genome.fa.s4.2.7.7.80.10.50.1000.15.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  15  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)
4773187--4773220	15	2.1	17	89	10	54	44	2	0	52	1.16
4776471--4776535	30	2.2	30	88	0	94	24	29	4	41	1.75
4778294--4778330	18	2.1	18	94	0	65	24	27	8	40	1.83
4780025--4780294	127	2.1	127	86	2	382	29	15	17	38	1.90
4780353--4780419	33	2.1	31	91	5	107	37	16	1	44	1.57
4784435--4784510	31	2.5	30	77	14	82	53	3	13	28	1.57
4786924--4786990	25	2.7	25	85	0	89	32	16	25	25	1.96
4786979--4787144	73	2.3	72	77	13	178	37	21	22	19	1.94
4787055--4787161	25	4.3	25	73	10	69	36	20	22	20	1.95
4787102--4787161	26	2.3	26	85	2	77	38	20	21	20	1.94
4787113--4787167	26	2.1	26	82	0	65	40	20	21	18	1.92
4795706--4795954	50	4.8	50	84	4	291	20	28	23	26	1.99
4795705--4795954	100	2.4	104	87	5	346	20	28	23	26	1.99
4796049--4796080	13	2.5	13	94	0	55	56	12	0	31	1.37
4796292--4796349	30	1.9	30	89	0	89	31	24	3	41	1.71
4801828--4801869	19	2.2	19	83	8	50	42	2	2	52	1.27
4803080--4803128	23	2.1	24	85	7	66	46	4	0	48	1.20
4811358--4811397	20	2.1	19	85	4	53	55	7	2	35	1.42
4815399--4815460	28	2.2	28	85	2	88	62	6	0	30	1.20
4815420--4815466	18	2.6	18	84	15	62	57	4	0	38	1.18
4815414--4815461	18	2.5	19	86	6	62	60	4	0	35	1.16
4815863--4815900	15	2.5	15	86	0	58	60	5	2	31	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4816060--4816114	24	2.2	23	78	15	56	41	1	1	54	1.21
4816067--4816124	25	2.3	25	76	5	64	50	3	0	46	1.18
4818271--4818311	20	2.0	20	100	0	82	48	9	0	41	1.36
4823033--4823063	11	2.7	11	95	5	53	3	35	6	54	1.42
4823167--4823200	17	2.0	17	88	0	50	0	38	5	55	1.24
4828347--4828375	3	9.7	3	100	0	58	65	0	0	34	0.93
4829910--4829969	18	3.4	16	78	17	57	68	3	0	28	1.05
4831241--4831279	20	1.9	21	89	5	62	41	0	2	56	1.13
4832253--4832280	2	14.0	2	100	0	56	50	0	0	50	1.00
4834878--4834983	37	2.8	37	87	7	144	35	2	0	61	1.11
4834935--4835026	28	3.2	29	76	14	100	38	1	0	60	1.04
4834952--4835031	11	7.9	11	74	20	77	42	1	0	56	1.07
4834963--4834996	17	2.0	17	100	0	68	41	0	0	58	0.98
4838886--4838925	8	4.6	8	82	17	53	22	5	0	72	1.04
4838870--4838925	27	2.0	28	93	6	96	26	7	0	66	1.18
4838870--4838962	29	3.2	28	80	11	91	32	4	0	63	1.14
4838942--4838975	17	2.0	17	94	0	59	44	0	0	55	0.99
4838923--4838989	29	2.3	28	90	10	100	40	1	0	58	1.07
4838930--4838999	10	7.0	10	72	18	65	42	1	0	55	1.08
4840095--4840152	30	1.9	31	82	10	75	37	15	5	41	1.70
4840149--4840259	29	3.8	29	96	1	195	30	17	8	44	1.77
4840126--4840259	59	2.3	58	87	3	171	32	16	8	42	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4840632--4840697	13	4.8	14	78	17	68	80	0	18	1	0.79
4840638--4840698	7	8.7	7	81	12	72	81	0	16	1	0.76
4840638--4840698	20	3.1	19	79	15	63	81	0	16	1	0.76
4840635--4840697	6	10.3	6	74	19	51	80	0	17	1	0.78
4840632--4840698	15	4.6	15	76	10	68	80	0	17	1	0.79
4840826--4840902	24	3.1	25	80	10	88	29	40	24	5	1.77
4840824--4840866	8	5.2	8	80	2	50	32	44	20	2	1.65
4841287--4841346	17	3.5	17	80	8	68	33	10	11	45	1.74
4841286--4841350	18	3.7	18	85	2	87	32	10	12	44	1.76
4841399--4841485	18	4.7	18	77	8	77	36	11	9	42	1.73
4841424--4841514	38	2.5	37	82	7	96	34	12	9	43	1.75
4841490--4841575	34	2.6	34	81	7	97	26	13	11	47	1.78
4842737--4842829	40	2.3	40	89	7	136	60	1	4	34	1.24
4851898--4852517	288	2.2	288	93	0	1051	38	15	17	28	1.90
4859395--4859420	2	13.0	2	100	0	52	50	0	0	50	1.00
4862071--4862105	17	2.0	18	88	5	54	40	0	5	54	1.24
