genome.fa.s9462.2.7.7.80.10.50.1000.3.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: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  20687664

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   79   80   
          81   82   83   84   85   86   87   88   89   90   91   

This is table  3  of  91  ( 10815 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)
458912--458960	19	2.7	17	84	9	53	26	20	28	24	1.99
458932--459076	64	2.2	65	85	6	188	26	19	24	29	1.98
459974--460010	16	2.3	16	100	0	74	24	32	5	37	1.78
464071--464155	45	1.9	44	92	2	143	32	15	11	40	1.83
466978--467035	6	9.0	6	80	14	62	15	0	3	81	0.83
466987--467035	7	7.3	7	81	9	66	14	0	2	83	0.73
466984--467035	13	3.9	13	87	12	79	15	0	1	82	0.75
468363--468664	155	1.9	155	86	1	426	31	17	22	27	1.97
482673--482703	16	1.9	16	93	0	53	61	0	9	29	1.28
483211--483290	23	3.4	24	83	13	87	52	1	3	42	1.27
483253--483302	23	2.2	22	82	3	55	46	4	6	44	1.47
484096--484150	7	8.1	7	80	10	53	5	50	0	43	1.25
484096--484150	13	4.1	14	81	13	62	5	50	0	43	1.25
493748--493784	18	2.0	20	89	10	60	48	16	0	35	1.46
494337--494366	14	2.1	14	93	0	51	40	10	0	50	1.36
496176--496299	62	2.0	62	98	0	239	47	6	18	27	1.73
498730--498902	84	2.1	84	94	0	301	32	22	21	22	1.98
499020--499105	18	4.8	19	79	12	101	46	13	8	31	1.73
499022--499108	35	2.5	35	86	1	120	47	13	8	31	1.72
501804--501869	29	2.3	29	81	5	80	37	6	4	51	1.47
501843--501938	31	3.1	31	80	3	104	40	5	0	54	1.23
501948--502035	28	3.1	28	80	11	92	50	1	3	45	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
502112--502149	13	3.0	13	80	3	51	50	0	5	44	1.24
502035--502301	30	8.9	30	76	6	195	52	1	9	37	1.41
503133--503232	48	2.1	48	88	0	146	38	7	6	49	1.55
503587--503636	24	2.1	24	100	0	100	58	8	30	4	1.45
503826--503867	21	2.0	21	95	0	75	38	16	23	21	1.93
503831--503880	21	2.4	21	82	0	64	34	22	20	24	1.97
504286--504384	29	3.5	28	83	8	121	25	20	10	44	1.82
506793--506840	19	2.5	20	86	3	62	50	2	14	33	1.55
510011--510121	28	4.2	28	63	21	78	16	21	11	50	1.76
511585--511651	26	2.5	26	85	2	80	74	1	16	7	1.11
511604--511656	21	2.7	20	80	8	65	81	1	13	3	0.92
511604--511656	22	2.5	21	79	8	63	81	1	13	3	0.92
512178--512293	60	1.9	60	91	0	187	36	12	19	31	1.90
514315--514357	21	2.0	21	90	0	68	25	16	25	32	1.96
515019--515350	185	1.8	183	84	5	463	44	6	8	40	1.60
517120--517178	30	2.0	30	93	0	100	28	10	25	35	1.89
517086--517223	73	1.9	72	82	4	170	28	15	23	31	1.96
517148--517293	43	3.4	43	84	11	217	33	19	21	25	1.97
520906--520931	6	4.3	6	100	0	52	69	15	0	15	1.20
521189--521469	41	6.9	41	78	4	264	34	19	18	27	1.95
521184--521426	80	3.0	82	81	6	287	35	20	17	26	1.95
521230--521467	123	1.9	122	82	4	291	34	19	17	27	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
522339--522374	2	18.5	2	94	5	65	50	0	0	50	1.00
522342--522371	15	2.0	15	100	0	60	53	0	0	46	1.00
522340--522373	17	2.0	17	100	0	68	52	0	0	47	1.00
523588--523623	18	1.9	19	88	5	56	77	2	0	19	0.88
524964--524996	2	17.0	2	93	6	59	48	0	0	51	1.00
524967--524998	15	2.1	15	100	0	64	46	0	0	53	1.00
524989--525037	19	2.4	20	83	13	64	65	0	0	34	0.93
528209--528265	21	2.7	21	75	0	60	35	15	24	24	1.95
529662--529712	20	2.5	21	77	3	59	60	3	0	35	1.15
530637--530684	9	5.0	9	83	14	60	41	25	29	4	1.74
530639--530684	21	2.3	21	85	10	62	41	26	28	4	1.74
553301--553345	3	14.7	3	90	4	72	33	0	0	66	0.92
563765--563792	9	3.1	9	100	0	56	53	0	46	0	1.00
571118--571274	64	2.5	63	79	10	167	28	18	17	35	1.94
