genome.fa.s3.2.7.7.80.10.50.1000.96.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  96  of  150  ( 17918 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)
30176466--30176775	44	7.0	44	67	12	197	29	18	24	27	1.98
30176466--30176845	132	2.9	132	95	0	670	28	19	23	27	1.98
30178977--30179015	21	1.9	21	84	5	53	28	5	10	56	1.54
30183509--30183578	34	2.1	34	97	0	131	38	27	8	25	1.85
30195017--30195058	22	1.9	22	95	0	75	9	21	28	40	1.84
30195122--30195263	43	3.3	43	90	7	234	30	33	16	18	1.93
30199259--30199585	41	8.0	41	84	3	378	30	30	17	21	1.96
30199259--30199579	81	3.9	81	83	5	382	30	29	18	21	1.97
30199262--30199579	122	2.6	123	85	5	414	30	29	17	22	1.97
30207300--30207344	24	1.9	24	90	4	74	35	0	2	62	1.08
30207441--30207468	9	3.1	9	100	0	56	57	10	0	32	1.33
30207411--30207552	68	2.1	66	94	2	248	45	9	4	40	1.58
30207541--30207582	16	2.6	16	92	0	66	42	7	2	47	1.43
30207556--30207611	23	2.5	23	82	2	69	44	1	1	51	1.22
30207411--30207574	68	2.5	66	86	10	216	45	9	4	40	1.55
30207878--30207974	13	7.4	13	75	2	77	42	3	17	37	1.65
30207865--30207924	26	2.3	26	85	2	75	45	1	18	35	1.60
30207878--30207989	53	2.1	53	81	3	127	42	2	17	36	1.64
30214357--30214437	42	1.9	42	82	9	103	50	1	12	35	1.48
30214493--30214548	22	2.6	22	88	2	78	57	0	10	32	1.33
30214471--30214501	2	15.5	2	93	0	53	48	0	3	48	1.17
30214514--30214554	22	2.0	20	90	9	64	60	0	7	31	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30214651--30214675	2	12.5	2	100	0	50	52	0	0	48	1.00
30219702--30220061	104	3.5	103	94	1	605	31	29	20	19	1.97
30231280--30231480	40	5.0	40	92	0	285	44	26	14	13	1.83
30233166--30233211	16	2.9	16	78	18	51	69	2	2	26	1.11
30233166--30233212	17	2.8	17	81	12	53	70	2	2	25	1.10
30233183--30233225	23	1.9	23	90	4	70	74	2	0	23	0.93
30236701--30236734	17	1.9	18	88	5	52	61	0	14	23	1.33
30240857--30240931	27	2.8	27	83	0	96	21	24	18	36	1.95
30240950--30241288	161	2.1	160	83	1	426	25	23	16	34	1.95
30243613--30243649	15	2.4	16	90	4	58	62	0	0	37	0.96
30245564--30245603	19	2.1	19	86	9	55	67	20	12	0	1.22
30257435--30257514	38	2.1	38	95	0	142	36	6	18	38	1.76
30257493--30257995	31	16.3	31	72	10	325	34	6	15	43	1.73
30257473--30257995	92	5.7	92	91	0	841	34	7	15	42	1.75
30257493--30257969	61	7.8	62	72	9	352	34	7	15	42	1.74
30258165--30258278	41	2.7	42	78	8	117	30	15	21	32	1.94
30263682--30263739	29	2.0	29	96	0	107	31	25	3	39	1.73
30267161--30267233	32	2.5	27	78	19	92	26	2	19	52	1.59
30267174--30267234	32	1.9	32	96	0	113	27	3	18	50	1.62
30269417--30269548	41	3.2	40	80	10	135	24	20	27	28	1.99
30279941--30279979	20	2.0	20	94	0	69	48	0	2	48	1.15
30280100--30280137	14	2.7	15	92	8	62	42	18	2	36	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30288904--30289018	50	2.2	52	76	4	126	38	13	13	35	1.83
30294568--30294646	39	2.0	39	87	0	113	36	10	27	25	1.88
30296190--30296281	45	2.0	45	95	0	166	26	17	23	32	1.97
30316817--30316856	20	2.0	20	85	0	53	25	15	0	60	1.35
30324305--30324346	18	2.3	18	95	0	75	45	19	0	35	1.50
30327513--30327547	16	2.2	16	89	0	52	17	5	0	77	0.96
30327513--30327559	23	2.0	23	87	4	67	21	4	0	74	0.99
30334043--30334692	44	14.8	44	62	8	158	27	27	24	21	1.99
30334028--30334703	263	2.6	263	89	0	1019	27	27	23	20	1.99
30334030--30334703	88	7.7	88	89	0	990	27	27	23	20	1.99
30334705--30334910	44	4.7	44	71	10	145	26	20	25	28	1.99
30334641--30334958	131	2.4	131	80	4	372	27	23	23	25	2.00
30335109--30335297	100	1.9	99	82	3	236	28	21	23	25	1.99
30335308--30335406	44	2.2	44	82	3	119	33	21	18	27	1.96
30337242--30337276	16	2.2	16	89	0	52	17	5	0	77	0.96
