genome.fa.s1.2.7.7.80.10.50.1000.145.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  145  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)
43364427--43364694	42	6.4	42	92	0	387	26	21	22	28	1.99
43364381--43364694	84	3.7	82	83	9	348	26	21	22	28	1.99
43365021--43365088	21	3.2	21	80	0	82	4	45	19	30	1.70
43370565--43370849	9	32.8	9	71	16	208	31	2	20	45	1.64
43370554--43370658	25	4.2	25	74	16	108	34	2	19	43	1.65
43370570--43370843	34	7.9	35	75	13	198	31	2	20	46	1.63
43370673--43370711	19	2.1	19	85	9	53	30	0	17	51	1.46
43370565--43370849	25	10.9	27	73	14	208	31	2	20	45	1.64
43373709--43373733	2	12.5	2	100	0	50	48	0	0	52	1.00
43375156--43375253	41	2.4	41	84	1	126	39	26	15	18	1.90
43375313--43375404	40	2.3	40	90	0	139	20	31	16	31	1.95
43376126--43376183	27	2.1	27	84	6	73	48	5	20	25	1.70
43383602--43383657	28	2.0	28	82	6	69	50	1	7	41	1.40
43391577--43391665	26	3.3	27	77	9	83	46	2	12	39	1.54
43391843--43391893	3	17.0	3	95	0	93	66	1	0	31	1.03
43392649--43392675	8	3.4	8	100	0	54	88	0	0	11	0.50
43393379--43393538	83	1.9	83	85	2	223	20	25	25	29	1.99
43393462--43393828	69	5.3	69	81	4	373	20	23	24	31	1.98
43393464--43393810	138	2.5	138	83	5	432	20	23	24	31	1.98
43394444--43394612	85	2.0	85	100	0	338	43	22	10	23	1.84
43397611--43397651	2	20.5	2	94	0	73	51	2	0	46	1.14
43397613--43397661	8	6.1	8	88	6	55	53	6	0	40	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43399999--43400031	14	2.3	15	89	5	50	24	3	6	66	1.28
43417446--43417733	152	1.9	152	82	4	366	34	17	14	32	1.91
43417816--43418014	83	2.4	82	90	4	312	26	7	15	51	1.68
43420024--43420063	18	2.1	19	86	9	55	27	2	2	67	1.16
43421110--43421174	3	20.7	3	75	9	58	69	1	4	24	1.16
43422959--43423262	51	6.3	51	72	13	218	30	16	17	35	1.92
43422959--43423172	95	2.2	95	84	0	275	31	15	17	35	1.91
43423002--43423256	140	1.8	140	81	3	316	30	18	16	35	1.92
43422985--43423903	44	19.9	44	71	11	477	30	18	16	34	1.93
43423322--43423592	140	1.9	140	84	2	357	29	18	15	36	1.92
43422988--43423903	89	9.9	89	71	14	382	30	18	16	34	1.93
43423415--43423903	229	2.1	228	81	6	551	30	19	15	33	1.93
43423545--43423903	140	2.6	134	81	3	416	30	20	15	33	1.94
43430701--43430766	4	16.5	4	90	0	96	69	3	3	24	1.16
43434336--43434389	21	2.6	21	69	0	54	64	9	18	7	1.45
43434854--43434900	19	2.7	17	81	15	60	42	0	4	53	1.20
43435120--43435156	3	12.3	3	100	0	74	32	0	0	67	0.91
43439940--43439966	14	1.9	14	100	0	54	29	25	7	37	1.83
43446956--43446990	15	2.2	16	90	5	54	5	11	0	82	0.82
43447551--43447616	3	21.3	3	76	17	64	30	1	4	63	1.23
43447766--43447833	33	2.0	34	83	8	86	33	5	0	60	1.21
43452304--43452339	18	1.9	18	88	5	54	58	2	0	38	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43452389--43452432	21	2.0	22	86	4	63	45	0	0	54	0.99
43452383--43452440	30	1.9	31	82	10	75	44	0	0	55	0.99
43452415--43452440	9	2.9	9	100	0	52	42	0	0	57	0.98
43454358--43454417	30	2.0	30	83	3	75	41	0	38	20	1.52
43454630--43454666	9	4.1	9	92	0	65	29	10	13	45	1.77
43454720--43454750	9	3.4	9	90	0	53	38	22	12	25	1.90
43457162--43457201	16	2.5	16	91	0	71	40	0	32	27	1.57
43457181--43457274	44	2.1	46	88	4	138	29	4	28	37	1.76
43457181--43457286	44	2.5	41	76	16	101	30	3	28	37	1.75
43457412--43457526	26	4.3	26	70	8	95	53	3	0	42	1.24
43457432--43457548	18	7.0	17	64	21	59	56	2	0	40	1.19
43468623--43468683	23	2.7	23	94	0	104	44	21	19	14	1.86
43470332--43470366	18	2.0	17	88	5	52	45	0	0	54	0.99
43470211--43470625	120	3.5	120	91	1	672	43	2	5	48	1.40
43470584--43470622	15	2.4	16	83	12	53	46	0	0	53	1.00
43472204--43472308	51	2.1	50	90	1	165	27	10	20	41	1.84