578015--578171	64	2.5	63	77	10	167	25	19	20	35	1.96
579592--579657	34	1.9	34	87	0	96	53	15	1	30	1.51
586408--586447	20	2.1	19	90	4	62	35	7	32	25	1.84
586600--586673	36	2.1	36	85	10	98	47	2	0	50	1.15
589915--590740	413	2.0	416	93	1	1419	28	19	14	38	1.91
593913--593990	16	4.9	16	68	6	68	51	26	10	11	1.70
593913--593995	32	2.6	32	84	3	114	50	26	10	12	1.72
594257--594294	20	2.0	20	89	5	60	60	0	5	34	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
599984--600062	32	2.5	32	89	4	115	34	16	10	39	1.82
600898--600968	19	3.6	19	70	10	61	28	16	28	26	1.97
601418--601549	34	3.6	34	70	21	113	36	11	23	28	1.90
601366--601595	78	3.0	76	86	10	321	37	11	23	27	1.89
609387--609457	20	3.5	20	73	16	58	26	16	28	28	1.97
609864--610106	79	3.1	79	91	0	378	37	11	23	28	1.89
609953--610096	45	3.5	44	73	20	155	33	11	25	29	1.90
623544--623587	22	2.1	22	83	8	56	45	4	0	50	1.22
623489--623599	35	3.2	34	88	5	145	39	2	0	56	1.19
623590--623616	13	2.1	13	100	0	54	33	0	0	66	0.92
623489--623614	35	3.7	35	85	8	138	38	2	0	58	1.17
637784--637828	20	2.2	20	92	0	72	33	17	17	31	1.94
638342--638645	151	2.0	151	98	0	581	42	14	15	27	1.85
638727--638766	21	1.9	22	90	10	66	17	10	35	37	1.83
638897--638949	21	2.5	21	96	0	97	26	26	22	24	2.00
638994--639092	21	4.8	20	82	13	119	22	21	34	22	1.97
639172--639229	30	2.0	29	90	10	91	44	17	5	32	1.70
639172--639231	29	2.0	30	93	6	104	43	16	6	33	1.74
640429--640476	19	2.5	20	82	3	62	29	12	6	52	1.63
641615--641654	21	1.9	22	90	10	66	12	10	40	37	1.77
641767--641863	21	4.7	21	85	1	124	29	24	21	23	1.99
641903--642001	21	4.8	20	83	13	119	21	19	36	23	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
642081--642139	30	2.0	30	86	6	84	44	16	5	33	1.70
648825--648867	13	3.4	13	83	6	52	23	23	2	51	1.60
648910--648984	19	3.9	19	82	3	89	29	18	8	44	1.78
652782--652936	78	2.0	78	97	2	296	31	18	10	40	1.84
654134--654191	20	2.8	20	77	17	55	65	3	27	3	1.25
654147--654188	19	2.2	19	86	4	57	66	2	30	0	1.04
657024--657066	21	2.0	21	82	8	52	16	23	27	32	1.96
660556--660600	23	2.0	23	90	0	72	22	26	28	22	1.99
672537--672767	118	2.0	114	94	3	408	34	5	12	47	1.64
673051--673079	13	2.2	13	100	0	58	51	17	6	24	1.69
678306--678419	36	3.3	35	78	17	141	20	25	21	32	1.98
678333--678409	29	2.6	30	87	2	111	18	24	23	33	1.96
678679--678727	20	2.5	20	93	0	80	22	22	8	46	1.77
686161--686236	29	2.5	30	87	4	100	22	6	17	53	1.66
686656--686722	30	2.2	31	89	2	100	52	14	10	22	1.72
690401--690476	22	3.5	22	92	0	125	28	1	2	67	1.12
690401--690507	22	4.3	25	80	16	109	29	2	2	64	1.22
690442--690507	30	2.2	29	86	2	96	30	4	3	62	1.30
690401--690489	4	20.8	4	75	13	70	28	3	2	66	1.20
690924--690973	26	2.0	25	84	4	64	28	0	8	64	1.22
692395--692451	3	18.7	3	85	3	60	8	0	56	35	1.31
692398--692469	9	7.6	9	80	11	72	12	0	52	34	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
692387--692472	6	13.7	6	79	9	64	15	0	51	33	1.44
696996--697038	20	2.2	20	87	8	61	13	2	4	79	1.00
705220--705254	15	2.4	14	86	9	52	65	2	31	0	1.07
712215--712250	16	2.1	18	90	10	58	47	2	0	50	1.15
712370--712400	2	15.5	2	100	0	62	48	0	0	51	1.00
712455--712479	2	12.5	2	100	0	50	52	0	0	48	1.00
714173--714210	5	7.6	5	100	0	76	39	0	0	60	0.97
714828--714866	19	2.1	19	86	13	55	12	10	0	76	1.01
715031--715065	18	1.9	18	88	0	52	40	0	17	42	1.49
722501--722525	6	4.2	6	100	0	50	36	0	32	32	1.58

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   79   80   
          81   82   83   84   85   86   87   88   89   90   91