genome.fa.s4.2.7.7.80.10.50.1000.13.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: CP032248.1 Gossypioides kirkii chromosome KI_06
Parameters: 2 7 7 80 10 50 1000
Length:  60359545

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   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   

This is table  13  of  193  ( 23090 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)
4547410--4547435	13	2.0	13	100	0	52	53	15	23	7	1.67
4547893--4547936	22	2.0	22	90	0	70	59	0	29	11	1.32
4548077--4548206	66	2.0	66	98	0	251	50	14	7	26	1.70
4548610--4548677	32	2.1	32	97	0	127	58	8	16	16	1.61
4556392--4556549	79	2.0	79	100	0	316	48	10	8	32	1.68
4557634--4557694	21	2.9	21	87	0	95	31	27	21	19	1.97
4558289--4558393	32	3.1	32	65	21	88	29	19	24	26	1.98
4559028--4559071	21	2.1	21	100	0	88	40	15	13	29	1.86
4559750--4559801	26	2.0	26	100	0	104	42	34	7	15	1.75
4559984--4560038	27	2.0	27	96	0	101	7	30	23	38	1.82
4561056--4561085	15	2.0	15	100	0	60	26	53	0	20	1.46
4560372--4561664	594	2.2	591	87	6	1851	38	20	14	26	1.91
4562191--4562216	13	2.0	13	100	0	52	53	15	7	23	1.67
4573659--4573712	27	2.0	27	88	0	81	16	29	29	24	1.97
4573729--4573776	14	3.4	14	74	5	51	70	12	0	16	1.16
4577050--4577142	26	3.5	26	73	8	80	34	1	10	53	1.43
4577208--4577242	6	5.8	6	93	0	61	65	14	0	20	1.26
4579656--4579703	17	2.8	17	87	6	62	58	2	2	37	1.22
4581795--4581824	1	30.0	1	100	0	60	0	0	100	0	0.00
4595306--4595340	16	2.2	16	90	5	54	34	2	0	62	1.10
4598041--4598074	3	11.3	3	100	0	68	32	35	0	32	1.58
4599057--4599116	31	1.9	31	90	6	95	43	10	11	35	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4599574--4599614	22	1.9	22	85	5	57	12	17	9	60	1.57
4607233--4607277	23	2.0	23	100	0	90	46	8	13	31	1.74
4608648--4608680	11	3.0	11	83	16	50	54	0	33	12	1.37
4616555--4616595	7	5.9	7	100	0	82	41	29	14	14	1.86
4623585--4623624	18	2.1	20	86	9	57	45	0	20	35	1.51
4623607--4623654	24	1.9	26	84	16	66	45	0	22	31	1.53
4623738--4623817	23	3.5	23	87	3	99	8	25	25	41	1.83
4627029--4627070	22	2.0	22	90	4	68	71	0	0	28	0.86
4627031--4627148	12	10.2	12	69	23	58	62	1	1	33	1.15
4632557--4632637	19	4.2	19	76	14	69	62	1	1	34	1.11
4632566--4632646	19	4.1	18	77	17	72	64	1	1	33	1.10
4632918--4632949	2	16.0	2	100	0	64	50	0	0	50	1.00
4639129--4639215	41	2.1	41	91	0	138	35	11	13	39	1.81
4645643--4645723	31	2.6	31	84	3	92	50	12	9	27	1.71
4649846--4649885	5	8.4	5	97	2	66	0	37	20	42	1.52
4654626--4654671	19	2.5	19	79	10	51	71	2	15	10	1.23
4659628--4659681	21	2.6	21	93	0	90	79	12	0	7	0.92
4660227--4660271	23	2.0	23	86	0	63	35	20	13	31	1.91
4669969--4670011	18	2.3	18	80	4	50	37	0	6	55	1.27
4673160--4673275	6	19.8	6	82	5	112	49	33	17	0	1.47
4673154--4673294	30	4.6	30	88	2	192	46	34	19	0	1.50
4673163--4673294	3	44.0	3	86	0	93	46	34	19	0	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4674054--4674092	13	2.9	13	82	17	53	17	23	5	53	1.63
4675047--4675097	6	9.2	6	77	14	56	49	31	17	1	1.58
4680117--4680155	18	2.0	20	90	9	64	64	0	0	35	0.94
4684915--4684958	22	2.0	22	100	0	88	50	9	9	31	1.65
4691396--4691422	8	3.4	8	100	0	54	85	0	0	14	0.61
4692329--4692383	25	2.2	25	80	6	58	9	23	0	67	1.19
4693083--4693122	17	2.3	18	83	12	57	10	7	25	57	1.57
4695296--4695449	59	2.6	59	83	9	192	44	2	1	51	1.23
4695609--4695646	16	2.4	16	86	8	51	28	23	5	42	1.76
4696508--4696532	12	2.1	12	100	0	50	60	0	0	40	0.97
4701848--4701873	2	13.0	2	100	0	52	50	0	0	50	1.00
4704921--4704949	13	2.2	13	100	0	58	20	31	20	27	1.98
4718144--4718206	31	2.0	31	96	0	117	39	14	22	23	1.91
4718942--4718975	17	2.0	17	100	0	68	47	11	11	29	1.76
