genome.fa.s1.2.7.7.80.10.50.1000.181.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: 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  181  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)
54375639--54375922	42	6.7	42	86	2	392	33	22	21	22	1.97
54375639--54375971	126	2.6	126	84	4	386	31	22	21	24	1.98
54375639--54375971	84	4.0	83	82	5	323	31	22	21	24	1.98
54376292--54376339	21	2.3	21	92	0	78	4	45	20	29	1.70
54377055--54377235	9	20.9	9	70	12	128	33	3	19	43	1.68
54377083--54377159	33	2.3	34	93	4	138	35	5	20	38	1.75
54377206--54377555	112	3.1	112	93	2	578	37	4	11	46	1.62
54377201--54377554	56	6.3	56	83	2	469	37	4	11	46	1.62
54377499--54377591	37	2.5	37	94	0	159	36	4	11	47	1.60
54377532--54377857	56	5.8	56	87	2	501	38	3	11	46	1.59
54377621--54377659	20	2.0	20	94	0	69	46	5	5	43	1.48
54377528--54377871	113	3.0	113	98	0	670	38	4	11	46	1.59
54378024--54378662	20	33.9	19	65	17	149	38	4	10	46	1.58
54377975--54378539	57	9.9	57	87	1	814	39	4	10	46	1.58
54377986--54378555	113	5.0	113	94	0	953	39	4	10	46	1.58
54378495--54378662	37	4.5	38	84	5	209	38	4	8	48	1.54
54378268--54378662	150	2.6	151	73	12	362	38	4	9	47	1.57
54380678--54380719	19	2.2	19	86	0	57	23	2	45	28	1.66
54381049--54381631	231	2.5	230	91	1	927	33	20	18	27	1.96
54382891--54382939	18	2.5	21	80	9	59	26	2	10	61	1.39
54383276--54383508	112	2.1	112	84	7	296	29	24	23	22	1.99
54394964--54395035	35	2.0	36	83	2	92	56	8	5	29	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54396183--54396219	19	2.0	19	89	5	58	32	2	10	54	1.49
54397465--54397501	18	2.1	17	90	5	56	59	0	5	35	1.20
54397467--54397524	29	2.0	30	89	3	91	62	1	5	31	1.27
54397625--54397707	9	9.7	9	70	18	61	27	2	2	67	1.16
54397625--54397709	42	2.0	40	86	6	116	29	2	2	65	1.17
54397653--54397689	15	2.4	16	95	4	67	29	0	2	67	1.04
54397723--54397752	15	2.0	15	93	0	51	30	0	0	70	0.88
54409400--54409445	22	2.0	23	87	4	67	21	10	0	67	1.21
54419552--54419597	3	15.3	3	100	0	92	67	0	0	32	0.91
54419896--54419946	25	1.9	25	84	11	66	17	3	3	74	1.12
54430736--54430791	25	2.2	25	80	6	58	32	25	25	17	1.97
54430943--54430998	26	2.2	26	90	0	85	39	19	23	17	1.92
54432531--54432572	21	2.1	21	86	8	61	52	4	4	38	1.44
54435403--54435489	43	2.0	43	84	4	113	19	16	28	35	1.93
54435900--54435932	16	1.9	18	88	11	52	33	18	15	33	1.92
54437226--54437282	28	2.0	28	100	0	114	42	3	14	40	1.62
54454950--54454974	2	12.5	2	100	0	50	52	0	0	48	1.00
54463668--54463757	39	2.3	39	94	3	146	18	14	12	54	1.71
54464753--54464814	24	2.6	24	84	5	81	19	30	17	32	1.95
54464752--54464859	24	4.5	24	73	16	71	20	28	18	32	1.96
54464898--54464979	26	3.2	26	77	8	87	20	23	20	35	1.96
54464961--54465038	25	3.2	26	69	10	74	17	24	20	37	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54464959--54465075	49	2.4	48	81	11	130	20	21	20	37	1.94
54467159--54467217	12	4.1	14	72	20	50	37	1	5	55	1.32
54475416--54475482	31	2.2	30	84	10	82	28	8	7	55	1.58
54477081--54477136	23	2.6	22	80	8	62	46	0	0	53	1.00
54482055--54482287	100	2.3	100	79	7	233	35	20	11	32	1.88
54487935--54487961	2	13.5	2	100	0	54	48	0	0	51	1.00
54488152--54488189	17	2.2	17	95	0	67	18	5	13	63	1.48
54489061--54489097	12	3.1	12	96	0	65	40	2	16	40	1.62
54494942--54494984	22	2.0	22	82	13	54	65	2	0	32	1.06
54496504--54496556	26	2.1	25	85	3	70	62	7	5	24	1.44
54498728--54498790	30	2.1	30	90	0	99	31	12	28	26	1.93
54502611--54502647	11	3.5	11	85	10	51	35	2	0	62	1.10
54502602--54502658	21	2.8	20	78	10	62	29	3	1	64	1.20
54502613--54502649	10	3.7	10	89	10	58	35	2	0	62	1.10
54502612--54502666	21	2.6	21	82	5	67	30	3	0	65	1.10
