genome.fa.s1129.2.7.7.80.10.50.1000.43.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   

This is table  43  of  89  ( 10573 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)
9505968--9506000	9	3.6	9	95	4	57	75	0	3	21	0.93
9508497--9508550	19	2.8	19	81	13	58	72	0	7	20	1.08
9511412--9511451	16	2.5	16	75	0	53	70	0	12	17	1.18
9512754--9512790	16	2.3	16	90	0	56	67	0	16	16	1.23
9514072--9514117	20	2.3	20	85	7	58	34	30	10	23	1.89
9520613--9520678	17	3.8	17	82	9	89	77	3	16	3	1.02
9520616--9520708	6	16.3	6	70	10	61	75	2	18	4	1.07
9520616--9520727	35	3.2	34	80	16	124	74	1	18	5	1.10
9520616--9520714	34	2.9	33	85	12	123	74	2	18	5	1.09
9520669--9520729	18	3.4	18	78	17	74	73	0	19	6	1.04
9520648--9520700	22	2.3	23	84	12	74	73	1	18	5	1.12
9520634--9520726	34	2.7	33	85	12	109	73	1	19	6	1.11
9524628--9524764	59	2.3	59	82	2	186	28	18	24	28	1.98
9524865--9524986	47	2.7	45	87	6	174	38	8	22	30	1.84
9525881--9525949	29	2.4	29	77	0	75	27	15	5	50	1.67
9526123--9526460	137	2.4	139	77	6	344	28	11	12	46	1.77
9528659--9528704	18	2.6	18	85	0	65	26	21	15	36	1.93
9532290--9532407	60	1.9	59	80	14	134	27	7	3	61	1.40
9532508--9532536	2	14.5	2	100	0	58	48	0	0	51	1.00
9532722--9532761	20	2.0	20	86	13	57	20	7	0	72	1.08
9536716--9537065	183	1.9	183	95	0	628	26	20	21	30	1.98
9538341--9538427	37	2.4	37	88	1	122	25	20	13	40	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9538246--9538493	102	2.4	105	86	6	353	31	20	13	35	1.91
9538377--9538556	66	2.8	66	91	4	278	31	21	12	35	1.90
9538508--9538593	37	2.4	36	82	5	104	29	20	11	38	1.88
9538273--9538658	166	2.3	169	90	4	615	31	20	12	36	1.90
9538609--9538694	36	2.4	36	86	3	111	25	18	13	41	1.88
9538443--9538789	100	3.5	100	87	5	469	31	19	12	37	1.88
9538677--9538735	30	2.0	30	86	6	84	40	16	10	32	1.82
9538749--9538863	36	3.1	36	82	4	158	29	19	11	40	1.86
9538902--9539016	33	3.5	33	88	5	153	37	19	10	33	1.86
9538971--9539157	67	2.7	67	81	4	214	30	21	11	36	1.89
9539470--9539676	106	1.9	107	89	0	317	35	26	17	20	1.95
9539473--9539720	106	2.3	106	82	4	295	35	25	16	22	1.95
9541043--9541083	2	20.5	2	100	0	82	48	0	0	51	1.00
9541259--9541309	21	2.4	21	84	12	61	21	7	1	68	1.25
9543698--9543758	23	2.7	24	85	10	83	21	22	8	47	1.77
9544171--9544211	17	2.3	18	87	4	57	39	2	2	56	1.26
9545672--9545723	22	2.4	22	80	3	61	63	3	1	30	1.23
9546771--9546820	21	2.4	20	83	12	57	24	18	20	38	1.93
9547582--9547644	21	2.9	21	73	4	63	38	25	11	25	1.89
9552056--9552096	20	2.0	20	85	0	55	24	24	24	26	2.00
9552062--9552105	20	2.2	20	83	0	52	25	15	27	31	1.96
9553758--9553802	21	2.1	21	84	8	56	26	11	22	40	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9555203--9555245	22	2.0	22	95	0	77	16	23	37	23	1.94
9557260--9557299	21	1.9	21	89	0	62	10	25	40	25	1.86
9557282--9557339	23	2.8	21	79	12	66	18	24	34	22	1.96
9568257--9568301	21	2.1	21	83	4	54	57	8	6	26	1.54
9584632--9584722	28	3.1	28	79	11	94	46	1	4	48	1.29
9585041--9585155	54	2.2	54	81	9	130	44	0	1	53	1.17
9587477--9587514	2	18.5	2	89	5	58	44	0	2	52	1.14
9589661--9589709	20	2.5	20	96	0	89	20	6	10	63	1.47
9590378--9590483	44	2.4	44	91	1	167	28	24	10	36	1.88
9593479--9593550	2	36.0	2	100	0	144	50	0	0	50	1.00
9594753--9594785	9	3.9	9	88	11	52	42	0	0	57	0.98
9594753--9594785	16	1.9	18	88	11	52	42	0	0	57	0.98
9595199--9595265	19	3.7	18	75	16	59	7	37	0	55	1.28
9598349--9598390	13	2.9	14	83	16	50	28	9	2	59	1.41
9600248--9600303	21	2.7	21	85	0	85	19	35	33	10	1.87
