genome.fa.s4.2.7.7.80.10.50.1000.124.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  124  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)
39809803--39809871	18	3.8	18	77	7	86	14	43	2	39	1.60
39812831--39812907	14	5.0	15	71	20	52	42	14	9	33	1.77
39812847--39812886	20	2.0	20	90	0	62	50	12	10	27	1.72
39812835--39812901	34	1.9	35	90	3	109	46	13	8	31	1.74
39813037--39813078	21	2.0	21	86	9	59	52	0	0	47	1.00
39819412--39819484	37	2.0	37	81	10	87	50	4	4	41	1.40
39820698--39820728	15	2.1	15	93	0	53	74	9	6	9	1.23
39822746--39822772	6	4.5	6	100	0	54	62	0	18	18	1.32
39825754--39825787	17	2.0	18	88	11	54	47	0	11	41	1.40
39832946--39832976	2	15.5	2	100	0	62	0	51	0	48	1.00
39842160--39842215	28	2.0	28	92	0	94	35	28	14	21	1.92
39859384--39859425	15	2.8	16	86	10	54	54	4	0	40	1.21
39865067--39865131	2	32.5	2	93	0	112	47	1	0	50	1.10
39865388--39865435	19	2.5	19	83	6	53	27	6	4	62	1.38
39866400--39866454	18	3.0	18	82	10	58	41	3	1	52	1.29
39868703--39868742	14	2.9	14	84	0	53	32	7	17	42	1.77
39868726--39868765	20	2.0	20	90	0	62	27	10	12	50	1.72
39868711--39868777	34	1.9	35	90	3	109	31	8	13	46	1.74
39868705--39868781	14	5.0	15	71	20	52	32	9	15	42	1.78
39873277--39873317	2	20.5	2	100	0	82	48	0	0	51	1.00
39895067--39895308	50	4.8	50	88	1	324	25	23	30	21	1.99
39895839--39895876	19	2.0	19	100	0	76	31	0	31	36	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39912840--39912911	27	2.7	27	80	4	74	37	15	25	22	1.93
39916826--39917293	151	3.1	151	85	5	554	41	5	10	41	1.64
39917206--39917265	32	1.9	31	86	6	86	36	6	6	50	1.55
39917952--39917982	2	15.5	2	100	0	62	48	0	0	51	1.00
39918749--39918905	81	2.0	80	86	6	219	24	19	24	31	1.98
39918824--39919539	113	6.3	113	89	3	1034	21	21	25	31	1.98
39922687--39922731	25	2.0	22	83	16	56	44	6	2	46	1.42
39922696--39923026	34	10.3	33	76	14	245	44	13	2	40	1.55
39922760--39923225	65	7.2	65	72	18	330	43	15	1	39	1.58
39922878--39923258	9	44.6	9	70	20	212	42	18	1	37	1.58
39922883--39923257	16	23.1	16	73	19	216	42	18	1	37	1.58
39922820--39923160	129	2.8	127	88	8	485	42	17	1	38	1.58
39923063--39923144	34	2.4	35	81	6	96	39	15	1	43	1.55
39928906--39929051	65	2.2	66	90	3	224	39	18	30	12	1.87
39929023--39929134	21	5.3	21	82	4	91	33	17	42	6	1.75
39929033--39929134	42	2.4	42	86	3	134	33	17	43	5	1.73
39929484--39929838	43	8.3	43	76	3	171	24	21	27	26	1.99
39929440--39929626	86	2.2	87	78	0	196	27	17	26	28	1.98
39930021--39930062	22	1.9	22	95	0	75	40	28	21	9	1.84
39940129--39940201	17	4.6	16	72	12	53	82	6	6	4	0.95
39940603--39941107	42	12.1	42	86	0	654	22	17	22	37	1.94
39941424--39941458	16	2.2	16	94	0	61	0	25	0	74	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39941885--39942603	153	4.8	150	85	6	879	41	5	10	42	1.62
39942558--39942616	32	1.9	32	82	6	77	33	5	6	54	1.49
39943129--39943175	24	1.9	24	83	12	60	31	6	6	55	1.51
39943334--39943375	3	14.0	3	94	0	66	28	0	4	66	1.12
39944646--39944747	43	2.4	43	83	0	132	32	24	14	28	1.95
39944776--39944824	22	2.2	22	82	7	55	61	4	0	34	1.15
39947059--39947101	14	3.3	14	81	12	56	46	11	6	34	1.67
39948386--39948425	14	2.8	14	80	3	53	40	12	0	47	1.41
39948386--39948425	15	2.8	15	81	11	57	40	12	0	47	1.41
39948918--39949007	40	2.2	40	86	7	121	22	23	24	30	1.99
39948941--39949027	40	2.2	40	89	0	129	24	22	22	29	1.99
39948802--39949182	155	2.4	154	84	5	473	27	21	20	29	1.98
39949111--39949211	40	2.5	40	84	6	125	28	23	18	28	1.98
39948918--39949367	195	2.4	186	83	6	521	27	22	21	28	1.99
39949120--39949222	40	2.6	40	84	1	118	30	23	16	30	1.96
