genome.fa.s1.2.7.7.80.10.50.1000.159.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  159  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)
47041202--47041234	3	11.0	3	100	0	66	66	0	33	0	0.92
47052967--47053018	15	3.4	15	77	17	54	40	0	0	59	0.97
47053737--47053853	56	1.9	62	83	14	156	54	11	11	22	1.68
47054428--47054466	17	2.3	18	86	8	55	61	0	5	33	1.18
47054946--47055007	24	2.4	25	82	12	65	58	4	3	33	1.36
47060559--47060637	31	2.6	30	73	13	81	50	6	12	30	1.65
47065217--47065262	23	2.0	23	100	0	92	21	21	17	39	1.93
47065572--47065662	46	2.0	46	86	2	130	47	15	2	35	1.58
47071141--47071349	92	2.3	90	84	9	262	46	3	2	46	1.35
47071277--47071324	26	1.9	25	84	16	64	45	0	2	52	1.12
47071616--47071659	16	2.8	16	83	13	56	45	0	2	52	1.13
47071618--47071908	156	1.9	156	94	0	510	48	5	3	42	1.43
47071941--47072047	45	2.6	40	75	13	108	31	29	5	32	1.81
47072031--47072066	16	2.2	16	100	0	72	38	36	0	25	1.56
47075272--47075314	19	2.2	19	83	4	50	44	13	9	32	1.76
47080653--47080741	13	6.8	13	83	7	108	32	3	6	57	1.41
47080776--47080817	15	2.7	16	85	7	59	42	14	2	40	1.58
47082958--47082997	18	2.2	18	90	0	62	30	7	42	20	1.79
47083839--47083886	25	1.9	25	100	0	96	39	4	8	47	1.53
47083950--47083983	16	2.1	16	94	0	59	50	5	2	41	1.42
47086279--47086315	17	2.4	16	86	13	51	43	2	5	48	1.40
47091291--47091330	2	20.0	2	100	0	80	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47092120--47092302	43	4.3	42	75	4	125	37	19	21	21	1.95
47092120--47092357	42	5.6	42	76	4	165	38	19	20	21	1.94
47092120--47092357	86	2.8	87	72	6	218	38	19	20	21	1.94
47093588--47093618	2	15.5	2	93	0	53	51	0	0	48	1.00
47095377--47095409	17	1.9	17	93	0	57	51	0	3	45	1.16
47095596--47095637	14	3.1	14	79	6	59	30	0	7	61	1.22
47095583--47095636	27	2.0	26	92	3	90	25	1	7	64	1.30
47096637--47096675	20	1.9	21	94	5	71	35	10	7	46	1.67
47102342--47102369	3	9.3	3	100	0	56	0	35	32	32	1.58
47113936--47113977	11	3.4	12	84	15	59	4	7	4	83	0.91
47116185--47116515	178	1.9	179	92	0	556	40	11	15	32	1.83
47120425--47120472	19	2.5	20	82	3	62	35	0	2	62	1.07
47130336--47130368	17	2.1	17	88	11	52	36	0	0	63	0.95
47139679--47139735	27	2.1	27	86	0	78	15	3	15	64	1.42
47144489--47144538	11	4.6	11	75	20	52	72	16	6	6	1.25
47146311--47146348	2	19.0	2	100	0	76	50	0	0	50	1.00
47146748--47146820	36	2.0	36	100	0	146	41	10	10	36	1.76
47155067--47155134	29	2.3	29	92	5	111	11	10	47	30	1.74
47158643--47158717	29	2.6	28	75	8	69	21	28	24	26	1.99
47160710--47160952	50	4.8	50	92	0	396	20	31	22	25	1.98
47161047--47161077	13	2.4	13	94	0	53	54	12	0	32	1.38
47165176--47165245	34	2.1	34	83	5	88	30	12	14	42	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47171330--47171391	2	30.5	2	96	3	115	48	1	0	50	1.10
47176461--47176516	17	3.4	17	78	14	55	67	0	3	28	1.07
47177122--47177383	129	2.0	129	99	0	515	36	17	22	23	1.95
47181240--47181289	24	2.1	24	96	0	91	22	4	46	28	1.70
47187032--47187071	10	3.8	11	87	9	57	12	7	2	77	1.07
47187026--47187072	5	9.4	5	77	9	51	14	6	2	76	1.08
47187026--47187071	21	2.3	20	88	7	67	13	6	2	78	1.04
47187663--47187691	15	1.9	15	100	0	58	31	0	0	68	0.89
47187687--47187739	24	2.3	23	83	9	63	32	11	5	50	1.61
47192692--47192737	7	6.7	7	76	14	51	69	0	15	15	1.19
47192702--47192736	13	2.7	13	86	0	52	71	0	14	14	1.15
47194048--47195294	44	28.3	43	87	4	1284	32	12	22	32	1.92
47196226--47196262	12	3.2	12	88	3	58	10	8	0	81	0.89
47196226--47196278	12	4.7	11	86	6	54	11	7	1	79	1.01
47199657--47199703	20	2.5	19	86	6	60	23	6	23	46	1.75
47200920--47201014	39	2.3	40	85	10	131	56	6	1	35	1.31
