genome.fa.s9.2.7.7.80.10.50.1000.128.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  128  of  226  ( 27023 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)
43110954--43111026	37	2.0	37	100	0	146	31	21	13	32	1.93
43115743--43115967	51	4.4	50	78	4	211	29	28	16	25	1.97
43117873--43117930	25	2.3	26	82	11	77	18	24	22	34	1.96
43117984--43118054	25	2.8	25	80	4	72	23	26	19	29	1.98
43120567--43120610	8	5.5	8	83	8	54	36	2	0	61	1.09
43123603--43123641	14	2.8	14	84	0	51	35	12	23	28	1.91
43124515--43124553	19	2.1	19	85	0	51	51	0	2	46	1.14
43124541--43124606	29	2.2	30	86	10	91	53	0	1	45	1.09
43124560--43124609	16	3.2	16	70	18	52	50	0	0	50	1.00
43131671--43131742	34	2.1	35	82	7	85	29	12	23	34	1.92
43133725--43134111	42	9.2	42	90	0	522	20	19	24	35	1.96
43134942--43135364	152	2.8	148	85	5	562	42	4	10	42	1.59
43135882--43135928	24	1.9	24	83	12	60	31	6	6	55	1.51
43138162--43138225	32	2.0	32	96	0	119	51	18	17	12	1.76
43147552--43147600	16	3.1	16	93	0	89	34	6	36	22	1.79
43147580--43147669	45	2.0	44	89	6	137	32	5	28	33	1.80
43148074--43148108	18	2.0	17	88	5	52	54	0	0	45	0.99
43147812--43148228	120	3.5	120	92	0	692	49	5	2	42	1.39
43153473--43153611	27	5.1	27	83	0	179	36	13	25	24	1.92
43153473--43153638	54	3.1	53	85	1	215	36	13	24	24	1.92
43153473--43153641	81	2.1	81	82	4	198	36	13	25	24	1.92
43156471--43156508	12	3.3	12	82	14	53	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43175220--43175354	40	3.4	40	89	2	200	11	16	28	44	1.81
43177624--43177710	25	3.5	25	75	6	86	33	19	26	20	1.97
43184094--43184160	25	2.7	24	75	11	64	32	20	29	16	1.95
43184106--43184198	24	3.8	24	69	9	73	33	21	27	17	1.96
43184266--43184320	25	2.2	25	86	0	83	38	18	25	18	1.93
43184467--43184522	20	2.7	21	72	10	53	50	12	0	37	1.41
43189038--43189166	42	3.1	42	76	8	127	44	14	22	18	1.86
43189058--43189160	21	4.9	21	62	8	57	42	15	22	19	1.88
43192165--43192203	18	2.2	18	86	9	53	58	2	2	35	1.25
43192458--43192640	94	1.9	97	87	5	273	50	3	2	43	1.32
43192815--43192850	2	18.0	2	100	0	72	50	0	0	50	1.00
43195377--43195426	20	2.5	19	75	9	55	52	2	12	34	1.50
43196041--43196169	25	5.2	24	68	15	75	20	25	20	32	1.97
43196179--43196226	24	2.0	23	88	4	69	16	22	20	39	1.92
43196046--43196222	73	2.4	72	80	6	203	19	25	20	34	1.96
43198184--43198220	15	2.4	16	82	13	51	72	5	0	21	1.04
43202922--43202951	6	5.0	6	100	0	60	66	0	0	33	0.92
43203369--43203416	21	2.2	22	85	7	71	58	2	2	37	1.22
43203358--43203435	30	2.6	30	81	6	77	58	1	1	38	1.14
43220673--43220750	25	3.2	24	75	14	79	42	1	3	52	1.27
43220690--43220889	62	3.1	62	67	13	147	43	3	5	48	1.41
43233055--43233088	17	2.1	17	88	5	52	76	11	0	11	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43233918--43233942	12	2.1	12	100	0	50	40	0	8	52	1.31
43249565--43249610	20	2.3	20	84	0	65	45	15	13	26	1.82
43251530--43251580	26	2.0	25	88	3	75	66	3	5	23	1.30
43252149--43252186	19	2.1	18	90	5	58	63	5	5	26	1.37
43253666--43253775	44	2.5	44	85	2	141	30	21	20	28	1.98
43253904--43254062	50	3.2	50	63	7	115	27	23	19	29	1.98
43253871--43254178	100	3.1	100	89	0	465	26	22	20	30	1.98
43253920--43254077	50	3.2	50	66	3	129	26	22	19	31	1.98
43254118--43254237	50	2.4	51	80	6	120	25	29	19	26	1.98
43254004--43254615	267	2.3	266	91	0	972	25	26	21	27	1.99
43266760--43266810	26	2.0	25	88	3	75	66	3	5	23	1.30
43267150--43267178	2	14.5	2	100	0	58	51	0	0	48	1.00
43267436--43267476	19	2.1	18	86	13	55	63	7	4	24	1.40
43267476--43267517	18	2.1	20	75	25	52	61	4	0	33	1.17
43272997--43273044	19	2.5	19	72	3	51	16	10	4	68	1.33
43273389--43273453	23	2.8	23	83	6	78	24	4	35	35	1.76
43274401--43274446	20	2.3	20	84	0	65	45	15	13	26	1.82
