genome.fa.s1.2.7.7.80.10.50.1000.174.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  174  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)
52062471--52062550	38	2.1	38	100	0	160	27	5	33	33	1.79
52066978--52067128	30	5.1	30	75	0	151	29	25	11	33	1.91
52066984--52067127	60	2.4	60	84	0	198	27	25	11	34	1.91
52073978--52074020	22	2.0	22	85	0	59	0	20	16	62	1.32
52074591--52074746	50	3.1	50	66	15	133	22	21	26	30	1.99
52074526--52075603	100	10.8	100	86	2	1074	23	20	24	31	1.98
52074610--52075584	50	19.5	50	67	6	434	23	21	23	31	1.98
52075626--52075996	44	8.5	44	70	11	201	29	19	17	32	1.95
52075597--52075996	219	1.8	219	91	1	658	29	19	17	33	1.95
52077355--52077387	14	2.4	14	90	5	50	15	15	0	69	1.19
52077363--52077396	7	4.7	7	96	3	59	11	14	0	73	1.10
52078251--52078309	31	1.9	31	86	3	84	16	10	6	66	1.43
52086437--52086465	8	3.6	8	100	0	58	24	0	0	75	0.80
52089727--52089798	28	2.6	28	95	2	128	51	0	6	41	1.29
52090166--52090198	6	5.7	6	92	7	59	84	0	0	15	0.61
52090166--52090198	11	2.8	12	90	9	59	84	0	0	15	0.61
52090166--52090198	17	1.9	17	100	0	66	84	0	0	15	0.61
52098310--52098511	33	5.6	32	68	22	125	22	18	25	33	1.97
52098342--52098554	33	5.5	41	70	21	181	23	17	25	33	1.96
52098306--52098591	75	3.8	75	91	0	457	23	18	26	32	1.97
52098306--52098579	151	1.8	149	92	1	458	22	17	26	32	1.97
52100129--52100153	11	2.3	11	100	0	50	8	36	0	56	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52105416--52105490	29	2.5	30	78	8	80	62	1	2	33	1.17
52105412--52105559	10	14.9	10	66	18	60	62	1	4	32	1.22
52105445--52105577	50	2.7	49	79	11	130	64	0	5	29	1.20
52105456--52105539	22	4.0	22	77	14	88	66	1	3	28	1.15
52105434--52105595	10	16.7	9	68	14	65	65	2	4	27	1.24
52105791--52105846	21	2.7	21	86	2	69	39	0	1	58	1.08
52105963--52106244	90	3.1	89	81	6	320	33	10	18	36	1.86
52106780--52106823	18	2.4	18	85	7	54	47	0	2	50	1.13
52108008--52108065	28	2.1	28	100	0	116	55	8	10	25	1.62
52108766--52108845	40	2.0	40	83	9	101	53	3	6	36	1.44
52108904--52109045	76	1.9	76	86	2	205	40	0	30	28	1.61
52108904--52109078	76	2.3	78	81	11	195	40	0	31	27	1.61
52111641--52111668	9	3.1	9	100	0	56	21	35	10	32	1.88
52118936--52119093	48	3.3	48	88	1	219	36	6	19	37	1.77
52152279--52152351	38	1.9	37	86	8	103	31	21	1	45	1.61
52152339--52152382	23	1.9	22	82	17	54	38	22	0	38	1.55
52152481--52152602	23	5.3	23	89	0	199	31	24	20	22	1.98
52160829--52160859	15	2.1	15	93	0	53	38	19	19	22	1.93
52164456--52164545	44	2.0	44	100	0	180	33	15	13	37	1.86
52172722--52172946	50	4.4	50	84	5	245	20	29	23	26	1.99
52173285--52173354	30	2.4	29	74	11	72	32	21	12	32	1.91
52177948--52177973	2	13.0	2	100	0	52	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)
52179412--52179450	15	2.7	14	80	7	51	20	0	38	41	1.53
52179385--52179451	14	4.9	14	77	14	59	26	0	31	41	1.56
52180762--52180836	2	40.5	2	69	15	54	45	0	8	46	1.32
52180762--52180836	23	3.4	22	92	7	118	45	0	8	46	1.32
52180763--52180827	23	2.8	23	100	0	130	43	0	9	47	1.35
52181837--52181863	11	2.5	11	100	0	54	25	18	0	55	1.43
52184756--52184858	9	12.0	9	66	20	60	40	19	3	35	1.70
52197946--52198098	22	7.0	22	90	0	225	26	26	14	32	1.94
52198273--52198323	13	3.8	13	75	14	50	35	1	5	56	1.35
52199339--52199385	4	11.8	4	100	0	94	25	0	23	51	1.49
52201173--52201236	23	2.7	22	76	7	56	64	4	1	29	1.23
52201380--52201424	20	2.2	21	84	11	58	55	0	8	35	1.31
52202234--52202265	3	10.7	3	100	0	64	68	0	31	0	0.90
52203066--52203119	24	2.2	24	86	0	72	35	3	5	55	1.41
52207641--52207694	18	2.8	19	86	5	74	40	1	9	48	1.46
