genome.fa.s4.2.7.7.80.10.50.1000.194.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  194  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)
60425802--60425848	3	15.3	3	86	4	58	0	31	6	61	1.21
60428004--60428066	32	1.9	34	87	12	96	30	1	0	68	0.99
60428019--60428092	26	2.9	25	82	7	87	32	1	1	64	1.10
60434407--60434956	223	2.5	223	93	0	913	43	18	12	24	1.85
60435577--60435626	24	2.1	24	100	0	100	28	6	24	42	1.78
60437761--60437794	16	2.1	16	100	0	68	38	5	0	55	1.24
60439847--60439884	2	19.0	2	88	0	58	52	2	0	44	1.14
60450406--60450507	30	3.4	29	73	8	87	49	1	10	38	1.49
60464835--60464861	1	27.0	1	100	0	54	0	0	0	100	0.00
60473847--60473871	13	1.9	13	100	0	50	48	0	0	52	1.00
60475415--60475531	60	2.0	60	98	0	225	31	0	14	53	1.41
60475726--60476013	103	2.8	100	86	8	388	25	1	17	55	1.50
60480852--60480889	20	1.9	20	94	0	67	44	39	0	15	1.47
60489257--60489331	31	2.4	31	86	4	98	30	6	9	53	1.59
60490698--60490767	29	2.4	30	81	13	83	30	7	8	54	1.58
60490914--60490985	29	2.4	30	80	15	78	47	8	15	29	1.74
60492759--60492812	20	2.7	19	80	8	63	62	3	0	33	1.12
60500083--60500119	3	12.3	3	100	0	74	67	0	0	32	0.91
60501100--60501124	2	12.5	2	100	0	50	48	0	0	52	1.00
60502764--60502791	13	2.2	13	100	0	56	57	0	28	14	1.38
60503817--60503841	12	2.1	12	100	0	50	16	8	8	68	1.38
60508163--60508208	15	3.1	15	78	12	51	41	0	2	56	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60509668--60509752	25	3.6	25	81	9	81	30	5	2	61	1.32
60511702--60511747	23	2.1	21	88	11	67	63	2	2	32	1.19
60512993--60513026	14	2.5	14	95	4	61	50	35	0	14	1.44
60523730--60523836	49	2.3	45	76	17	103	46	2	0	49	1.22
60523774--60523844	15	4.6	15	72	16	56	49	1	1	47	1.18
60525065--60525120	21	2.8	20	78	10	60	62	0	10	26	1.28
60525389--60525438	20	2.5	21	87	9	77	44	0	0	56	0.99
60525805--60525830	4	6.5	4	100	0	52	23	0	0	76	0.78
60534497--60534639	45	3.2	45	87	4	207	40	20	18	19	1.92
60534491--60534666	45	4.2	39	75	17	131	39	21	19	19	1.92
60545764--60545862	31	3.3	30	68	16	89	25	16	15	43	1.86
60552070--60552154	28	3.0	28	78	13	84	30	2	5	61	1.32
60554330--60554361	3	10.7	3	93	0	55	62	0	3	34	1.11
60554644--60554677	17	2.0	17	88	0	50	47	5	5	41	1.52
60562084--60562119	14	2.4	16	90	9	58	55	2	11	30	1.49
60562115--60562149	17	2.1	17	88	0	52	48	0	14	37	1.44
60562084--60562171	14	6.5	14	70	17	53	52	1	12	34	1.47
60568606--60568631	2	13.0	2	100	0	52	50	0	0	50	1.00
60573867--60573892	4	6.5	4	100	0	52	23	0	0	76	0.78
60580399--60580470	30	2.4	30	80	2	81	36	6	12	44	1.69
60580393--60580470	31	2.5	31	79	2	95	35	6	12	44	1.68
60596098--60596142	18	2.6	17	82	6	56	55	6	0	37	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60600253--60600288	16	2.1	18	90	10	58	58	0	0	41	0.98
60601246--60601319	29	2.5	30	86	4	96	51	14	14	18	1.77
60603697--60603736	18	2.2	18	86	8	55	45	0	0	55	0.99
60607689--60607716	6	4.7	6	100	0	56	17	64	0	17	1.30
60607735--60607774	2	20.0	2	100	0	80	50	0	0	50	1.00
60609365--60609686	159	2.0	159	98	0	626	35	21	14	28	1.92
60610629--60610713	39	2.3	36	81	6	98	43	14	16	25	1.85
60614225--60614265	20	2.0	20	90	0	64	12	2	21	63	1.40
60621617--60621641	2	12.5	2	100	0	50	52	0	0	48	1.00
60625145--60625298	43	3.6	42	77	4	139	29	25	18	26	1.98
60625145--60625336	43	4.5	43	75	7	122	29	25	19	26	1.99
60627078--60627702	9	71.9	9	64	19	154	34	2	18	45	1.62
60627054--60627124	29	2.3	31	83	11	85	32	0	19	47	1.50
60627076--60627172	25	3.9	24	73	16	90	34	0	20	45	1.52
60627111--60627197	34	2.6	34	83	3	113	31	2	21	44	1.65
