009	51	2.4	50	82	6	138	19	10	12	57	1.63
3798669--3798983	54	5.9	54	86	4	415	35	19	16	27	1.94
3798669--3798983	107	2.9	106	88	3	427	35	19	16	27	1.94
3798669--3798983	161	2.0	162	85	6	435	35	19	16	27	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