54502613--54502668	20	2.8	20	84	7	53	32	3	0	64	1.11
54508674--54508972	146	2.0	146	96	0	553	42	24	6	26	1.79
54510467--54510512	24	1.9	24	82	8	58	34	0	2	63	1.07
54511950--54511994	21	2.1	21	100	0	90	8	8	17	64	1.47
54515516--54515593	39	2.0	39	100	0	156	35	33	10	20	1.86
54515870--54516363	174	2.8	180	89	3	723	35	20	13	31	1.91
54516979--54517007	15	1.9	15	100	0	58	34	6	6	51	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54518324--54518353	15	2.0	15	100	0	60	40	13	20	26	1.89
54519924--54519970	9	5.4	9	82	10	53	14	0	25	59	1.36
54519923--54519970	17	2.9	16	75	9	51	14	0	27	58	1.37
54532966--54533091	55	2.3	54	90	2	198	23	9	33	33	1.87
54543078--54543115	19	2.0	19	100	0	76	26	15	15	42	1.87
54545203--54545296	47	2.0	47	93	0	161	44	7	9	38	1.65
54561483--54561507	2	12.5	2	100	0	50	48	0	0	52	1.00
54561652--54561681	2	15.0	2	100	0	60	50	0	0	50	1.00
54561783--54561819	2	18.5	2	100	0	74	48	0	0	51	1.00
54562750--54562777	2	14.0	2	100	0	56	50	0	0	50	1.00
54567326--54567389	22	2.9	22	92	0	101	31	28	15	25	1.96
54570871--54570914	23	1.9	23	86	9	63	36	2	0	61	1.09
54570866--54570928	23	2.6	24	73	9	58	39	3	0	57	1.15
54589005--54589029	2	12.5	2	100	0	50	52	0	0	48	1.00
54589683--54589727	22	2.0	22	83	8	56	33	2	4	60	1.29
54593957--54594019	5	11.6	5	85	12	81	19	22	0	58	1.39
54593957--54594019	28	2.3	27	89	5	99	19	22	0	58	1.39
54593965--54594062	22	4.3	22	78	10	72	23	18	0	58	1.39
54594014--54594104	19	4.4	21	77	17	77	27	9	1	61	1.34
54594012--54594104	41	2.3	41	80	12	111	26	9	1	62	1.33
54594041--54594084	18	2.6	18	89	7	65	20	11	2	65	1.35
54594095--54594201	28	3.8	28	79	7	119	31	18	0	49	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54594106--54594149	5	8.2	5	80	14	52	25	20	0	54	1.45
54594273--54594316	16	2.9	15	86	6	61	22	13	0	63	1.29
54594606--54594706	5	18.6	5	80	13	69	19	11	2	65	1.38
54594606--54594706	22	4.4	22	74	16	87	19	11	2	65	1.38
54594605--54594706	27	3.7	26	80	10	107	19	11	2	65	1.37
54594693--54595063	47	7.9	47	89	4	520	26	12	0	61	1.31
54594719--54595063	68	4.9	69	71	21	234	26	12	0	60	1.32
54594843--54595061	21	9.5	21	69	20	125	26	13	0	60	1.33
54594693--54595063	95	3.9	95	90	3	556	26	12	0	61	1.31
54595110--54595179	22	3.2	22	66	22	65	38	0	12	48	1.42
54595105--54595253	44	3.4	44	95	0	262	37	2	11	48	1.51
54596652--54596882	46	5.0	46	95	0	399	29	26	8	35	1.86
54601477--54601679	111	1.8	112	88	6	313	33	22	17	27	1.96
54602530--54602566	18	2.1	18	90	10	58	67	0	0	32	0.91
54624811--54624835	2	12.5	2	100	0	50	0	0	48	52	1.00
54631626--54631663	19	2.0	20	94	5	69	26	0	2	71	1.00
54631641--54631679	15	2.5	16	84	16	55	25	0	5	69	1.09
54632313--54632338	13	2.0	13	100	0	52	53	15	7	23	1.67
54632357--54632414	20	2.9	19	76	5	62	43	8	8	39	1.66
54632373--54632410	19	2.0	19	90	10	60	39	10	7	42	1.69
54638142--54638208	7	9.7	7	73	3	64	55	26	1	16	1.50
54638163--54638246	21	4.0	21	68	7	55	51	29	2	16	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54638149--54638202	28	1.9	28	84	0	72	53	27	1	16	1.53
54638267--54638308	7	6.1	7	78	15	52	54	26	0	19	1.44
54651926--54651952	2	13.5	2	100	0	54	48	0	0	51	1.00
54653283--54653309	10	2.7	10	100	0	54	55	29	7	7	1.55
54655385--54655417	2	16.5	2	100	0	66	51	48	0	0	1.00
54657597--54657680	44	1.9	44	87	0	123	27	10	16	45	1.81
54657673--54657702	15	1.9	16	93	6	53	26	6	6	60	1.47
54658241--54658316	21	3.4	21	81	7	80	21	28	15	34	1.94
54673183--54673222	21	1.9	21	89	0	62	17	7	5	70	1.30
54673747--54673834	19	4.5	19	69	13	72	38	2	0	59	1.10

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