genome.fa.s4.2.7.7.80.10.50.1000.136.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  136  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)
43393133--43393163	15	2.1	15	93	0	53	12	0	29	58	1.35
43393068--43393393	43	7.5	43	81	6	327	16	0	32	50	1.50
43393262--43393316	15	3.7	15	80	11	69	16	0	30	52	1.44
43393999--43394038	18	2.2	18	90	0	62	42	7	30	20	1.79
43395941--43395984	11	3.8	12	80	19	58	43	0	31	25	1.55
43404726--43404763	18	2.2	18	86	9	53	57	2	0	39	1.12
43409747--43409852	33	3.2	33	82	2	133	27	14	42	16	1.86
43409747--43409886	66	2.1	66	80	7	151	25	14	42	17	1.87
43411891--43411929	16	2.6	16	88	8	55	61	12	0	25	1.31
43411889--43412353	106	4.5	103	79	10	484	53	16	0	28	1.48
43412674--43412716	21	2.0	23	86	9	63	0	27	0	72	0.85
43412661--43412720	31	2.0	29	87	12	86	0	26	0	73	0.84
43412661--43412719	28	2.1	29	81	15	70	0	25	0	74	0.82
43413043--43413082	20	2.0	21	90	5	64	52	0	2	45	1.14
43413038--43413083	20	2.4	19	82	14	58	56	0	2	41	1.11
43415789--43415873	39	2.3	37	91	6	136	25	15	20	38	1.91
43418464--43418520	13	4.4	13	84	0	69	38	24	8	28	1.85
43418460--43418520	26	2.4	25	83	8	77	36	22	8	32	1.84
43424086--43424332	50	4.8	50	80	4	228	23	27	20	27	1.99
43424670--43424733	30	2.1	30	82	0	74	34	21	7	35	1.83
43433361--43433459	38	2.6	38	76	9	103	50	9	4	36	1.53
43436594--43436637	11	3.9	11	87	3	61	20	25	2	52	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43436721--43436751	16	2.0	16	93	6	55	54	0	0	45	0.99
43437864--43437889	7	3.7	7	100	0	52	26	0	15	57	1.38
43438537--43438579	18	2.4	18	92	0	68	20	27	6	44	1.77
43439047--43439080	7	4.9	7	85	0	50	64	0	0	35	0.94
43439133--43439379	127	1.9	127	95	0	440	28	22	17	32	1.96
43439152--43439412	127	2.1	125	84	7	330	31	22	16	29	1.96
43440190--43440249	26	2.5	22	71	19	57	51	3	5	40	1.40
43440405--43440475	30	2.4	29	77	11	72	38	7	1	53	1.37
43441956--43442055	31	3.1	30	71	20	76	45	9	1	45	1.42
43441941--43442033	36	2.5	38	84	5	127	47	6	1	45	1.35
43445774--43445813	3	13.3	3	94	0	71	65	0	35	0	0.93
43448071--43448140	27	2.6	27	80	8	79	51	20	2	25	1.61
43449879--43449945	20	3.2	23	61	30	58	43	10	8	37	1.71
43458352--43458797	218	2.0	218	91	3	718	30	18	15	35	1.92
43470288--43470495	101	2.1	101	97	1	391	22	12	4	60	1.51
43470298--43470530	101	2.3	100	91	6	364	24	12	4	59	1.51
43471189--43471233	5	9.0	5	95	0	72	40	4	20	35	1.72
43471989--43472122	66	2.0	66	84	2	171	49	14	22	14	1.79
43482496--43482553	23	2.6	23	80	2	73	56	1	0	41	1.09
43484819--43484870	21	2.5	21	87	0	68	40	5	19	34	1.75
43491027--43491102	3	24.7	3	84	5	98	38	2	0	59	1.12
43491636--43491666	12	2.6	12	94	0	53	70	3	25	0	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43492363--43492452	37	2.4	37	85	7	112	41	3	23	32	1.71
43495170--43495307	27	5.1	27	84	1	161	43	21	18	16	1.88
43495170--43495308	54	2.6	54	84	0	179	43	21	17	16	1.87
43495374--43495428	24	2.3	24	78	6	67	25	7	20	47	1.75
43495619--43495808	32	5.9	32	76	7	154	20	20	22	36	1.95
43495635--43495814	64	2.8	64	82	3	175	20	21	22	36	1.95
43495635--43495814	96	1.9	96	85	6	249	20	21	22	36	1.95
43496729--43497251	273	1.9	272	81	5	641	28	5	12	53	1.61
43497657--43497695	14	2.8	14	80	0	51	41	10	15	33	1.81
43497287--43497902	315	2.0	310	89	4	943	32	10	12	44	1.75
43498048--43498131	33	2.8	29	77	13	96	50	9	15	25	1.74
43498060--43498126	33	2.0	33	91	0	107	52	10	11	25	1.70
43498291--43498379	39	2.3	39	81	11	94	50	1	1	47	1.15
43502117--43502141	12	2.1	12	100	0	50	8	44	0	48	1.32
43502755--43502789	17	2.1	17	100	0	70	40	34	5	20	1.76
