genome.fa.s8.2.7.7.80.10.50.1000.54.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  54  of  190  ( 22705 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)
15259630--15259658	15	1.9	15	100	0	58	34	3	6	55	1.44
15259793--15259847	27	2.0	27	92	0	92	32	25	10	30	1.90
15266935--15266977	18	2.3	20	80	15	56	72	0	6	20	1.08
15267059--15267121	6	10.5	6	81	13	58	65	0	0	34	0.93
15267059--15267103	11	4.3	11	83	16	60	71	0	0	28	0.87
15267087--15267122	2	18.0	2	88	0	54	55	0	0	44	0.99
15268454--15268601	44	3.4	43	73	9	120	28	19	17	34	1.95
15268608--15268701	44	2.1	44	84	2	116	29	21	11	37	1.89
15268939--15269121	44	4.2	44	73	12	160	27	22	19	30	1.98
15268953--15269162	44	4.8	44	77	5	158	26	21	19	31	1.97
15268961--15269162	87	2.3	89	84	4	257	26	21	20	31	1.98
15268961--15269216	87	2.9	86	80	7	248	27	19	19	33	1.96
15271036--15271070	17	2.1	17	88	0	52	40	2	0	57	1.14
15271045--15271084	14	2.7	15	84	7	55	35	10	0	55	1.34
15273729--15273973	45	5.4	45	89	0	346	40	20	19	19	1.91
15276953--15276998	21	2.2	21	84	0	56	36	34	4	23	1.75
15287468--15287584	39	3.0	39	92	0	198	46	21	3	29	1.68
15289129--15289168	20	2.0	20	95	4	73	35	17	5	42	1.71
15289145--15289196	27	1.9	27	96	0	95	40	13	3	42	1.62
15289776--15289819	23	1.9	23	85	0	61	34	2	4	59	1.30
15290153--15290178	12	2.2	12	100	0	52	30	0	19	50	1.48
15291070--15291114	2	22.5	2	90	0	72	48	2	0	48	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15297699--15297733	17	2.0	18	88	5	54	20	2	0	77	0.90
15304441--15304484	23	1.9	22	82	17	54	36	25	0	38	1.56
15304530--15304617	45	2.0	45	90	0	140	32	20	18	28	1.96
15304628--15304814	51	3.7	49	77	7	196	31	26	17	24	1.97
15304626--15304810	101	1.8	101	88	5	284	31	26	17	24	1.97
15315285--15315371	28	3.1	27	75	6	93	35	21	22	19	1.96
15315727--15316115	27	14.5	26	80	5	357	25	20	18	35	1.95
15315744--15316115	54	6.9	54	83	2	401	25	19	19	35	1.95
15315727--15316100	81	4.6	81	80	3	414	25	19	18	35	1.95
15315759--15316115	134	2.7	134	84	2	457	25	20	18	35	1.95
15315728--15316115	188	2.1	188	83	2	485	25	20	18	36	1.95
15318417--15318658	37	6.6	37	78	7	201	42	28	9	20	1.83
15318429--15318498	18	3.8	19	71	14	58	38	30	10	21	1.86
15318435--15318654	74	3.0	75	79	9	222	42	27	9	20	1.82
15321068--15321144	26	2.9	26	78	3	82	31	19	5	44	1.73
15321290--15321314	12	2.1	12	100	0	50	16	24	0	60	1.36
15321895--15321943	16	3.1	16	77	11	64	42	22	20	14	1.88
15334664--15335003	51	6.7	51	83	3	393	29	25	15	28	1.96
15334660--15335003	102	3.4	101	88	2	467	29	25	15	28	1.96
15341280--15341327	19	2.5	19	100	0	96	20	43	0	35	1.52
15341341--15341378	8	4.8	8	100	0	76	13	36	0	50	1.42
15354418--15354538	29	4.2	29	92	0	206	36	14	25	23	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15357527--15357576	23	2.1	23	85	3	64	44	16	20	20	1.87
15361389--15361424	15	2.5	14	86	8	54	55	0	5	38	1.23
15367690--15367738	21	2.3	20	89	6	71	59	0	4	36	1.17
15367688--15367751	31	2.1	31	82	11	78	59	1	3	35	1.23
15367756--15367816	25	2.4	27	75	10	74	62	0	3	34	1.12
15367757--15367829	24	2.8	26	74	16	71	61	0	2	35	1.10
15367898--15367946	19	2.7	19	87	9	68	69	0	8	22	1.14
15367837--15367957	18	6.6	19	73	19	71	61	0	4	33	1.18
15368435--15368467	12	2.5	13	85	14	50	33	0	0	66	0.92
15368436--15368482	24	2.0	24	82	0	58	31	0	0	68	0.90
15368449--15368507	26	2.4	24	80	11	57	30	1	1	66	1.12
15368604--15368629	12	2.2	12	100	0	52	23	0	0	76	0.78
15369398--15369438	3	13.7	3	100	0	82	65	0	0	34	0.93
15369631--15369661	9	3.4	9	90	0	53	25	12	22	38	1.90
15369715--15369751	9	4.1	9	92	0	65	45	13	10	29	1.77
