genome.fa.s1.2.7.7.80.10.50.1000.38.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  38  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)
11915865--11916039	25	7.0	24	72	10	120	20	25	19	34	1.96
11915995--11916063	25	2.7	25	81	2	75	27	24	17	30	1.97
11923581--11923608	2	14.0	2	100	0	56	50	0	0	50	1.00
11926670--11926704	17	2.1	17	88	0	52	74	2	2	20	1.08
11930115--11930139	2	12.5	2	100	0	50	52	0	0	48	1.00
11933262--11933334	19	3.9	18	75	8	56	57	20	8	13	1.62
11934194--11934238	21	2.0	23	83	8	58	33	2	0	64	1.06
11939549--11939591	14	3.0	14	81	15	52	37	4	0	58	1.19
11939581--11939653	11	6.9	11	70	22	50	45	1	1	52	1.18
11943621--11943686	33	2.0	33	93	0	114	37	10	10	40	1.74
11945613--11945694	3	28.3	3	72	16	57	29	4	1	64	1.22
11945652--11945694	15	2.8	16	86	6	63	32	2	0	65	1.06
11945728--11945783	22	2.5	22	80	13	60	35	7	7	50	1.57
11945708--11945785	26	3.0	26	69	19	74	34	8	7	48	1.63
11946436--11946481	19	2.4	19	85	0	65	39	2	4	54	1.32
11949978--11950016	21	1.9	19	90	10	60	71	7	15	5	1.26
11950726--11950755	7	4.4	7	95	4	53	76	0	0	23	0.78
11950753--11950804	18	2.8	18	78	13	61	65	5	1	26	1.26
11964104--11964141	16	2.4	16	90	0	58	31	0	34	34	1.58
11964120--11964210	45	2.0	44	87	2	128	31	5	28	34	1.80
11964565--11964756	90	2.1	90	84	2	242	30	1	14	53	1.50
11964658--11964916	105	2.5	105	86	5	366	27	0	14	57	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11964878--11964914	16	2.3	16	86	13	58	29	2	5	62	1.31
11972820--11972860	12	3.4	12	83	9	57	80	2	17	0	0.82
11974153--11974588	45	9.8	45	74	7	309	29	23	22	24	1.99
11974146--11974410	134	2.0	134	85	4	356	30	21	21	25	1.98
11974206--11974599	89	4.4	89	85	1	450	29	23	23	24	1.99
11974793--11975074	50	5.6	50	74	0	240	29	20	22	27	1.98
11974793--11975082	100	2.9	100	88	0	427	29	20	22	27	1.98
11975111--11975348	44	5.6	42	71	8	151	33	20	18	27	1.96
11975091--11975339	129	1.9	129	89	1	383	34	21	17	26	1.95
11977538--11977681	74	2.0	73	85	1	198	35	15	17	31	1.91
11978754--11978829	18	4.3	17	75	9	55	46	9	13	31	1.74
11978789--11978873	22	4.0	22	79	11	99	43	9	10	36	1.72
11979040--11979102	33	1.9	34	90	6	103	60	11	6	22	1.53
11979224--11979263	16	2.4	17	91	4	64	0	17	0	82	0.67
11979344--11979389	24	1.9	24	95	0	83	8	34	34	21	1.84
11979524--11979572	16	2.8	18	82	14	66	4	22	53	20	1.63
11979597--11979640	20	2.1	22	91	8	74	0	22	0	77	0.77
11979596--11979643	24	2.0	23	84	11	62	0	22	0	77	0.78
11979604--11979646	20	2.2	20	87	8	61	0	25	0	74	0.82
11979757--11979788	14	2.2	15	94	5	57	21	9	9	59	1.57
11980001--11980144	30	4.9	29	83	5	182	43	5	15	35	1.71
11980001--11980145	59	2.5	59	87	7	199	42	5	15	35	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11980241--11980285	16	2.5	19	79	13	51	46	4	13	35	1.63
11980351--11980406	28	2.0	28	85	0	76	41	1	12	44	1.53
11980526--11980568	22	2.0	22	90	0	68	11	20	25	41	1.86
11980623--11980859	127	1.9	128	84	2	325	26	31	19	23	1.98
11980623--11980874	85	3.0	85	81	2	276	27	30	18	23	1.97
11980616--11980874	42	6.1	42	82	4	252	27	30	17	23	1.97
11980786--11981015	115	2.0	116	93	1	392	40	21	11	26	1.88
11985024--11985068	17	2.8	16	80	16	56	33	0	6	60	1.23
11985024--11985101	35	2.3	37	80	17	105	34	2	6	56	1.39
11986838--11987074	41	5.8	41	88	0	330	31	31	20	17	1.95
11987134--11987250	40	3.0	40	79	7	123	22	19	21	36	1.95
11987256--11987281	12	2.2	12	100	0	52	46	30	15	7	1.74
12004108--12004168	19	3.2	18	73	17	61	24	3	4	67	1.26
12004825--12004882	11	5.2	11	87	2	80	22	32	1	43	1.64
12004825--12004879	22	2.4	23	90	6	94	23	30	1	43	1.64
12004860--12004959	51	2.0	51	88	4	148	28	26	3	43	1.69
