genome.fa.s4.2.7.7.80.10.50.1000.16.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  16  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)
4963386--4963446	21	3.0	21	80	2	61	49	24	3	22	1.65
4963456--4963496	20	2.0	21	90	4	66	26	4	26	41	1.76
4974936--4974986	22	2.3	22	100	0	102	27	33	0	39	1.57
4974963--4975046	40	2.1	40	86	4	116	34	22	0	42	1.54
4975032--4975096	31	2.1	31	94	0	112	33	0	0	66	0.92
4976177--4976201	7	3.6	7	100	0	50	28	0	12	60	1.32
4976853--4976887	18	1.9	18	88	0	52	25	34	8	31	1.86
4977047--4977871	29	28.1	29	83	7	995	50	26	0	22	1.52
4977047--4977871	57	14.1	57	84	7	985	50	26	0	22	1.52
4977047--4977871	86	9.7	86	83	5	1009	50	26	0	22	1.52
4977665--4977698	6	5.7	6	100	0	68	35	50	0	14	1.44
4977636--4977726	47	1.9	47	88	0	137	42	39	0	17	1.49
4980976--4981316	126	2.7	127	93	0	585	32	20	15	31	1.94
4982481--4982510	15	2.0	15	93	0	51	30	0	0	70	0.88
4987342--4987386	22	2.0	22	83	8	56	22	2	8	66	1.30
4987671--4987740	35	2.0	34	81	8	79	54	2	4	38	1.35
4987994--4988076	37	2.3	37	81	6	89	63	4	3	27	1.31
4991738--4991787	3	16.7	3	95	0	91	64	0	2	34	1.05
4994146--4994190	18	2.6	17	83	13	56	35	2	0	62	1.08
5000593--5000698	53	2.0	51	89	3	158	32	15	9	43	1.78
5004536--5004596	28	2.2	28	97	2	115	29	13	26	31	1.93
5005610--5005665	28	2.0	28	96	0	103	30	21	19	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5011918--5012279	69	5.2	69	78	3	328	25	17	23	33	1.96
5020940--5020995	16	3.3	17	78	9	53	50	1	5	42	1.35
5021678--5021759	39	2.1	38	82	8	94	39	1	0	59	1.05
5024312--5024345	17	2.1	17	88	5	52	44	0	0	55	0.99
5029535--5029580	20	2.2	20	80	3	56	69	6	2	21	1.22
5031028--5031201	90	1.9	90	89	4	271	31	18	18	30	1.96
5035695--5035727	14	2.4	14	100	0	66	36	0	15	48	1.45
5035836--5035907	26	2.8	26	82	2	74	51	0	12	36	1.40
5036041--5036082	3	14.3	3	80	14	52	61	0	2	35	1.09
5036044--5036082	8	4.9	8	81	12	53	61	0	2	35	1.10
5037180--5037411	41	5.7	40	81	5	227	20	24	24	30	1.98
5037163--5037411	82	3.0	78	78	9	255	20	25	23	30	1.98
5037388--5037498	41	2.7	41	83	4	127	28	23	26	21	1.99
5039211--5039236	7	3.7	7	100	0	52	15	0	26	57	1.38
5041813--5041848	15	2.5	15	90	4	56	11	16	8	63	1.49
5042496--5042551	9	6.8	9	73	19	59	48	16	0	35	1.46
5042449--5042551	43	2.5	40	84	7	127	48	12	0	37	1.48
5042505--5042554	16	3.2	16	94	2	84	48	16	0	36	1.46
5048129--5048296	66	2.5	66	85	1	203	41	17	27	13	1.87
5048267--5048316	21	2.4	21	86	0	64	36	18	42	4	1.69
5048650--5048754	42	2.5	42	81	9	115	20	18	31	30	1.96
5048651--5048817	43	3.9	42	77	10	142	21	19	29	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5048698--5048838	43	3.3	43	85	3	169	19	21	27	31	1.98
5049192--5049252	25	2.5	24	82	10	70	57	1	1	39	1.18
5063583--5063612	6	4.8	6	95	4	51	30	0	0	70	0.88
5063717--5064113	73	5.4	73	82	5	469	24	21	15	37	1.93
5063716--5064113	147	2.7	145	83	5	487	24	21	16	37	1.93
5066951--5066996	15	3.2	14	79	14	58	41	2	2	54	1.25
5067058--5067082	4	6.2	4	100	0	50	24	0	0	76	0.80
5070436--5071705	86	14.7	86	87	0	1748	26	23	20	29	1.99
5070700--5070921	43	5.2	42	63	18	98	28	23	20	27	1.99
5070436--5071699	258	4.9	258	90	0	1936	26	23	20	29	1.99
5072876--5072962	33	2.5	35	79	3	106	10	10	10	68	1.39
5084340--5084380	21	1.9	22	90	5	66	24	7	9	58	1.55
5086419--5086997	44	13.2	44	62	7	199	27	27	24	20	1.99
5086414--5087045	88	7.2	88	89	0	931	26	28	24	20	1.99
5086832--5086974	43	3.3	42	67	9	115	27	29	26	16	1.97
5087008--5087219	44	4.9	43	73	4	201	26	24	23	25	2.00