43504035--43504095	24	2.6	24	79	7	63	57	1	0	40	1.08
43504046--43504096	23	2.2	22	83	13	59	54	0	0	45	0.99
43508777--43508820	3	15.0	3	81	13	56	34	2	0	63	1.07
43513851--43513901	6	7.9	7	93	6	74	76	0	7	15	1.00
43513852--43513901	13	3.9	12	89	7	64	76	0	8	16	1.02
43514839--43515432	44	13.4	44	77	5	545	31	12	23	32	1.92
43514839--43515435	133	4.5	132	86	3	763	31	12	23	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43514806--43515358	89	6.2	89	82	3	614	30	13	23	33	1.92
43514839--43515432	89	6.7	86	80	6	469	31	12	23	32	1.92
43515438--43515855	44	9.8	42	74	12	291	28	22	22	26	1.99
43515484--43515859	85	4.4	85	73	10	343	29	22	22	26	1.99
43515436--43515850	129	3.2	129	94	0	733	28	22	22	26	1.99
43517191--43517228	3	13.0	3	94	5	69	34	0	0	65	0.93
43519330--43519376	18	2.7	17	81	18	53	25	2	0	72	0.96
43519330--43519377	17	2.7	17	78	15	53	25	2	0	72	0.95
43520004--43520146	19	7.4	19	69	19	82	60	5	2	32	1.32
43520085--43520146	20	3.2	19	77	6	63	62	8	0	29	1.23
43520073--43520125	10	5.4	10	80	13	56	62	7	1	28	1.33
43521985--43522045	19	3.3	19	78	17	58	29	0	8	62	1.24
43526048--43526139	29	3.3	29	69	14	86	38	4	6	51	1.48
43529714--43529748	18	1.9	18	88	0	52	20	2	2	74	1.08
43534963--43535042	22	3.7	22	90	6	112	36	17	8	37	1.81
43534989--43535042	19	2.7	19	91	8	63	35	16	11	37	1.84
43535802--43536028	50	4.5	50	72	3	152	28	21	20	29	1.98
43535814--43535999	100	1.9	100	81	5	232	27	20	19	31	1.97
43535962--43536346	168	2.3	168	89	1	594	28	24	17	29	1.98
43536296--43536482	50	3.7	50	77	4	198	28	19	20	31	1.97
43536301--43536535	100	2.3	100	88	1	328	27	20	20	31	1.97
43536323--43536536	50	4.3	50	78	2	178	28	21	19	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43536373--43536536	50	3.3	50	79	3	195	28	21	18	31	1.97
43539631--43539663	9	3.8	9	88	4	50	42	15	21	21	1.89
43541608--43541637	3	10.0	3	100	0	60	66	0	0	33	0.92
43542575--43542641	22	3.0	22	88	2	89	35	16	8	38	1.80
43542613--43542664	19	2.9	17	78	10	59	32	15	11	40	1.83
43542598--43542654	22	2.8	19	82	14	78	33	15	12	38	1.85
43543866--43543943	33	2.4	33	78	8	86	26	23	15	34	1.94
43543818--43544079	101	2.6	101	85	1	348	27	27	15	30	1.96
43545745--43545961	111	2.0	111	93	0	371	33	26	10	29	1.89
43547339--43547377	5	7.8	5	100	0	78	17	0	0	82	0.68
43548668--43548725	5	10.8	5	75	14	53	43	3	17	36	1.66
43548673--43548725	22	2.4	22	87	0	70	43	3	16	35	1.67
43548647--43548717	27	2.7	27	77	12	76	46	5	16	30	1.70
43552816--43552841	13	2.0	13	100	0	52	46	7	7	38	1.61
43552852--43552917	18	3.8	18	64	22	50	42	15	13	28	1.85
43552828--43552907	34	2.4	34	85	4	108	43	15	11	30	1.81
43564234--43564283	3	17.0	3	79	4	57	0	32	0	68	0.90
43564228--43564295	9	7.4	9	75	18	52	0	27	0	72	0.85
43566200--43566391	50	3.9	50	89	0	269	21	31	20	26	1.98
43580854--43580878	13	1.9	13	100	0	50	68	0	8	24	1.16
43588074--43588117	22	2.0	23	90	4	72	22	31	11	34	1.90
43588321--43588419	41	2.4	41	84	0	117	32	18	22	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43592979--43593012	5	7.0	5	93	6	61	58	0	0	41	0.98
43592975--43593012	15	2.7	14	88	11	60	57	0	0	42	0.98
43593041--43593077	18	2.1	18	90	5	58	40	0	24	35	1.55
43601540--43601586	20	2.3	21	82	13	62	65	0	2	31	1.04
43601629--43601683	20	2.7	21	82	5	67	65	7	3	23	1.34
43602409--43602487	16	4.9	16	75	17	65	72	6	15	6	1.26
43607227--43607264	16	2.3	17	86	4	51	57	5	2	34	1.35
43608473--43608589	53	2.2	53	90	3	182	41	9	8	40	1.68
43612263--43612315	18	2.9	18	80	2	61	41	45	1	11	1.51
43612419--43612458	9	4.4	9	87	0	62	25	7	22	45	1.78

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