genome.fa.s1.2.7.7.80.10.50.1000.36.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  36  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)
11355910--11355935	12	2.2	12	100	0	52	38	7	0	53	1.30
11355944--11356001	25	2.4	25	80	8	68	58	3	0	37	1.15
11357707--11357853	75	2.0	75	95	0	267	25	20	12	40	1.88
11361271--11361317	22	2.1	22	85	14	62	65	4	6	23	1.33
11363158--11363633	44	10.2	44	65	19	157	30	18	18	31	1.96
11363129--11363586	94	4.9	93	82	2	470	31	19	18	30	1.96
11363123--11363554	189	2.3	189	83	4	523	31	19	18	31	1.96
11370226--11370282	3	19.0	3	96	0	105	66	0	1	31	1.02
11371955--11371981	7	3.9	7	100	0	54	14	0	0	85	0.61
11380453--11380485	2	16.5	2	93	0	57	45	0	0	54	0.99
11382012--11382054	21	2.0	22	86	8	63	79	4	9	6	1.06
11382905--11382979	29	2.5	31	76	4	82	45	14	13	26	1.82
11383229--11383280	23	2.3	23	86	6	70	44	7	0	48	1.31
11383229--11383290	23	2.7	23	78	11	58	48	6	0	45	1.28
11383386--11383437	26	2.0	26	100	0	104	61	11	0	26	1.30
11383395--11383466	26	2.8	25	82	14	76	62	8	0	29	1.24
11398774--11399622	51	18.6	44	69	16	383	34	17	18	28	1.94
11398914--11399316	45	8.9	43	73	11	249	34	17	19	28	1.94
11398783--11399316	181	2.9	181	89	0	816	33	17	19	28	1.95
11399141--11399442	45	6.3	50	70	17	171	33	17	18	29	1.94
11399432--11399567	41	3.1	41	69	19	119	36	19	17	27	1.94
11399377--11399593	92	2.4	92	88	1	319	36	17	17	28	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11403023--11403071	22	2.2	22	100	0	98	26	18	28	26	1.98
11407181--11407263	42	2.0	43	83	11	109	31	28	20	19	1.97
11408125--11408175	27	2.0	27	92	7	88	43	5	0	50	1.26
11422990--11423338	125	2.8	125	94	0	626	30	16	21	32	1.95
11426445--11426469	10	2.5	10	100	0	50	48	0	8	44	1.32
11426453--11426578	55	2.3	55	98	0	243	46	4	11	38	1.61
11426573--11426794	29	7.6	29	86	7	313	28	0	26	44	1.61
11426573--11426790	59	3.7	58	83	8	298	29	0	25	44	1.61
11426573--11426790	89	2.5	88	92	1	364	29	0	25	44	1.61
11426676--11426809	29	5.0	23	74	25	97	26	0	26	46	1.58
11426764--11426816	23	2.7	18	85	14	61	28	0	20	50	1.48
11426815--11426999	71	2.6	71	93	0	316	45	14	2	37	1.59
11427856--11427886	15	2.1	15	100	0	62	35	38	6	19	1.77
11429189--11429253	30	2.2	30	91	5	105	61	0	0	38	0.96
11429195--11429236	21	2.0	21	85	0	57	59	0	0	40	0.97
11429254--11429375	51	2.4	51	90	4	183	42	0	28	27	1.61
11445121--11445164	19	2.3	19	84	7	54	38	4	0	56	1.20
11446719--11446769	17	2.9	17	77	11	59	70	3	0	25	1.04
11451769--11452558	400	2.0	400	95	0	1409	28	16	21	33	1.95
11453830--11453966	63	2.2	62	79	6	143	41	17	23	17	1.90
11475086--11475123	20	1.9	20	84	10	51	50	0	2	47	1.15
11477164--11477194	16	1.9	16	100	0	62	38	6	3	51	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11488966--11488990	7	3.6	7	100	0	50	32	16	12	40	1.84
11490229--11490257	11	2.5	12	94	5	51	13	0	6	79	0.93
11494131--11494175	20	2.3	20	96	3	83	40	0	0	60	0.97
11497882--11497918	17	2.2	17	90	4	58	18	2	10	67	1.32
11504095--11504238	72	2.0	72	87	2	209	45	11	9	32	1.73
11513844--11513868	13	1.9	13	100	0	50	24	8	32	36	1.84
11514686--11514741	21	2.7	21	94	0	94	30	37	8	23	1.85
11515258--11515521	130	2.0	130	97	0	492	33	16	17	33	1.92
11517595--11517695	30	3.2	30	76	15	112	28	13	24	32	1.94
11518190--11518220	3	10.3	3	100	0	62	35	0	0	64	0.94
11528072--11528149	38	2.1	38	97	0	147	52	3	7	35	1.48
11544011--11544045	17	2.1	17	88	0	52	28	5	0	65	1.15
11549226--11549700	124	3.8	124	92	2	758	30	16	21	32	1.95
11552875--11553011	21	6.4	21	81	12	147	26	0	29	43	1.55
11552855--11553052	67	2.9	70	80	15	243	26	0	28	43	1.59
