genome.fa.s4.2.7.7.80.10.50.1000.46.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  46  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)
13789211--13789624	132	3.1	132	87	1	580	29	17	24	28	1.97
13790063--13790107	23	2.0	23	86	4	65	37	4	15	42	1.67
13790075--13790117	22	1.9	23	85	4	61	34	4	11	48	1.60
13792871--13792957	25	3.5	24	78	10	95	56	5	4	33	1.44
13798892--13798931	20	2.0	20	85	0	53	45	2	2	50	1.28
13801838--13801880	18	2.4	18	96	0	77	27	27	20	23	1.99
13813944--13813983	17	2.4	17	100	0	80	87	0	0	12	0.54
13813944--13813981	8	4.6	8	93	6	67	89	0	0	10	0.49
13813950--13814026	9	8.4	9	72	13	50	83	1	7	7	0.88
13813987--13814032	20	2.4	19	81	3	56	78	0	19	2	0.86
13815011--13815071	11	5.4	11	77	13	52	78	1	19	0	0.83
13815158--13815267	43	2.5	44	85	2	134	32	12	28	26	1.93
13816391--13817435	100	10.5	100	89	0	1482	32	25	19	22	1.98
13816456--13817761	50	26.1	50	69	7	587	32	25	19	22	1.97
13817741--13817843	51	2.1	51	81	15	130	34	17	17	30	1.93
13821133--13821297	40	4.1	40	77	11	140	29	18	24	26	1.98
13821149--13821297	80	1.9	80	80	5	176	31	19	23	25	1.98
13821356--13821453	40	2.4	41	85	6	121	21	23	28	26	1.99
13821326--13821801	196	2.4	195	81	7	581	26	20	23	28	1.99
13822209--13822245	15	2.6	14	87	8	56	18	0	40	40	1.51
13822316--13822366	23	2.1	26	82	10	63	35	1	5	56	1.35
13822543--13822585	14	2.9	15	82	6	52	16	0	46	37	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13825082--13825146	9	7.7	9	71	13	57	43	16	0	40	1.49
13825078--13825167	25	3.8	24	83	13	107	43	15	0	41	1.47
13825110--13825179	12	6.0	12	70	18	58	44	15	0	40	1.47
13830277--13830369	21	4.4	21	87	0	123	36	16	43	4	1.67
13830219--13830455	129	1.8	129	86	0	339	40	17	31	11	1.85
13830782--13830970	43	4.4	43	87	2	274	24	16	32	25	1.96
13831246--13831345	43	2.3	43	81	3	130	25	18	30	27	1.98
13832478--13832598	3	40.7	3	73	4	93	32	5	2	59	1.34
13837193--13837220	12	2.3	12	100	0	56	0	21	50	28	1.49
13842824--13842887	29	2.2	29	88	0	92	43	17	9	29	1.80
13843423--13843480	25	2.3	25	96	0	107	25	12	12	50	1.74
13844774--13844821	19	2.5	19	83	10	53	25	2	0	72	0.95
13844787--13844828	14	3.3	13	81	15	52	23	4	0	71	1.05
13847435--13847468	16	2.1	16	89	10	52	35	2	20	41	1.68
13857944--13858015	22	3.3	22	94	0	117	30	16	27	25	1.97
13869015--13869051	14	2.6	14	91	0	56	27	2	2	67	1.17
13875809--13876016	104	2.0	104	100	0	416	43	7	16	32	1.76
13880404--13880465	28	2.2	29	88	2	90	56	8	1	33	1.38
13883740--13883776	9	4.1	9	92	0	65	45	13	10	29	1.77
13883986--13884044	30	2.0	30	86	6	84	20	38	0	40	1.53
13884719--13884744	5	5.2	5	100	0	52	23	19	19	38	1.93
13886291--13886380	26	3.4	26	72	14	67	33	23	17	25	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13886423--13886469	24	2.0	24	82	0	58	27	27	21	23	1.99
13890447--13890476	14	2.2	13	94	5	51	13	16	0	70	1.18
13890420--13890579	57	2.7	57	83	8	191	30	16	6	46	1.72
13901218--13901279	27	2.3	27	94	2	106	22	16	14	46	1.83
13904305--13904366	3	20.7	3	96	0	115	67	1	0	30	1.00
13906238--13906272	2	18.0	2	94	5	63	51	0	0	48	1.00
13909187--13909219	14	2.3	15	89	5	50	39	0	3	57	1.14
13910899--13910956	29	2.0	29	86	3	80	56	3	1	37	1.26
13913302--13913382	40	2.0	41	85	7	112	23	19	25	30	1.98
13916982--13917028	17	2.8	17	78	9	51	19	25	0	55	1.43
13927651--13927848	86	2.3	85	81	5	238	27	16	25	30	1.97
13927651--13927818	43	3.9	43	88	3	225	25	16	27	30	1.97
13931696--13931740	24	1.9	24	86	4	65	31	0	0	68	0.89
13931758--13931813	25	2.2	25	83	6	67	26	5	5	62	1.39
13933069--13933116	19	2.5	18	83	12	60	16	12	12	58	1.63
13938220--13938704	41	10.8	44	69	17	232	30	18	21	29	1.97
