genome.fa.s8.2.7.7.80.10.50.1000.16.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  16  of  190  ( 22705 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)
4645601--4645918	51	6.0	51	76	17	274	44	23	1	30	1.61
4648998--4649277	123	2.3	124	84	5	386	31	22	15	30	1.95
4651106--4651143	18	2.1	18	95	0	67	18	28	23	28	1.98
4655745--4655901	24	6.5	24	68	18	94	34	5	6	53	1.50
4655825--4655941	46	2.5	46	95	2	209	32	5	6	54	1.51
4655855--4655930	24	3.2	24	70	7	84	31	6	5	56	1.47
4656898--4656941	7	6.4	7	92	5	54	25	0	6	68	1.14
4657047--4657079	14	2.4	14	94	0	57	18	57	6	18	1.60
4658668--4658692	8	3.1	8	100	0	50	64	0	12	24	1.27
4658767--4658818	25	2.1	25	96	0	95	40	3	9	46	1.55
4658917--4658946	8	3.9	8	91	8	53	86	0	0	13	0.57
4659023--4659063	18	2.3	18	100	0	82	19	14	26	39	1.90
4659924--4659948	11	2.3	11	100	0	50	56	16	0	28	1.41
4660659--4660693	6	5.8	6	96	0	61	65	34	0	0	0.93
4680918--4681016	23	4.3	23	90	0	162	31	27	21	20	1.98
4680918--4681016	46	2.2	46	94	0	180	31	27	21	20	1.98
4682892--4682916	10	2.5	10	100	0	50	32	0	0	68	0.90
4683018--4683047	14	2.1	15	93	6	53	16	0	6	76	0.99
4685355--4685485	23	5.6	23	77	16	110	27	0	27	44	1.60
4685379--4685532	21	6.8	21	79	15	105	26	0	28	44	1.54
4685419--4685711	29	8.9	33	72	20	176	29	0	24	46	1.53
4685355--4685527	95	1.8	95	92	2	294	27	0	27	45	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4685574--4685715	30	4.7	29	74	13	99	30	0	22	46	1.52
4685656--4685730	23	3.0	23	80	9	78	34	1	17	46	1.56
4685528--4685691	30	5.1	34	86	11	183	29	0	23	46	1.53
4688384--4688682	50	5.8	50	86	4	366	26	23	29	20	1.99
4695764--4695820	30	1.9	30	86	10	82	40	5	24	29	1.77
4696158--4696456	50	5.8	50	87	2	364	26	23	29	20	1.99
4698476--4698509	15	2.3	15	90	5	52	67	5	0	26	1.13
4698812--4698870	29	2.1	27	87	9	84	44	16	13	25	1.85
4699729--4699762	14	2.5	14	95	4	61	14	0	35	50	1.44
4699891--4699939	25	1.9	26	83	4	64	69	6	6	18	1.31
4700575--4700608	3	11.3	3	100	0	68	0	32	0	67	0.91
4702562--4702619	29	2.0	29	83	6	73	39	0	6	53	1.28
4702577--4702623	23	2.0	23	84	8	60	38	0	4	57	1.18
4702608--4702653	3	15.7	3	78	13	51	34	0	0	65	0.93
4702612--4702644	14	2.4	14	90	5	50	33	0	0	66	0.92
4702605--4702653	18	2.8	18	84	9	66	36	0	0	63	0.95
4707215--4707275	26	2.3	26	81	13	72	27	0	3	68	1.05
4707793--4707854	30	2.0	30	84	9	81	45	3	3	48	1.34
4711060--4711182	44	2.8	44	77	13	117	24	22	21	31	1.98
4711169--4711527	132	2.7	132	93	0	612	26	22	20	30	1.98
4723404--4723443	20	2.0	20	90	0	62	50	12	10	27	1.72
4723392--4723458	34	1.9	35	90	3	109	46	13	8	31	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4723427--4723466	14	2.9	14	84	0	53	42	17	7	32	1.77
4726232--4726287	28	2.0	28	100	0	112	42	17	3	35	1.67
4728679--4728727	25	2.0	25	88	8	73	48	16	16	18	1.81
4735426--4735502	29	2.7	29	100	0	154	49	9	11	29	1.70
4735426--4735525	29	3.4	29	90	5	121	49	10	13	28	1.73
4736185--4736255	29	2.4	29	78	4	79	35	7	9	47	1.64
4736207--4736265	29	2.0	30	86	3	84	30	3	11	54	1.53
4739792--4739825	15	2.3	15	90	5	52	17	0	29	52	1.45
4739807--4739851	23	2.0	23	86	0	63	20	0	22	57	1.40
4746643--4746675	6	5.5	6	100	0	66	15	0	0	84	0.61
4747390--4747467	3	26.0	3	100	0	156	33	0	0	66	0.92
4747915--4748316	108	3.7	108	92	2	664	30	16	18	34	1.93
4749602--4749644	15	2.9	15	86	6	61	27	0	2	69	1.00
4749602--4749645	14	3.1	14	86	3	61	27	0	2	70	0.99
4751805--4752018	99	2.2	100	92	4	353	37	3	8	50	1.49
4751847--4752057	99	2.1	99	82	6	250	41	2	9	46	1.50
