genome.fa.s9634.2.7.7.80.10.50.1000.16.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

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   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   

This is table  16  of  78  ( 9351 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)
3506482--3506530	20	2.6	18	90	6	71	4	20	0	75	0.96
3506455--3506582	60	2.1	58	80	12	143	6	21	0	71	1.13
3506459--3506530	27	2.8	26	82	17	82	5	19	0	75	1.00
3506457--3506539	44	1.9	43	87	7	123	4	20	1	73	1.08
3506458--3506558	44	2.4	45	82	11	115	5	19	0	73	1.10
3515946--3516042	44	2.1	47	88	7	146	40	20	11	27	1.87
3520088--3520173	3	28.7	3	78	4	84	39	0	1	59	1.05
3520880--3520912	12	2.8	12	100	0	66	57	9	27	6	1.53
3521310--3521349	21	1.9	21	85	10	55	32	5	0	62	1.17
3521464--3521498	2	18.0	2	94	5	63	51	48	0	0	1.00
3521498--3521549	2	26.0	2	96	0	95	50	0	1	48	1.12
3522483--3522545	29	2.3	28	78	19	71	31	3	1	63	1.19
3523015--3523105	46	1.9	49	82	6	116	36	13	20	29	1.91
3523856--3523938	43	1.9	44	82	2	105	30	13	22	33	1.92
3531516--3531557	22	1.9	22	90	0	66	35	19	14	30	1.91
3532043--3532378	123	2.7	122	88	2	476	40	16	18	25	1.90
3532294--3532651	139	2.6	139	78	2	364	40	15	16	27	1.88
3532876--3532962	3	29.0	3	74	4	77	35	0	1	63	1.02
3534065--3534105	2	20.5	2	100	0	82	48	0	0	51	1.00
3534227--3534266	21	1.9	21	85	10	55	32	5	0	62	1.17
3534383--3534420	2	19.0	2	88	0	58	52	2	0	44	1.14
3534548--3534831	149	1.9	149	85	9	398	38	7	5	48	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3535827--3535874	23	2.1	23	88	0	69	35	12	18	33	1.89
3536265--3536327	23	2.7	23	90	0	90	38	19	6	36	1.77
3536722--3536846	39	3.2	39	97	0	232	17	13	20	48	1.80
3537384--3537433	25	2.0	25	88	3	75	40	18	8	34	1.79
3537707--3537769	23	2.7	23	90	0	90	38	19	6	36	1.77
3537908--3537974	30	2.2	29	82	10	73	43	0	4	52	1.21
3538113--3538161	22	2.2	22	89	7	73	42	18	2	36	1.62
3538125--3538177	22	2.4	22	90	0	79	35	18	7	37	1.80
3538543--3538594	22	2.3	22	86	3	68	40	17	5	36	1.73
3537465--3539109	417	4.0	422	93	5	2786	38	12	8	40	1.73
3538943--3539014	23	3.2	22	86	5	90	40	19	5	34	1.75
3538953--3539014	22	2.7	23	90	2	90	38	17	6	37	1.76
3542116--3542617	181	2.8	183	89	6	803	33	15	14	36	1.88
3543715--3543786	3	24.0	3	78	0	72	26	34	4	34	1.76
3545206--3546557	392	3.4	395	97	2	2518	30	15	17	36	1.91
3545206--3546557	197	6.9	198	97	1	2538	30	15	17	36	1.91
3545206--3546557	589	2.3	589	97	2	2544	30	15	17	36	1.91
3546669--3546712	18	2.4	18	84	0	61	59	11	2	27	1.44
3548586--3548627	21	2.0	21	85	0	57	14	30	16	38	1.89
3550852--3550898	19	2.4	19	80	13	60	21	17	10	51	1.75
3551020--3551065	20	2.3	20	89	10	76	17	17	10	54	1.70
3552000--3552050	14	3.4	14	75	20	50	72	0	21	5	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3555762--3555799	20	1.9	20	94	0	67	42	18	2	36	1.64
3562073--3562106	18	1.9	17	88	5	50	64	5	0	29	1.17
3570090--3570123	18	1.9	17	88	5	50	64	5	0	29	1.17
3577567--3577626	23	2.7	23	82	10	72	28	26	20	25	1.99
3578342--3578373	16	2.0	16	100	0	64	12	25	18	43	1.85
3587669--3587698	7	4.3	7	100	0	60	56	26	0	16	1.40
3590166--3590231	21	3.1	21	80	0	78	25	9	36	28	1.87
3590235--3590379	42	3.5	42	82	1	157	22	7	43	26	1.80
3590220--3590437	21	10.4	21	77	1	132	22	9	41	26	1.84
3590221--3590442	84	2.6	84	77	6	207	22	9	40	26	1.84
3590427--3590509	42	2.0	42	80	0	94	21	10	42	25	1.85
3590460--3590509	21	2.4	21	89	0	73	26	10	36	28	1.88
3590598--3590656	21	2.8	21	86	0	73	20	16	47	15	1.83
3590625--3590704	21	3.8	21	79	0	70	26	15	38	20	1.91
3595857--3595976	29	4.1	29	93	2	197	37	20	10	32	1.85
