genome.fa.s1.2.7.7.80.10.50.1000.37.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  37  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)
11696019--11696182	81	2.0	81	89	2	249	33	18	22	25	1.96
11696228--11696296	24	2.9	24	80	6	70	18	7	24	49	1.73
11696468--11696672	32	6.4	32	80	4	162	21	20	21	35	1.96
11696757--11696808	26	2.0	26	84	0	68	25	23	17	34	1.96
11713941--11713990	23	2.2	23	100	0	100	32	28	12	28	1.92
11714369--11714418	23	2.2	23	88	0	73	74	12	8	6	1.22
11714369--11714424	23	2.5	22	82	5	69	71	16	7	5	1.27
11716935--11716980	23	2.0	22	84	12	58	47	21	0	30	1.51
11717744--11717783	21	1.9	21	89	0	62	37	7	0	55	1.29
11721744--11721797	18	3.0	18	80	0	63	42	5	16	35	1.72
11724945--11725379	27	16.2	27	75	7	305	41	17	16	24	1.90
11725584--11725678	26	3.7	26	75	2	102	13	23	26	36	1.92
11725798--11725900	30	3.5	29	84	2	118	22	26	24	27	2.00
11727105--11727142	16	2.4	16	100	0	76	23	18	26	31	1.97
11734527--11734558	15	2.0	17	88	11	50	43	0	6	50	1.27
11734774--11734811	13	2.8	14	76	8	51	63	0	0	36	0.95
11735322--11735367	14	3.4	14	82	17	62	76	0	23	0	0.79
11735319--11735367	22	2.2	23	88	3	73	75	0	24	0	0.80
11737641--11737734	49	1.9	49	95	0	170	42	8	25	23	1.82
11738754--11738778	13	1.9	13	100	0	50	64	4	0	32	1.12
11740170--11740200	10	3.1	10	95	0	53	38	45	0	16	1.47
11742882--11742925	22	2.0	22	86	4	61	36	4	4	54	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11743714--11743754	2	21.5	2	85	9	59	51	0	0	48	1.00
11743701--11743753	16	3.2	17	84	10	56	50	0	1	47	1.12
11744440--11744499	17	3.4	17	69	24	52	31	3	1	63	1.20
11744445--11744509	20	3.5	20	71	16	66	33	3	1	61	1.21
11744488--11744517	15	1.9	16	93	6	53	40	0	6	53	1.27
11744628--11744656	2	14.5	2	100	0	58	51	0	0	48	1.00
11745335--11745394	21	3.0	20	80	7	59	33	6	5	55	1.48
11748929--11749275	72	4.7	72	78	6	268	36	12	24	26	1.91
11749017--11749274	75	3.5	73	79	7	263	37	10	25	25	1.88
11749471--11749522	22	2.4	21	78	6	59	21	3	9	65	1.38
11751004--11751081	27	2.9	27	75	3	86	19	23	33	24	1.97
11751138--11751186	18	2.6	18	87	9	62	71	2	24	2	1.07
11751260--11751295	17	2.1	17	89	0	54	22	5	13	58	1.56
11754156--11754218	27	2.3	28	88	5	101	55	6	0	38	1.25
11754167--11754224	27	2.1	27	96	0	107	48	8	0	43	1.34
11756219--11756262	16	2.8	15	83	10	61	59	2	2	36	1.23
11756374--11756495	60	2.0	60	87	3	174	54	13	0	30	1.45
11756489--11756550	29	2.1	30	93	3	108	53	12	1	32	1.49
11756518--11756670	22	6.9	22	83	12	206	55	12	1	30	1.45
11756518--11756670	41	3.5	41	87	8	189	55	12	1	30	1.45
11756483--11756661	49	3.7	49	78	14	212	55	11	1	31	1.43
11756739--11756764	12	2.2	12	100	0	52	46	15	0	38	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11756849--11756894	14	3.2	14	84	3	56	0	43	2	54	1.12
11756865--11756894	15	2.1	15	93	6	53	0	46	0	53	1.00
11762720--11762789	16	4.3	16	73	8	52	41	5	4	48	1.46
11762921--11762976	16	3.4	17	85	4	62	39	7	5	48	1.54
11765096--11765144	24	2.0	24	96	0	89	40	28	6	24	1.79
11772512--11772538	3	9.0	3	100	0	54	66	0	0	33	0.92
11772601--11772649	23	2.3	21	80	20	57	65	0	6	28	1.16
11772617--11772646	14	2.1	15	93	6	53	66	0	6	26	1.16
11772639--11772699	27	2.3	25	81	10	68	67	3	9	19	1.34
11772656--11772728	32	2.2	34	82	7	87	68	2	8	20	1.28
11772692--11772779	23	3.9	24	72	21	75	64	1	11	22	1.32
11772625--11772787	59	2.7	58	80	12	147	65	1	10	22	1.33
11772744--11772821	14	5.8	13	77	18	56	70	2	7	19	1.23
11772778--11772807	12	2.5	12	88	0	51	73	6	3	16	1.18
11774679--11775173	44	10.9	44	74	9	332	29	21	16	32	1.96
11774679--11774849	45	3.8	45	82	3	193	32	22	15	29	1.95
