genome.fa.s4.2.7.7.80.10.50.1000.102.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  102  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)
32712563--32712598	13	2.8	13	82	0	54	50	0	5	44	1.25
32713224--32713309	25	3.4	25	75	4	84	27	24	19	27	1.99
32716006--32716124	54	2.2	54	81	0	139	29	17	15	37	1.90
32715968--32716375	28	14.7	28	67	10	156	28	19	18	33	1.95
32716077--32716260	56	3.3	55	77	6	172	28	19	20	32	1.96
32715965--32716368	84	4.8	84	71	10	247	28	19	18	33	1.95
32716291--32716377	30	3.0	28	75	12	79	28	14	17	39	1.89
32725186--32725269	42	2.0	42	83	4	107	51	5	5	36	1.51
32725385--32725460	6	12.7	6	100	0	152	17	0	0	82	0.66
32729684--32729708	13	1.9	13	100	0	50	44	8	0	48	1.32
32732087--32732293	26	7.5	26	69	12	110	24	17	21	36	1.95
32732087--32732293	29	7.5	29	71	12	141	24	17	21	36	1.95
32732218--32732306	29	3.2	28	69	12	69	29	16	20	33	1.95
32736148--32736210	25	2.5	26	87	7	87	17	23	19	39	1.92
32739636--32739678	14	2.7	15	83	16	52	41	2	0	55	1.12
32745085--32745137	25	2.1	25	100	0	106	30	0	11	58	1.33
32746411--32746528	50	2.3	50	85	5	148	33	16	13	37	1.87
32748690--32748716	12	2.2	12	100	0	54	29	7	22	40	1.81
32749084--32749122	19	2.1	18	85	4	51	33	12	0	53	1.39
32750602--32750644	21	2.0	21	90	0	68	46	4	2	46	1.36
32755214--32755249	18	2.0	18	88	0	54	52	0	8	38	1.32
32755752--32755789	2	19.0	2	100	0	76	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32756146--32756247	49	2.2	47	80	7	118	30	17	7	44	1.77
32757775--32757949	42	4.2	42	83	2	174	42	17	22	17	1.88
32757778--32757900	21	5.9	21	64	3	68	43	19	21	15	1.88
32757775--32757946	84	2.0	84	80	2	193	42	17	22	17	1.89
32763093--32763121	15	1.9	15	100	0	58	68	0	3	27	1.05
32763134--32763180	23	2.1	23	85	14	64	57	0	8	34	1.29
32763109--32763173	14	4.6	14	74	16	55	60	3	6	30	1.37
32770405--32770580	93	1.9	93	80	6	205	29	18	23	28	1.98
32770502--32770605	44	2.4	44	81	0	118	30	22	20	26	1.98
32770495--32770647	44	3.5	44	75	5	112	31	20	20	27	1.98
32771047--32771085	20	1.9	19	85	10	51	46	25	5	23	1.73
32773957--32773981	13	1.9	13	100	0	50	64	0	4	32	1.12
32784158--32784205	25	1.9	25	83	8	62	58	0	10	31	1.32
32787997--32788047	26	2.0	26	100	0	102	21	11	15	50	1.76
32789269--32789339	28	2.5	29	90	2	108	36	12	0	50	1.41
32789402--32789485	27	3.1	27	98	1	161	23	30	27	17	1.97
32789618--32789794	37	4.8	37	99	0	345	38	11	0	49	1.40
32789849--32789895	18	2.6	18	86	6	60	46	0	10	42	1.38
32789835--32789895	19	3.3	19	79	4	70	47	0	8	44	1.33
32790395--32790478	27	3.1	27	87	1	125	16	29	28	25	1.97
32790537--32790634	29	3.5	26	82	12	115	52	0	11	36	1.38
32790537--32790634	28	3.5	28	87	6	137	52	0	11	36	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32793964--32793990	10	2.7	10	100	0	54	81	0	7	11	0.87
32794051--32794115	32	2.0	32	93	0	112	40	18	21	20	1.92
32794258--32794302	19	2.3	20	88	7	67	53	11	8	26	1.65
32804121--32804193	37	2.0	37	86	2	103	31	21	0	46	1.52
32804527--32804570	23	1.9	24	90	9	74	22	22	0	54	1.45
32805469--32805494	13	2.0	13	100	0	52	30	0	30	38	1.58
32807242--32807320	41	1.9	41	89	5	124	24	17	26	31	1.97
32808348--32808379	2	16.5	2	93	6	57	50	0	0	50	1.00
32809805--32809989	51	3.6	51	82	0	208	24	24	8	42	1.83
32811752--32812061	158	2.0	158	88	0	467	30	23	15	30	1.95
32821097--32821172	29	2.5	30	83	10	93	31	5	11	51	1.61
32821094--32821172	31	2.6	31	82	9	101	31	5	11	51	1.59
32828344--32828376	16	2.1	16	94	0	57	27	3	24	45	1.68
32833797--32833829	17	1.9	17	100	0	66	72	3	0	24	0.98
32833787--32833829	19	2.2	20	84	12	54	74	4	0	20	1.00
32836526--32836551	3	8.7	3	100	0	52	65	0	0	34	0.93
