genome.fa.s1.2.7.7.80.10.50.1000.132.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  132  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)
40003684--40003968	86	3.3	86	83	4	353	30	30	16	22	1.95
40003682--40003968	129	2.2	129	81	4	339	31	30	16	22	1.95
40008729--40008757	8	3.8	8	90	9	51	37	41	0	20	1.53
40008729--40008757	15	1.9	15	100	0	58	37	41	0	20	1.53
40008769--40008820	27	1.9	27	92	0	86	40	38	1	19	1.63
40009227--40009336	41	2.7	41	94	1	184	28	29	23	19	1.98
40009315--40009357	21	2.0	21	100	0	86	37	30	18	13	1.90
40009274--40009398	62	2.0	62	96	0	232	31	29	22	16	1.96
40009233--40009439	103	2.0	104	95	0	371	29	29	23	16	1.97
40009336--40009470	41	3.3	41	98	0	261	28	31	22	17	1.96
40009227--40009489	144	1.8	145	91	0	438	29	29	22	18	1.97
40009518--40009653	41	3.4	39	80	5	148	21	19	20	38	1.93
40009530--40009670	41	3.5	41	78	7	130	24	20	19	36	1.95
40009659--40009684	12	2.2	12	100	0	52	46	30	15	7	1.74
40012197--40012245	25	1.9	26	87	4	73	34	20	6	38	1.77
40012391--40012420	12	2.5	12	94	0	51	16	20	0	63	1.31
40012768--40012806	17	2.2	17	86	4	51	30	0	23	46	1.53
40013692--40013731	20	1.9	20	85	10	53	37	17	22	22	1.94
40014593--40014747	71	2.2	71	81	4	168	21	14	11	52	1.72
40014674--40014807	60	2.2	61	81	4	153	20	17	13	47	1.81
40016955--40016998	23	1.9	23	95	0	79	47	9	20	22	1.78
40025100--40025141	14	3.1	13	86	13	50	45	0	7	47	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40025100--40025141	19	2.3	18	84	8	57	45	0	7	47	1.30
40037584--40037627	22	2.0	22	90	0	70	59	0	2	38	1.10
40037602--40037631	16	1.9	15	93	6	51	60	0	0	40	0.97
40037647--40037688	13	2.9	14	80	13	50	52	0	2	45	1.13
40037722--40037769	19	2.6	19	77	6	55	50	2	0	47	1.12
40044204--40044248	19	2.4	19	80	0	54	28	6	4	60	1.42
40060111--40060169	27	2.1	28	84	6	75	59	1	1	37	1.18
40060186--40060232	11	4.4	11	74	15	53	59	2	4	34	1.29
40066920--40066996	33	2.6	28	75	18	82	22	0	23	54	1.45
40069524--40069618	26	3.8	24	79	13	95	30	18	26	24	1.98
40069524--40069618	49	1.9	49	83	8	122	30	18	26	24	1.98
40070241--40070407	43	3.9	42	73	8	124	34	24	12	28	1.92
40074937--40075022	13	6.5	13	72	6	66	33	18	2	45	1.62
40075198--40075364	45	3.7	45	87	6	223	20	20	17	41	1.91
40077846--40077884	19	2.1	19	85	0	51	41	7	0	51	1.31
40080718--40080762	20	2.2	20	80	0	54	40	13	17	28	1.88
40083985--40084041	18	3.3	17	76	16	55	10	19	1	68	1.28
40084032--40084109	40	1.9	41	82	7	97	11	19	1	67	1.28
40086509--40086553	22	2.0	22	86	0	63	33	8	24	33	1.86
40087511--40087555	20	2.2	20	88	0	63	44	13	13	28	1.81
40088370--40089395	514	2.0	514	97	0	1926	30	18	13	37	1.89
40091773--40091801	9	3.3	9	95	4	51	13	0	6	79	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40098179--40098363	101	1.8	102	89	3	293	23	16	27	32	1.96
40098179--40098363	51	3.6	51	78	3	187	23	16	27	32	1.96
40098367--40098461	45	2.1	45	90	0	154	26	18	25	29	1.98
40106063--40106089	7	3.9	7	100	0	54	14	0	0	85	0.61
40110063--40110118	26	2.2	25	81	6	67	44	1	0	53	1.11
40109972--40110117	61	2.5	57	80	8	170	44	1	3	50	1.27
40110279--40110303	12	2.1	12	100	0	50	40	8	8	44	1.63
40110767--40110849	18	4.5	17	69	20	51	51	3	1	43	1.26
40110799--40110880	18	4.8	17	74	17	64	54	3	1	40	1.26
40110858--40110907	21	2.4	22	83	6	59	62	2	4	32	1.25
40115809--40115896	42	2.1	42	91	0	140	37	15	23	22	1.93
40117821--40117855	18	1.9	18	100	0	70	28	31	17	22	1.96
40119942--40119973	12	2.5	13	95	5	57	59	18	3	18	1.51
40134856--40134911	21	2.7	21	83	5	69	73	1	7	17	1.15
40134906--40134938	7	4.6	7	96	3	57	69	0	3	27	1.03
40134858--40134922	21	3.2	20	77	16	62	73	1	6	18	1.11