52211956--52212068	47	2.4	47	84	0	154	10	17	26	45	1.81
52211956--52212036	25	3.4	23	69	17	67	9	17	25	46	1.78
52212029--52212085	22	2.6	22	88	0	87	14	19	26	40	1.89
52214755--52214787	16	2.1	16	100	0	66	24	24	6	45	1.75
52219244--52219287	2	22.0	2	85	0	61	45	4	2	47	1.35
52239197--52239238	22	1.9	22	85	0	57	35	7	4	52	1.50
52242291--52242340	25	2.0	25	92	0	82	38	14	8	40	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52263487--52263703	73	3.0	73	94	0	371	38	17	16	28	1.91
52267307--52267344	6	6.2	6	93	6	67	18	0	0	81	0.69
52267307--52267343	13	2.9	13	96	4	67	16	0	0	83	0.64
52267308--52267344	19	1.9	19	100	0	74	16	0	0	83	0.64
52267351--52267395	20	2.2	20	88	7	65	37	0	2	60	1.09
52273851--52273902	20	2.8	18	78	21	63	51	3	1	42	1.31
52273809--52273943	68	1.9	72	88	5	206	50	5	2	42	1.37
52276503--52276562	22	2.7	21	75	10	66	60	6	11	21	1.54
52285395--52285565	43	4.0	42	81	14	208	21	18	28	30	1.97
52285408--52285565	84	1.9	84	87	7	232	21	19	29	29	1.98
52286492--52286518	2	13.5	2	100	0	54	48	0	0	51	1.00
52287773--52287806	12	2.9	12	86	4	52	35	2	0	61	1.11
52287808--52287847	18	2.2	18	86	8	55	67	12	0	20	1.22
52296164--52296270	53	2.0	53	94	0	187	44	14	15	24	1.85
52296956--52296980	12	2.1	12	100	0	50	16	24	0	60	1.36
52310093--52310120	3	9.3	3	100	0	56	35	32	0	32	1.58
52312207--52312232	5	5.2	5	100	0	52	19	0	0	80	0.71
52320206--52320414	52	4.1	51	85	9	293	34	14	23	27	1.93
52320258--52320451	46	4.3	46	79	15	226	37	14	21	26	1.92
52320192--52320414	98	2.3	98	95	0	392	34	14	23	27	1.94
52320378--52320486	37	3.0	37	93	2	186	36	16	22	24	1.94
52338003--52338035	16	2.1	16	100	0	66	36	6	0	57	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52338227--52338290	33	1.9	33	90	0	101	46	3	21	28	1.66
52338238--52338371	33	4.1	32	73	11	101	37	3	23	35	1.73
52344774--52344812	18	2.2	18	86	4	53	64	5	10	20	1.44
52348316--52348365	4	12.2	4	78	19	50	4	20	0	76	0.95
52348325--52348365	17	2.4	17	88	8	57	4	21	0	73	1.02
52348316--52348365	13	4.1	12	80	19	50	4	20	0	76	0.95
52364685--52364762	19	4.3	19	90	6	117	41	10	12	35	1.77
52364685--52364762	18	4.3	18	87	12	115	41	10	12	35	1.77
52364685--52364796	18	6.3	18	78	12	92	38	9	13	38	1.78
52364853--52364901	17	2.8	17	82	11	64	44	10	16	28	1.80
52365283--52365317	14	2.6	14	90	4	54	65	2	11	20	1.37
52365412--52365494	43	2.0	42	83	7	105	9	27	36	26	1.88
52365505--52365558	13	4.2	13	75	22	51	0	22	5	72	1.05
52365498--52365565	23	3.0	23	83	10	86	1	23	5	69	1.19
52365676--52365750	7	10.3	7	78	17	64	0	24	0	76	0.80
52365685--52365742	31	1.9	30	92	3	98	0	24	0	75	0.80
52365687--52365754	13	5.0	13	78	16	57	0	26	0	73	0.83
52365888--52365926	17	2.2	17	86	9	51	0	15	17	66	1.25
52366317--52366456	30	4.7	30	81	9	153	40	1	25	32	1.64
52366317--52366463	59	2.5	60	80	9	158	40	2	23	34	1.67
52368502--52368557	10	5.7	10	74	18	55	28	0	1	69	0.98
52368475--52368579	39	2.8	39	78	13	114	35	0	1	61	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52368504--52368559	27	2.0	29	86	6	80	32	0	1	66	1.03
52373532--52373569	2	19.0	2	88	0	58	47	2	2	47	1.30
52384398--52384423	3	8.7	3	100	0	52	30	0	0	69	0.89
52385936--52386072	9	15.2	8	68	22	51	63	5	0	30	1.18
52385983--52386061	29	2.7	29	98	0	149	64	8	0	26	1.23
52385936--52386182	19	13.1	18	67	19	96	59	5	0	33	1.26
52385983--52386074	29	3.2	29	93	3	141	65	7	0	27	1.20
52386044--52386094	22	2.3	23	79	6	59	62	3	0	33	1.13
52385936--52386182	10	26.2	9	69	17	96	59	5	0	33	1.26
52386737--52386810	20	3.7	20	75	12	71	24	2	2	70	1.14

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