genome.fa.s1.2.7.7.80.10.50.1000.130.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  130  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)
39490564--39490682	59	2.0	59	98	0	229	39	15	5	39	1.70
39492838--39492918	44	2.0	42	85	11	114	30	6	14	48	1.69
39495086--39495166	41	2.0	41	100	0	162	37	19	17	25	1.94
39497579--39497770	74	2.6	73	76	5	188	32	20	16	31	1.94
39499265--39499304	16	2.5	16	95	0	71	32	7	12	47	1.69
39508131--39508179	19	2.6	19	77	6	55	67	0	22	10	1.20
39530897--39530934	13	2.9	13	88	7	51	57	0	2	39	1.12
39533242--39533294	22	2.3	23	87	3	72	66	3	0	30	1.10
39533248--39533313	28	2.3	29	84	7	82	59	1	1	37	1.16
39538411--39538622	87	2.4	88	87	6	306	45	10	11	32	1.75
39538997--39539028	14	2.3	14	100	0	64	28	34	18	18	1.95
39540044--39540082	20	2.0	20	100	0	78	30	10	7	51	1.64
39540061--39540127	29	2.3	29	82	5	82	29	10	5	53	1.59
39542593--39542644	19	2.8	18	82	5	59	32	1	0	65	1.04
39544585--39544778	59	3.3	59	89	0	298	34	3	8	53	1.48
39544830--39544908	29	2.7	29	84	3	97	36	13	5	44	1.67
39544937--39544981	24	1.9	23	86	4	63	53	26	0	20	1.46
39545603--39545643	22	2.0	20	85	9	55	60	0	0	39	0.96
39546393--39546454	31	2.0	31	84	6	81	43	6	8	41	1.60
39554702--39554732	9	3.4	9	90	0	53	25	12	22	38	1.90
39562667--39562815	69	2.2	70	84	7	191	26	26	14	32	1.94
39562696--39563114	69	6.1	69	74	9	180	23	23	15	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39562850--39563114	138	1.9	137	82	2	316	23	22	16	37	1.93
39565500--39565583	41	2.1	39	88	4	123	53	16	0	29	1.43
39565517--39565578	21	3.0	22	70	15	69	51	17	0	30	1.46
39565524--39565601	12	7.0	12	71	19	62	53	15	1	29	1.50
39565551--39565601	25	2.0	25	84	0	66	54	15	1	27	1.52
39568089--39568126	20	2.0	20	84	5	51	50	0	2	47	1.15
39570510--39570553	19	2.3	19	84	0	52	70	0	4	25	1.06
39570546--39570598	17	3.2	17	86	2	63	54	0	3	41	1.18
39570868--39570957	17	4.9	18	74	16	78	31	3	2	63	1.23
39570861--39570938	19	4.2	20	75	16	69	33	2	1	62	1.17
39570823--39570966	56	2.5	56	82	8	148	29	6	2	61	1.35
39570869--39570957	9	9.9	8	71	17	52	30	3	2	64	1.22
39571054--39571276	91	2.5	89	88	2	338	30	9	22	36	1.87
39572714--39572843	42	3.1	42	91	2	215	27	20	19	32	1.97
39573143--39573209	21	3.2	21	86	0	89	2	47	19	29	1.64
39573532--39573910	25	15.3	25	77	19	168	34	0	20	45	1.54
39573650--39573892	51	4.8	52	84	11	310	33	0	19	46	1.50
39573543--39574001	9	52.4	9	68	21	230	33	0	21	44	1.54
39576436--39576597	83	2.0	83	93	0	279	29	19	12	38	1.88
39576936--39577016	39	2.0	40	88	2	119	38	39	2	19	1.65
39577699--39577775	39	2.0	40	87	7	113	38	38	2	19	1.66
39577927--39577958	15	2.1	16	94	5	57	50	3	0	46	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39578045--39578087	8	5.6	8	83	10	63	39	46	0	13	1.44
39578122--39578146	7	3.6	7	100	0	50	48	36	0	16	1.46
39578040--39578146	14	7.2	14	69	14	63	41	41	0	16	1.55
39578368--39578797	114	3.8	113	77	10	423	28	24	22	24	1.99
39580253--39580294	21	2.0	20	86	4	57	26	0	4	69	1.08
39580527--39580591	21	3.1	21	73	16	64	38	7	0	53	1.30
39582484--39582527	19	2.3	20	84	7	56	27	20	11	40	1.86
39584417--39584456	18	2.2	18	86	8	55	12	15	5	67	1.38
39586609--39587370	133	5.8	132	85	5	925	28	20	24	27	1.99
39589921--39589972	24	2.2	24	89	0	77	36	1	5	55	1.35
39593031--39593071	21	2.0	21	85	4	57	26	4	21	46	1.72
39602363--39602438	32	2.4	31	82	10	100	46	0	0	53	1.00
39602366--39602436	5	13.2	6	75	24	70	47	0	0	52	1.00
39602366--39602435	16	4.4	16	76	20	74	47	0	0	52	1.00
39602384--39602436	21	2.5	21	90	6	81	45	0	0	54	0.99
39602477--39602525	20	2.7	18	77	22	57	51	4	2	42	1.32