40154154--40154197	22	2.0	22	82	8	54	36	0	18	45	1.49
40159189--40159268	38	2.0	40	92	4	137	28	1	38	31	1.65
40160764--40160831	34	2.0	34	91	5	111	35	19	22	23	1.96
40171148--40171179	16	2.0	16	93	0	55	25	15	0	59	1.36
40171397--40171597	51	4.0	51	80	8	248	30	27	16	24	1.97
40171814--40171844	16	1.9	16	93	0	53	45	9	9	35	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40173876--40173915	18	2.2	18	86	8	55	12	25	42	20	1.86
40174180--40174212	16	2.0	17	88	5	50	39	12	9	39	1.74
40176903--40176944	21	2.0	20	86	4	57	52	2	11	33	1.51
40178381--40178416	3	11.7	3	88	5	54	69	0	30	0	0.89
40178875--40178925	6	8.5	6	78	8	50	80	0	0	19	0.71
40178875--40178920	13	3.1	14	84	15	58	80	0	0	19	0.71
40187869--40187898	15	2.0	15	100	0	60	40	13	6	40	1.71
40188869--40188967	34	3.2	33	65	21	86	50	13	2	34	1.53
40188860--40188978	60	2.0	60	94	0	211	52	13	1	31	1.50
40189636--40189701	23	2.7	23	76	9	69	57	1	1	39	1.17
40192691--40192743	25	2.1	25	100	0	106	54	0	7	37	1.29
40203723--40203790	35	1.9	35	87	0	100	39	17	19	23	1.92
40207015--40207059	18	2.7	16	82	6	54	6	20	4	68	1.29
40210738--40210799	20	3.0	20	72	9	52	51	14	4	29	1.63
40211850--40211885	18	2.0	19	89	10	58	72	8	0	19	1.10
40213893--40213933	10	4.0	10	84	6	55	60	9	0	29	1.28
40213894--40213933	21	1.9	21	89	0	62	62	7	0	30	1.23
40218962--40219018	24	2.4	24	73	5	62	57	7	1	33	1.36
40219520--40219606	44	2.0	44	90	0	138	20	16	31	32	1.94
40220038--40220090	13	4.1	13	76	9	63	32	5	24	37	1.79
40226767--40226813	22	2.1	22	88	7	69	65	0	0	34	0.93
40226782--40226823	18	2.3	18	83	0	57	66	2	0	30	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40231535--40231581	24	2.0	24	91	0	76	6	19	36	38	1.77
40231990--40232460	50	9.4	50	73	3	374	24	25	20	29	1.99
40232006--40232477	100	4.7	100	93	1	768	25	24	21	28	1.99
40232527--40232725	45	4.4	44	71	16	133	25	26	18	30	1.98
40232555--40232757	45	4.5	45	79	7	214	25	24	19	30	1.98
40232527--40232725	89	2.2	91	87	6	296	25	26	18	30	1.98
40233995--40234083	47	1.9	46	90	2	142	10	22	20	47	1.80
40233997--40234095	47	2.1	46	81	1	108	10	25	18	46	1.80
40244603--40244649	24	2.0	24	91	0	76	6	19	36	38	1.77
40255962--40256012	24	2.1	24	85	7	68	29	0	1	68	1.00
40257543--40257579	18	2.1	18	94	0	65	24	27	8	40	1.83
40257977--40258093	62	1.9	60	82	3	144	36	3	9	50	1.52
40261124--40261644	126	4.1	126	89	2	751	27	16	17	38	1.91
40261124--40261644	251	2.1	253	88	2	780	27	16	17	38	1.91
40261704--40261838	34	4.3	31	82	10	148	43	14	0	42	1.45
40261764--40261831	29	2.4	29	92	2	111	42	11	0	45	1.40
40268197--40268309	51	2.2	51	88	4	174	46	7	18	28	1.75
40269298--40269386	9	9.9	9	91	0	142	34	23	11	30	1.90
40269288--40269386	27	3.7	27	89	1	137	36	24	10	29	1.88
40269388--40269499	37	3.0	37	92	2	172	47	13	6	33	1.68
40269434--40269494	17	3.4	17	68	12	50	50	13	4	31	1.62
40273069--40273162	44	2.1	45	92	2	154	22	3	31	42	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40273320--40273355	18	2.0	18	100	0	72	27	11	22	38	1.88
40274679--40274872	97	2.0	97	98	0	379	28	11	18	40	1.86
40275747--40275789	21	2.0	21	86	0	59	16	23	23	37	1.94
40278801--40278828	14	2.0	14	100	0	56	7	21	0	71	1.09
40278819--40278889	26	2.8	27	75	10	69	14	25	5	54	1.61
40282077--40282181	54	1.9	55	86	1	149	39	13	16	31	1.87
40288573--40288618	24	1.9	24	86	0	65	30	28	19	21	1.98
40288783--40288853	24	3.0	24	66	6	63	21	22	21	35	1.96
40288832--40288891	25	2.5	24	77	2	66	15	30	21	33	1.94
40291235--40291306	26	2.7	27	80	4	76	43	11	15	30	1.81

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