genome.fa.s1129.2.7.7.80.10.50.1000.42.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  42  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)
9217070--9217137	24	2.8	24	88	0	73	39	20	16	23	1.91
9217777--9217814	17	2.2	17	95	0	67	26	2	36	34	1.71
9218084--9218129	19	2.4	19	85	3	56	21	17	30	30	1.96
9218095--9218131	19	1.9	19	94	0	65	21	16	29	32	1.95
9223164--9223194	3	10.7	3	93	6	55	67	0	0	32	0.91
9223792--9223847	27	2.2	26	83	6	69	42	26	14	16	1.86
9224095--9224178	31	2.7	31	77	12	93	44	22	3	29	1.70
9233537--9233624	29	3.0	30	83	6	92	42	2	18	37	1.63
9233941--9233993	14	3.8	14	100	0	106	43	18	15	22	1.87
9234348--9234379	3	10.7	3	100	0	64	34	0	0	65	0.93
9234890--9234932	2	21.5	2	100	0	86	51	0	0	48	1.00
9247770--9247815	20	2.3	19	85	14	58	50	8	15	26	1.73
9270306--9270351	20	2.3	19	85	14	58	50	8	15	26	1.73
9274078--9274889	134	6.1	134	83	5	852	31	25	15	28	1.96
9276449--9276480	2	16.0	2	100	0	64	0	50	0	50	1.00
9276480--9276523	2	22.5	2	95	4	81	50	0	0	50	1.00
9286477--9286528	20	2.6	20	90	0	86	36	17	17	28	1.92
9289068--9289231	20	7.6	20	72	16	123	22	25	6	45	1.77
9289056--9289255	46	4.5	46	85	6	261	23	24	7	46	1.77
9294919--9294949	16	1.9	16	93	0	53	29	29	6	35	1.82
9295941--9296100	46	3.5	46	87	3	232	20	20	10	49	1.77
9301576--9301628	16	3.3	16	97	0	97	43	11	18	26	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9304054--9304220	65	2.5	69	78	11	177	40	4	8	46	1.55
9316737--9316806	35	2.0	35	94	0	122	32	10	22	34	1.88
9317839--9317869	8	3.8	8	95	4	53	90	0	0	9	0.46
9317839--9317871	9	3.8	9	92	8	59	87	0	0	12	0.53
9317801--9317868	25	2.7	25	73	6	66	77	4	5	11	1.08
9317839--9317871	17	1.9	17	100	0	66	87	0	0	12	0.53
9317923--9317970	17	2.7	18	74	6	53	70	0	10	18	1.15
9318038--9318115	41	1.9	40	82	12	97	71	0	3	24	1.02
9317996--9318136	58	2.4	62	80	16	142	68	1	4	24	1.17
9318065--9318154	39	2.4	36	80	10	101	64	1	3	31	1.17
9318201--9318280	2	40.5	2	91	7	128	51	0	2	46	1.14
9318270--9318338	20	3.3	20	74	18	61	68	0	4	27	1.09
9319674--9320047	106	3.5	106	84	7	522	23	19	24	32	1.97
9320742--9320890	67	2.2	67	83	7	194	38	8	20	33	1.82
9321071--9321373	106	2.9	106	89	0	435	21	17	24	35	1.95
9321964--9322036	31	2.3	31	83	2	92	35	24	13	26	1.93
9322936--9323073	69	2.0	69	97	0	258	26	15	21	37	1.92
9323131--9323183	19	2.7	19	80	8	54	5	15	3	75	1.13
9327581--9327647	26	2.6	27	79	15	79	74	5	5	13	1.19
9327907--9327972	18	3.5	18	74	11	69	63	1	6	28	1.27
9327999--9328049	8	6.4	8	95	0	57	49	5	0	45	1.26
9328006--9328068	2	32.0	2	85	9	85	50	1	3	44	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9328011--9328083	24	2.9	27	80	9	75	56	0	2	41	1.14
9328062--9328130	21	3.3	20	75	21	63	68	0	2	28	1.04
9328060--9328140	38	2.3	35	76	17	85	66	0	2	30	1.05
9328843--9328886	22	2.0	22	82	8	54	40	2	0	56	1.11
9332098--9332135	3	12.3	3	94	5	67	36	0	0	63	0.95
9333588--9333665	30	2.6	30	87	0	93	17	11	6	64	1.47
9338624--9338753	37	3.6	36	82	6	154	32	18	11	37	1.87
9339008--9339366	134	2.7	131	84	2	423	25	31	16	27	1.96
9341300--9341347	19	2.5	19	89	0	78	43	14	4	37	1.65
9351098--9351142	18	2.5	18	100	0	90	42	0	0	57	0.98
9352418--9352456	18	2.1	18	85	4	51	35	0	7	56	1.28
9353927--9353968	22	1.9	22	90	0	66	45	2	0	52	1.13
9354460--9354498	10	3.9	10	86	0	51	28	30	0	41	1.57
9354515--9354583	26	3.0	22	76	21	61	31	0	2	65	1.08
9354542--9354595	9	6.3	9	77	12	60	31	1	1	64	1.14
9354544--9354593	17	3.1	16	91	2	73	34	2	2	62	1.18