3597376--3597413	15	2.4	16	82	8	51	65	0	2	31	1.06
3599532--3599571	21	1.9	21	89	0	62	32	27	15	25	1.95
3599597--3599635	19	2.1	19	95	0	69	20	38	15	25	1.92
3599552--3599761	64	3.3	64	80	9	216	30	26	16	27	1.96
3599713--3599761	19	2.6	19	84	9	57	24	30	18	26	1.98
3608105--3608144	21	1.9	21	94	0	71	32	30	15	22	1.94
3608170--3608208	19	2.1	19	90	0	60	23	38	12	25	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3608105--3608269	64	2.5	65	83	4	199	33	25	14	26	1.94
3608286--3608334	19	2.6	19	84	9	57	24	30	18	26	1.98
3615558--3615612	21	2.9	17	84	13	56	12	45	14	27	1.81
3615558--3615604	21	2.2	21	100	0	94	14	42	14	27	1.86
3616568--3616697	23	5.7	23	86	3	172	31	25	23	20	1.98
3616909--3616958	25	2.0	25	100	0	100	32	28	4	36	1.76
3617483--3617624	64	2.2	63	79	7	153	26	22	17	33	1.96
3618102--3618160	7	8.6	7	94	1	93	57	0	40	1	1.09
3618431--3618506	15	4.8	15	73	16	55	64	1	25	9	1.31
3621081--3621324	121	2.0	121	91	1	391	47	3	9	38	1.54
3621313--3621387	30	2.5	29	80	6	87	53	0	2	44	1.14
3621367--3621445	30	2.7	28	75	9	86	55	0	3	40	1.18
3626641--3626707	20	3.2	20	68	15	64	35	19	16	28	1.93
3626631--3626715	42	2.0	42	100	0	170	36	23	14	25	1.93
3626881--3626916	17	2.1	17	89	0	54	27	0	11	61	1.30
3643614--3643715	3	33.7	3	94	2	177	35	0	0	63	1.01
3645080--3645114	18	1.9	18	88	0	52	37	2	0	60	1.12
3645796--3645842	14	3.3	15	82	5	53	21	0	2	76	0.89
3645796--3645840	19	2.3	20	81	11	58	22	0	2	75	0.91
3654945--3655730	83	9.5	83	95	0	1373	27	11	23	37	1.90
3656474--3657104	113	5.6	113	96	1	1124	36	12	20	30	1.89
3657350--3657415	3	22.7	3	90	6	109	34	1	0	63	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3658839--3658876	19	2.0	20	84	5	51	39	2	0	57	1.12
3667123--3667153	2	15.5	2	100	0	62	48	0	0	51	1.00
3682071--3682176	2	53.5	2	98	1	205	50	0	0	50	1.00
3684125--3684183	26	2.3	26	76	5	66	59	8	1	30	1.37
3689621--3689739	56	2.1	56	96	0	220	42	8	24	25	1.82
3702270--3702322	25	2.1	25	96	0	97	37	30	15	16	1.90
3709978--3710271	30	9.8	30	87	2	353	35	4	35	24	1.77
3709978--3710287	90	3.4	90	86	3	394	35	4	35	24	1.76
3713398--3713437	21	1.9	21	85	10	55	60	10	12	17	1.59
3716418--3716457	15	2.7	15	88	3	64	12	12	32	42	1.80
3717400--3717425	3	8.7	3	100	0	52	69	0	30	0	0.89
3717992--3718483	200	2.5	199	83	2	569	31	14	13	40	1.86
3719503--3719540	18	2.1	18	95	0	67	34	18	15	31	1.92
3722555--3722624	10	7.3	9	75	10	59	15	28	28	27	1.96
3722555--3722622	19	3.5	19	88	6	93	16	26	29	27	1.97
3722620--3722658	17	2.3	17	100	0	78	17	46	23	12	1.83
3729841--3729918	19	4.1	19	81	8	68	19	25	26	28	1.99
3729876--3729918	19	2.3	19	95	0	77	18	25	27	27	1.98
3729841--3729920	29	2.8	29	81	5	83	18	27	26	27	1.98
3731945--3732089	21	6.9	21	77	7	141	24	35	16	24	1.95
3733391--3733438	19	2.5	20	86	3	62	50	6	14	29	1.67
3734765--3734864	21	4.7	21	73	16	89	21	35	18	26	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3736223--3737419	198	6.1	199	90	3	1622	30	16	14	38	1.89
3736219--3737419	392	3.0	390	87	4	1657	29	16	14	38	1.89
3736223--3737419	590	2.0	591	86	3	1685	30	16	14	38	1.89
3738480--3738528	19	2.6	19	96	0	89	55	10	2	32	1.45
3740284--3740350	33	2.0	33	97	0	125	23	46	0	29	1.53
3740791--3740846	24	2.4	23	80	8	69	50	7	0	42	1.30
3744156--3744251	31	3.1	31	80	3	93	41	17	5	35	1.72
3744747--3744779	7	4.7	7	100	0	66	12	0	0	87	0.53
3744935--3744981	23	2.0	23	95	0	85	48	25	10	14	1.76
3745610--3745929	46	6.9	46	82	3	340	31	21	20	25	1.98

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   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78