32836758--32836802	19	2.6	18	82	10	58	60	0	0	40	0.97
32836973--32837104	49	2.6	49	79	9	131	59	9	3	28	1.45
32836993--32837104	49	2.2	50	82	7	138	58	8	2	30	1.43
32836993--32837135	49	2.8	49	76	14	130	58	7	2	30	1.40
32837948--32837993	25	1.9	23	82	8	56	43	6	2	47	1.41
32846343--32846435	47	2.0	47	91	0	150	36	10	2	50	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32846970--32847029	30	2.0	29	93	3	102	58	11	3	26	1.49
32855727--32855765	2	19.5	2	100	0	78	48	0	0	51	1.00
32862316--32862453	44	3.1	44	85	7	190	26	14	26	32	1.95
32862543--32862684	51	2.8	51	71	0	122	27	21	25	26	1.99
32862406--32862951	264	2.1	264	95	0	984	28	18	25	27	1.98
32862737--32863074	169	2.0	168	92	1	561	29	19	25	25	1.98
32862807--32862948	51	2.8	51	73	0	131	28	20	25	26	1.99
32865069--32865120	26	2.0	26	88	7	79	25	5	3	65	1.32
32871403--32871700	50	5.8	50	85	2	335	27	20	29	22	1.99
32871403--32871736	150	2.2	151	81	5	370	28	20	28	22	1.99
32875143--32875193	25	2.0	25	84	3	66	45	9	13	31	1.76
32882903--32882931	12	2.3	13	94	5	51	65	6	6	20	1.40
32889995--32890125	39	3.4	39	86	4	183	44	20	3	31	1.69
32913576--32913617	13	3.2	13	82	0	57	33	21	4	40	1.74
32913517--32913617	51	1.9	54	82	9	129	32	17	4	44	1.71
32914682--32914841	43	3.7	43	93	0	259	23	30	15	31	1.95
32914964--32915056	30	3.1	30	77	1	114	50	15	6	27	1.68
32916174--32916416	45	5.4	45	80	6	215	22	16	13	48	1.80
32933599--32933630	15	2.1	15	100	0	64	21	12	18	46	1.82
32936363--32936404	23	1.9	22	85	9	59	9	28	2	59	1.41
32950856--32950890	17	2.1	17	88	0	52	40	2	2	54	1.30
32953821--32953868	23	2.1	23	84	7	62	45	0	6	47	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32957647--32957812	42	4.0	42	90	4	248	25	16	27	30	1.96
32974903--32974985	33	2.5	32	84	5	103	13	25	20	40	1.88
32974924--32974998	33	2.3	33	86	4	98	20	28	13	38	1.90
32975074--32975103	7	4.3	7	91	0	51	26	26	3	43	1.70
32983282--32983333	22	2.4	22	80	0	59	48	19	15	17	1.82
32983325--32983460	32	4.3	32	86	4	177	38	19	19	22	1.94
32983459--32983519	26	2.3	26	88	0	86	36	24	21	18	1.95
32983635--32983768	24	5.6	24	82	3	135	44	19	6	29	1.76
32983635--32983768	48	2.8	48	81	0	151	44	19	6	29	1.76
32983789--32984264	81	5.9	80	83	3	537	25	22	18	33	1.96
32983789--32984264	27	17.6	27	81	4	487	25	22	18	33	1.96
32984189--32984280	27	3.4	27	82	5	114	20	19	19	40	1.92
32985480--32985521	20	2.1	20	100	0	84	33	19	9	38	1.84
32989031--32989311	43	6.6	43	76	11	269	23	16	25	34	1.95
32989034--32989311	85	3.3	85	94	0	468	23	16	25	34	1.95
32991324--32991377	27	2.0	28	85	3	74	44	3	9	42	1.54
32993559--32993598	2	20.0	2	94	0	71	47	0	2	50	1.14
32995349--32995409	24	2.5	26	81	10	74	37	8	11	42	1.71
32997641--32997684	20	2.2	20	91	0	70	20	13	25	40	1.89
33000128--33000278	74	2.0	74	100	0	302	34	15	13	36	1.87
33008995--33009034	20	2.0	20	100	0	80	25	5	15	55	1.60
33009144--33009202	26	2.3	26	82	5	66	18	15	33	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33009222--33009354	26	5.1	26	80	3	124	23	13	27	36	1.92
33009252--33009353	52	2.0	52	86	0	141	24	14	24	36	1.93
33019645--33019686	21	2.0	21	85	0	57	11	21	45	21	1.84
33034517--33034556	6	6.7	6	100	0	80	15	0	0	85	0.61
33042022--33043100	360	3.0	360	97	0	2025	33	18	14	33	1.91
33049168--33049275	20	5.3	20	60	8	56	20	31	13	34	1.92
33049149--33049355	41	5.1	41	88	1	290	20	30	15	33	1.93
33050515--33050548	12	2.9	12	86	4	52	32	0	0	67	0.91
33054958--33054982	12	2.1	12	100	0	50	68	24	0	8	1.16
33063071--33063172	52	2.0	51	84	7	136	40	8	12	38	1.75

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