genome.fa.s1.2.7.7.80.10.50.1000.138.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  138  of  187  ( 22383 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)
41388536--41388701	66	2.5	66	86	1	208	15	30	16	37	1.90
41390505--41390780	9	32.4	9	74	13	237	32	0	21	45	1.55
41390505--41390770	25	10.5	25	77	10	215	32	0	21	45	1.55
41390575--41390748	69	2.6	69	93	2	300	32	0	21	45	1.52
41390505--41390765	69	4.1	64	83	9	229	32	0	21	45	1.55
41390520--41390748	69	3.4	69	86	5	288	32	0	21	45	1.56
41392672--41392787	23	5.0	22	69	12	72	36	2	36	25	1.70
41393218--41393270	21	2.5	21	78	6	63	52	24	0	22	1.47
41393507--41393551	22	2.0	22	87	8	65	33	42	6	17	1.76
41393585--41393629	13	3.4	13	84	6	63	51	33	2	13	1.53
41393716--41393761	23	2.0	24	83	8	60	39	26	8	26	1.85
41393879--41393935	21	2.8	19	75	15	51	52	24	1	21	1.56
41394175--41394808	156	4.0	156	85	4	829	24	21	22	31	1.98
41394487--41394821	166	2.0	166	91	0	546	25	21	21	31	1.98
41394105--41394801	321	2.2	312	83	6	867	25	21	22	30	1.99
41397431--41397467	9	4.1	9	92	0	65	48	8	10	32	1.67
41404444--41404485	21	2.0	22	85	4	59	57	4	0	38	1.20
41407820--41407854	3	11.7	3	100	0	70	31	0	0	68	0.90
41409113--41409178	21	2.9	23	75	11	82	65	4	1	28	1.21
41409113--41409181	22	3.1	21	69	22	61	62	4	1	31	1.24
41409115--41409184	23	3.1	23	71	22	67	61	5	1	31	1.28
41411809--41411907	51	1.9	51	83	4	128	37	13	6	43	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41411980--41412027	25	2.0	24	83	4	60	54	0	6	39	1.26
41414263--41414292	2	15.0	2	100	0	60	50	0	0	50	1.00
41414814--41414974	39	4.0	39	79	13	141	21	19	20	37	1.94
41414841--41414989	45	3.4	45	78	12	177	21	19	19	39	1.92
41419136--41419283	43	3.5	43	79	8	144	35	24	16	22	1.95
41419138--41419283	42	3.5	42	79	6	152	36	24	16	22	1.94
41419262--41419313	26	2.0	26	96	0	95	28	34	19	17	1.94
41419286--41419436	41	3.7	41	91	3	232	25	24	20	29	1.99
41419222--41419353	67	2.0	68	86	4	187	30	28	17	24	1.97
41423554--41423643	37	2.4	38	84	1	110	17	14	41	26	1.88
41437026--41437108	26	3.2	26	76	8	73	65	8	6	20	1.42
41437236--41437272	2	18.5	2	100	0	74	51	0	0	48	1.00
41439283--41439328	22	2.0	22	84	12	58	36	10	0	52	1.37
41439927--41439971	22	2.1	21	84	12	56	55	4	0	40	1.20
41440395--41440428	18	1.9	17	94	5	59	20	55	11	11	1.67
41440559--41440601	20	2.0	20	82	8	50	65	13	2	18	1.38
41441180--41441224	3	15.0	3	100	0	90	33	0	0	66	0.92
41441322--41441361	18	2.2	18	90	0	62	37	0	7	55	1.29
41443145--41443217	8	8.2	8	81	16	83	49	1	1	47	1.18
41444574--41444636	18	3.4	17	76	12	54	33	15	7	42	1.76
41452127--41452181	16	3.4	16	74	0	65	20	21	5	52	1.66
41452076--41452209	41	3.5	40	77	20	162	21	23	6	47	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41452127--41452198	32	2.2	32	90	4	119	22	22	6	48	1.74
41455818--41455853	18	2.0	18	100	0	72	33	16	22	27	1.95
41457143--41457179	16	2.3	16	86	13	58	40	0	0	59	0.97
41460070--41460139	24	3.0	24	91	2	115	44	18	7	30	1.76
41465790--41465841	17	3.1	17	82	0	68	38	21	7	32	1.82
41472175--41472261	44	2.0	44	86	0	120	29	14	20	34	1.93
41472240--41472417	88	2.0	88	82	3	214	32	20	15	30	1.94
41472296--41472643	44	7.8	44	70	11	190	32	21	15	31	1.94
41472206--41472600	44	8.9	45	69	11	136	32	20	15	31	1.94
41472302--41472738	223	1.9	224	84	6	580	31	20	16	32	1.94
41472577--41472739	92	1.8	87	81	6	200	30	15	18	35	1.92
41477120--41477194	37	2.0	37	89	5	116	50	0	17	32	1.46
41480849--41480885	19	2.0	18	89	5	56	35	8	24	32	1.85
41484469--41484527	3	19.7	3	76	13	59	62	5	3	28	1.32
41484455--41484527	36	2.0	36	84	5	94	60	5	6	27	1.45
