genome.fa.s8.2.7.7.80.10.50.1000.171.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  171  of  190  ( 22705 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)
49895086--49895220	25	5.6	25	80	10	133	39	19	22	19	1.93
49896157--49896194	3	13.0	3	84	15	53	63	0	0	36	0.95
49896151--49896194	9	5.0	8	86	13	52	61	0	0	38	0.96
49898944--49899039	23	4.2	23	78	5	113	32	26	18	22	1.97
49898951--49899041	46	2.0	46	88	0	137	31	25	20	21	1.98
49901974--49902048	38	2.0	38	91	0	123	30	20	24	25	1.98
49901975--49902039	19	3.4	19	75	8	78	29	20	26	24	1.99
49902788--49902812	5	5.0	5	100	0	50	80	0	0	20	0.72
49903663--49903720	22	2.6	22	81	7	64	41	17	5	36	1.72
49908437--49908468	11	2.9	11	95	0	55	81	0	0	18	0.70
49908691--49908739	25	2.0	24	88	7	73	61	2	0	36	1.08
49908691--49908844	46	3.4	45	74	11	143	57	1	4	36	1.31
49908712--49908773	24	2.7	23	83	13	76	59	1	3	35	1.23
49908691--49908848	23	6.9	23	72	15	105	56	1	4	36	1.30
49915419--49915530	42	2.7	42	84	0	125	42	20	21	15	1.88
49915461--49915541	21	3.9	21	66	0	54	44	18	18	18	1.87
49919056--49919099	11	3.8	11	80	11	52	34	0	2	63	1.07
49922558--49922679	23	5.3	23	84	0	172	22	20	26	31	1.98
49922560--49922679	46	2.6	46	91	0	195	21	20	26	30	1.98
49930008--49930106	23	4.3	23	90	0	162	20	21	27	31	1.98
49931343--49931463	21	5.8	21	72	0	98	17	24	17	40	1.90
49931337--49931477	42	3.4	42	82	0	147	18	25	17	39	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49933076--49933125	24	2.0	26	84	7	68	38	22	22	18	1.94
49933086--49933137	25	2.1	24	82	10	61	36	25	23	15	1.93
49933165--49933222	24	2.3	26	76	5	66	43	22	20	13	1.87
49934218--49934248	9	3.4	9	90	0	53	25	12	22	38	1.90
49934300--49934336	9	4.1	9	92	0	65	45	13	10	29	1.77
49934550--49934607	29	2.0	30	86	3	82	22	34	0	43	1.54
49934660--49934696	20	1.9	19	89	10	58	24	32	0	43	1.55
49937120--49937177	25	2.2	26	79	14	66	29	24	27	18	1.98
49937134--49937275	24	5.8	25	72	8	114	32	18	28	21	1.96
49940443--49940467	5	5.0	5	100	0	50	20	0	0	80	0.72
49941962--49942010	6	7.8	6	84	6	62	44	16	20	18	1.86
49941990--49942118	45	2.9	44	89	2	186	41	22	17	18	1.91
49945688--49945726	19	2.1	19	85	9	53	43	0	12	43	1.42
49945807--49946053	46	5.5	46	91	2	394	34	14	22	28	1.94
49945807--49946052	91	2.7	91	92	1	406	34	15	22	28	1.94
49945807--49946055	137	1.8	135	89	4	369	34	14	22	28	1.94
49953847--49953901	3	18.3	3	80	0	65	29	3	3	63	1.28
49954196--49954295	10	10.0	10	79	14	93	81	0	18	1	0.76
49954196--49954293	22	4.6	21	84	10	112	81	0	17	1	0.74
49954196--49954291	44	2.2	42	85	10	133	81	0	17	1	0.75
49954618--49955224	18	34.1	18	69	15	243	30	12	10	46	1.74
49954643--49955140	17	28.2	16	69	15	138	29	12	10	47	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49954618--49955212	35	16.7	35	70	13	238	30	12	10	46	1.75
49967185--49967699	78	6.6	78	79	8	482	29	16	19	34	1.94
49967193--49967694	158	3.2	157	80	9	523	29	16	19	33	1.94
49967898--49968030	30	4.5	29	79	7	142	33	18	6	41	1.75
49967897--49968025	59	2.2	58	80	5	143	34	18	5	41	1.73
49968270--49968324	16	3.7	15	83	13	69	65	0	32	1	1.03
49968386--49968419	3	11.3	3	93	0	59	70	0	29	0	0.87
49968704--49968764	18	3.3	18	86	11	88	81	0	18	0	0.68
49968700--49968768	30	2.3	30	92	2	113	82	0	17	0	0.67
49968902--49968946	8	6.0	8	75	15	51	24	0	4	71	1.05
49969038--49969416	18	21.1	18	69	16	173	30	12	11	46	1.76
49969040--49969078	20	1.9	21	94	5	71	33	15	10	41	1.81
49969042--49969427	35	10.8	34	72	15	221	30	12	10	46	1.75
49969109--49969425	53	6.0	50	74	15	207	29	11	10	47	1.74
49972564--49972733	18	9.6	18	75	10	152	43	11	12	31	1.79