12006771--12006810	18	2.2	18	86	0	53	17	30	7	45	1.76
12007052--12007098	21	2.2	21	85	7	60	36	34	21	8	1.84
12007377--12007432	7	7.9	7	76	23	55	50	35	0	14	1.43
12007351--12007705	22	16.0	22	76	13	138	43	31	0	24	1.54
12007380--12007440	15	3.6	15	73	26	59	52	34	0	13	1.40
12007417--12007705	43	6.9	43	83	7	387	43	31	0	24	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12007489--12007702	65	3.3	64	88	3	338	42	30	0	26	1.55
12007799--12007966	37	4.4	38	65	14	114	42	9	6	41	1.63
12007705--12007983	114	2.4	114	98	0	540	41	9	7	41	1.64
12010996--12011436	125	3.5	126	90	4	673	29	23	17	29	1.97
12013254--12013293	19	2.1	19	90	0	62	37	15	10	37	1.80
12019285--12019323	3	13.0	3	83	0	51	66	0	30	2	1.05
12031493--12031528	15	2.4	15	90	9	56	80	0	0	19	0.71
12033693--12033718	2	13.0	2	100	0	52	50	0	0	50	1.00
12039715--12039835	43	2.8	43	75	12	104	33	28	18	19	1.96
12049390--12049420	2	15.5	2	100	0	62	51	0	48	0	1.00
12052195--12052282	46	1.9	46	86	4	124	48	11	20	19	1.79
12056339--12056395	26	2.2	26	100	0	114	49	24	12	14	1.77
12071381--12071408	8	3.5	8	100	0	56	75	0	0	25	0.81
12079881--12079921	19	2.1	20	86	4	57	31	9	2	56	1.45
12080778--12080822	16	2.6	18	79	13	58	57	6	2	33	1.37
12081041--12081081	19	2.1	20	86	4	57	31	9	2	56	1.45
12081552--12081636	41	2.1	39	81	12	93	49	2	1	47	1.22
12083734--12083817	36	2.3	36	85	2	105	40	17	7	34	1.77
12084063--12084144	43	1.9	43	82	9	105	32	29	19	18	1.95
12090364--12090443	36	2.2	36	88	0	124	18	10	22	48	1.77
12091134--12091185	21	2.5	21	84	6	61	17	5	42	34	1.73
12091898--12091952	28	2.0	28	88	0	83	49	16	3	30	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12091923--12091983	26	2.4	26	86	2	79	54	11	4	29	1.57
12091903--12092170	96	2.8	96	84	3	357	48	17	6	26	1.72
12092019--12092085	26	2.6	26	88	2	91	47	13	8	29	1.73
12092105--12092170	26	2.6	26	87	2	98	50	13	7	28	1.69
12093323--12093451	62	2.1	61	94	1	222	48	20	7	23	1.76
12093662--12093749	6	14.7	6	78	0	77	55	10	11	22	1.65
12093668--12093750	18	4.6	18	83	0	94	55	10	10	22	1.65
12104016--12104050	18	2.0	18	88	5	54	54	5	0	40	1.24
12104063--12104102	17	2.3	18	86	4	55	57	7	0	35	1.27
12115754--12115878	56	2.2	56	90	2	189	41	7	13	37	1.72
12115872--12115979	23	4.7	23	95	0	180	33	0	22	44	1.53
12115947--12116762	29	28.3	29	91	2	1261	29	0	26	44	1.56
12119083--12119149	32	2.2	31	91	5	109	64	0	1	34	1.03
12119089--12119130	21	2.0	20	86	4	57	64	0	0	35	0.94
12119183--12119254	22	3.3	22	94	3	119	36	0	33	30	1.58
12134305--12134338	13	2.6	13	85	0	50	64	2	0	32	1.08
12140826--12140881	29	2.0	28	82	10	69	41	3	5	50	1.43
12141797--12142046	42	5.9	41	83	2	275	32	21	20	26	1.98
12141795--12142001	85	2.4	84	85	7	292	31	22	20	25	1.98
12144303--12144353	26	1.9	27	96	4	95	11	25	19	43	1.85
12144517--12144799	149	1.9	148	94	0	494	38	13	17	30	1.89
12145635--12145695	7	7.9	7	73	20	50	31	47	0	21	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12145635--12145696	15	3.9	16	91	4	99	32	46	0	20	1.51
12145952--12146224	114	2.4	113	87	3	379	27	27	20	23	1.99
12146156--12146265	41	2.7	41	91	0	166	30	30	20	20	1.97
12146042--12146380	156	2.2	156	87	5	474	28	27	21	23	1.99
12146197--12146565	114	3.2	113	87	1	515	26	26	22	24	2.00
12145952--12146488	270	2.0	269	84	4	715	27	27	21	24	1.99
12146634--12146659	12	2.2	12	100	0	52	46	30	15	7	1.74
12153015--12153134	64	1.9	64	85	0	168	35	23	20	20	1.96
12153529--12153558	5	5.8	5	96	4	51	36	20	0	43	1.52
12156288--12156345	22	2.9	19	85	14	89	46	18	6	27	1.75

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