genome.fa.s4.2.7.7.80.10.50.1000.121.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  121  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)
38972706--38972962	45	5.7	45	70	14	163	31	21	20	27	1.98
38973698--38973722	5	5.0	5	100	0	50	80	0	20	0	0.72
38974529--38974607	21	3.8	21	73	16	60	39	8	2	49	1.48
38975117--38975256	72	1.9	73	94	1	246	28	18	17	35	1.94
38978644--38978704	3	20.7	3	96	3	115	32	0	0	67	0.91
38993710--38993753	23	1.9	23	90	0	70	36	11	13	38	1.81
38997908--38997950	22	2.0	22	100	0	86	37	13	25	23	1.92
39016616--39016668	24	2.1	25	82	6	63	22	3	5	67	1.28
39017452--39017521	32	2.2	32	82	10	81	57	8	12	21	1.62
39023818--39023888	31	2.3	31	97	0	133	29	18	18	33	1.95
39023920--39024056	9	15.4	9	83	3	170	33	20	8	37	1.84
39023920--39024053	53	2.5	53	92	0	223	32	20	8	37	1.84
39024079--39024216	20	7.3	20	65	14	96	45	16	5	31	1.71
39024136--39024196	17	3.4	17	68	12	50	50	16	3	29	1.61
39024056--39024238	37	4.9	37	95	0	312	46	14	5	32	1.68
39027061--39027085	7	3.6	7	100	0	50	52	16	16	16	1.76
39027141--39027192	7	7.3	7	78	4	59	55	11	15	17	1.68
39027139--39027186	15	3.3	15	79	5	62	56	10	16	16	1.67
39028217--39028267	25	2.0	25	96	0	93	13	17	23	45	1.84
39035576--39035673	26	3.8	25	78	6	90	38	11	16	33	1.84
39038964--39039001	20	1.9	20	88	0	58	50	2	5	42	1.39
39044016--39044143	49	2.6	49	79	0	121	29	28	18	22	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39048672--39048717	2	23.0	2	90	0	74	52	2	0	45	1.13
39049105--39049190	8	9.2	9	67	20	52	59	0	3	37	1.15
39049157--39049279	17	6.9	19	73	16	68	53	1	4	39	1.32
39055265--39055493	62	3.7	62	65	11	144	29	6	19	43	1.77
39055268--39055515	124	2.0	124	84	3	329	29	6	19	43	1.77
39057762--39057945	42	4.4	42	79	4	192	34	24	16	24	1.95
39057754--39057945	85	2.3	84	85	5	255	34	23	17	24	1.96
39057925--39057974	26	1.9	26	87	0	73	28	34	20	18	1.95
39061229--39061308	29	2.7	29	75	19	85	32	8	5	53	1.53
39062076--39062426	42	8.4	42	79	3	332	34	21	16	26	1.95
39062076--39062358	126	2.3	124	84	3	370	34	21	17	26	1.95
39062807--39062896	21	4.3	21	88	0	108	4	41	18	35	1.71
39068258--39068578	9	36.8	9	73	14	271	32	1	20	45	1.61
39068258--39068578	88	3.7	88	83	6	368	32	1	20	45	1.61
39068437--39068608	45	3.9	44	78	14	144	30	1	20	47	1.58
39068673--39068697	13	1.9	13	100	0	50	48	8	0	44	1.32
39069783--39069820	18	2.1	18	100	0	76	47	15	10	26	1.78
39070470--39071183	365	2.0	366	92	1	1189	34	20	15	30	1.93
39071230--39071310	24	3.2	24	73	13	81	46	8	0	44	1.34
39071689--39071749	28	2.2	26	83	11	77	36	44	1	18	1.59
39071691--39071748	27	2.1	29	87	6	84	34	46	1	17	1.58
39071873--39071912	7	6.0	7	85	11	57	30	52	0	17	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39071873--39071911	12	3.1	12	82	13	51	30	51	0	17	1.46
39071904--39071978	14	5.1	14	75	10	60	38	32	1	28	1.65
39072551--39072795	115	2.1	115	87	3	343	29	24	22	22	1.99
39072708--39072922	73	3.0	72	90	0	340	26	23	23	26	2.00
39072709--39072929	72	3.1	71	88	3	325	27	23	23	26	2.00
39072854--39073167	114	2.8	114	88	2	443	27	26	22	23	1.99
39073404--39073443	13	3.1	13	81	0	53	47	0	2	50	1.14
39074260--39074311	19	2.8	18	74	8	50	63	5	1	28	1.28
39081844--39081908	29	2.3	28	89	5	96	29	29	4	36	1.77
39083482--39083583	51	2.0	51	100	0	204	15	5	21	56	1.60
39084444--39084486	21	2.0	21	82	8	52	34	11	2	51	1.51
39092256--39092300	18	2.5	17	80	13	54	71	6	4	17	1.25
39096794--39096842	20	2.4	21	83	10	66	48	6	8	36	1.58
39096814--39096877	30	2.1	30	91	0	101	59	4	6	29	1.42
39098075--39098105	16	1.9	16	100	0	62	48	0	0	51	1.00
39098096--39098130	9	3.7	9	85	14	52	37	0	2	60	1.12