4725142--4725169	2	14.0	2	100	0	56	0	50	0	50	1.00
4745967--4746001	3	12.0	3	93	6	63	65	0	34	0	0.93
4775040--4775106	31	2.2	31	91	0	107	41	10	10	37	1.74
4779675--4779767	30	3.1	30	81	6	100	25	21	21	31	1.98
4780586--4780632	18	2.6	18	93	3	76	36	0	23	40	1.55
4788894--4788935	18	2.2	19	87	12	59	38	0	4	57	1.20
4788894--4788936	19	2.3	18	84	11	52	37	0	6	55	1.27
4790349--4790649	152	2.0	152	93	1	514	36	17	12	32	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4793209--4793319	57	1.9	58	88	1	170	29	19	12	37	1.89
4800558--4800591	16	2.1	17	88	5	52	14	14	11	58	1.63
4821903--4821953	25	2.0	25	100	0	102	35	0	15	49	1.45
4825639--4825669	3	10.3	3	100	0	62	67	0	32	0	0.91
4837661--4837697	18	2.1	18	94	0	65	37	27	21	13	1.91
4841886--4841910	3	8.3	3	100	0	50	32	0	0	68	0.90
4844085--4844182	23	4.2	23	87	10	144	12	24	23	39	1.89
4844085--4844182	48	2.1	46	88	7	144	12	24	23	39	1.89
4844147--4844221	39	1.9	39	91	0	123	12	22	21	44	1.85
4844181--4844274	23	4.0	23	75	16	86	11	25	19	43	1.84
4849922--4849985	30	2.1	30	85	5	85	65	3	1	29	1.17
4857853--4857938	25	3.2	24	78	16	64	61	1	5	31	1.27
4858187--4858245	30	2.0	30	100	0	118	38	3	6	50	1.45
4866463--4866499	15	2.5	15	86	0	56	27	8	0	64	1.21
4869799--4869843	22	2.0	22	82	8	54	42	2	2	53	1.25
4877541--4877580	16	2.5	16	91	0	71	35	5	32	27	1.79
4877751--4877833	26	3.0	26	69	19	76	50	1	0	48	1.08
4877749--4877894	58	2.5	56	85	11	188	50	0	2	47	1.18
4887397--4887438	22	1.9	22	85	0	57	59	0	11	28	1.33
4890428--4890473	20	2.3	20	84	0	56	19	10	0	69	1.17
4892075--4892114	9	4.7	9	84	9	57	35	0	0	65	0.93
4892075--4892114	17	2.4	17	83	12	55	35	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4900388--4900412	1	25.0	1	100	0	50	0	0	0	100	0.00
4908253--4908292	12	3.6	12	74	19	50	65	0	2	32	1.06
4908255--4908296	21	2.0	21	100	0	84	61	0	4	33	1.17
4908939--4908982	20	2.2	20	84	8	54	56	0	4	38	1.20
4908926--4909034	51	2.1	51	83	5	130	56	0	5	37	1.22
4913494--4913534	21	2.0	21	85	0	55	51	2	2	43	1.28
4922763--4922814	20	2.7	20	80	14	63	30	5	17	46	1.71
4931196--4931508	96	3.3	93	77	8	301	31	20	18	29	1.96
4931182--4931537	188	1.9	192	81	4	445	31	20	17	30	1.96
4931691--4931731	19	2.2	19	90	0	64	39	7	24	29	1.82
4932104--4932185	42	2.0	42	90	0	128	28	14	20	36	1.92
4934855--4934927	26	2.8	25	85	4	92	16	10	34	38	1.84
4936066--4936105	19	2.0	21	85	9	57	50	5	7	37	1.53
4942705--4942755	24	2.1	24	96	0	93	56	9	11	21	1.63
4952265--4952303	17	2.3	17	90	0	60	15	12	25	46	1.81
4956958--4957002	17	2.6	17	89	0	63	71	2	4	22	1.15
4958500--4958573	27	2.7	27	80	2	76	63	2	4	29	1.26
4958759--4958829	27	2.5	28	76	13	67	25	2	1	70	1.09
4958759--4958815	28	2.0	28	83	6	71	21	3	1	73	1.07
4958794--4958827	15	2.2	16	94	5	61	29	0	0	70	0.87
4962646--4962686	10	4.4	10	84	9	52	78	0	0	21	0.76
4986545--4986575	16	2.0	15	93	6	53	32	6	0	61	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4986780--4986828	22	2.2	23	82	10	66	46	4	2	46	1.33
4987782--4987838	30	2.0	28	82	6	69	64	1	1	31	1.13
4992883--4992912	3	10.0	3	100	0	60	33	0	0	66	0.92
5009748--5009826	23	3.4	23	85	0	113	11	20	22	45	1.83
5009735--5009828	23	4.1	23	81	2	100	11	21	21	45	1.83
5014176--5014360	23	8.2	23	77	16	190	12	23	22	41	1.88
5014176--5014355	48	4.0	45	77	15	194	12	22	22	41	1.88
5014261--5014337	41	1.9	39	86	5	109	12	22	22	42	1.87
5014194--5014405	87	2.4	84	76	11	232	11	22	22	43	1.85
5014359--5014452	23	4.0	23	75	16	86	11	25	19	43	1.84

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   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193