4864122--4864165	21	2.0	22	95	4	81	34	18	13	34	1.90
4881614--4881706	30	3.1	29	74	10	87	39	17	7	35	1.78
4883087--4883158	36	2.0	36	100	0	144	36	19	11	33	1.87
4884161--4884211	19	2.8	18	85	11	68	52	0	0	47	1.00
4884161--4884214	18	3.0	17	86	8	72	55	0	0	44	0.99
4884167--4884214	9	5.3	9	87	7	71	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4887847--4887877	11	2.8	11	90	0	53	67	0	0	32	0.91
4894325--4894369	20	2.3	19	82	14	56	40	8	2	48	1.47
4897406--4897449	23	1.9	23	90	0	70	72	0	15	11	1.11
4908895--4908920	13	2.0	13	100	0	52	46	0	0	53	1.00
4910875--4910899	13	1.9	13	100	0	50	48	0	8	44	1.32
4915806--4915854	16	3.1	16	87	0	71	38	2	34	24	1.67
4916066--4916120	16	3.4	17	78	12	55	54	1	0	43	1.10
4916185--4916236	15	3.6	15	80	12	56	53	1	0	44	1.11
4916069--4916240	59	2.9	58	68	14	152	51	4	1	42	1.31
4916553--4916591	20	2.0	20	84	0	51	43	2	12	41	1.56
4916864--4916899	12	3.1	12	92	4	56	25	2	2	69	1.15
4916853--4916915	23	2.7	24	73	11	76	28	4	4	61	1.36
4926321--4926351	6	5.2	6	100	0	62	16	35	32	16	1.91
4926837--4926878	3	14.0	3	100	0	84	33	33	0	33	1.58
4936549--4936581	16	2.1	16	94	0	57	3	15	6	75	1.11
4936607--4936637	3	10.3	3	100	0	62	64	0	0	35	0.94
4938698--4938779	30	2.6	31	73	5	85	25	15	10	47	1.78
4939417--4939722	17	17.5	17	70	13	158	44	12	12	30	1.80
4939426--4939723	18	16.9	17	67	15	126	44	12	12	30	1.80
4939414--4939722	35	8.8	33	75	14	223	44	12	12	30	1.80
4939839--4939904	20	3.6	18	75	17	55	45	7	13	33	1.72
4940119--4940175	26	2.2	25	84	3	69	66	8	3	21	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4940258--4940307	16	2.9	17	82	8	66	0	22	0	78	0.76
4940263--4940314	7	7.7	7	76	6	54	0	17	0	82	0.66
4940278--4940316	12	3.1	12	82	10	51	0	15	0	84	0.62
4940259--4940316	8	7.2	8	74	14	57	0	18	0	81	0.70
4940259--4940316	17	3.6	17	82	11	61	0	18	0	81	0.70
4940624--4940694	10	7.1	10	72	21	60	0	23	0	76	0.79
4940776--4940852	14	4.4	17	71	23	54	0	16	6	76	0.98
4940777--4940849	20	3.8	19	75	21	73	0	16	6	76	0.99
4941189--4941335	59	2.5	58	82	7	179	38	3	23	34	1.72
4941189--4941336	30	5.0	31	79	8	164	38	3	23	34	1.72
4941528--4942713	75	15.7	72	89	3	1159	36	20	15	27	1.93
4941587--4942330	78	9.7	78	89	3	703	35	19	15	29	1.93
4941605--4942731	227	5.0	226	83	8	873	37	19	15	27	1.92
4943588--4943626	15	2.6	14	84	11	51	0	5	10	84	0.76
4949887--4949938	16	3.2	16	78	10	61	48	11	9	30	1.72
4949887--4949975	17	5.2	17	73	14	58	43	13	10	32	1.77
4949919--4949959	20	2.0	21	90	9	68	39	12	7	41	1.70
4949885--4950000	52	2.3	51	79	10	130	46	12	7	32	1.71
4950031--4950314	18	16.1	18	71	16	202	42	11	14	31	1.81
4950035--4950314	35	8.0	35	77	9	241	43	11	13	31	1.81
4950035--4950314	17	15.9	17	70	15	151	43	11	13	31	1.81
4950432--4950475	21	2.2	20	87	4	61	40	9	9	40	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4950460--4950499	19	2.0	20	85	4	55	60	10	10	20	1.57
4950659--4950708	6	8.7	6	80	10	52	66	0	2	32	1.03
4950713--4950769	26	2.2	25	84	3	69	66	8	3	21	1.34
4953669--4953809	30	4.8	28	81	10	149	40	2	23	34	1.67
4953661--4953809	59	2.5	58	82	6	172	39	2	22	35	1.66
4954603--4954654	25	2.2	25	86	6	72	65	1	7	25	1.30
4958181--4958259	36	2.4	33	82	16	92	45	0	12	41	1.42
4960268--4960339	24	2.8	26	81	6	76	16	29	23	30	1.96
4960359--4960422	25	2.6	24	75	5	65	18	20	26	34	1.96
4963388--4963440	20	2.6	21	81	3	63	50	26	3	18	1.64

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