genome.fa.s4.2.7.7.80.10.50.1000.197.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  197  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)
61529965--61530305	155	2.2	154	91	5	562	29	10	7	51	1.65
61530440--61530505	27	2.4	27	87	0	96	13	34	25	25	1.93
61530566--61530615	22	2.2	23	82	10	59	20	0	6	74	1.03
61536019--61536072	15	3.3	15	74	18	54	44	0	1	53	1.11
61536343--61536424	11	7.5	11	72	4	58	6	6	21	65	1.37
61537507--61538052	270	2.0	270	100	0	1092	34	13	15	35	1.87
61542530--61542720	96	2.0	96	98	0	373	45	5	25	23	1.75
61542923--61543130	42	5.0	43	80	10	144	29	23	28	18	1.97
61542951--61543287	42	8.0	42	85	2	318	32	26	24	17	1.97
61548367--61548406	20	2.0	20	100	0	80	60	0	0	40	0.97
61548349--61548404	20	2.6	22	83	13	73	53	3	0	42	1.18
61551852--61551887	18	2.0	18	94	0	63	63	5	0	30	1.17
61553255--61553293	12	3.3	12	78	7	53	5	7	17	69	1.32
61553258--61553305	24	2.0	24	88	4	71	6	6	16	70	1.28
61559559--61559631	29	2.4	31	77	4	78	39	15	12	32	1.84
61559590--61559656	31	2.3	27	76	14	62	43	11	8	35	1.73
61564801--61564841	22	1.9	22	90	5	66	43	12	0	43	1.41
61566812--61566837	12	2.2	12	100	0	52	7	69	15	7	1.35
61566825--61567119	141	2.1	141	95	0	536	27	26	24	22	2.00
61575998--61576025	14	2.0	14	100	0	56	78	7	7	7	1.09
61593379--61593410	11	2.9	11	95	0	55	15	3	0	81	0.82
61598740--61598775	14	2.6	13	87	12	54	30	0	2	66	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61615392--61615437	7	6.6	7	100	0	92	13	15	0	71	1.14
61615392--61615448	21	2.7	21	89	5	62	19	12	0	68	1.20
61616061--61616105	4	11.2	4	100	0	90	51	24	0	24	1.49
61616037--61616186	71	2.1	70	85	9	198	50	12	10	27	1.72
61616892--61616939	22	2.1	22	81	11	53	60	4	2	33	1.27
61622193--61622232	19	2.1	19	86	9	55	35	2	0	62	1.09
61624122--61624171	27	1.9	25	84	15	66	54	18	6	22	1.65
61628003--61628036	17	2.0	17	88	0	50	44	0	2	52	1.16
61638358--61638402	23	2.0	23	82	8	56	40	0	2	57	1.11
61640475--61640504	9	3.3	9	95	0	51	46	30	0	23	1.52
61642783--61643181	192	2.1	192	88	0	584	28	16	21	33	1.95
61643798--61643885	42	2.1	42	97	0	167	23	31	20	23	1.98
61646067--61646132	31	2.2	29	82	17	73	34	0	3	62	1.11
61661461--61661499	20	2.0	20	89	0	60	33	10	15	41	1.81
61664021--61664062	21	2.0	21	86	9	59	21	0	4	73	1.01
61666900--61666931	7	4.6	7	96	0	55	40	9	31	18	1.83
61666856--61666972	58	2.0	58	96	0	216	33	13	23	29	1.93
61669805--61669838	7	4.9	7	100	0	68	0	14	55	29	1.40
61670900--61671055	84	1.9	84	89	2	242	34	16	16	32	1.91
61681117--61681154	14	2.6	15	83	4	51	42	15	5	36	1.70
61694448--61694474	11	2.5	11	100	0	54	22	0	0	77	0.76
61701139--61701170	10	3.2	10	100	0	64	0	9	0	90	0.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61714137--61714161	2	12.5	2	100	0	50	52	0	0	48	1.00
61718079--61718104	3	8.7	3	100	0	52	69	0	0	30	0.89
61727038--61727066	12	2.3	13	94	5	51	37	0	6	55	1.27
61737238--61737413	83	2.1	81	86	8	241	22	6	19	52	1.68
61739640--61739695	27	2.0	28	83	10	71	50	0	1	48	1.11
61741172--61741204	3	11.0	3	100	0	66	33	0	0	66	0.92
61744793--61744835	22	2.0	22	81	9	52	34	2	2	60	1.22
61745723--61745758	18	2.0	18	94	0	63	25	0	5	69	1.10
61745832--61745880	25	1.9	25	84	12	64	71	0	0	28	0.86
61745822--61745882	30	2.1	30	84	9	81	70	0	0	29	0.88
61749787--61750114	126	2.6	127	82	7	375	45	20	12	21	1.83
61749787--61750102	127	2.5	125	82	7	388	46	20	12	20	1.83
61763145--61763178	5	6.4	5	96	3	50	0	23	0	76	0.79
61763733--61763806	31	2.5	29	78	10	78	45	14	2	36	1.60
61764816--61764874	22	2.8	21	72	12	57	33	5	6	54	1.49
61767753--61767877	58	2.1	59	79	4	137	47	13	15	24	1.81