11553048--11553160	25	4.8	24	72	20	103	44	14	0	40	1.51
11553048--11553204	70	2.3	69	94	1	269	45	13	0	40	1.48
11553128--11553214	44	2.0	45	90	2	140	49	12	0	37	1.41
11553635--11553669	18	1.9	18	94	0	61	34	8	31	25	1.86
11558953--11559499	292	1.9	291	90	1	873	32	27	11	28	1.91
11567344--11567376	16	2.0	17	88	5	50	39	12	0	48	1.40
11572314--11572358	17	2.6	17	83	10	56	20	2	0	77	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11572310--11572356	24	2.0	24	83	8	60	21	2	0	76	0.89
11572309--11572358	6	8.5	6	80	12	50	20	2	0	78	0.86
11572334--11572358	11	2.3	11	100	0	50	16	0	0	84	0.63
11574534--11574616	41	2.0	41	100	0	166	42	26	9	21	1.84
11581186--11581219	16	2.1	16	88	0	50	67	0	2	29	1.05
11581203--11581230	12	2.3	12	100	0	56	60	0	7	32	1.24
11593428--11593505	32	2.5	30	80	13	95	37	2	7	52	1.44
11594313--11594358	24	2.0	22	83	8	56	4	23	6	65	1.35
11602030--11602095	31	2.2	31	84	13	84	24	1	7	66	1.26
11602257--11602298	21	2.0	21	86	13	61	57	9	0	33	1.31
11602287--11602330	22	1.9	24	86	9	65	59	9	4	27	1.48
11604227--11604342	36	3.2	35	82	4	135	31	49	5	14	1.65
11604325--11604356	3	10.7	3	93	0	55	31	65	0	3	1.08
11604244--11604340	36	2.7	37	87	6	137	29	49	6	14	1.67
11613361--11613417	30	1.9	30	82	13	73	45	3	1	49	1.29
11614422--11614461	20	2.0	21	95	5	73	30	0	0	70	0.88
11620153--11620194	18	2.5	17	80	7	50	50	26	0	23	1.50
11620165--11620191	6	4.5	6	100	0	54	51	33	0	14	1.43
11621522--11621606	42	2.0	42	97	0	161	24	17	16	41	1.90
11624743--11624798	28	2.0	28	100	0	112	21	21	17	39	1.93
11625416--11625473	5	10.0	6	80	15	61	81	0	15	3	0.83
11625416--11625471	11	4.9	11	83	12	69	82	0	14	3	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11625419--11625472	24	2.2	26	87	12	87	81	0	14	3	0.82
11625416--11625473	17	3.4	17	82	17	75	81	0	15	3	0.83
11626994--11627155	43	3.7	43	72	8	130	31	24	22	21	1.98
11626991--11627200	87	2.4	87	91	0	339	31	22	22	23	1.98
11626991--11627279	44	6.7	43	71	8	160	30	23	22	23	1.99
11627184--11627489	129	2.4	129	88	1	470	32	21	20	25	1.98
11627432--11627534	45	2.3	45	82	0	116	31	21	22	25	1.98
11629432--11629470	12	3.2	12	85	0	51	48	20	0	30	1.50
11631724--11631787	3	22.0	3	73	17	55	31	3	3	62	1.26
11631862--11631888	2	13.5	2	100	0	54	51	0	0	48	1.00
11638800--11638838	21	1.9	20	84	5	51	28	5	5	61	1.39
11641937--11641994	18	3.4	18	86	6	68	29	6	24	39	1.81
11649132--11649182	21	2.4	20	78	12	57	29	19	13	37	1.90
11655227--11655277	25	2.1	24	89	7	77	1	33	0	64	1.05
11657274--11657555	95	2.9	98	78	10	281	42	3	6	47	1.46
11657498--11657555	28	2.0	29	86	3	82	34	1	8	55	1.41
11661892--11661976	35	2.4	35	86	2	107	40	28	14	17	1.88
11669963--11670083	23	5.3	23	93	0	197	19	21	26	33	1.97
11672653--11672694	17	2.6	17	81	7	52	35	2	16	45	1.61
11674269--11674318	20	2.6	19	71	20	50	54	0	4	42	1.19
11674264--11674303	16	2.5	16	83	0	53	60	0	5	35	1.19
11677763--11677800	20	1.9	20	84	10	51	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11682297--11682321	13	1.9	13	100	0	50	52	0	8	40	1.31
11686302--11686498	97	2.0	97	96	0	358	36	23	18	21	1.95
11687147--11687397	74	3.5	72	84	6	262	33	20	21	24	1.97
11687187--11687374	35	5.3	35	67	18	118	32	21	21	24	1.97
11688552--11688598	17	2.8	17	79	20	62	55	6	2	36	1.37
11689132--11689168	9	4.1	9	89	0	56	32	10	10	45	1.74
11692856--11693032	74	2.4	75	80	4	180	35	21	22	21	1.96
11692897--11693069	40	4.5	39	79	9	194	36	20	20	22	1.95
11694118--11694161	7	6.4	7	85	15	65	54	0	0	45	0.99
11696005--11696193	27	7.1	27	81	2	195	34	17	22	24	1.95

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