39098516--39098546	15	2.1	15	94	5	55	54	0	6	38	1.26
39098690--39098731	20	2.1	20	86	0	57	7	26	21	45	1.77
39102179--39102244	28	2.3	28	84	2	87	40	24	15	19	1.90
39102376--39102521	70	2.1	70	81	2	168	31	21	24	21	1.98
39102391--39102561	70	2.4	70	79	5	184	32	22	23	21	1.98
39106344--39106380	14	2.6	15	83	12	51	29	2	5	62	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39110815--39110854	16	2.5	16	91	0	62	35	10	40	15	1.80
39112321--39112359	7	5.6	7	90	9	62	74	0	12	12	1.08
39113658--39113990	127	2.6	128	90	2	526	31	19	24	24	1.98
39114761--39114797	14	2.6	15	83	12	51	29	2	5	62	1.31
39119024--39119142	27	4.4	27	78	5	89	35	17	27	19	1.94
39119173--39119273	27	3.7	27	75	5	96	29	12	32	24	1.93
39119173--39119289	54	2.2	54	85	3	155	30	12	30	25	1.93
39119189--39119322	54	2.5	53	80	3	142	29	11	30	27	1.92
39119335--39119459	27	4.7	27	76	5	94	34	18	24	22	1.96
39119372--39119476	54	2.0	53	82	1	129	35	20	25	19	1.95
39127635--39127672	13	2.9	13	85	11	51	71	26	0	2	1.00
39127635--39127666	14	2.3	15	89	10	50	68	28	0	3	1.04
39128948--39129048	27	3.7	27	90	1	139	25	27	12	33	1.93
39135459--39135512	19	2.9	19	86	2	74	53	5	12	27	1.61
39137764--39137828	27	2.4	27	84	5	78	30	16	24	27	1.97
39145555--39145622	33	2.1	33	100	0	136	23	25	14	36	1.93
39148473--39149174	44	15.9	45	76	5	628	28	15	26	30	1.96
39148473--39149207	264	2.8	265	91	0	1177	28	15	25	29	1.96
39148473--39149207	133	5.5	133	90	0	1161	28	15	25	29	1.96
39158233--39158262	3	10.0	3	92	0	51	33	3	0	63	1.11
39158420--39158456	9	4.2	9	83	16	51	40	2	0	56	1.13
39166844--39166945	51	2.0	51	94	0	177	43	12	7	36	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39168829--39168879	25	2.0	25	100	0	102	15	11	23	49	1.78
39171604--39171666	32	2.0	31	87	3	90	46	6	12	34	1.68
39185486--39185518	17	1.9	17	93	0	57	57	9	15	18	1.63
39192567--39192595	15	2.0	15	93	6	51	48	20	0	31	1.50
39197713--39197752	16	2.5	16	87	0	62	17	5	17	60	1.54
39200691--39200762	31	2.1	34	78	19	96	30	12	12	44	1.79
39200701--39200762	31	2.0	31	96	0	115	29	12	14	43	1.83
39202243--39202286	18	2.4	18	84	3	61	47	13	15	22	1.81
39205607--39205646	2	20.0	2	100	0	80	50	0	0	50	1.00
39205745--39205769	2	12.5	2	100	0	50	52	0	0	48	1.00
39237789--39237827	14	2.8	14	80	0	51	30	23	20	25	1.98
39244698--39244730	16	2.1	16	100	0	66	30	6	33	30	1.82
39244963--39245019	28	2.0	28	96	0	105	29	14	12	43	1.81
39251171--39251200	15	1.9	16	93	6	53	76	0	6	16	0.99
39252592--39252752	24	7.0	24	66	22	94	33	5	3	57	1.40
39252602--39252670	23	2.9	23	81	10	86	31	5	4	57	1.42
39252654--39252736	22	3.8	21	79	14	87	36	6	2	55	1.38
39252557--39252820	69	3.7	68	76	14	182	33	6	5	54	1.47
39252632--39252727	22	4.1	24	80	12	94	34	6	3	56	1.40
39252556--39252761	45	4.4	45	73	16	143	33	5	4	55	1.43
39257503--39257549	24	2.0	24	87	8	69	0	57	0	42	0.98
39257615--39257664	25	2.0	25	88	0	73	6	36	2	56	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39259294--39259333	13	3.0	13	83	16	55	30	2	2	65	1.19
39261204--39261237	12	2.8	12	81	0	50	44	17	23	14	1.86
39263561--39263616	14	3.5	15	76	23	60	78	0	21	0	0.75
39263561--39263618	5	11.8	5	82	10	75	79	0	20	0	0.74
39263561--39263618	19	3.2	19	79	20	79	79	0	20	0	0.74
39265012--39265116	45	2.3	44	91	1	165	25	14	26	33	1.94
39265198--39265430	43	5.4	42	75	8	173	31	21	19	27	1.97
39265112--39265471	130	2.8	129	91	0	567	31	21	19	27	1.97
39265559--39265904	173	2.0	173	90	1	541	30	19	22	28	1.98
39265773--39266090	147	2.2	146	84	4	397	29	16	21	31	1.96

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