genome.fa.s1129.2.7.7.80.10.50.1000.45.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  45  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)
9956979--9957322	46	7.5	46	89	0	508	42	12	21	23	1.87
9965067--9965103	18	2.1	18	85	14	51	43	10	13	32	1.79
9968213--9968434	53	4.2	53	85	2	284	39	17	15	27	1.90
9972466--9972495	7	4.3	7	100	0	60	30	13	0	56	1.37
9975189--9975383	53	3.7	53	83	0	255	38	14	16	30	1.89
9981109--9981169	28	2.2	28	93	0	104	36	18	6	39	1.76
9981313--9981579	131	2.0	131	83	2	331	33	16	15	35	1.90
9982647--9982786	63	2.2	64	91	3	221	43	4	9	42	1.56
9986702--9986862	88	1.8	86	93	2	277	46	6	11	36	1.65
9994565--9994646	23	3.7	21	78	12	83	8	8	0	82	0.83
9994573--9994638	8	8.9	8	73	15	61	10	4	0	84	0.75
9994573--9994638	14	4.5	14	80	15	80	10	4	0	84	0.75
9997934--9997999	14	4.6	14	77	3	60	59	7	10	22	1.56
10001797--10001849	3	19.0	3	81	14	60	66	1	0	32	1.03
10001797--10001852	19	3.0	18	79	7	67	66	1	0	32	1.03
10001797--10001859	22	2.8	22	85	2	81	68	3	0	28	1.05
10001913--10001986	37	2.0	37	100	0	148	29	10	16	43	1.82
10003208--10003356	2	77.0	2	68	22	61	50	6	2	40	1.40
10003186--10003308	22	5.6	22	68	20	71	48	9	0	40	1.42
10003186--10003357	94	1.9	88	80	11	195	50	6	1	41	1.40
10003499--10003573	38	2.0	38	89	0	114	37	13	25	24	1.91
10012528--10012591	31	2.1	31	96	0	119	31	25	25	18	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10012531--10012614	31	2.7	31	87	3	98	32	25	26	16	1.96
10014151--10014186	2	18.0	2	100	0	72	50	0	0	50	1.00
10033744--10033779	16	2.2	16	90	0	54	75	0	11	13	1.06
10034644--10035430	82	9.6	82	83	3	951	37	21	17	23	1.94
10035552--10035603	27	1.9	27	92	0	86	32	1	1	63	1.16
10035555--10035604	3	16.7	3	83	8	66	32	2	2	64	1.16
10038498--10038537	17	2.4	17	95	0	71	37	30	7	25	1.83
10046465--10046504	6	6.7	6	85	0	53	25	15	7	52	1.68
10046465--10046504	12	3.3	12	100	0	80	25	15	7	52	1.68
10046478--10046534	28	2.0	28	86	0	78	21	10	7	61	1.52
10048619--10048686	2	34.0	2	100	0	136	50	0	0	50	1.00
10048976--10049027	26	1.9	28	92	7	90	71	7	17	3	1.25
10049010--10049096	17	5.2	16	82	9	102	81	0	10	8	0.87
10049033--10049125	1	93.0	1	73	0	51	83	0	8	7	0.80
10049033--10049102	8	8.5	8	87	12	106	85	0	4	10	0.72
10049015--10049096	34	2.4	34	93	2	139	82	0	8	8	0.83
10049015--10049126	42	2.6	42	85	8	145	81	0	10	8	0.88
10048984--10049125	8	17.4	8	74	11	76	79	1	12	6	0.98
10049731--10049793	32	2.0	32	96	0	117	42	17	17	22	1.89
10051415--10051637	114	2.0	114	93	0	383	33	15	21	30	1.94
10052456--10052579	54	2.3	54	88	0	176	22	24	31	21	1.98
10055195--10055234	21	1.9	21	89	0	62	10	25	40	25	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10061041--10061249	75	2.8	76	85	5	271	20	24	32	22	1.98
10063876--10063930	22	2.5	22	84	0	74	34	10	12	41	1.78
10064606--10064787	76	2.4	76	93	1	303	24	20	21	32	1.97
10064798--10065547	113	6.6	113	90	3	1073	37	15	19	28	1.91
10065500--10065565	20	3.3	20	69	23	66	50	12	22	15	1.77
10065488--10065629	40	3.5	41	89	9	220	47	10	22	19	1.80
10069605--10069660	27	2.1	27	100	0	112	48	7	3	41	1.48
10069913--10069942	14	2.1	14	100	0	60	20	13	10	56	1.65
10069960--10070916	317	3.0	316	96	1	1776	42	13	8	34	1.76
10071060--10071104	18	2.4	19	88	3	65	64	4	2	28	1.25
10073178--10073213	17	2.1	17	90	10	56	44	0	0	55	0.99
10076467--10076544	3	26.0	3	94	5	140	67	0	0	32	0.90
10079071--10079192	66	1.9	64	86	6	174	36	18	18	26	1.94
10080542--10080729	22	8.5	22	92	0	304	15	25	29	28	1.96
10088789--10088820	3	11.0	3	93	6	57	68	0	0	31	0.90
10096177--10096246	24	2.9	24	77	12	72	42	15	18	22	1.88