39609710--39609748	18	2.2	17	86	13	53	33	0	20	46	1.51
39609867--39609895	8	3.6	8	100	0	58	24	13	27	34	1.93
39609982--39610057	23	3.3	23	100	0	152	22	21	26	30	1.99
39621468--39621624	42	3.8	42	79	8	151	40	16	22	19	1.91
39621536--39621603	21	3.2	21	75	8	75	44	19	19	17	1.88
39634387--39634547	83	2.0	80	86	3	223	27	12	19	40	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39643414--39643481	24	2.8	24	88	0	109	25	20	25	29	1.99
39643597--39643640	23	1.9	24	86	9	65	38	18	9	34	1.82
39646513--39646559	15	2.9	16	73	20	53	36	2	0	61	1.08
39646577--39646603	10	2.7	10	100	0	54	40	0	0	59	0.98
39647648--39647689	20	2.2	20	82	4	50	69	23	4	2	1.20
39649471--39649561	45	2.0	45	100	0	182	35	6	0	58	1.24
39649480--39649577	45	2.4	41	83	11	103	38	8	0	53	1.31
39650221--39650253	2	17.0	2	87	6	50	48	0	0	51	1.00
39651286--39651324	21	1.9	21	89	5	62	46	5	5	43	1.48
39651656--39651759	51	2.0	51	88	0	154	20	33	17	28	1.95
39656246--39656277	14	2.3	14	100	0	64	34	6	21	37	1.79
39659445--39659505	27	2.3	27	91	0	95	32	19	16	31	1.94
39664410--39664451	18	2.3	18	100	0	84	42	0	33	23	1.55
39677670--39677701	17	2.0	17	88	11	50	28	40	12	18	1.87
39679103--39679143	22	1.9	22	90	5	66	51	7	0	41	1.30
39679106--39679178	29	2.5	29	78	8	76	58	5	1	34	1.29
39680668--39680707	19	2.2	17	83	12	53	25	0	2	72	0.97
39680673--39680708	18	1.9	19	94	5	65	22	0	2	75	0.94
39680681--39680731	24	2.1	24	88	0	75	25	0	1	72	0.95
39681765--39681809	20	2.2	20	80	7	56	62	2	0	35	1.08
39681781--39681832	27	1.9	27	88	7	79	63	3	0	32	1.12
39682549--39682623	31	2.4	31	93	0	132	33	8	13	45	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39682550--39682647	31	3.2	31	85	2	90	34	7	15	42	1.74
39682776--39682845	29	2.3	30	87	4	97	32	8	14	44	1.75
39686362--39686402	21	1.9	22	85	5	57	24	12	31	31	1.92
39688632--39688791	68	2.3	69	85	5	209	24	8	24	42	1.82
39689248--39689487	20	11.9	20	69	6	115	40	8	13	37	1.75
39689243--39689366	41	3.0	40	70	3	104	42	8	13	34	1.76
39689268--39689458	61	3.2	60	78	8	145	41	8	13	36	1.75
39689330--39689446	40	2.9	40	82	6	137	43	8	12	35	1.74
39689357--39689489	61	2.2	62	85	5	173	41	9	12	36	1.75
39689247--39689473	101	2.2	101	83	6	273	40	8	12	38	1.74
39689527--39689765	112	2.1	113	80	7	281	37	15	14	33	1.88
39691762--39691801	16	2.5	16	91	0	62	47	2	7	42	1.45
39691790--39691928	68	2.1	67	97	2	262	40	5	9	44	1.60
39691874--39691901	9	3.1	9	100	0	56	32	0	10	57	1.33
39693122--39693154	16	2.1	16	100	0	66	69	12	0	18	1.18
39694896--39694930	2	17.5	2	100	0	70	51	48	0	0	1.00
39695200--39695315	43	2.7	43	79	11	139	37	27	14	19	1.91
39698182--39698216	6	5.7	6	86	6	52	0	14	0	85	0.59
39698167--39698216	19	2.5	20	78	18	59	2	12	2	84	0.80
39699370--39699467	33	2.9	33	77	8	108	32	11	14	41	1.81
39702382--39702436	19	3.0	19	81	5	51	45	3	0	50	1.19
39704888--39704929	20	2.2	19	86	4	57	73	0	26	0	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39705887--39705927	21	2.0	21	90	9	66	26	17	26	29	1.97
39707426--39707503	17	4.8	17	86	10	83	0	33	0	66	0.92
39707432--39707504	3	25.3	3	82	8	80	0	34	0	65	0.93
39707431--39707481	26	2.0	26	88	0	75	0	39	0	60	0.97
39707432--39707504	29	2.6	29	84	2	85	0	34	0	65	0.93
39710979--39711045	27	2.5	27	100	0	134	20	8	32	37	1.84
39710988--39711037	17	3.4	17	65	35	51	22	12	32	34	1.90
39711309--39711378	21	3.4	21	72	18	67	37	1	8	52	1.41
39711395--39711440	18	2.6	18	86	3	58	43	0	2	54	1.12
39711343--39711516	59	2.9	59	69	11	167	40	1	5	52	1.33

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