genome.fa.s4.2.7.7.80.10.50.1000.17.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   194   195   196   197   198   

This is table  17  of  198  ( 23681 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)
5159092--5159166	22	3.5	22	70	14	66	26	25	36	12	1.91
5159937--5159965	5	5.8	5	100	0	58	62	17	0	20	1.33
5159936--5159975	15	2.7	15	84	7	55	65	12	0	22	1.26
5160350--5160395	14	3.3	14	93	0	83	41	0	2	56	1.11
5160522--5160556	3	11.7	3	100	0	70	34	0	0	65	0.93
5161467--5161535	24	2.7	27	82	10	83	42	0	26	31	1.56
5161679--5161774	39	2.5	39	80	6	108	19	23	29	27	1.99
5165462--5165495	17	2.0	17	88	11	52	32	0	2	64	1.08
5167566--5167599	17	2.0	17	100	0	68	35	0	11	52	1.38
5167583--5167608	12	2.2	12	100	0	52	34	0	15	50	1.45
5167624--5167680	24	2.2	27	78	9	66	59	1	5	33	1.30
5167668--5167774	24	4.2	25	78	6	99	62	2	3	30	1.27
5167668--5167781	51	2.2	50	87	6	158	62	2	4	30	1.28
5169229--5169500	44	6.1	43	69	15	176	28	20	19	31	1.97
5169603--5170055	45	10.0	44	69	11	222	31	21	15	31	1.95
5169467--5170055	181	3.2	181	86	1	793	30	19	16	32	1.94
5169378--5169946	89	6.4	85	73	11	327	30	20	17	32	1.95
5169333--5170042	44	15.7	45	70	11	328	30	20	17	32	1.95
5176153--5176235	25	3.4	23	77	11	85	69	4	1	24	1.14
5176276--5176384	26	4.2	26	76	8	105	63	1	3	31	1.22
5176276--5176384	51	2.1	50	89	6	164	63	1	3	31	1.22
5179300--5179336	9	4.1	9	92	0	65	45	13	10	29	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5179395--5179434	19	2.1	19	90	4	62	25	42	0	32	1.55
5187562--5187604	11	3.5	11	77	22	50	51	4	0	44	1.22
5187551--5187604	26	2.1	26	100	0	108	50	7	0	42	1.30
5191709--5191816	54	2.0	54	83	0	135	50	10	12	27	1.72
5192748--5192824	31	2.5	31	82	2	84	44	10	16	28	1.81
5194272--5194323	20	2.7	18	82	11	59	67	9	1	21	1.29
5194894--5194999	49	2.2	46	85	5	140	42	12	13	32	1.81
5198756--5198811	23	2.5	22	77	16	62	42	0	1	55	1.10
5198756--5198811	22	2.5	21	77	16	60	42	0	1	55	1.10
5199044--5199076	17	1.9	17	88	11	50	21	0	0	78	0.75
5201373--5201406	14	2.5	14	95	4	61	14	0	35	50	1.44
5201718--5201781	29	2.1	29	83	11	76	48	17	12	21	1.80
5201819--5201861	21	2.0	21	83	16	54	30	2	4	62	1.28
5203115--5203150	18	2.0	18	94	0	63	19	11	5	63	1.46
5212663--5212713	18	2.9	18	80	13	61	62	1	0	35	1.06
5213026--5213069	16	2.9	16	86	6	65	40	0	0	59	0.98
5228851--5228876	12	2.2	12	100	0	52	61	0	0	38	0.96
5236365--5236462	46	2.2	46	94	1	171	43	19	3	33	1.66
5240978--5241075	46	2.2	46	94	1	171	43	19	3	33	1.66
5242560--5242591	2	16.0	2	93	0	55	46	0	0	53	1.00
5244397--5244435	9	4.3	9	90	6	53	71	5	0	23	1.05
5245840--5245916	39	2.0	39	92	0	127	37	29	20	11	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5248157--5248191	15	2.2	16	90	5	54	37	0	14	48	1.44
5248825--5248878	24	2.4	21	80	14	63	16	9	16	57	1.64
5249525--5249552	12	2.3	12	100	0	56	50	7	0	42	1.30
5250888--5250933	7	6.6	7	78	16	51	60	10	0	28	1.30
5250888--5250933	15	3.3	15	82	11	62	60	10	0	28	1.30
5250929--5250986	21	2.8	20	84	7	80	43	17	3	36	1.66
5250972--5250999	14	2.0	14	100	0	56	50	7	0	42	1.30
5251008--5251425	9	46.7	9	82	2	502	51	15	0	32	1.49
5251645--5251695	22	2.3	22	86	6	68	33	33	0	33	1.58
5251882--5251915	15	2.3	15	90	5	52	26	0	5	67	1.13
5254059--5254219	30	5.2	30	84	10	202	45	24	0	30	1.54
5254069--5254154	35	2.4	35	88	7	120	44	29	0	26	1.55
5254054--5254191	65	2.1	65	93	0	231	44	22	0	32	1.58
5254177--5254228	24	2.2	24	86	6	70	46	25	0	28	1.53
5254333--5254502	30	5.6	30	78	15	197	43	24	0	31	1.59