10098837--10098911	4	18.2	4	81	10	53	24	9	1	65	1.30
10100739--10100786	13	3.7	13	94	0	87	27	20	18	33	1.96
10100900--10100942	2	21.5	2	100	0	86	48	0	0	51	1.00
10101554--10101624	32	2.2	32	97	2	133	23	15	5	54	1.62
10105583--10105798	53	4.1	53	85	0	270	37	18	16	27	1.92
10107120--10107248	10	13.3	9	75	13	114	14	27	27	30	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10107120--10107248	30	4.4	29	90	5	181	14	27	27	30	1.95
10107120--10107248	19	6.7	19	79	13	115	14	27	27	30	1.95
10107245--10107309	22	3.0	22	90	0	112	20	47	21	10	1.80
10108239--10108315	31	2.4	32	73	14	79	19	27	27	25	1.99
10108192--10108315	63	2.0	62	81	12	146	17	26	29	26	1.98
10114478--10114576	10	10.3	9	76	12	90	15	27	28	29	1.96
10114478--10114576	19	5.2	19	80	13	89	15	27	28	29	1.96
10114477--10114576	29	3.4	30	85	9	127	16	27	28	29	1.97
10114573--10114637	22	3.0	22	90	0	103	20	47	21	10	1.80
10114627--10114657	7	4.4	7	100	0	62	16	29	29	25	1.96
10115568--10115644	31	2.4	32	73	14	79	19	27	27	25	1.99
10115521--10115644	63	2.0	62	81	12	146	17	26	29	26	1.98
10122044--10122092	3	16.3	3	100	0	98	67	0	0	32	0.91
10122609--10122817	53	4.0	53	78	6	235	38	18	16	26	1.91
10122613--10122804	105	1.8	105	84	4	262	39	17	15	27	1.90
10126205--10126450	132	1.9	131	82	5	309	34	17	12	35	1.88
10127963--10128226	83	3.2	80	76	9	194	31	13	20	34	1.91
10127987--10128222	83	2.9	82	81	5	246	31	12	21	34	1.90
10128203--10128435	41	5.6	40	71	8	171	26	18	17	37	1.93
10131393--10131760	42	8.8	43	73	10	262	25	22	17	34	1.96
10131395--10131732	124	2.7	124	89	0	498	25	21	17	35	1.95
10134549--10134593	20	2.3	20	88	3	65	37	0	24	37	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10145879--10145927	6	8.2	6	100	0	98	32	0	67	0	0.91
10147012--10147175	17	9.5	17	81	5	159	36	20	5	37	1.76
10146996--10147108	51	2.2	51	85	0	154	35	23	3	37	1.73
10152278--10152365	23	4.0	22	83	5	88	20	27	28	23	1.99
10152298--10152343	23	2.0	23	100	0	92	21	26	30	21	1.99
10157449--10157481	12	2.8	12	86	13	50	42	0	6	51	1.26
10160258--10160300	17	2.5	17	76	0	50	27	16	13	41	1.86
10160279--10160355	34	2.3	35	77	6	86	35	20	6	37	1.79
10160293--10160432	17	8.1	17	79	4	120	37	17	7	37	1.78
10162430--10162467	20	1.9	20	88	0	58	42	0	0	57	0.98
10165382--10165469	17	5.1	17	78	19	60	48	2	2	46	1.27
10165415--10165532	15	7.9	15	69	16	50	44	5	5	44	1.50
10165388--10165446	18	3.3	17	82	15	66	47	3	1	47	1.29
10165412--10165457	18	2.5	17	83	13	56	47	4	0	47	1.21
10165460--10165532	13	5.3	13	72	9	56	43	6	6	42	1.58
10165656--10165731	39	1.9	39	89	5	118	44	0	28	26	1.54
10165655--10165736	19	4.2	20	84	6	116	43	0	29	26	1.55
10166165--10166238	27	2.7	28	83	6	89	52	27	0	20	1.46
10166185--10166242	14	4.2	14	82	2	73	53	27	0	18	1.45
10166171--10166242	21	3.5	20	79	9	74	52	26	0	20	1.47
10166185--10166242	7	8.4	7	81	9	57	53	27	0	18	1.45
10166601--10166637	2	18.0	2	94	5	65	48	0	2	48	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10166944--10166990	14	3.7	14	71	26	50	51	4	0	44	1.21
10166942--10166991	23	2.1	24	96	3	93	48	4	0	48	1.20
10176578--10176640	21	2.9	21	83	4	72	15	25	38	20	1.92
10183217--10183257	16	2.6	16	84	0	55	63	4	7	24	1.40
10183428--10183470	16	2.7	16	81	0	59	32	6	27	32	1.84
10183796--10183827	4	8.0	4	100	0	64	75	0	0	25	0.81
10183826--10183904	29	2.7	28	86	3	104	49	2	17	30	1.60
10185978--10186026	19	2.6	19	84	9	66	32	18	24	24	1.97
10185996--10186119	46	2.7	47	83	12	143	29	16	23	30	1.97
10185996--10186119	45	2.7	46	82	13	141	29	16	23	30	1.97

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