30337242--30337288	23	2.0	24	87	4	69	21	4	0	74	0.99
30337355--30337401	17	2.5	19	76	20	53	31	0	6	61	1.21
30346850--30346892	17	2.5	17	100	0	86	16	20	32	30	1.95
30347263--30347303	20	2.0	20	90	0	64	41	17	4	36	1.71
30351151--30351194	22	2.0	22	81	0	52	56	2	0	40	1.11
30351807--30351878	34	2.1	34	87	5	101	13	16	9	59	1.60
30351859--30351897	6	6.5	6	100	0	78	0	15	0	84	0.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30354797--30354826	15	1.9	16	93	6	53	56	0	0	43	0.99
30357972--30358002	15	2.1	15	100	0	62	25	25	6	41	1.79
30359591--30359633	21	2.0	21	100	0	86	44	13	13	27	1.83
30361198--30361227	2	15.0	2	100	0	60	50	0	0	50	1.00
30361270--30361295	7	3.7	7	100	0	52	42	0	0	57	0.98
30363873--30364150	144	1.9	144	94	1	486	30	16	27	25	1.97
30373822--30374197	45	9.0	45	70	16	218	29	19	25	26	1.98
30373877--30374030	81	1.9	81	93	0	263	27	20	25	25	1.99
30382990--30383041	24	2.2	24	85	0	68	38	3	7	50	1.50
30389682--30389717	14	2.6	14	86	0	54	25	38	2	33	1.70
30390032--30390087	17	3.7	17	67	30	54	33	12	10	42	1.77
30390027--30390085	27	2.2	27	87	0	82	37	11	8	42	1.72
30390037--30390090	27	2.0	27	100	0	108	29	11	11	48	1.73
30392728--30392760	17	2.0	17	88	5	50	39	21	0	39	1.53
30398408--30398454	25	2.0	24	83	8	60	46	29	0	23	1.52
30399597--30399653	29	2.0	29	89	0	87	21	40	15	22	1.91
30401787--30401840	16	3.3	16	76	2	54	42	16	3	37	1.66
30402375--30402439	29	2.3	28	94	5	121	21	16	23	38	1.93
30406662--30406686	10	2.5	10	100	0	50	16	8	8	68	1.38
30407508--30407544	11	3.3	11	96	3	65	56	0	2	40	1.13
30407521--30407627	8	12.3	9	73	19	61	57	0	1	40	1.09
30410315--30410347	14	2.3	15	89	5	50	24	0	0	75	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30417115--30417181	27	2.5	26	81	11	82	62	0	1	35	1.04
30418361--30418496	41	3.4	41	77	9	156	32	24	17	25	1.97
30418618--30418677	17	3.6	16	73	22	52	51	11	0	36	1.38
30423001--30423054	28	1.9	28	81	7	65	33	14	12	38	1.85
30423209--30423342	64	2.1	64	94	0	232	36	9	13	40	1.77
30423967--30424020	16	3.4	16	89	0	81	33	1	35	29	1.69
30423999--30424108	45	2.6	43	80	9	129	33	5	29	31	1.80
30424234--30424275	15	2.7	16	82	14	52	52	2	0	45	1.13
30424243--30424284	15	2.9	15	82	10	52	52	0	0	47	1.00
30424271--30424413	22	6.9	21	67	23	70	51	3	2	43	1.30
30424328--30424368	13	3.2	12	80	12	55	58	0	0	41	0.98
30424232--30424500	103	2.6	103	86	7	400	52	3	1	42	1.28
30424458--30424495	18	2.3	17	86	13	53	57	0	2	39	1.12
30426059--30426088	13	2.3	13	94	0	51	30	13	6	50	1.67
30452172--30452206	2	17.5	2	100	0	70	51	0	0	48	1.00
30452402--30452562	41	3.9	41	94	0	259	30	22	19	26	1.98
30460031--30460084	19	2.8	19	94	0	99	37	9	16	37	1.81
30460020--30460091	38	2.0	36	84	10	94	37	9	16	36	1.82
30460031--30460107	38	1.9	40	87	10	113	36	7	16	38	1.78
30460289--30460333	23	2.0	23	81	0	54	22	0	15	62	1.33
30460543--30460587	3	14.7	3	81	4	54	28	0	2	68	1.01
30475217--30475251	18	1.9	19	88	11	56	65	8	0	25	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30476834--30476881	25	2.0	25	83	4	62	18	25	18	37	1.94
30479066--30479095	16	1.9	16	93	6	53	50	20	0	30	1.49
30486305--30486417	59	1.9	59	92	0	190	45	9	20	24	1.81
30495422--30495457	18	2.0	18	100	0	72	38	27	16	16	1.90
30499627--30499661	15	2.4	15	90	4	54	34	8	0	57	1.29
30500386--30501117	105	6.9	105	84	5	940	30	17	19	32	1.95
30500396--30501117	212	3.4	212	96	0	1284	30	18	19	31	1.96
30507459--30507493	18	1.9	18	88	0	52	2	28	0	68	1.04
30511168--30511206	17	2.4	16	84	16	53	41	2	7	48	1.45
30516994--30517041	19	2.5	20	80	10	55	31	14	16	37	1.89

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