39949259--39949381	40	3.1	39	79	11	133	27	23	21	26	1.99
39955493--39955820	162	2.0	162	99	0	647	39	16	19	24	1.91
39955988--39956027	20	2.0	20	85	5	53	32	35	2	30	1.71
39956030--39956091	25	2.5	25	86	0	88	19	38	16	25	1.92
39956563--39956605	21	2.0	21	100	0	86	41	18	9	30	1.82
39958263--39958794	59	9.0	58	90	2	803	45	5	3	46	1.41
39958263--39958879	177	3.4	176	88	5	875	45	5	3	45	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39958628--39958715	20	4.4	20	68	13	74	45	2	3	48	1.31
39958777--39958806	12	2.5	12	94	0	51	60	0	0	40	0.97
39958717--39958861	71	2.1	69	87	5	204	48	5	2	42	1.40
39958759--39958893	55	2.4	54	73	15	132	45	5	3	45	1.43
39959336--39959360	7	3.6	7	100	0	50	32	12	16	40	1.84
39966776--39966848	27	2.7	27	76	0	92	23	34	32	9	1.87
39966908--39966961	20	2.7	20	88	5	83	62	0	37	0	0.95
39967362--39968426	457	2.3	462	86	7	1464	51	8	9	30	1.64
39967709--39968413	156	4.5	156	92	1	1105	52	7	10	29	1.63
39970481--39970539	6	9.8	6	100	0	118	49	16	16	16	1.81
39973485--39973571	37	2.3	39	86	7	117	50	10	4	34	1.57
39973485--39973693	76	2.7	77	77	10	230	48	11	4	34	1.61
39973558--39973604	23	2.0	23	84	8	60	59	14	2	23	1.46
39973901--39973957	3	18.3	3	78	3	51	1	42	1	54	1.21
39973900--39973957	9	6.6	9	75	11	57	1	43	1	53	1.21
39975264--39975335	3	24.0	3	100	0	144	0	33	0	66	0.92
39977652--39977853	102	2.0	102	92	3	336	31	28	19	20	1.97
39977756--39977892	42	3.5	40	72	20	137	33	26	17	22	1.96
39977754--39977927	75	2.3	76	91	4	282	33	27	18	20	1.96
39977620--39977959	177	1.9	177	93	2	594	31	27	19	21	1.97
39985236--39985434	102	2.0	102	91	4	330	31	27	20	21	1.97
39985338--39985513	75	2.4	74	92	3	282	32	26	19	21	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39985204--39985543	177	1.9	177	93	1	583	31	27	19	21	1.98
39992546--39992608	32	2.0	32	87	0	90	44	7	3	44	1.49
39993191--39993220	16	1.9	16	93	6	53	36	6	6	50	1.55
40003102--40003164	32	2.0	32	87	0	90	44	6	3	46	1.45
40004814--40004839	6	4.3	6	100	0	52	84	0	0	15	0.62
40012837--40012884	18	2.6	18	96	3	87	54	12	6	27	1.61
40014908--40014968	22	2.7	22	87	2	77	49	1	1	47	1.21
40014944--40014983	16	2.5	16	91	0	62	47	2	7	42	1.45
40014972--40015113	68	2.1	67	94	2	250	40	4	9	45	1.58
40015056--40015083	9	3.1	9	100	0	56	32	0	10	57	1.33
40015180--40015222	23	1.9	22	95	4	77	62	0	0	37	0.95
40021599--40021625	2	13.5	2	100	0	54	51	0	0	48	1.00
40021705--40021738	3	11.0	3	87	6	50	61	0	2	35	1.11
40023349--40023400	25	2.0	26	82	10	63	38	13	9	38	1.77
40023502--40023647	17	8.8	17	63	24	71	52	2	2	43	1.27
40030150--40030194	21	2.2	20	84	4	54	26	11	26	35	1.90
40031812--40032054	50	4.8	50	85	1	290	20	30	22	26	1.98
40031812--40032049	100	2.4	101	87	2	336	21	29	23	26	1.99
40035922--40036079	39	4.1	40	75	8	146	44	18	3	32	1.68
40035904--40036083	78	2.3	78	83	5	222	43	19	3	33	1.69
40038635--40038688	24	2.4	24	81	9	60	61	3	0	35	1.14
40039536--40039569	16	2.1	16	89	10	52	76	0	0	23	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40042864--40042971	3	37.0	3	73	7	71	28	6	1	62	1.30
40043359--40043390	9	3.8	9	84	16	50	37	0	0	62	0.95
40043368--40043419	22	2.5	19	75	19	50	38	5	0	55	1.24
40043337--40043509	51	3.3	52	68	10	131	36	9	2	51	1.49
40046825--40046852	5	5.6	5	100	0	56	82	17	0	0	0.68
40047273--40047325	23	2.2	26	86	10	76	81	3	11	3	0.96
40047273--40047325	28	1.9	26	85	11	70	81	3	11	3	0.96
40047605--40047691	45	1.9	45	81	4	104	27	12	10	49	1.73
40048726--40049166	50	8.8	48	80	8	332	34	21	18	26	1.96
40048723--40049166	100	4.4	98	81	3	422	34	21	18	26	1.96

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