genome.fa.s3.2.7.7.80.10.50.1000.9.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: CP032247.1 Gossypioides kirkii chromosome KI_05
Parameters: 2 7 7 80 10 50 1000
Length:  50980411

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   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   

This is table  9  of  171  ( 20472 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)
3983405--3983458	15	3.3	15	74	18	54	44	0	1	53	1.11
3985928--3985952	2	12.5	2	100	0	50	52	0	0	48	1.00
3988508--3988546	20	2.0	19	85	14	53	56	10	2	30	1.46
4001161--4001187	14	1.9	14	100	0	54	51	14	7	25	1.68
4001243--4001322	41	2.0	40	82	7	99	61	20	1	17	1.42
4033182--4033374	96	2.0	96	92	2	325	34	16	24	24	1.95
4039536--4039576	20	2.0	20	95	0	73	29	24	9	36	1.87
4042397--4042837	59	7.7	59	72	13	284	30	17	13	38	1.88
4042396--4042800	111	3.6	110	81	7	379	32	17	12	38	1.87
4042713--4042827	60	1.9	60	89	3	178	31	15	12	40	1.84
4045081--4045128	12	3.7	12	75	20	51	54	0	8	37	1.31
4045432--4045580	48	3.1	48	67	14	146	40	4	5	48	1.47
4045222--4045611	93	4.2	93	93	1	683	43	5	4	46	1.44
4057419--4057447	7	4.1	7	100	0	58	41	0	44	13	1.44
4058499--4058536	20	1.9	20	89	10	60	39	0	5	55	1.23
4058838--4058882	20	2.2	21	84	4	56	26	8	2	62	1.37
4059064--4059099	17	2.1	17	89	0	54	22	22	0	55	1.44
4059556--4059623	34	2.0	35	88	2	102	26	8	22	42	1.82
4064503--4064548	24	1.9	24	82	8	58	19	32	2	45	1.62
4064558--4064593	17	2.1	17	89	0	54	19	22	0	58	1.40
4064853--4064942	28	3.2	28	81	4	110	38	5	4	51	1.46
4065939--4065963	12	2.1	12	100	0	50	32	0	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4068056--4068107	3	17.0	3	84	4	59	26	7	65	0	1.20
4071616--4071655	22	1.9	21	85	10	55	25	15	37	22	1.93
4078816--4078866	24	2.0	24	81	11	57	11	17	15	54	1.70
4081591--4081616	1	26.0	1	100	0	52	0	100	0	0	0.00
4089106--4089166	28	2.2	27	94	2	104	21	22	14	40	1.90
4091094--4091161	32	2.3	30	82	10	77	27	4	10	57	1.51
4091113--4091180	32	2.1	32	100	0	136	25	7	8	58	1.54
4102296--4102342	24	2.0	24	100	0	94	25	25	14	34	1.94
4120478--4120503	3	8.7	3	100	0	52	69	0	30	0	0.89
4140653--4140678	2	13.0	2	100	0	52	50	0	0	50	1.00
4154929--4154966	17	2.2	18	85	4	51	21	2	18	57	1.52
4157223--4157247	6	4.2	6	100	0	50	16	0	84	0	0.63
4157151--4157322	87	2.0	87	94	0	299	28	4	48	18	1.67
4177031--4177063	2	16.5	2	100	0	66	51	0	48	0	1.00
4203124--4203187	30	2.1	30	100	0	128	9	26	15	48	1.75
4208852--4208887	2	18.0	2	100	0	72	50	0	0	50	1.00
4210189--4210243	22	2.5	22	87	0	74	65	18	7	9	1.44
4210850--4210893	11	3.9	11	76	5	52	75	18	2	4	1.09
4210835--4210882	20	2.3	21	78	7	53	70	14	8	6	1.31
4211181--4211336	62	2.5	65	85	10	209	43	0	3	52	1.19
4231934--4231981	20	2.4	20	96	0	87	31	8	18	41	1.80
4247426--4247467	20	2.1	20	82	8	50	23	21	0	54	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4256502--4256539	13	3.0	13	84	3	51	36	0	0	63	0.95
4258329--4258391	22	2.9	22	83	9	76	9	12	15	61	1.55
4258402--4258450	22	2.2	22	77	0	53	10	2	12	75	1.13
4258441--4258495	21	2.5	23	88	5	78	5	3	21	69	1.25
4258424--4258518	12	8.3	12	72	10	65	6	3	18	71	1.21
4260314--4260381	11	6.2	11	70	13	50	25	1	5	67	1.21
4272102--4272171	23	3.0	23	76	18	72	47	1	0	51	1.09
4273090--4273125	10	3.6	10	92	0	63	30	5	0	63	1.17
4276929--4277010	30	2.8	30	76	9	87	54	8	9	26	1.61
4276902--4277012	30	3.8	29	71	13	84	54	7	10	27	1.61
4304491--4304521	3	10.3	3	100	0	62	67	0	0	32	0.91
4304993--4305019	4	6.8	4	100	0	54	77	0	0	22	0.76
4311236--4311361	65	1.9	65	96	0	234	15	16	18	49	1.80
4325366--4325439	35	2.1	35	80	9	80	59	5	1	33	1.29