13938313--13938659	137	2.6	134	83	6	425	32	18	20	29	1.96
13937929--13938607	321	2.1	328	84	7	902	31	17	21	29	1.96
13938540--13938704	44	3.8	44	79	3	147	29	20	20	29	1.98
13938761--13938841	44	2.0	41	83	11	103	30	18	22	28	1.97
13940192--13940235	23	2.0	23	86	4	63	31	0	0	68	0.90
13952118--13952154	15	2.5	15	90	0	56	45	10	8	35	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13954986--13955360	105	3.6	105	84	4	494	32	17	12	37	1.88
13961081--13961216	63	2.2	63	84	7	172	41	5	16	36	1.73
13961501--13961582	31	2.6	30	79	7	74	29	19	8	42	1.81
13961945--13962051	31	3.5	30	70	19	87	41	9	21	28	1.84
13961916--13962108	59	3.2	58	80	10	187	45	10	17	26	1.81
13963983--13964575	296	2.0	297	96	1	1102	31	13	15	39	1.87
13968674--13968740	11	5.9	12	70	18	54	43	2	0	53	1.16
13975005--13975107	47	2.3	46	80	14	108	2	23	8	65	1.35
13979821--13979845	12	2.1	12	100	0	50	8	16	32	44	1.76
13980023--13980226	41	5.0	41	85	4	252	21	21	26	29	1.99
13980022--13980226	83	2.5	83	86	6	274	21	21	27	29	1.98
13980025--13980258	40	5.8	39	84	4	218	22	21	25	31	1.98
13980478--13980520	14	3.0	14	86	3	50	25	0	30	44	1.55
13980483--13980526	7	6.1	7	84	5	61	25	0	31	43	1.55
13981199--13981252	22	2.5	21	81	3	63	22	0	29	48	1.51
13981205--13981233	15	1.9	15	100	0	58	20	0	34	44	1.52
13981240--13981279	21	1.9	21	89	0	62	20	0	37	42	1.52
13981894--13981941	24	2.0	24	84	8	62	58	8	6	27	1.51
13984165--13984197	17	1.9	17	93	0	57	18	0	24	57	1.40
13986395--13986641	43	5.8	43	82	5	279	22	17	30	29	1.97
13986705--13986746	22	1.9	22	95	0	75	40	28	21	9	1.84
13990586--13990646	21	3.0	21	61	29	51	19	27	4	47	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13997744--13997781	5	7.6	5	85	11	51	44	21	13	21	1.85
13997736--13997781	20	2.3	20	88	7	67	41	21	13	23	1.88
13998722--13998767	23	2.0	23	100	0	92	26	21	17	34	1.95
13998833--13998888	28	2.0	28	92	0	94	25	10	28	35	1.89
14001256--14001293	16	2.6	16	84	16	55	23	7	0	68	1.16
14001432--14001456	10	2.5	10	100	0	50	24	0	12	64	1.27
14007255--14007543	125	2.3	125	90	1	463	32	20	20	26	1.97
14009159--14009200	13	3.0	14	82	6	50	2	11	11	73	1.18
14012512--14012551	21	1.9	21	90	10	64	5	22	42	30	1.75
14013497--14013535	7	5.6	7	85	11	53	58	15	0	25	1.37
14013497--14013549	14	3.8	14	83	14	65	58	15	0	26	1.37
14013497--14013549	21	2.5	21	90	0	88	58	15	0	26	1.37
14014644--14014678	14	2.6	14	86	4	54	68	0	0	31	0.90
14014729--14014776	11	4.4	11	80	17	55	45	0	33	20	1.52
14014720--14014776	22	2.6	22	81	13	64	45	0	31	22	1.53
14014737--14014779	11	4.0	10	85	14	59	48	0	30	20	1.50
14015801--14015825	13	1.9	13	100	0	50	48	0	4	48	1.20
14016464--14016569	41	2.6	40	88	7	144	33	6	4	54	1.47
14020007--14020046	21	1.9	21	85	10	55	37	2	32	27	1.70
14028258--14028302	21	2.0	22	91	8	74	60	2	4	33	1.29
14029625--14029706	16	5.4	16	74	14	84	17	0	25	57	1.40
14029607--14029691	14	5.8	14	71	13	64	18	0	24	56	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14029624--14029724	8	13.0	8	67	21	54	16	0	27	55	1.42
14029597--14029707	30	3.6	30	89	4	152	17	0	25	57	1.40
14034746--14034770	13	1.9	13	100	0	50	56	12	16	16	1.68
14037030--14037182	43	3.6	43	78	7	132	24	15	26	33	1.95
14037030--14037159	44	3.0	44	83	3	122	23	16	29	31	1.96
14042100--14042145	23	2.0	24	82	4	58	39	2	4	54	1.32
14042160--14042202	9	4.6	9	80	8	50	23	9	0	67	1.19
14044073--14044116	21	2.2	20	83	4	52	61	0	2	36	1.09
14044084--14044141	8	8.3	7	78	14	50	58	0	1	39	1.08
14044240--14044317	24	3.3	23	77	7	77	44	0	1	53	1.08

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