5254341--5254518	35	5.6	35	76	21	212	44	22	0	32	1.57
5254376--5254451	23	3.0	23	76	23	89	44	23	1	30	1.62
5257765--5258169	125	3.2	125	90	4	633	31	22	15	30	1.95
5258363--5258421	29	2.1	27	84	9	75	44	15	15	25	1.85
5258445--5258512	9	7.8	9	74	12	70	42	20	0	36	1.52
5258511--5258572	25	2.5	25	94	0	106	46	22	1	29	1.61
5258722--5258761	21	1.9	21	94	0	71	30	20	47	2	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5259173--5259315	41	3.5	41	89	0	214	23	17	21	37	1.94
5266924--5266969	20	2.3	20	81	3	58	43	2	2	52	1.25
5268218--5268269	26	2.0	26	96	0	95	30	17	11	40	1.85
5268407--5268510	51	2.1	50	92	3	174	29	8	20	41	1.82
5280061--5280103	22	2.0	22	85	0	59	65	0	18	16	1.28
5284383--5284537	46	3.5	46	90	4	246	33	14	23	28	1.94
5285488--5285539	24	2.2	24	82	6	61	42	7	34	15	1.75
5286370--5286411	18	2.3	18	87	0	66	21	19	21	38	1.94
5291387--5291542	37	4.3	37	78	16	130	35	1	0	62	1.07
5291417--5291483	21	3.3	21	74	20	70	35	2	0	61	1.12
5291417--5291543	38	3.1	38	84	12	139	37	2	0	60	1.10
5293204--5293237	14	2.4	14	90	0	50	35	17	2	44	1.64
5301432--5301470	19	2.1	19	85	9	53	43	0	2	53	1.14
5307853--5307886	18	1.9	18	94	5	61	76	2	2	17	1.04
5307991--5308105	10	11.5	10	73	17	87	65	0	34	0	0.93
5307983--5308112	25	5.4	25	79	15	157	64	0	35	0	0.94
5307983--5308102	45	2.7	45	97	0	222	65	0	35	0	0.93
5307970--5308095	20	6.2	20	81	16	143	64	0	35	0	0.94
5308217--5308271	28	2.0	27	86	6	76	30	3	5	60	1.37
5308359--5308393	17	2.1	17	88	0	52	74	2	0	22	0.95
5308534--5308799	129	2.0	131	91	1	428	52	7	10	29	1.63
5308680--5308726	13	3.6	13	77	11	51	61	4	6	27	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5308663--5309403	153	4.9	152	89	3	1068	51	7	9	30	1.62
5308663--5309403	305	2.4	303	89	3	1130	51	7	9	30	1.62
5309451--5309565	42	2.8	40	75	17	110	46	13	4	35	1.62
5309640--5309713	29	2.5	29	84	4	94	24	14	14	45	1.83
5310583--5310616	3	11.3	3	87	0	50	0	29	0	70	0.87
5311179--5311211	16	2.1	16	88	11	50	54	6	30	9	1.56
5311254--5311306	21	2.5	20	82	11	70	66	5	26	1	1.25
5312880--5312951	16	4.4	16	72	10	65	44	1	2	51	1.24
5319690--5319800	45	2.5	46	82	4	136	22	17	15	45	1.85
5321174--5321227	13	4.1	13	78	4	63	37	22	7	33	1.82
5324545--5324606	29	2.1	30	85	8	83	41	9	11	37	1.74
5328125--5328213	40	2.2	40	82	11	119	31	8	11	48	1.70
5346000--5346219	111	2.0	111	86	1	309	30	13	19	36	1.90
5346213--5346256	22	2.0	22	100	0	88	45	9	22	22	1.80
5346116--5346362	129	1.9	129	94	2	433	32	13	21	32	1.92
5346234--5346482	106	2.4	105	90	2	392	32	14	20	32	1.93
5357812--5357901	26	3.3	26	66	22	67	46	15	16	21	1.84
5360166--5360232	33	2.0	33	100	0	134	47	19	11	20	1.81
5368200--5368244	18	2.4	19	85	3	56	48	2	2	46	1.26
5369448--5369528	41	2.0	41	100	0	162	16	19	14	49	1.80
5374449--5374480	13	2.3	15	89	10	50	3	9	3	84	0.84
5385060--5385100	2	20.5	2	94	0	73	53	46	0	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5390377--5390420	20	2.2	20	87	0	61	50	11	2	36	1.51
5390378--5390412	18	1.9	18	88	0	52	51	11	2	34	1.53
5393644--5393684	21	2.0	21	100	0	82	39	21	19	19	1.93
5407256--5407291	9	4.1	9	89	7	56	61	0	0	38	0.96
5408530--5408678	76	2.0	76	97	0	280	34	17	2	46	1.60
5408694--5408742	18	2.7	18	78	6	55	46	10	0	42	1.37
5413603--5413637	15	2.4	15	90	4	54	48	0	8	42	1.33
5414225--5414282	28	2.1	28	96	0	107	32	22	13	31	1.93
5419284--5419475	50	3.8	50	88	0	267	20	29	22	27	1.98
5422237--5422277	21	1.9	22	85	5	57	7	17	2	73	1.17

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   194   195   196   197   198