49972528--49972701	54	3.2	51	81	11	197	43	11	13	31	1.79
49972480--49972682	109	1.9	107	82	11	252	44	10	14	30	1.79
49972527--49972732	36	5.8	35	76	8	175	43	11	12	33	1.78
49972724--49972765	20	2.0	22	86	9	61	38	2	16	42	1.61
49973333--49973380	7	6.9	7	81	9	62	0	16	0	83	0.65
49973638--49973703	6	10.3	6	79	8	51	0	22	0	77	0.77
49973651--49973706	9	6.1	9	84	10	60	0	25	0	75	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49973644--49973707	16	3.9	16	78	13	67	0	25	0	75	0.81
49973668--49973707	3	13.0	3	89	5	62	0	32	0	67	0.91
49973638--49973706	19	3.6	19	84	2	84	0	23	0	76	0.78
49973655--49973714	19	3.2	19	87	0	84	0	31	0	68	0.90
49974050--49974207	30	5.2	29	87	6	226	37	1	23	37	1.66
49974049--49974207	60	2.6	60	94	1	273	37	1	23	37	1.66
49974388--49976176	155	11.6	155	84	8	1959	35	20	16	26	1.94
49974369--49976182	77	23.5	78	86	6	2068	36	20	16	26	1.94
49974369--49976177	232	7.8	232	85	7	2066	36	20	16	26	1.94
49976156--49976206	20	2.5	20	87	0	84	43	11	13	31	1.80
49976444--49976491	19	2.6	18	77	9	51	16	27	10	45	1.80
49977047--49977088	9	4.8	9	82	5	59	0	0	11	88	0.53
49977047--49977088	14	3.2	13	87	9	59	0	0	11	88	0.53
49983042--49983347	55	5.5	55	79	9	187	44	10	14	31	1.78
49983085--49983347	37	7.1	37	75	10	198	44	10	14	30	1.78
49983044--49983347	18	16.6	18	73	13	210	44	10	14	30	1.78
49983788--49983814	5	5.4	5	100	0	54	62	0	0	37	0.95
49983947--49983989	7	5.9	7	78	10	50	0	16	0	83	0.64
49983947--49983978	16	2.0	16	100	0	64	0	12	0	87	0.54
49983947--49983991	23	2.0	23	90	0	72	0	15	0	84	0.62
49984077--49984137	24	2.5	25	84	10	81	9	24	37	27	1.87
49984268--49984320	7	6.9	7	87	12	61	13	11	0	75	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49984269--49984321	8	6.6	8	85	14	74	11	11	0	77	1.00
49984269--49984340	33	2.2	32	90	9	110	8	15	0	76	1.01
49984321--49984350	4	7.5	4	100	0	60	0	23	0	76	0.78
49984346--49984375	3	10.0	3	100	0	60	0	33	0	66	0.92
49984722--49984878	30	5.2	30	89	3	253	38	2	22	36	1.68
49984874--49984905	8	3.9	8	92	8	55	12	0	9	78	0.97
49987190--49987234	23	2.0	22	82	4	54	40	4	17	37	1.70
49990997--49991043	22	2.2	21	84	3	58	46	21	14	17	1.83
49991009--49991070	29	2.1	29	96	0	115	41	22	20	14	1.89
49996287--49996311	12	2.1	12	100	0	50	60	16	8	16	1.58
49999796--49999844	25	1.9	25	84	12	64	55	10	2	32	1.45
50003743--50003771	15	1.9	15	100	0	58	27	27	13	31	1.94
50004453--50004502	25	2.0	25	100	0	100	28	32	20	20	1.97
50006691--50006794	3	34.7	3	100	0	208	33	0	0	66	0.92
50007586--50007624	20	2.0	20	100	0	78	35	17	20	25	1.95
50009334--50009488	36	4.0	36	78	15	166	28	20	14	37	1.91
50009370--50009524	46	3.6	46	76	16	195	28	21	12	37	1.90
50009291--50009524	82	2.9	82	93	1	393	28	21	13	36	1.92
50016423--50016475	23	2.3	23	93	0	97	32	26	20	20	1.98
50016922--50016980	30	2.0	30	83	6	75	28	25	6	38	1.81
50019905--50020058	36	4.0	36	79	16	175	28	20	14	36	1.92
50019941--50020094	46	3.6	46	75	18	186	28	22	13	35	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50019862--50020094	81	2.9	82	93	2	384	28	21	14	35	1.93
50019987--50020058	35	2.0	36	94	2	128	26	20	15	37	1.92
50024712--50024760	24	2.0	24	96	0	89	42	0	6	51	1.27
50035306--50035337	5	6.4	5	100	0	64	0	0	59	40	0.97
50043943--50043967	7	3.6	7	100	0	50	28	28	28	16	1.97
50048097--50048122	12	2.2	12	100	0	52	7	15	30	46	1.74
50048129--50048261	39	3.4	39	79	9	130	35	21	21	22	1.96
50048302--50048415	40	2.8	41	85	6	151	26	21	21	30	1.98
50048943--50048978	15	2.4	15	95	0	63	16	11	16	55	1.68
50050637--50050792	41	4.1	36	78	18	172	23	25	19	31	1.98

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