61782492--61782579	31	2.9	31	68	8	72	35	11	12	40	1.79
61785580--61785635	26	2.2	26	93	3	96	41	7	17	33	1.77
61790726--61790768	22	1.9	22	90	4	68	44	0	0	55	0.99
61790944--61790983	3	13.3	3	100	0	80	65	0	0	35	0.93
61791560--61791600	21	1.9	22	90	5	66	56	4	0	39	1.21
61793927--61793992	20	3.2	19	77	16	60	50	1	1	46	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61803361--61803429	33	2.1	33	81	7	79	55	1	2	40	1.24
61813220--61813276	28	2.0	28	96	0	105	33	8	14	43	1.76
61813316--61813447	59	2.2	60	87	1	185	37	9	17	34	1.83
61827782--61827866	31	2.8	29	72	8	71	41	10	10	37	1.74
61828234--61828274	18	2.2	20	91	8	68	21	2	4	70	1.18
61831001--61831040	16	2.5	16	88	8	55	47	2	2	47	1.29
61833586--61834927	682	2.0	654	87	8	1910	33	13	15	38	1.86
61836239--61836319	39	2.1	39	86	4	110	37	4	7	50	1.52
61836346--61836376	15	2.1	15	100	0	62	32	0	25	41	1.56
61839830--61839874	21	2.1	22	87	4	65	2	13	6	77	1.05
61840365--61840394	2	15.5	2	93	6	53	50	0	0	50	1.00
61845345--61845370	6	4.3	6	100	0	52	50	19	15	15	1.79
61845353--61845457	45	2.3	45	83	6	142	42	18	17	21	1.89
61851667--61851722	22	2.7	20	81	13	67	26	3	3	66	1.25
61859612--61859642	3	10.3	3	100	0	62	67	0	0	32	0.91
61864550--61864601	27	1.9	27	84	7	70	55	11	1	30	1.46
61866161--61866258	44	2.2	45	88	1	144	26	27	15	30	1.96
61866337--61866526	44	4.3	44	67	12	120	25	24	18	31	1.98
61866276--61866524	132	1.9	132	92	1	419	27	23	19	28	1.98
61866611--61867134	45	11.7	45	79	4	540	29	22	18	29	1.97
61866611--61867156	89	6.1	89	79	3	551	29	22	18	29	1.97
61866609--61867156	134	4.1	134	95	0	979	29	22	18	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61867417--61867499	44	1.9	43	87	2	121	16	22	18	42	1.89
61875123--61875173	26	1.9	26	84	4	66	54	11	1	31	1.47
61878047--61878092	18	2.6	18	92	0	74	30	2	2	65	1.16
61885391--61885471	39	2.1	39	86	4	110	37	4	7	50	1.52
61885498--61885528	15	2.1	15	100	0	62	32	0	25	41	1.56
61894680--61894726	12	3.7	12	83	11	58	27	2	2	68	1.13
61894877--61894939	26	2.5	26	82	12	78	44	9	0	46	1.36
61894908--61894945	18	2.1	19	90	5	60	39	10	0	50	1.37
61896272--61896314	3	14.3	3	100	0	86	67	0	0	32	0.91
61896623--61896666	25	1.9	24	82	17	58	40	9	0	50	1.34
61901611--61901656	22	2.1	22	100	0	92	21	26	8	43	1.81
61903244--61903304	21	2.7	22	76	19	63	14	11	9	63	1.51
61911688--61911730	22	2.0	20	83	16	52	55	6	2	34	1.39
61927332--61927468	70	2.0	69	95	1	247	42	5	12	39	1.67
61929269--61929293	13	1.9	13	100	0	50	40	0	0	60	0.97
61929265--61929302	20	1.9	20	88	0	58	47	0	0	52	1.00
61929286--61929331	20	2.4	19	81	3	56	65	0	2	32	1.05
61931111--61931167	29	2.0	29	82	6	71	40	15	7	36	1.75
61938044--61938091	23	2.1	23	84	0	60	47	0	6	45	1.27
61942405--61942447	21	2.0	21	86	8	61	34	0	6	58	1.25
61943558--61943622	23	2.9	22	76	17	62	29	4	1	64	1.22
61945832--61945873	21	2.0	21	86	9	59	40	7	11	40	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61958446--61958535	45	2.0	45	100	0	180	24	20	31	24	1.98
61959113--61959169	30	1.9	30	100	0	114	26	17	26	29	1.97
61963775--61963818	2	23.5	2	82	13	58	52	0	47	0	1.00
61965285--61965336	27	1.9	27	96	0	95	17	38	19	25	1.93
61974192--61974216	2	12.5	2	100	0	50	0	0	48	52	1.00
61983656--61983732	29	2.5	31	87	4	104	46	11	12	28	1.77
61983686--61983754	29	2.3	29	85	5	84	47	11	15	24	1.79
61988994--61989048	24	2.4	23	82	8	60	50	1	0	47	1.11
61992179--61992281	18	5.6	20	74	19	64	66	0	6	26	1.16
61992215--61992310	27	3.5	27	72	14	79	61	1	6	31	1.27

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