43275855--43275947	27	3.4	27	82	2	107	21	23	31	23	1.99
43276186--43276231	3	15.3	3	100	0	92	32	0	0	67	0.91
43279368--43279392	11	2.3	11	100	0	50	44	16	8	32	1.76
43281485--43282253	160	4.8	155	70	16	479	30	11	8	50	1.67
43281485--43282260	320	2.4	317	92	1	1259	30	10	8	50	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43282628--43282725	44	2.2	45	83	7	130	1	26	0	72	0.91
43282637--43282725	10	8.3	10	72	17	54	1	28	0	70	0.94
43282618--43282778	34	4.8	33	79	14	120	0	29	0	69	0.97
43282824--43282889	27	2.4	27	85	5	80	21	34	24	19	1.96
43285382--43285420	12	3.2	12	85	0	51	20	23	5	51	1.67
43285668--43285865	50	3.8	50	83	4	216	23	28	20	27	1.99
43287071--43287229	52	3.1	52	98	0	309	32	9	29	28	1.88
43287104--43287186	25	3.2	25	64	18	62	32	8	30	28	1.87
43291964--43292147	50	3.6	50	79	5	163	21	28	22	27	1.99
43299038--43299193	49	3.2	48	73	12	163	23	17	20	38	1.93
43299024--43299245	99	2.2	99	90	1	347	23	21	20	34	1.97
43299087--43299356	50	5.3	50	75	9	208	22	25	21	30	1.99
43300145--43300449	43	7.2	43	73	12	204	17	25	32	24	1.97
43300116--43300551	85	5.2	84	73	13	315	19	25	31	24	1.98
43300145--43300551	128	3.2	127	82	5	409	18	25	30	24	1.98
43302154--43302226	36	2.0	36	100	0	146	21	21	10	45	1.83
43302393--43302536	50	2.9	50	86	1	198	20	30	24	25	1.98
43306047--43306072	13	2.0	13	100	0	52	61	7	0	30	1.24
43308540--43308584	23	2.0	23	86	4	65	46	11	4	37	1.60
43308552--43308594	22	1.9	23	85	4	61	41	11	4	41	1.62
43312964--43313006	23	1.9	23	90	4	70	46	13	4	34	1.65
43312961--43313018	22	2.6	22	81	7	73	43	17	3	36	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43316535--43322871	85	74.6	85	79	3	5473	17	25	35	21	1.95
43323703--43327057	85	39.5	85	73	4	1960	16	25	33	21	1.94
43323711--43329065	127	42.2	127	70	5	1778	16	25	33	20	1.93
43323703--43329077	212	25.4	210	70	5	1859	16	25	33	20	1.93
43325065--43325941	42	20.6	43	78	7	328	15	25	35	23	1.94
43324865--43329065	170	24.9	170	72	7	1859	16	25	34	20	1.94
43325730--43325813	43	2.1	37	72	24	89	17	28	29	23	1.97
43327283--43328008	43	17.0	43	81	2	766	16	27	34	20	1.94
43327283--43329412	85	25.4	85	71	10	1025	17	26	34	20	1.95
43328034--43329065	43	24.3	43	77	5	790	17	27	35	20	1.94
43329185--43329412	42	5.4	42	79	6	203	17	25	34	22	1.96
43330729--43331954	42	28.9	42	74	10	619	17	26	34	21	1.96
43330715--43331954	85	14.6	85	77	4	991	17	26	34	21	1.95
43330736--43331919	467	2.5	467	78	6	1105	17	26	34	21	1.96
43330715--43331954	382	3.2	379	78	6	1202	17	26	34	21	1.95
43330715--43331953	297	4.2	292	78	5	1036	17	26	34	21	1.96
43339188--43339593	42	9.6	43	73	6	326	17	25	34	21	1.95
43339218--43339503	85	3.4	85	84	6	427	17	24	35	22	1.95
43339191--43339593	169	2.4	170	88	1	585	17	25	35	22	1.95
43341346--43344730	42	80.2	42	76	5	2741	17	25	35	21	1.95
43341346--43344730	85	40.1	84	78	4	2640	17	25	35	21	1.95
43344831--43345155	43	7.6	43	73	5	257	17	24	34	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43344832--43345165	85	3.9	85	77	7	331	17	24	34	23	1.96
43344831--43345153	128	2.5	128	75	8	291	17	25	33	23	1.96
43345958--43353777	85	92.3	85	77	4	4455	17	26	34	21	1.95
43345958--43380579	255	136.3	254	74	5	13286	16	25	33	21	1.94
43345958--43380579	170	204.4	169	74	5	13693	16	25	33	21	1.94
43349298--43349456	76	2.1	76	85	2	212	20	27	32	20	1.97
43354545--43380579	85	307.5	84	75	5	13582	17	25	33	21	1.95
43354545--43380579	127	205.0	125	74	6	13153	17	25	33	21	1.95
43355313--43370243	212	70.5	213	72	9	1163	17	25	34	22	1.96
43365550--43365666	32	3.3	32	69	26	101	16	17	40	25	1.90

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226