genome.fa.s4.2.7.7.80.10.50.1000.181.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  181  of  198  ( 23681 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)
56507793--56507903	25	4.5	25	71	3	91	37	22	21	18	1.94
56507948--56507995	23	2.1	23	92	0	78	31	18	29	20	1.97
56507893--56508062	26	6.8	26	73	14	101	32	21	27	18	1.97
56509866--56509916	21	2.4	21	93	0	93	35	21	13	29	1.92
56510087--56510422	148	2.3	148	83	3	410	26	30	13	30	1.94
56512555--56512609	24	2.3	24	78	12	60	18	21	21	38	1.94
56512591--56512673	25	3.3	25	81	0	94	20	25	19	34	1.96
56512603--56512693	25	3.6	25	79	5	76	21	24	21	31	1.98
56525188--56525213	9	2.9	9	100	0	52	30	11	34	23	1.90
56530492--56530550	19	3.2	19	75	15	61	61	5	3	30	1.34
56531502--56531526	2	12.5	2	100	0	50	52	0	0	48	1.00
56532167--56532209	4	10.8	4	89	0	68	51	0	23	25	1.49
56532347--56532589	120	2.0	120	98	0	468	38	20	12	28	1.89
56532768--56532792	10	2.5	10	100	0	50	64	0	0	36	0.94
56533503--56533537	14	2.6	14	90	4	54	28	0	0	71	0.86
56533502--56533536	15	2.4	14	90	9	52	25	0	0	74	0.82
56549173--56549495	160	2.0	160	98	0	619	31	13	21	34	1.92
56550701--56550753	18	3.0	17	91	5	79	39	1	1	56	1.21
56550548--56550773	99	2.3	97	85	8	291	42	1	3	52	1.27
56550901--56551006	44	2.5	41	76	18	126	34	31	3	30	1.75
56550914--56551006	44	2.1	46	91	4	154	36	30	4	29	1.77
56550901--56551020	46	2.8	42	80	12	129	36	31	5	26	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56558311--56558336	13	2.0	13	100	0	52	23	7	23	46	1.78
56558565--56558755	97	2.0	98	81	5	226	35	21	11	31	1.89
56565064--56565124	19	3.4	17	79	20	63	72	3	0	24	1.00
56565065--56565126	18	3.4	18	82	13	74	72	3	0	24	0.99
56565061--56565124	27	2.4	27	84	5	94	71	3	0	25	1.00
56565741--56565799	26	2.3	26	85	5	75	64	6	0	28	1.19
56565886--56565942	26	2.2	25	84	3	69	63	5	1	29	1.27
56565965--56566014	22	2.3	22	82	0	64	42	0	32	26	1.56
56569171--56569228	30	1.9	30	89	0	89	15	36	32	15	1.89
56570094--56570118	10	2.5	10	100	0	50	40	8	12	40	1.72
56571393--56571457	26	2.8	22	78	17	76	33	21	3	41	1.69
56571392--56571462	22	3.0	22	73	15	70	30	21	2	45	1.66
56574588--56574688	29	3.3	29	72	14	96	34	6	10	47	1.66
56577721--56577999	94	3.0	93	77	6	265	24	19	20	35	1.96
56577878--56578137	143	1.8	143	82	3	335	26	20	21	31	1.97
56577955--56578146	93	2.1	94	80	10	216	28	20	20	30	1.98
56577963--56578139	50	3.7	48	74	17	145	29	22	19	28	1.98
56584246--56584278	16	2.1	16	100	0	66	30	33	12	24	1.91
56587098--56587129	2	16.0	2	100	0	64	50	0	0	50	1.00
56587505--56587537	15	2.3	15	89	5	50	63	12	6	18	1.48
56587514--56587577	15	4.3	15	77	15	69	62	7	3	26	1.38
56587519--56587574	12	4.7	12	75	16	53	62	7	3	26	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56592789--56592950	41	4.0	41	83	7	159	35	26	17	20	1.95
56592789--56592946	82	1.9	82	83	5	203	34	26	18	20	1.95
56605256--56605440	92	2.0	92	91	4	302	23	19	7	49	1.72
56605950--56606461	253	2.0	254	95	1	929	26	17	15	40	1.89
56616746--56616862	57	2.1	54	87	4	171	42	8	5	42	1.59
56618038--56618100	32	2.0	32	87	6	92	19	19	14	47	1.82
56618152--56618406	140	1.8	135	79	11	293	35	6	9	48	1.63
56618388--56618432	24	1.9	23	86	4	63	48	6	11	33	1.65
56618656--56618727	36	2.0	35	81	7	83	40	1	5	52	1.33
56618834--56618870	10	3.7	10	89	10	58	27	0	8	64	1.21
56618832--56618870	21	1.9	20	89	5	60	28	0	7	64	1.21
56619096--56619133	20	2.0	20	89	5	60	65	5	2	26	1.27
56619861--56619910	25	2.0	25	96	0	91	44	24	6	26	1.76
56624605--56624657	27	1.9	28	84	3	72	33	1	1	62	1.17
56640360--56640550	90	2.1	90	99	0	373	32	17	25	23	1.97
56640487--56640685	102	2.0	99	87	3	281	30	18	31	19	1.96