4754383--4754670	126	2.3	126	90	1	452	28	20	17	33	1.95
4754713--4755098	192	2.0	184	86	7	526	40	16	1	41	1.58
4754713--4755098	95	4.1	96	84	8	508	40	16	1	41	1.58
4782049--4782082	2	17.0	2	100	0	68	50	0	0	50	1.00
4782161--4782231	33	2.2	33	85	5	92	40	11	11	36	1.77
4785036--4785279	120	2.1	118	83	7	298	31	20	7	40	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4786977--4787081	8	12.4	8	89	7	138	36	20	11	31	1.89
4786986--4787082	17	5.6	18	89	7	148	35	21	11	31	1.89
4786986--4787082	9	11.2	9	91	4	148	35	21	11	31	1.89
4786977--4787081	51	2.1	51	90	3	167	36	20	11	31	1.89
4787128--4787225	17	5.4	17	65	13	52	48	13	4	33	1.61
4787098--4787234	20	7.3	20	64	14	76	48	13	5	33	1.64
4787081--4787251	37	4.6	37	89	1	245	47	13	4	33	1.63
4787707--4787814	45	2.4	45	98	0	207	42	15	12	29	1.83
4787717--4787792	23	3.3	23	62	3	64	47	15	10	26	1.78
4787740--4787814	22	3.4	22	64	3	60	41	14	13	30	1.84
4788256--4788326	29	2.4	29	95	2	124	33	15	45	5	1.70
4788402--4788519	44	2.4	50	77	18	149	22	1	32	44	1.63
4788431--4788507	25	3.3	25	70	20	85	16	2	33	46	1.61
4788418--4788531	44	2.6	44	94	1	203	20	1	35	42	1.62
4788456--4788528	19	3.5	19	68	20	56	19	1	36	42	1.60
4788515--4788539	13	1.9	13	100	0	50	16	0	44	40	1.47
4791011--4791056	24	1.9	24	86	0	65	45	0	34	19	1.51
4791624--4791792	16	10.5	17	63	20	60	54	2	1	41	1.23
4791700--4791778	17	4.8	17	67	14	58	54	2	2	40	1.27
4791699--4791792	48	2.0	48	89	0	143	55	2	2	40	1.24
4792124--4792154	3	10.7	3	93	6	55	35	0	0	64	0.94
4792899--4793202	43	7.1	43	84	7	325	29	26	19	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4792899--4793149	86	2.9	85	90	1	358	27	26	21	24	1.99
4796421--4796457	19	2.0	19	89	5	58	59	5	0	35	1.20
4802105--4802137	15	2.1	16	88	5	50	24	3	24	48	1.65
4802186--4802278	41	2.3	41	84	3	116	24	27	26	20	1.99
4805397--4805423	4	6.8	4	100	0	54	74	0	0	25	0.83
4810395--4810450	29	1.9	29	82	13	71	50	1	1	46	1.22
4812314--4812355	17	2.5	17	96	0	75	47	26	14	11	1.78
4813686--4813743	28	2.1	28	96	3	109	34	0	29	36	1.58
4816142--4816197	15	3.9	15	75	6	55	37	1	0	60	1.07
4816136--4816197	21	2.9	21	80	4	70	33	1	0	64	1.03
4820355--4820386	11	2.8	12	90	9	50	28	31	0	40	1.57
4824585--4824649	32	2.0	32	93	0	112	29	13	23	33	1.93
4827281--4827305	5	5.0	5	100	0	50	20	0	0	80	0.72
4834702--4834800	23	4.3	23	90	0	153	31	26	21	21	1.98
4839549--4839581	18	1.9	18	88	11	52	30	0	3	66	1.06
4840052--4840127	29	2.6	29	76	15	77	27	10	5	56	1.54
4840656--4840706	26	1.9	27	84	4	68	54	0	9	35	1.33
4840859--4840919	21	3.0	20	76	6	52	34	6	0	59	1.24
4840896--4840935	17	2.3	17	86	4	53	47	5	0	47	1.24
4845838--4846546	113	6.3	113	90	2	1079	22	22	24	30	1.99
4845838--4846546	227	3.1	224	90	3	1077	22	22	24	30	1.99
4847020--4847172	77	1.9	77	84	6	198	32	0	22	43	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4847082--4847115	14	2.4	14	90	9	52	20	0	41	38	1.53
4847055--4847372	91	3.8	81	79	16	319	27	1	26	45	1.61
4847103--4847351	91	2.8	88	94	3	437	26	1	26	45	1.63
4847337--4847375	7	5.4	7	81	6	51	12	0	43	43	1.42
4847389--4847427	18	2.2	18	86	4	53	38	7	17	35	1.79
4847744--4847788	21	2.2	20	88	11	65	80	0	6	13	0.91
4849437--4849647	56	3.7	56	72	17	152	45	12	2	39	1.56
4849477--4849528	22	2.4	21	83	6	68	44	13	0	42	1.44
4849549--4849852	9	34.7	9	66	19	90	42	15	2	39	1.59
4849554--4849667	16	7.1	16	71	23	71	44	16	1	36	1.58

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