genome.fa.s4.2.7.7.80.10.50.1000.40.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  40  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)
11967417--11967471	20	2.8	20	72	10	58	36	16	5	41	1.71
11967532--11967653	40	3.0	40	87	0	181	41	15	5	36	1.71
11967298--11967657	195	1.8	195	80	5	433	37	19	6	36	1.79
11967542--11967657	20	5.8	20	80	4	126	40	16	5	37	1.71
11967719--11967760	21	2.0	21	86	4	59	47	4	7	40	1.52
11967727--11967771	21	2.2	21	84	4	56	48	6	6	37	1.56
11967936--11968078	20	7.2	20	67	6	85	41	16	8	34	1.78
11967937--11968079	40	3.6	40	75	9	114	41	15	8	34	1.77
11968295--11968356	20	3.0	20	70	11	54	37	14	9	38	1.79
11968393--11968445	20	2.6	22	69	19	53	39	7	3	49	1.49
11970332--11970567	119	2.0	118	85	0	319	30	9	22	38	1.86
11975826--11975927	30	3.1	33	77	17	106	45	0	14	40	1.45
11975793--11975926	65	2.2	61	82	9	164	43	0	13	42	1.49
11976017--11976414	126	3.2	125	88	4	554	36	17	17	27	1.93
11979742--11979779	18	2.1	18	95	0	67	42	7	26	23	1.81
11982763--11982828	31	2.1	31	100	0	132	33	31	18	16	1.93
11985560--11985625	31	2.1	31	82	0	78	36	3	4	56	1.35
11985682--11985728	24	2.0	24	83	8	60	46	6	0	46	1.28
11993213--11993265	19	2.8	19	83	13	65	30	20	5	43	1.75
11996400--11996457	26	2.2	27	93	3	100	43	18	24	13	1.87
12001047--12001286	44	5.5	44	83	3	259	30	18	20	30	1.96
12001050--12001286	88	2.7	88	84	0	285	31	18	20	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12002724--12002772	22	2.2	21	79	10	53	28	10	2	59	1.41
12002765--12002843	35	2.2	34	79	16	81	22	8	1	67	1.26
12004746--12004789	21	2.1	21	86	0	61	25	6	2	65	1.28
12004858--12004904	21	2.4	21	83	13	57	31	4	2	61	1.27
12004896--12004926	15	2.1	15	100	0	62	38	0	0	61	0.96
12024078--12024154	38	2.0	38	100	0	154	25	12	12	48	1.78
12025052--12025121	22	3.2	22	63	25	58	32	12	27	27	1.93
12032354--12032448	25	3.8	25	77	5	93	25	22	23	29	1.99
12034548--12034603	22	2.5	23	82	2	69	51	1	1	44	1.22
12034579--12034618	16	2.5	16	91	0	62	47	2	7	42	1.45
12034691--12034718	9	3.1	9	100	0	56	32	0	10	57	1.33
12034607--12034816	68	3.1	68	96	1	379	40	4	8	45	1.56
12034759--12034786	9	3.1	9	100	0	56	32	0	10	57	1.33
12037029--12037053	2	12.5	2	100	0	50	48	0	0	52	1.00
12037785--12037823	17	2.3	17	100	0	78	28	0	10	61	1.28
12038355--12038689	97	3.5	97	99	0	661	41	13	6	38	1.71
12038727--12038771	23	2.0	23	82	8	56	44	6	2	46	1.42
12038778--12038804	11	2.5	11	100	0	54	48	25	0	25	1.52
12041167--12041375	92	2.3	91	85	5	269	45	3	4	46	1.41
12041303--12041350	26	1.9	25	84	16	64	45	0	2	52	1.12
12041527--12041567	15	2.8	15	82	10	50	43	0	2	53	1.13
12041740--12042052	153	2.0	156	91	2	515	46	5	4	43	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12042198--12042236	15	2.6	15	95	0	69	69	7	0	23	1.14
12047509--12047616	25	4.3	25	77	4	101	25	19	25	29	1.98
12048963--12049020	24	2.5	24	86	8	75	46	13	6	32	1.70
12053888--12053917	13	2.3	13	94	0	51	40	26	3	30	1.72
12055969--12056021	2	26.5	2	100	0	106	50	0	0	49	1.00
12058971--12059014	18	2.5	18	96	3	81	15	0	20	63	1.31
12062265--12062353	17	5.2	16	81	8	79	38	2	13	46	1.56
12062269--12062375	34	3.2	34	81	6	112	35	3	14	46	1.62
12062291--12062376	17	5.1	18	80	10	76	34	3	15	46	1.62
12062308--12062405	17	5.9	16	73	19	69	31	6	15	46	1.70
12070322--12070347	2	13.0	2	100	0	52	50	0	0	50	1.00
12077124--12077174	27	1.9	27	84	4	68	15	9	11	62	1.53
12082967--12083055	45	2.0	45	86	0	124	32	23	16	26	1.96
12083066--12083252	51	3.7	51	72	11	168	32	25	17	25	1.97
12083064--12083247	101	1.8	101	86	3	271	32	26	16	25	1.96
12084676--12084706	15	2.1	15	100	0	62	25	6	41	25	1.79