43477966--43478005	20	2.0	21	85	5	55	32	17	15	35	1.91
43478105--43478160	19	2.9	19	86	0	67	28	5	17	48	1.69
43478128--43478165	19	2.0	19	100	0	76	26	5	26	42	1.76
43478317--43478353	10	3.8	10	92	7	67	24	0	21	54	1.45
43478317--43478353	19	1.9	19	100	0	74	24	0	21	54	1.45
43478331--43478450	64	1.9	64	92	0	204	25	4	22	47	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43484876--43484949	38	1.9	38	94	0	130	39	9	18	32	1.83
43488529--43488569	18	2.3	18	100	0	82	43	0	4	51	1.23
43491785--43491837	19	2.8	18	75	18	54	41	1	13	43	1.54
43493946--43493997	14	3.7	14	76	0	50	73	0	5	21	1.04
43495289--43495350	31	2.0	31	100	0	124	32	12	6	48	1.67
43497594--43497657	30	2.1	30	88	5	94	35	21	20	21	1.96
43498030--43498246	53	4.1	54	86	2	251	23	21	14	41	1.89
43499259--43499536	27	10.3	27	82	8	282	19	19	17	42	1.89
43499260--43499536	81	3.4	80	88	4	369	19	19	17	42	1.89
43502812--43502989	54	3.3	55	75	12	161	29	25	30	14	1.94
43506219--43506252	9	3.8	9	96	0	59	38	0	0	61	0.96
43506228--43506299	28	2.8	25	74	13	74	37	0	2	59	1.12
43516215--43516547	50	6.6	50	78	7	253	23	28	19	27	1.98
43519944--43519982	20	1.9	21	84	5	53	48	5	2	43	1.38
43533669--43533712	22	2.0	22	95	0	79	38	22	4	34	1.75
43536644--43536672	2	14.5	2	100	0	58	48	0	0	51	1.00
43537025--43537128	41	2.5	41	88	0	145	29	24	20	25	1.99
43537387--43537440	12	4.2	12	77	13	63	44	9	3	42	1.54
43542770--43542798	14	2.0	15	93	6	51	27	20	20	31	1.98
43544562--43545041	238	2.0	238	90	2	750	33	13	15	36	1.87
43545312--43545364	21	2.5	20	79	11	61	41	0	15	43	1.46
43551829--43551880	26	2.0	26	96	0	95	23	13	19	44	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43563545--43563693	61	2.3	66	84	7	182	34	10	6	48	1.63
43563783--43563849	33	2.0	33	100	0	134	34	14	11	38	1.84
43565102--43565143	9	4.6	9	87	3	57	71	11	7	9	1.31
43569630--43569671	9	4.6	9	87	3	57	71	11	7	9	1.31
43585652--43585719	34	2.0	34	100	0	136	47	8	11	32	1.71
43591373--43591407	15	2.3	15	90	0	52	5	14	11	68	1.37
43593994--43594083	37	2.4	37	82	12	103	42	2	4	51	1.34
43593993--43594121	11	11.4	11	65	25	56	42	1	3	51	1.29
43593993--43594171	95	1.9	92	87	7	263	42	2	4	50	1.34
43600216--43600240	13	1.9	13	100	0	50	24	24	36	16	1.94
43601458--43601663	91	2.2	91	82	3	234	31	13	24	30	1.93
43606196--43606489	41	7.1	41	95	0	471	28	21	26	24	1.99
43610688--43610747	30	2.0	31	83	9	79	41	0	40	18	1.50
43610927--43610972	9	5.1	9	100	0	92	32	10	10	45	1.74
43611167--43611240	33	2.1	36	80	11	84	50	5	12	32	1.62
43611347--43611420	3	24.3	3	88	2	103	62	2	2	32	1.23
43613092--43613295	44	4.7	43	72	9	153	29	25	17	27	1.97
43613024--43613807	126	6.1	126	92	1	1097	30	22	18	28	1.97
43613432--43613745	38	7.4	44	66	13	156	29	23	17	29	1.97
43615061--43615135	12	6.2	12	77	11	64	1	20	0	78	0.82
43615054--43615138	8	10.5	8	73	16	77	1	18	0	80	0.79
43615053--43615136	15	5.3	15	77	14	64	1	20	0	78	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43615066--43615138	7	9.4	7	76	19	65	0	19	0	80	0.71
43618247--43618271	13	1.9	13	100	0	50	24	24	36	16	1.94
43619466--43619671	91	2.2	91	84	3	252	32	12	24	31	1.92
43624122--43624322	21	10.8	20	69	20	64	45	10	9	33	1.72
43624193--43624428	18	13.2	17	76	12	172	46	10	11	32	1.73
43624267--43624322	20	2.7	20	76	15	60	42	10	7	39	1.67
43624261--43624322	21	3.0	22	81	9	76	38	9	8	43	1.67
43624192--43624428	36	6.6	36	76	13	211	45	10	10	32	1.73
43624390--43624468	40	1.9	40	84	7	104	43	7	10	39	1.67
43625232--43625299	28	2.5	28	83	7	77	0	29	0	70	0.87

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