4330129--4330175	2	24.0	2	95	4	87	51	0	0	48	1.00
4336154--4336266	30	3.8	27	76	14	82	38	6	9	45	1.62
4336222--4336282	31	2.0	31	87	6	88	36	8	9	45	1.67
4336667--4336709	18	2.5	17	81	7	52	44	6	0	48	1.29
4362596--4362671	39	1.9	39	82	12	93	53	2	1	42	1.23
4373365--4373392	13	2.2	13	100	0	56	32	0	14	53	1.41
4373429--4373505	31	2.6	30	77	4	84	54	6	0	38	1.26
4373836--4373867	4	8.0	4	92	0	55	71	0	3	25	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4386538--4386566	14	2.1	14	100	0	58	72	0	6	20	1.07
4387296--4387330	16	2.2	16	90	10	54	57	14	0	28	1.38
4392865--4392904	5	8.0	5	94	0	71	0	57	0	42	0.98
4405498--4406327	411	2.0	411	94	0	1464	26	24	15	34	1.95
4411960--4411985	6	4.3	6	100	0	52	15	0	53	30	1.42
4417530--4417586	29	1.9	30	92	3	98	57	10	0	31	1.32
4418560--4418619	33	2.0	31	81	15	72	50	5	3	41	1.41
4420036--4420071	19	1.9	19	88	5	56	36	0	2	61	1.11
4420048--4420089	16	2.8	15	83	16	52	40	0	0	59	0.97
4423398--4423428	12	2.6	12	94	0	53	22	35	6	35	1.80
4425385--4425433	22	2.3	20	79	6	53	48	0	2	48	1.12
4426627--4426654	9	3.1	9	100	0	56	0	21	0	78	0.75
4434357--4434412	29	2.0	27	83	13	69	44	1	8	44	1.45
4437695--4437789	41	2.3	41	94	0	163	21	7	32	38	1.81
4443552--4443584	2	16.5	2	100	0	66	51	0	48	0	1.00
4444585--4444614	16	1.9	15	93	6	51	0	13	0	86	0.57
4448833--4448871	11	3.6	11	79	6	53	43	25	10	20	1.83
4448833--4448874	21	2.0	21	100	0	84	42	23	9	23	1.83
4451697--4451776	24	3.3	24	87	3	99	1	31	18	48	1.56
4451697--4451760	12	5.3	12	73	14	51	0	34	18	46	1.49
4451685--4451798	48	2.4	48	82	2	131	2	35	15	46	1.60
4451734--4451798	24	2.7	24	87	0	94	3	32	13	50	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4451809--4451872	24	2.6	25	80	4	69	1	31	21	45	1.62
4452227--4452263	18	2.1	18	89	0	56	13	32	27	27	1.94
4464311--4464349	18	2.1	19	90	4	62	10	12	0	76	1.01
4464710--4464752	22	2.0	20	86	8	59	65	2	0	32	1.06
4477167--4477205	20	2.0	19	85	14	53	43	15	0	41	1.46
4477167--4477210	21	2.2	20	84	12	54	43	13	0	43	1.44
4486018--4486042	2	12.5	2	100	0	50	52	0	0	48	1.00
4498994--4499029	12	3.0	12	95	0	63	38	25	2	33	1.70
4500086--4500147	28	2.2	28	83	13	76	46	0	1	51	1.10
4507080--4507111	14	2.3	14	100	0	64	53	0	0	46	1.00
4518136--4518244	56	1.9	56	92	0	182	33	28	14	23	1.94
4518519--4518552	2	18.0	2	88	11	54	50	0	0	50	1.00
4527435--4527465	11	2.8	11	95	0	53	64	0	0	35	0.94
4532999--4533062	23	2.7	23	90	2	101	6	26	23	43	1.77
4534123--4534430	153	2.0	153	98	0	598	36	17	11	34	1.86
4553095--4553198	30	3.5	30	76	2	93	22	19	25	33	1.97
4553911--4553978	33	2.1	33	97	0	127	42	23	2	30	1.69
4553996--4554034	14	2.8	14	92	0	60	33	23	7	35	1.83
4580176--4580218	6	7.2	6	91	0	68	2	65	0	32	1.06
4581688--4581733	14	3.2	14	80	17	58	56	4	0	39	1.19
4586285--4586316	15	2.1	15	94	0	55	25	0	3	71	1.00
4586285--4586323	14	2.7	14	88	4	51	25	2	2	69	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4586751--4586808	31	1.9	30	89	3	89	34	12	6	46	1.68
4586929--4586968	16	2.6	16	84	4	55	62	0	0	37	0.95
4589629--4589656	2	14.0	2	100	0	56	50	0	0	50	1.00
4590196--4590588	126	3.1	126	96	1	714	38	14	13	32	1.85
4590194--4590586	128	3.1	128	96	1	718	38	14	13	33	1.85
4592635--4592700	28	2.3	29	81	5	71	39	6	7	46	1.57
4615434--4615486	2	26.5	2	100	0	106	0	49	0	50	1.00
4616414--4616445	7	4.4	7	92	7	55	84	0	15	0	0.63
4616414--4616445	15	2.2	14	94	5	55	84	0	15	0	0.63
4622995--4623072	33	2.4	32	81	8	86	46	2	1	50	1.23

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   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171