genome.fa.s1.2.7.7.80.10.50.1000.32.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  32  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)
10172702--10172741	12	3.5	11	84	15	55	22	5	0	72	1.04
10173708--10173744	19	1.9	19	88	0	56	59	0	8	32	1.27
10180148--10180216	3	23.0	3	100	0	138	33	0	0	66	0.92
10180829--10180855	2	13.5	2	100	0	54	48	0	0	51	1.00
10183876--10183999	50	2.5	50	77	6	126	30	18	19	31	1.96
10183977--10184957	89	10.8	90	76	9	715	30	21	15	33	1.94
10184126--10184907	184	4.3	183	77	9	468	30	20	14	34	1.93
10184031--10184917	140	6.5	133	75	9	531	30	20	15	33	1.94
10183871--10184957	44	23.7	47	73	11	568	30	20	15	33	1.94
10188522--10188622	33	3.1	33	94	0	184	15	24	12	46	1.81
10192978--10193020	19	2.2	20	87	4	61	44	6	18	30	1.76
10197428--10197559	66	2.0	66	100	0	264	46	6	3	43	1.43
10202221--10202271	21	2.4	21	90	3	75	25	0	5	68	1.12
10205025--10205065	6	6.8	6	97	0	73	53	0	12	34	1.38
10208244--10208608	46	8.0	46	78	7	278	33	4	23	38	1.75
10208270--10208600	23	14.4	23	72	10	212	32	4	23	38	1.75
10208514--10208622	46	2.4	46	85	3	139	33	7	23	35	1.83
10211482--10212297	44	18.7	42	71	12	383	26	22	20	29	1.99
10211470--10212253	217	3.6	217	87	2	1022	26	22	20	29	1.98
10211475--10212297	89	9.4	88	69	14	418	26	22	20	30	1.98
10211741--10212299	261	2.1	258	85	5	734	27	22	20	28	1.99
10215165--10215398	46	5.6	44	81	13	230	35	14	21	28	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10215203--10215313	37	3.0	37	91	0	177	38	12	19	28	1.89
10236199--10236230	15	2.2	15	94	5	57	50	0	0	50	1.00
10246704--10246732	2	14.5	2	100	0	58	51	0	0	48	1.00
10252670--10252699	12	2.4	13	94	5	53	56	0	0	43	0.99
10256663--10256821	45	3.6	45	78	5	180	27	25	15	30	1.96
10256831--10257082	132	1.9	132	85	1	353	28	23	17	29	1.97
10257065--10257433	50	7.4	50	70	2	274	24	24	20	30	1.99
10257065--10257452	100	3.9	100	90	0	589	25	23	20	30	1.99
10258695--10258736	7	6.0	7	79	20	52	11	16	0	71	1.14
10258695--10258736	21	2.0	21	90	9	68	11	16	0	71	1.14
10268099--10268266	86	2.0	84	89	4	257	46	9	5	38	1.61
10268752--10268803	22	2.3	20	76	20	50	55	7	0	36	1.29
10269484--10269560	31	2.5	31	91	4	120	45	9	16	28	1.78
10269731--10269773	15	2.8	15	80	16	52	46	2	2	48	1.27
10274414--10274503	39	2.4	37	74	18	94	33	1	0	65	1.00
10276865--10276923	31	1.9	31	89	6	93	52	10	10	27	1.67
10281769--10281794	9	2.9	9	100	0	52	80	7	11	0	0.89
10281766--10281815	15	3.3	15	78	10	57	76	4	18	2	1.04
10281765--10281816	9	5.4	9	80	13	50	73	3	21	1	1.10
10286410--10286448	20	2.0	20	85	10	53	61	5	0	33	1.18
10287050--10287209	85	1.9	85	84	0	212	38	16	16	28	1.90
10289384--10289436	26	2.0	26	89	7	81	47	1	0	50	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10297454--10297521	31	2.2	31	89	0	100	42	4	14	38	1.66
10300897--10300928	16	1.9	16	93	6	55	59	0	0	40	0.97
10300889--10300929	16	2.7	16	82	17	52	53	0	0	46	1.00
10308067--10308121	28	2.0	28	92	0	92	27	25	20	27	1.99
10318482--10318536	25	2.2	25	96	0	101	34	0	9	56	1.31
10323115--10323187	38	1.9	37	86	8	103	31	21	1	45	1.61
10323317--10323392	23	3.3	23	96	0	143	30	25	21	23	1.99
10324221--10324264	24	1.9	24	90	9	74	36	0	2	61	1.09
10324361--10324388	9	3.1	9	100	0	56	57	10	0	32	1.33
10324331--10324540	68	3.1	68	95	1	379	45	9	4	40	1.57
10324529--10324570	16	2.6	16	92	0	66	42	7	2	47	1.43
10324544--10324604	22	2.8	22	84	0	77	47	1	1	49	1.21
10326168--10326197	2	15.0	2	100	0	60	50	0	0	50	1.00
10326942--10327074	19	6.8	19	90	4	194	36	9	15	38	1.80
10326943--10327074	59	2.3	59	91	1	212	37	9	14	38	1.79