11774680--11775132	140	3.3	136	76	9	404	30	21	16	32	1.95
11778164--11778324	84	1.9	84	93	0	277	24	28	13	34	1.92
11780059--11780097	15	2.6	15	95	0	69	5	33	5	56	1.43
11783242--11783292	19	2.7	20	84	6	70	43	5	23	27	1.77
11783649--11783689	21	1.9	22	85	5	57	14	26	12	46	1.80
11786970--11786998	3	9.7	3	100	0	58	68	0	31	0	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11787058--11787106	23	2.3	21	80	20	57	65	0	6	28	1.16
11787075--11787113	3	13.0	3	84	10	53	64	0	5	30	1.15
11787175--11787322	4	36.5	4	68	9	68	66	3	7	22	1.31
11788917--11788952	15	2.4	15	100	0	72	11	11	13	63	1.51
11796321--11796362	22	2.0	22	85	4	59	52	4	9	33	1.55
11803614--11803656	13	3.4	13	78	18	54	65	2	0	32	1.06
11803615--11803658	12	3.6	12	82	14	54	61	2	0	36	1.09
11816566--11816608	21	2.0	22	86	13	63	32	13	0	53	1.41
11817533--11817585	27	1.9	28	84	3	72	26	5	1	66	1.25
11820249--11820317	26	2.6	25	73	11	66	44	5	2	46	1.42
11829184--11829233	26	1.9	26	95	0	91	34	10	10	46	1.71
11829282--11829406	62	2.0	62	96	0	232	40	10	8	40	1.70
11829621--11829796	93	1.9	93	86	0	253	38	11	19	30	1.88
11831340--11831400	24	2.4	25	79	17	65	39	0	0	60	0.97
11835235--11835277	21	2.0	22	90	4	70	39	34	9	16	1.80
11838226--11838250	2	12.5	2	100	0	50	48	0	0	52	1.00
11838630--11838699	15	4.7	15	71	10	54	74	2	18	4	1.11
11838640--11838711	28	2.6	28	77	16	69	73	2	16	6	1.17
11852173--11852277	41	2.5	40	81	3	129	26	27	20	25	1.99
11852701--11852751	2	26.0	2	78	11	52	43	3	3	49	1.39
11859152--11859256	41	2.6	41	84	3	149	25	28	20	24	1.99
11859734--11859770	2	18.5	2	94	0	65	48	0	2	48	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11860038--11860090	12	4.2	12	77	13	52	43	7	3	45	1.50
11869607--11869665	18	3.2	19	75	13	52	22	3	3	71	1.16
11869844--11869874	14	2.1	15	94	5	55	83	0	16	0	0.64
11871611--11871657	23	2.1	23	84	4	60	0	23	2	74	0.93
11874446--11874502	13	4.4	12	74	20	53	50	0	5	43	1.24
11874467--11874519	12	4.5	11	81	11	52	52	1	3	41	1.30
11882610--11882643	16	2.1	17	94	5	61	17	0	11	70	1.16
11884670--11884710	18	2.3	18	87	4	57	34	12	17	36	1.87
11886399--11886584	93	2.0	93	98	0	363	29	25	16	29	1.96
11889574--11889614	18	2.3	18	87	4	57	34	12	17	36	1.87
11890494--11890708	92	2.3	92	94	0	376	38	10	9	40	1.73
11893305--11893349	18	2.5	18	100	0	90	57	6	4	31	1.44
11893381--11893424	9	5.1	9	89	10	74	56	11	0	31	1.35
11893390--11893427	16	2.4	16	95	0	67	55	10	0	34	1.34
11893497--11893538	16	2.6	16	88	0	57	45	2	2	50	1.27
11893399--11893519	66	1.9	66	85	14	166	46	8	4	41	1.53
11894898--11894966	31	2.3	31	89	2	104	37	11	5	44	1.65
11907122--11907148	6	4.5	6	100	0	54	18	18	14	48	1.82
11907004--11907234	45	5.0	45	88	7	311	19	18	21	40	1.92
11907031--11907249	96	2.3	96	93	0	375	19	18	20	41	1.91
11907218--11907260	6	6.8	6	83	2	50	18	20	16	44	1.87
11907748--11907779	15	2.3	15	89	10	50	40	0	18	40	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11910275--11910352	27	2.9	27	84	3	104	19	23	34	23	1.96
11911736--11911765	6	5.0	6	91	0	51	3	33	33	30	1.74
11913778--11913839	19	3.2	19	86	8	88	53	12	3	30	1.55
11913773--11913838	21	3.2	21	85	10	91	56	12	3	28	1.51
11914011--11914050	14	2.9	13	85	10	53	0	35	0	65	0.93
11914172--11914236	27	2.4	27	94	5	114	16	30	23	29	1.96
11914401--11914468	28	2.6	25	79	18	77	27	14	7	50	1.70
11915848--11915924	25	3.1	25	79	3	75	19	24	20	35	1.96
11915887--11916030	50	2.9	48	77	15	143	20	27	18	33	1.96
11915841--11916039	74	2.7	75	74	10	192	20	25	19	34	1.96

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