12085617--12085805	94	2.0	94	100	0	378	24	7	24	43	1.79
12086082--12086124	23	1.9	23	86	13	63	37	0	0	62	0.95
12089883--12089935	26	2.0	26	100	0	106	28	18	22	30	1.98
12091211--12091781	127	4.5	127	91	2	877	30	17	23	28	1.97
12094954--12095107	21	7.2	21	83	2	191	27	0	29	42	1.60
12094954--12095105	43	3.5	42	85	2	205	27	0	29	42	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12094954--12095110	65	2.5	64	88	2	217	27	0	29	42	1.60
12096072--12096182	43	2.5	44	86	4	145	23	1	26	48	1.61
12096072--12096182	22	5.1	22	85	2	143	23	1	26	48	1.61
12096723--12096765	18	2.4	18	80	7	52	46	11	27	13	1.78
12098517--12098566	19	2.6	19	77	3	55	62	0	0	38	0.96
12098620--12098694	11	6.7	11	74	18	66	44	2	28	25	1.68
12098620--12098694	22	3.3	23	83	9	93	44	2	28	25	1.68
12107250--12107278	14	2.0	15	93	6	51	48	20	3	27	1.66
12107469--12107602	40	3.4	39	80	7	155	32	26	17	23	1.96
12114330--12114405	5	15.2	5	100	0	152	59	0	0	40	0.98
12114991--12115023	17	1.9	17	88	11	50	36	0	0	63	0.95
12117604--12117647	20	2.2	20	84	4	54	70	2	2	25	1.10
12117622--12117655	16	2.2	15	89	5	50	70	0	0	29	0.87
12117620--12117657	15	2.5	15	84	12	51	65	0	0	34	0.93
12117616--12117680	27	2.3	27	84	5	85	66	0	0	33	0.92
12118308--12118436	27	4.7	27	83	4	152	37	10	22	29	1.88
12127241--12127270	2	15.0	2	100	0	60	50	0	0	50	1.00
12129386--12129580	105	1.9	105	81	2	239	33	15	23	27	1.95
12131717--12131819	48	2.1	48	94	0	179	34	16	12	35	1.87
12133027--12133070	2	22.0	2	90	0	70	45	0	50	4	1.22
12137940--12137989	12	4.1	12	79	10	57	34	0	2	64	1.05
12140581--12140676	50	1.9	50	95	0	174	34	13	9	42	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12149319--12149394	37	2.1	37	82	9	93	44	2	2	50	1.30
12149312--12149543	124	1.9	123	82	10	294	42	3	5	49	1.40
12149400--12149543	62	2.3	62	93	0	252	40	2	5	50	1.40
12150766--12150796	14	2.2	14	100	0	62	32	6	19	41	1.77
12152924--12152954	15	2.1	15	93	0	53	25	32	3	38	1.72
12156872--12156902	15	2.1	15	93	0	53	25	32	3	38	1.72
12157059--12157153	47	2.1	45	96	4	172	56	6	9	27	1.55
12168771--12168809	20	2.0	20	94	0	69	33	7	33	25	1.84
12173912--12174111	105	1.9	105	84	2	267	33	17	23	26	1.96
12176166--12176248	41	2.0	43	88	4	125	32	13	27	26	1.93
12189368--12189444	33	2.3	32	82	6	91	32	18	23	25	1.97
12189263--12189492	105	2.3	99	82	6	255	32	17	24	25	1.97
12198263--12198527	72	3.7	71	75	6	228	39	15	19	26	1.91
12198257--12198465	48	4.3	48	77	4	179	39	15	19	25	1.91
12198433--12198570	47	3.0	46	77	13	131	39	15	18	26	1.91
12198257--12198559	24	12.7	23	70	12	148	38	15	19	26	1.92
12199878--12200047	43	4.0	44	78	4	150	29	15	22	31	1.95
12201895--12202198	59	5.2	59	75	7	226	37	9	21	31	1.86
12203655--12203716	31	2.0	31	100	0	124	22	22	35	19	1.96
12205270--12205327	30	1.9	30	85	0	80	17	43	27	12	1.84
12208295--12208349	5	11.0	5	81	14	69	23	0	0	76	0.79
12208296--12208347	9	5.3	9	80	15	59	23	0	0	76	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12208296--12208406	42	2.6	40	78	14	98	25	2	0	71	1.05
12209387--12209422	13	2.8	13	91	0	54	75	2	2	19	1.06
12216339--12216375	16	2.3	16	86	13	58	40	0	0	59	0.97
12216383--12216443	20	3.0	20	79	9	59	49	1	0	49	1.10
12219267--12219302	19	1.9	19	88	5	56	27	11	2	58	1.46
12220690--12221060	130	2.8	131	81	8	369	24	9	9	55	1.63
12220819--12221077	141	1.8	141	82	7	321	25	10	10	54	1.66
12221853--12221878	13	2.0	13	100	0	52	23	15	15	46	1.83
12223900--12223927	3	9.3	3	100	0	56	32	0	0	67	0.91
12224796--12224857	27	2.3	27	81	10	81	32	25	20	20	1.98

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