47201441--47201479	21	1.9	20	84	5	51	43	12	17	25	1.85
47201735--47201772	17	2.2	17	86	9	51	42	0	0	57	0.98
47201775--47201817	18	2.4	18	84	7	61	46	0	2	51	1.13
47201816--47201849	12	2.9	11	91	8	50	23	0	8	67	1.18
47210204--47210249	21	2.2	21	85	11	60	26	41	21	10	1.86
47217661--47217694	17	2.0	17	94	0	59	44	11	38	5	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47217915--47217959	6	7.3	6	95	5	81	66	0	0	33	0.92
47223120--47223155	6	6.0	6	90	0	54	0	16	33	50	1.46
47226466--47226531	21	3.1	20	74	10	60	10	15	1	72	1.18
47227786--47227828	19	2.2	20	91	4	70	60	0	0	39	0.97
47227769--47227854	27	3.0	29	75	19	81	65	1	1	32	1.08
47231135--47231166	14	2.3	14	100	0	64	46	6	12	34	1.67
47231225--47231259	12	2.8	12	91	4	52	34	5	11	48	1.63
47233656--47233680	8	3.1	8	100	0	50	52	24	12	12	1.72
47234703--47234775	36	2.0	36	94	0	128	43	2	19	34	1.65
47234706--47234791	36	2.6	32	83	10	95	39	3	20	36	1.70
47237624--47237652	14	2.0	15	93	6	51	10	13	0	75	1.04
47240673--47240951	144	2.0	137	88	9	417	46	17	4	31	1.67
47240831--47240862	12	2.7	12	95	0	55	43	21	0	34	1.53
47243489--47243546	23	2.5	23	85	0	80	51	25	6	15	1.68
47248262--47248298	2	19.0	2	94	5	67	48	0	0	51	1.00
47249467--47249497	2	15.5	2	100	0	62	51	0	0	48	1.00
47256355--47256391	2	18.5	2	100	0	74	48	0	0	51	1.00
47259035--47259122	43	2.0	43	97	0	167	39	15	12	31	1.85
47263848--47263885	2	19.0	2	100	0	76	50	0	0	50	1.00
47266368--47266411	15	2.8	16	79	6	54	68	6	0	25	1.14
47266559--47266599	21	1.9	22	85	5	57	26	0	4	68	1.10
47269109--47269450	51	6.7	50	79	6	343	30	26	15	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47269112--47269450	102	3.3	101	88	3	432	30	26	15	28	1.96
47269109--47269450	153	2.2	152	83	3	429	30	26	15	28	1.96
47272025--47272204	45	4.0	45	86	4	231	35	27	15	22	1.93
47277396--47277435	7	5.7	7	100	0	80	15	0	40	45	1.46
47285916--47286063	72	2.1	72	97	0	278	45	14	13	27	1.82
47288464--47288489	8	3.2	8	100	0	52	11	0	0	88	0.52
47288749--47288851	29	3.5	28	73	17	84	57	0	2	38	1.20
47288886--47288947	20	3.0	21	77	13	67	59	0	8	32	1.26
47288966--47289015	10	5.4	9	75	20	50	26	2	4	68	1.18
47289133--47289269	9	14.5	10	65	24	57	32	2	2	62	1.19
47289134--47289271	29	4.9	28	73	12	122	32	2	2	63	1.19
47289134--47289272	10	14.6	10	71	16	82	32	2	2	63	1.18
47289222--47289285	25	2.5	24	85	12	76	32	0	1	65	1.02
47289134--47289272	19	7.3	19	70	15	99	32	2	2	63	1.18
47289192--47289285	28	3.5	27	81	9	86	32	1	3	62	1.18
47289257--47289285	15	1.9	15	100	0	58	31	0	0	68	0.89
47298237--47298269	16	2.1	16	88	5	50	3	12	12	72	1.23
47300108--47300198	25	3.6	25	74	5	76	32	20	23	23	1.98
47300240--47300380	25	5.6	25	67	15	78	37	22	20	19	1.94
47300321--47300395	26	2.9	26	86	4	98	38	22	20	18	1.93
47301759--47301783	12	2.1	12	100	0	50	24	36	24	16	1.94
47301943--47302005	9	6.9	9	81	3	81	39	30	7	22	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47302150--47302179	13	2.3	13	100	0	60	16	0	43	40	1.48
47302892--47302937	23	2.0	23	100	0	92	30	17	30	21	1.96
47308282--47308317	15	2.4	15	95	0	63	47	0	19	33	1.50
47311082--47311114	10	3.0	11	86	13	50	27	0	0	72	0.85
47314732--47314777	23	2.0	23	91	0	74	54	6	0	39	1.26
47314820--47315022	88	2.3	88	81	10	247	40	17	7	34	1.77
47314820--47315042	87	2.6	85	82	9	238	38	18	8	35	1.80
47315138--47315194	23	2.7	22	84	12	75	71	0	5	22	1.05
47315118--47315292	19	8.7	21	68	18	79	62	1	6	28	1.30
47315117--47315231	10	11.4	10	70	15	58	65	0	5	29	1.14

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