60627315--60627702	25	16.3	25	70	15	202	34	2	17	45	1.60
60627394--60627454	20	3.1	20	81	9	72	36	0	14	49	1.44
60627413--60627623	93	2.3	89	86	4	278	36	0	15	46	1.53
60627345--60627609	113	2.3	115	86	4	351	35	1	16	45	1.59
60627655--60627715	20	3.1	20	81	9	72	36	0	14	49	1.44
60627705--60627775	30	2.4	28	79	9	79	50	0	4	45	1.21
60627758--60627802	23	2.0	22	86	4	63	46	0	6	46	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60627751--60627811	30	2.0	30	84	6	79	47	0	6	45	1.28
60629505--60629554	22	2.3	22	96	0	91	46	16	16	22	1.84
60646598--60646666	25	2.9	22	73	14	57	60	5	1	31	1.29
60648138--60648189	2	26.0	2	96	0	95	51	0	0	48	1.00
60648274--60648300	6	4.5	6	100	0	54	37	0	0	62	0.95
60649835--60649877	21	2.0	21	86	8	61	60	0	2	37	1.10
60650257--60650315	31	1.9	31	89	0	91	40	15	3	40	1.64
60658325--60658365	2	20.5	2	94	0	73	46	0	2	51	1.14
60668197--60668222	13	2.0	13	100	0	52	30	15	15	38	1.88
60672859--60672905	22	2.1	23	84	4	60	57	4	8	29	1.48
60673528--60673570	22	2.0	20	82	8	50	48	9	0	41	1.35
60675125--60675153	2	14.5	2	100	0	58	51	0	0	48	1.00
60676367--60676397	16	1.9	16	93	0	53	41	22	16	19	1.89
60679688--60679712	6	4.2	6	100	0	50	84	0	0	16	0.63
60682350--60682389	18	2.1	20	86	9	57	35	5	0	60	1.19
60682713--60682749	2	18.5	2	100	0	74	48	0	0	51	1.00
60683406--60683435	3	10.0	3	100	0	60	0	33	0	66	0.92
60687265--60687322	25	2.3	26	94	5	102	39	13	12	34	1.82
60692612--60692648	16	2.4	15	86	8	56	56	29	0	13	1.37
60692903--60692941	20	2.0	20	90	10	62	51	33	2	12	1.54
60692899--60692932	12	2.8	12	95	0	59	50	38	0	11	1.39
60692882--60692921	8	5.4	8	77	17	50	52	35	0	12	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60695308--60695344	19	1.9	19	88	0	56	35	0	0	64	0.94
60709020--60709098	39	2.0	39	97	0	149	25	18	20	35	1.95
60717698--60717727	2	15.0	2	100	0	60	50	0	0	50	1.00
60724430--60724501	30	2.4	29	77	6	72	50	6	1	41	1.38
60730268--60730320	21	2.5	21	82	11	56	58	0	0	41	0.98
60730902--60730937	18	2.0	18	89	10	56	36	0	0	63	0.94
60731296--60731335	18	2.2	18	86	8	55	40	5	2	52	1.37
60736884--60736915	15	2.1	15	94	0	55	9	18	59	12	1.59
60744070--60744112	21	1.9	23	86	13	63	39	2	11	46	1.53
60745417--60745443	9	3.0	9	100	0	54	33	0	0	66	0.92
60748627--60748658	12	2.7	12	95	0	55	18	65	12	3	1.38
60756681--60756706	6	4.3	6	100	0	52	84	0	0	15	0.62
60757414--60757622	44	4.9	43	72	9	185	22	20	22	34	1.96
60757762--60757968	87	2.4	87	85	1	299	22	24	23	29	1.99
60758399--60758594	108	1.8	108	88	2	304	46	10	17	25	1.80
60758560--60758660	45	2.3	44	80	10	107	53	8	11	25	1.66
60758930--60758983	12	4.4	12	82	13	58	0	14	3	81	0.82
60758932--60758985	18	3.1	17	84	12	65	0	14	3	81	0.82
60758931--60758986	25	2.3	23	85	8	85	0	16	3	80	0.85
60760703--60760885	62	3.0	62	94	0	321	31	6	21	39	1.79
60766391--60766430	20	2.0	20	90	4	64	52	15	20	12	1.74
60766595--60766625	3	10.3	3	100	0	62	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60766675--60766732	29	2.0	29	89	0	89	36	6	12	44	1.68
60767357--60767401	22	2.1	21	87	4	63	48	2	2	46	1.26
60780227--60780258	17	2.0	17	88	11	50	62	15	21	0	1.32
60780925--60780977	3	17.7	3	92	0	88	35	0	1	62	1.06
60782595--60782678	30	2.8	32	80	12	97	42	3	1	52	1.26
60784042--60784081	14	2.6	15	84	15	55	22	15	5	57	1.57
60784506--60784579	28	2.6	29	83	16	102	40	10	0	48	1.38
60784627--60784685	27	2.2	27	84	6	75	28	27	27	16	1.97
60784859--60784994	19	7.3	19	78	5	161	38	13	0	48	1.42
60784859--60784994	37	3.7	37	97	0	263	38	13	0	48	1.42

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