41484547--41484590	23	2.0	22	81	4	52	65	13	2	18	1.36
41485803--41485837	17	2.1	17	88	0	52	20	5	14	60	1.54
41488232--41488288	29	2.0	29	89	0	87	24	28	26	21	1.99
41493014--41493066	22	2.5	21	84	9	63	71	5	0	22	1.06
41495453--41495535	32	2.6	31	87	7	114	55	1	2	40	1.21
41499616--41499645	14	2.1	14	93	0	51	23	16	6	53	1.66
41500403--41500435	5	6.6	5	96	0	57	18	3	0	78	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41501088--41501117	15	1.9	16	93	6	53	60	33	0	6	1.23
41502528--41502553	2	13.0	2	100	0	52	50	0	0	50	1.00
41502640--41502678	18	2.2	18	90	0	60	43	5	2	48	1.38
41508780--41508812	15	2.1	17	88	11	52	78	0	21	0	0.75
41508953--41509118	45	3.8	44	67	4	118	27	17	26	28	1.98
41509030--41510193	132	8.8	132	92	0	1749	28	20	25	25	1.99
41509036--41509637	44	13.7	44	65	14	204	27	19	25	27	1.99
41509301--41510166	44	19.7	44	65	14	266	28	20	25	25	1.99
41510462--41510491	15	1.9	16	93	6	53	60	33	0	6	1.23
41511982--41512020	18	2.2	18	85	0	51	43	7	2	46	1.46
41521683--41521720	12	3.2	12	85	7	51	78	0	2	18	0.86
41526989--41527049	25	2.4	25	86	0	77	37	16	22	22	1.93
41528069--41528151	10	8.2	10	77	17	64	46	1	1	50	1.16
41528105--41528150	5	9.2	5	100	0	92	41	0	0	58	0.98
41528952--41528986	2	17.5	2	100	0	70	0	0	48	51	1.00
41529128--41529288	22	7.0	22	76	10	144	18	24	18	38	1.93
41529119--41529291	47	3.7	47	91	2	271	17	24	19	38	1.92
41533743--41533790	18	2.8	18	87	6	64	41	6	0	52	1.27
41533757--41533797	18	2.3	18	86	0	55	39	9	0	51	1.35
41536753--41536808	27	2.1	27	96	0	103	8	55	19	16	1.67
41537295--41537319	13	1.9	13	100	0	50	0	12	0	88	0.53
41540537--41540561	12	2.1	12	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41541679--41541907	115	2.0	114	99	0	449	40	17	12	29	1.86
41544335--41544360	7	3.7	7	100	0	52	76	0	0	23	0.78
41548461--41548497	5	7.2	5	90	3	56	75	0	2	21	0.92
41551518--41551547	12	2.5	12	94	0	51	86	3	10	0	0.67
41572190--41572227	5	7.4	5	96	3	67	78	0	0	21	0.74
41572983--41573027	18	2.6	17	82	6	63	51	2	2	44	1.26
41578389--41578431	17	2.5	18	74	11	54	18	11	0	69	1.17
41592157--41592214	3	19.7	3	81	13	68	65	1	0	32	1.03
41593673--41594011	128	2.7	127	89	1	500	24	21	21	32	1.98
41593683--41593986	44	7.1	42	67	16	135	24	22	21	32	1.98
41594127--41594713	87	6.7	87	90	0	913	25	23	22	29	1.99
41594390--41594529	42	3.2	44	67	17	137	25	25	23	25	2.00
41596821--41596853	11	3.0	11	87	12	50	0	18	0	81	0.68
41596823--41596865	17	2.4	17	92	7	68	2	16	0	81	0.79
41599501--41599552	19	2.7	20	82	5	63	46	11	17	25	1.81
41601728--41601760	16	2.1	16	100	0	66	39	6	18	36	1.75
41601780--41601834	3	18.7	3	76	14	53	63	3	0	32	1.12
41606764--41606792	14	2.1	14	100	0	58	37	20	34	6	1.80
41608420--41608485	33	2.0	33	96	0	123	30	1	24	43	1.63
41608427--41608484	18	3.4	18	66	22	52	31	1	22	44	1.63
41608714--41608761	20	2.3	20	82	10	53	50	6	0	43	1.27
41611645--41611988	72	4.8	72	88	2	464	53	15	6	24	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41614683--41614736	22	2.5	22	81	0	63	50	5	24	20	1.69
41617850--41617910	24	2.5	24	81	0	77	45	11	14	27	1.80
41617902--41617998	23	4.2	22	85	7	106	50	28	10	10	1.69
41617902--41618006	46	2.3	46	83	8	133	50	29	9	10	1.68
41619250--41619311	28	2.2	28	91	5	99	38	17	9	33	1.83
41619258--41619317	28	2.2	28	96	3	113	35	16	11	36	1.85
41619652--41619681	2	15.0	2	92	0	51	53	0	46	0	1.00
41620378--41620485	40	2.7	40	75	5	101	44	2	1	50	1.27
41621669--41621712	20	2.2	20	88	4	63	4	22	9	63	1.42
41621759--41621788	5	6.0	5	100	0	60	0	20	0	80	0.72

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