5087034--5087268	44	5.4	44	71	6	190	28	22	21	27	1.99
5087008--5087283	87	3.2	87	89	0	408	28	22	23	25	1.99
5090211--5090309	23	4.3	23	88	0	144	21	22	26	30	1.99
5093311--5093353	20	2.2	20	92	8	72	30	0	4	65	1.13
5093571--5093632	15	3.9	15	70	8	52	58	3	0	38	1.15
5093733--5093770	14	2.4	17	87	12	55	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5093750--5093788	12	3.4	11	80	13	51	46	0	2	51	1.14
5099008--5099038	4	7.8	4	100	0	62	25	0	0	74	0.82
5105166--5105469	44	7.0	44	62	21	142	25	22	23	28	1.99
5105149--5105586	86	5.1	86	90	0	671	26	22	23	27	1.99
5105190--5105499	45	7.2	43	62	22	114	27	22	23	26	2.00
5105323--5105555	44	5.4	42	65	23	137	24	23	24	27	2.00
5105557--5105741	46	4.1	46	64	13	114	27	21	23	28	1.99
5105534--5107139	134	12.0	133	93	1	2590	27	20	23	29	1.99
5105534--5107139	535	3.0	536	92	1	2693	27	20	23	29	1.99
5105534--5107158	669	2.4	669	93	1	2747	27	20	23	29	1.98
5106815--5107011	46	4.4	45	65	8	114	27	18	23	29	1.98
5106980--5107078	46	2.2	46	83	3	128	23	20	25	31	1.98
5107142--5107267	40	2.9	44	79	12	163	35	23	20	20	1.96
5107357--5107667	44	7.2	44	65	7	116	30	18	24	26	1.98
5107235--5107787	130	4.3	130	90	1	840	28	19	24	26	1.99
5107235--5107787	260	2.1	260	93	0	928	28	19	24	26	1.99
5107562--5107739	43	4.1	43	64	4	97	26	19	26	26	1.99
5107581--5107751	43	4.0	43	65	7	121	27	18	27	26	1.98
5109679--5109705	4	6.8	4	100	0	54	25	0	0	74	0.83
5115858--5115896	20	2.0	20	90	10	62	15	23	5	56	1.59
5116098--5116290	50	3.8	50	77	4	181	28	24	19	27	1.98
5116604--5116657	26	2.1	26	100	0	108	33	31	7	27	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5118610--5118685	23	3.3	23	80	5	91	30	26	19	23	1.98
5125082--5125146	5	13.8	5	83	16	86	38	0	0	61	0.96
5125082--5125142	9	6.6	9	82	14	63	37	0	0	62	0.96
5125086--5125146	14	4.3	14	91	8	97	37	0	0	62	0.96
5126102--5126165	22	2.9	22	80	0	74	17	25	18	39	1.92
5126773--5126811	19	2.1	18	85	4	51	38	0	17	43	1.50
5128545--5128582	20	1.9	20	94	0	67	39	15	2	42	1.61
5130454--5130542	41	2.2	41	97	0	169	41	15	20	22	1.90
5132653--5132782	40	3.3	40	74	7	122	24	16	25	33	1.95
5133712--5133789	27	2.9	27	92	0	129	29	21	32	16	1.96
5133864--5133933	19	3.7	19	82	3	97	37	10	0	52	1.35
5133869--5133939	37	1.9	37	100	0	142	39	11	0	49	1.39
5134225--5134283	19	3.2	18	80	4	73	38	10	1	49	1.47
5134233--5134283	18	2.7	19	81	3	68	37	11	0	50	1.39
5134280--5134326	18	2.6	19	83	6	53	55	0	8	36	1.31
5134402--5134479	27	2.9	27	82	3	95	19	28	20	32	1.97
5134542--5134587	24	1.9	24	95	0	83	58	2	6	32	1.36
5135504--5135529	5	5.2	5	100	0	52	42	19	19	19	1.90
5135627--5135683	7	8.1	7	96	0	105	43	29	0	26	1.55
5147534--5147585	18	2.9	18	75	16	54	34	1	1	61	1.18
5148530--5148566	19	1.9	19	88	0	56	62	0	2	35	1.10
5148558--5148664	54	2.0	54	80	10	121	47	4	0	46	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5149024--5149063	20	2.0	21	90	9	66	52	5	0	42	1.23
5149019--5149065	20	2.5	19	80	19	62	48	4	0	46	1.21
5151863--5151903	18	2.3	18	91	8	66	21	4	31	41	1.74
5154094--5154136	23	2.0	23	81	9	54	34	2	25	37	1.69
5154639--5154668	11	2.8	11	95	5	53	43	0	0	56	0.99
5154802--5154836	17	2.1	16	94	5	61	28	0	0	71	0.86
5154803--5154857	26	2.1	27	86	10	78	27	1	1	69	1.09
5155718--5155776	21	2.9	21	76	16	61	67	1	0	30	1.00
5155862--5155948	23	3.7	23	75	9	86	47	0	0	52	1.00
5156556--5156607	26	2.0	26	85	7	70	34	7	3	53	1.48

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