15374915--15374945	14	2.1	15	94	5	55	0	25	0	74	0.82
15375518--15375561	23	1.9	23	95	0	79	29	11	22	36	1.89
15376706--15376733	12	2.3	12	100	0	56	0	14	0	85	0.59
15376706--15376739	15	2.3	15	85	14	52	0	11	0	88	0.52
15377239--15377290	5	10.8	5	85	6	72	23	1	34	40	1.66
15383261--15383410	9	16.6	9	69	23	68	33	1	3	62	1.20
15383261--15383337	18	4.6	16	77	15	75	31	1	2	64	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15383455--15383526	31	2.4	29	83	4	90	25	12	13	48	1.78
15383653--15383696	13	3.4	12	81	12	52	13	9	0	77	0.99
15385622--15385660	16	2.4	16	82	0	51	74	7	15	2	1.15
15389694--15389732	16	2.4	16	82	0	51	74	7	15	2	1.15
15405767--15405794	13	2.2	13	100	0	56	64	0	0	35	0.94
15406622--15406728	11	10.4	11	73	17	61	37	3	0	58	1.16
15406644--15406706	10	6.4	10	78	14	60	31	1	0	66	1.01
15406615--15406762	40	3.5	40	83	9	181	35	2	0	61	1.10
15407137--15407189	19	2.7	21	80	14	67	33	0	7	58	1.26
15411296--15411337	22	1.9	22	85	0	57	52	2	19	26	1.58
15418866--15418926	24	2.6	23	72	12	61	40	8	22	27	1.82
15424637--15424691	28	1.9	29	85	3	76	36	10	5	47	1.62
15428118--15428157	18	2.2	18	86	8	55	60	2	0	37	1.11
15428128--15428178	17	2.8	19	82	11	54	60	0	0	39	0.97
15428260--15428288	9	3.2	9	100	0	58	48	0	0	51	1.00
15434994--15435181	68	2.8	68	86	0	250	35	16	23	23	1.95
15443415--15443495	6	13.3	6	77	10	76	76	13	7	2	1.10
15448428--15448543	37	3.1	37	84	7	146	18	15	31	35	1.92
15478899--15478939	21	2.0	21	81	18	50	12	12	14	60	1.58
15486023--15486142	24	4.8	25	74	11	104	16	24	24	35	1.95
15486102--15486151	24	2.1	24	88	0	73	16	26	22	36	1.94
15494528--15494566	19	2.1	19	100	0	78	74	0	10	15	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15496505--15496546	16	2.5	17	84	7	59	47	0	11	40	1.40
15505717--15505789	20	3.7	20	74	15	64	10	30	17	41	1.84
15505711--15505789	40	2.0	39	85	11	108	11	31	16	40	1.84
15509604--15509811	25	8.3	25	75	10	156	35	21	18	25	1.95
15509588--15509797	50	4.2	50	75	10	187	36	23	18	21	1.95
15509628--15509812	75	2.5	75	81	3	212	35	21	17	25	1.95
15512791--15512842	26	2.0	27	84	3	70	26	1	3	67	1.18
15512811--15512854	17	2.6	17	89	10	65	29	0	2	68	1.02
15512861--15512891	16	1.9	16	93	0	53	38	0	0	61	0.96
15517486--15517547	22	2.7	22	87	5	79	48	0	1	50	1.10
15517521--15517562	16	2.6	16	96	0	75	47	0	7	45	1.30
15517492--15517547	23	2.5	23	85	2	78	51	0	1	46	1.11
15517684--15517727	23	1.9	23	86	9	63	61	2	0	36	1.09
15523162--15523444	27	10.6	27	84	5	333	18	17	21	42	1.89
15523162--15523444	81	3.5	80	86	4	383	18	17	21	42	1.89
15525324--15525348	2	12.5	2	100	0	50	52	0	0	48	1.00
15532622--15532976	180	2.0	180	92	0	593	30	17	20	31	1.96
15540244--15540283	20	2.0	21	85	5	55	80	5	5	10	1.02
15544764--15544837	24	3.2	24	64	24	68	24	32	13	29	1.93
15544765--15544872	45	2.4	45	96	0	198	24	30	12	32	1.93
15544765--15544894	45	2.9	45	91	0	179	23	28	12	35	1.91
15547062--15547196	30	4.5	30	77	3	146	20	26	14	38	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15547062--15547225	60	2.8	60	82	4	181	21	26	14	37	1.92
15547182--15547249	29	2.3	29	87	2	91	26	25	13	35	1.92
15554302--15554335	16	2.1	16	100	0	68	64	23	5	5	1.38
15554657--15554816	30	5.4	30	73	5	137	23	26	10	38	1.88
15554592--15554776	90	2.1	90	85	0	244	23	26	11	38	1.89
15554657--15554814	60	2.7	60	75	8	162	23	27	10	38	1.88
15554758--15554816	29	2.0	29	83	6	75	25	27	10	37	1.88
15554807--15554863	29	2.0	29	82	0	69	24	22	19	33	1.97
15555993--15556040	21	2.4	20	93	6	80	29	14	16	39	1.88
15557045--15557085	20	2.0	20	95	0	73	60	0	31	7	1.24

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