9601423--9601496	37	2.0	37	100	0	148	32	29	2	35	1.72
9604512--9604561	19	2.6	19	81	12	66	74	2	4	20	1.08
9605022--9605051	12	2.5	12	88	0	51	66	3	23	6	1.30
9607003--9607038	5	7.2	5	87	12	56	80	0	0	19	0.71
9607003--9607038	9	3.6	10	88	11	56	80	0	0	19	0.71
9607006--9607037	14	2.2	15	94	5	57	81	0	0	18	0.70
9610530--9610657	65	2.0	65	87	6	188	55	14	0	28	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9611796--9611837	22	1.9	22	85	0	57	9	16	23	50	1.75
9619931--9620079	77	1.9	78	80	5	176	42	6	10	40	1.64
9620051--9620129	27	2.9	26	90	7	106	46	1	3	48	1.28
9620051--9620115	27	2.4	27	97	0	121	44	0	4	50	1.22
9625375--9625413	18	2.2	18	95	0	69	43	15	5	35	1.69
9626854--9627010	65	2.4	64	90	1	242	31	21	16	31	1.95
9630069--9630113	18	2.5	18	89	7	65	44	13	6	35	1.70
9631201--9631259	24	2.5	24	80	0	64	22	18	28	30	1.97
9633906--9633937	15	2.1	15	94	0	55	68	3	3	25	1.18
9636337--9636530	5	39.8	5	67	25	96	55	5	2	37	1.34
9636377--9636520	7	20.1	7	68	20	77	54	5	2	37	1.35
9636340--9636530	8	22.8	8	66	21	65	55	5	2	37	1.34
9636377--9636517	24	5.5	25	71	20	103	54	5	2	37	1.36
9636371--9636513	39	3.7	39	73	17	118	54	5	2	37	1.36
9637484--9637509	3	8.7	3	100	0	52	0	34	0	65	0.93
9638342--9638403	19	3.2	19	79	4	61	32	12	20	33	1.91
9638443--9638483	20	2.0	20	85	0	55	39	4	19	36	1.73
9643473--9643531	29	2.0	29	90	0	91	52	13	11	22	1.72
9648154--9648212	29	2.0	29	90	6	93	50	13	10	25	1.72
9648282--9648310	12	2.5	12	94	5	51	62	0	17	20	1.33
9651308--9651552	43	5.7	43	77	11	195	26	17	3	52	1.61
9651190--9651552	86	4.2	85	75	11	242	26	16	4	51	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9651190--9651553	43	8.4	43	72	14	170	26	16	5	51	1.65
9651285--9651569	129	2.2	129	78	11	298	25	17	5	51	1.65
9651373--9651552	85	2.1	85	83	11	217	27	17	4	50	1.65
9653821--9653870	21	2.4	21	89	0	82	30	14	20	36	1.91
9655109--9655181	23	3.2	23	90	0	110	38	20	5	35	1.76
9655599--9655671	23	3.2	23	92	0	119	38	21	5	34	1.77
9659782--9659847	33	2.0	33	87	0	96	22	46	1	28	1.61
9659881--9659945	21	3.1	21	93	0	103	16	30	10	41	1.83
9662169--9662211	20	2.3	18	85	14	61	20	16	11	51	1.75
9662174--9662220	20	2.4	19	82	10	67	19	17	10	53	1.72
9662355--9662401	20	2.3	20	86	10	69	17	14	10	57	1.65
9662141--9662613	181	2.6	182	88	0	678	27	16	13	42	1.86
9663544--9663574	5	6.2	5	100	0	62	0	19	0	80	0.71
9663933--9664045	42	2.6	43	77	15	117	19	12	14	53	1.71
9664551--9664858	41	7.5	39	71	11	116	30	19	19	29	1.97
9664551--9664928	206	1.8	205	86	2	544	30	18	19	31	1.96
9664878--9664968	41	2.2	41	82	3	112	28	14	19	37	1.91
9667529--9667608	21	3.8	21	96	0	142	22	7	17	52	1.69
9667727--9667879	42	3.6	43	81	7	134	22	13	22	41	1.88
9667770--9668033	43	6.2	42	76	5	158	23	18	20	37	1.94
9667895--9668028	42	3.2	41	71	17	103	23	22	18	35	1.96
9669051--9669077	14	1.9	14	100	0	54	51	0	25	22	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9670862--9671024	81	2.0	81	96	0	299	41	19	13	25	1.88
9673290--9673360	21	3.5	20	67	25	60	30	15	16	36	1.90
9673284--9673359	39	1.9	39	91	0	125	30	15	17	36	1.91
9679094--9679143	20	2.6	19	81	15	59	30	24	16	30	1.96
9684055--9684117	2	31.5	2	90	0	99	49	4	0	46	1.23
9693733--9693759	4	6.8	4	100	0	54	25	0	22	51	1.48
9694794--9694863	21	3.5	21	72	18	76	30	20	17	32	1.95
9694902--9694941	21	1.9	21	94	0	71	40	25	10	25	1.86
9700798--9700822	13	1.9	13	100	0	50	88	12	0	0	0.53
9700794--9700860	8	8.0	8	81	15	82	82	13	4	0	0.82

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