56650971--56650998	13	2.2	13	100	0	56	32	21	14	32	1.93
56657515--56657553	6	6.5	6	96	0	60	0	61	0	38	0.96
56660070--56660146	14	5.0	15	71	20	52	42	15	9	32	1.78
56660086--56660125	20	2.0	20	90	0	62	50	12	10	27	1.72
56660074--56660140	34	1.9	35	90	3	109	46	13	8	31	1.74
56660109--56660148	14	2.9	14	84	0	53	42	17	7	32	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56660593--56660617	11	2.3	11	100	0	50	40	0	28	32	1.57
56660602--56661031	125	3.5	125	93	0	747	29	15	22	32	1.95
56663207--56663285	27	2.9	27	90	0	122	29	20	34	16	1.94
56663445--56663513	19	3.7	19	80	5	88	52	1	8	37	1.42
56663439--56663497	18	3.2	18	80	4	73	50	0	10	38	1.36
56663439--56663509	37	1.9	37	97	0	133	49	1	9	39	1.45
56663482--56663522	19	2.1	19	86	4	55	53	4	7	34	1.50
56663735--56663803	19	3.7	19	80	5	88	52	1	8	37	1.42
56663729--56663799	37	1.9	37	97	0	133	49	1	9	39	1.45
56663729--56663787	18	3.2	18	80	4	73	50	0	10	38	1.36
56664024--56664094	37	1.9	37	100	0	142	49	0	11	39	1.39
56664030--56664098	19	3.7	19	82	5	97	52	0	10	37	1.36
56664315--56664385	37	1.9	37	100	0	142	49	0	11	39	1.39
56664321--56664389	19	3.7	19	82	5	97	52	0	10	37	1.36
56663338--56664459	295	3.8	291	97	1	2084	43	10	13	32	1.78
56664465--56664543	27	2.9	27	92	0	131	16	32	21	29	1.95
56665679--56665753	38	2.0	37	84	7	98	46	2	8	42	1.47
56665794--56665861	17	3.8	17	71	16	57	48	1	5	44	1.36
56665676--56666150	115	4.1	115	94	1	828	43	7	8	40	1.64
56665677--56666150	228	2.1	231	94	1	837	43	7	8	40	1.64
56666155--56666305	23	6.8	22	87	4	164	26	0	24	49	1.51
56666155--56666309	43	3.5	44	81	7	172	25	0	25	48	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56666372--56666483	25	4.7	25	71	14	92	47	11	0	41	1.40
56666360--56666493	70	1.9	70	95	0	241	48	11	0	39	1.40
56667602--56667626	7	3.6	7	100	0	50	60	12	0	28	1.32
56667796--56667833	20	1.9	20	84	10	51	55	7	2	34	1.43
56669025--56669115	42	2.2	42	85	0	119	12	32	29	25	1.92
56670857--56670881	13	1.9	13	100	0	50	40	16	8	36	1.77
56671198--56671247	25	2.1	22	85	10	64	40	2	8	50	1.43
56671430--56671464	18	1.9	18	88	0	52	48	0	0	51	1.00
56673886--56673932	25	1.9	25	86	4	69	17	25	19	38	1.92
56674093--56674144	25	2.1	25	89	7	79	19	26	23	30	1.98
56676329--56676362	12	2.9	11	87	12	50	38	17	17	26	1.92
56676378--56677130	250	3.0	250	99	0	1488	23	24	28	23	1.99
56681497--56681556	30	2.0	31	93	3	104	35	8	13	43	1.74
56683494--56683519	6	4.3	6	100	0	52	15	0	46	38	1.46
56684014--56684065	25	2.0	28	88	11	83	51	3	11	32	1.56
56688163--56688196	14	2.5	14	90	4	52	52	17	2	26	1.58
56689415--56689439	7	3.6	7	100	0	50	56	16	0	28	1.41
56690628--56690688	11	5.6	11	90	5	90	44	1	32	21	1.62
56697921--56697967	24	1.9	25	86	4	69	70	4	6	19	1.26
56698075--56698142	29	2.3	31	87	5	95	52	7	5	33	1.53
56701184--56701208	2	12.5	2	100	0	50	52	0	0	48	1.00
56706681--56706705	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56710380--56710420	3	13.7	3	84	0	55	29	2	4	63	1.28
56710388--56710436	15	3.3	15	79	0	53	32	2	6	59	1.34
56715323--56715369	10	4.5	10	79	10	58	65	0	0	34	0.93
56731294--56731326	17	1.9	17	100	0	66	42	21	0	36	1.53
56731899--56731931	17	2.0	17	88	5	50	45	0	21	33	1.52
56733255--56733319	30	2.2	29	83	10	78	43	0	10	46	1.38
56735534--56735610	37	2.1	38	82	2	93	29	15	23	31	1.95
56736506--56736543	20	1.9	20	94	0	67	18	15	10	55	1.68
56739228--56739263	2	18.0	2	94	0	63	47	0	0	52	1.00
56741997--56742044	25	1.9	25	87	8	71	50	6	0	43	1.27

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   188   189   190   191   192   
          193   194   195   196   197   198