9354552--9354597	16	2.9	16	87	6	58	30	2	2	65	1.16
9360374--9360437	21	3.0	21	81	4	65	23	35	25	15	1.94
9360376--9360457	21	3.8	21	74	17	62	23	37	24	14	1.92
9362700--9362732	16	2.1	16	100	0	66	36	0	18	45	1.49
9367974--9368006	15	2.2	15	100	0	66	54	6	12	27	1.60
9370778--9370817	16	2.5	16	100	0	80	30	27	0	42	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9375031--9375066	17	2.1	17	89	0	54	8	8	19	63	1.47
9375288--9375424	64	2.1	65	83	12	176	32	16	21	30	1.95
9375308--9375447	65	2.2	64	80	6	167	31	16	20	31	1.95
9378086--9378210	24	5.5	23	81	12	145	26	21	22	29	1.99
9384009--9384164	65	2.4	64	84	11	187	32	16	21	30	1.95
9384048--9384212	65	2.5	63	81	10	181	31	17	21	29	1.96
9384998--9385144	77	1.9	77	82	0	186	44	4	11	40	1.60
9387836--9388046	40	5.1	40	69	20	123	35	17	17	30	1.92
9387833--9388059	84	2.7	83	82	6	289	35	17	17	29	1.93
9389206--9389253	22	2.2	22	92	0	78	29	14	10	45	1.78
9391203--9391233	15	2.1	15	93	0	53	25	19	29	25	1.99
9396994--9397438	229	1.9	228	94	0	791	44	7	7	40	1.61
9397509--9397554	20	2.3	19	89	10	74	54	10	17	17	1.70
9399362--9399400	17	2.3	17	100	0	78	33	20	23	23	1.97
9399498--9399546	19	2.6	19	93	0	80	30	2	10	57	1.43
9399665--9400491	199	4.2	199	98	0	1586	36	15	17	31	1.91
9399665--9400491	397	2.1	397	98	0	1584	36	15	17	31	1.91
9400660--9400724	25	2.6	25	75	0	76	35	9	12	43	1.74
9401069--9401132	23	2.8	23	87	0	92	35	6	20	37	1.78
9401069--9401141	23	3.2	23	82	7	85	34	5	20	39	1.76
9411648--9411771	66	1.9	66	89	0	194	20	22	20	35	1.96
9420259--9420291	17	1.9	17	93	0	57	51	3	3	42	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9420654--9420719	32	2.2	29	83	8	78	24	12	25	37	1.90
9420712--9420931	33	6.6	32	68	20	130	14	9	34	42	1.77
9420712--9420788	32	2.4	32	86	6	102	12	9	36	41	1.75
9420824--9420924	28	3.4	28	79	12	121	14	7	33	43	1.75
9421473--9421513	18	2.3	18	91	0	64	31	26	4	36	1.78
9431105--9431132	14	2.0	14	100	0	56	57	7	21	14	1.61
9431573--9431752	53	3.4	52	86	4	220	35	21	17	26	1.95
9436954--9437079	53	2.4	53	81	4	146	34	21	15	28	1.94
9442659--9442724	32	2.1	32	91	0	105	37	15	16	30	1.90
9447658--9447720	21	3.2	19	75	20	67	39	14	12	33	1.84
9448556--9448709	29	5.2	28	63	16	71	33	6	18	42	1.76
9448547--9448712	59	2.8	58	92	1	269	33	6	17	43	1.73
9451534--9451583	23	2.2	23	100	0	100	26	4	32	38	1.75
9452166--9452210	21	2.1	21	88	8	65	48	8	17	24	1.75
9452760--9452926	59	2.8	59	88	0	237	34	5	15	44	1.69
9456096--9456297	99	2.0	98	82	7	239	35	14	18	31	1.91
9457643--9457855	61	3.6	56	82	8	205	40	20	14	24	1.90
9458140--9458503	85	4.3	85	85	2	466	35	20	18	25	1.95
9459142--9459177	18	2.1	17	89	5	54	41	2	5	50	1.40
9460350--9460375	2	13.0	2	100	0	52	50	0	0	50	1.00
9460525--9460727	9	22.2	9	70	19	77	20	6	1	71	1.16
9460541--9460586	19	2.3	20	92	3	76	21	6	0	71	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9460493--9460654	27	6.2	26	72	19	83	24	4	1	69	1.13
9460555--9460632	33	2.4	33	82	16	92	24	2	2	70	1.12
9460485--9460619	19	6.8	21	73	13	74	26	3	1	68	1.15
9460516--9460689	93	1.9	93	80	11	205	21	5	1	71	1.16
9469595--9469631	18	2.1	18	100	0	74	48	13	0	37	1.43
9472195--9472237	13	3.3	13	81	18	54	72	4	4	18	1.20
9472195--9472251	25	2.4	24	80	8	62	71	3	8	15	1.24
9500383--9500408	6	4.3	6	100	0	52	69	0	0	30	0.89
9503111--9503172	22	2.8	22	97	0	115	22	0	25	51	1.48
9503911--9503949	21	1.9	20	84	5	51	33	10	15	41	1.81

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