10326942--10327074	40	3.4	40	91	5	202	36	9	15	38	1.80
10328446--10328635	98	1.9	98	94	2	337	27	10	25	36	1.89
10333156--10333212	25	2.3	23	81	18	71	52	3	0	43	1.18
10335413--10335470	30	2.0	29	93	3	98	39	1	27	31	1.67
10346293--10346332	17	2.4	17	87	8	55	30	0	12	57	1.36
10348144--10348549	188	2.1	190	83	9	504	44	19	11	24	1.84
10349402--10349630	126	1.8	126	93	1	397	29	16	22	31	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10351669--10351693	11	2.3	11	100	0	50	48	28	16	8	1.74
10352510--10352711	55	3.6	56	84	7	279	46	5	11	35	1.65
10352713--10352884	29	5.6	29	85	10	209	20	0	32	47	1.51
10352707--10352884	64	2.9	62	83	9	224	20	0	32	46	1.55
10352945--10352993	25	1.9	25	87	4	71	38	16	4	40	1.67
10353392--10353437	18	2.6	18	82	0	56	39	8	30	21	1.84
10354082--10354106	7	3.6	7	100	0	50	60	12	0	28	1.32
10355065--10355095	15	2.0	16	93	6	55	67	6	0	25	1.14
10355196--10355235	21	1.9	21	84	0	53	62	0	0	37	0.95
10355188--10355254	31	2.2	31	94	2	118	62	0	0	37	0.95
10360908--10360982	31	2.5	30	80	18	84	44	10	0	45	1.38
10363529--10363555	2	13.5	2	100	0	54	51	0	0	48	1.00
10365882--10365950	31	2.2	31	84	5	86	43	8	13	34	1.74
10373283--10373361	39	2.0	39	100	0	158	34	22	7	35	1.83
10381868--10381939	31	2.3	31	83	13	85	54	0	1	44	1.08
10382195--10382261	31	2.1	31	84	13	84	47	1	0	50	1.10
10386883--10386930	21	2.3	21	81	0	60	41	8	4	45	1.53
10387623--10387681	31	1.9	31	85	0	82	49	8	3	38	1.50
10387989--10388163	78	2.3	76	94	2	305	36	8	12	43	1.72
10390995--10391047	26	2.0	26	82	7	63	45	3	1	49	1.31
10395779--10395808	15	2.1	15	93	6	53	66	0	6	26	1.16
10396751--10396787	19	1.9	19	89	10	58	24	10	10	54	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10398199--10398236	19	2.0	20	94	5	69	73	2	0	23	0.95
10399948--10400490	78	7.0	78	86	4	670	27	16	20	34	1.95
10399948--10400502	233	2.4	230	84	4	724	27	16	20	34	1.95
10399948--10400490	155	3.5	153	83	7	634	27	16	20	34	1.95
10400561--10400585	13	1.9	13	100	0	50	76	8	0	16	1.02
10401474--10401511	4	9.8	4	83	16	53	76	0	23	0	0.79
10401474--10401528	23	2.3	23	84	9	67	74	0	25	0	0.82
10401474--10401525	7	7.0	7	84	6	50	75	0	25	0	0.81
10401477--10401528	19	2.7	19	85	8	52	75	0	25	0	0.81
10402249--10402571	17	17.8	18	68	15	168	31	13	10	45	1.77
10402242--10402587	38	9.5	36	70	11	158	32	13	10	43	1.77
10402429--10402575	73	2.0	74	85	2	197	34	11	9	44	1.73
10402427--10402588	37	4.4	36	77	8	148	32	13	9	44	1.77
10402599--10402638	21	2.0	20	90	5	62	42	5	7	45	1.54
10402652--10402689	20	1.9	20	88	0	58	47	5	10	36	1.61
10402641--10402695	20	2.8	20	77	0	56	41	10	12	34	1.78
10402717--10402814	36	2.7	35	82	14	112	37	6	9	46	1.61
10402738--10402817	20	4.2	20	65	22	55	41	6	8	43	1.61
10403918--10404003	40	2.1	41	82	6	104	29	10	16	44	1.81
10413632--10413671	17	2.3	18	86	4	55	60	2	5	32	1.32
10413683--10413725	19	2.2	20	83	8	52	83	9	2	4	0.87
10420890--10420999	25	4.4	25	75	15	95	30	20	26	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10420890--10420999	49	2.2	50	85	4	143	30	20	26	23	1.98
10424110--10424143	2	17.0	2	100	0	68	50	0	0	50	1.00
10424708--10424852	41	3.5	41	89	1	202	28	15	24	30	1.96
10424707--10424935	82	2.8	82	79	6	216	28	17	25	27	1.98
10424831--10424934	41	2.5	41	95	0	181	26	20	29	23	1.98
10426956--10427022	23	2.9	23	93	0	116	38	4	29	26	1.76
10427193--10427307	57	2.0	57	93	0	194	35	11	24	28	1.90
10430051--10430096	24	1.9	24	95	0	83	17	28	4	50	1.65
10433988--10434033	9	4.5	10	80	20	51	28	2	6	63	1.31
10433988--10434033	20	2.2	20	82	17	51	28	2	6	63	1.31

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