genome.fa.s4.2.7.7.80.10.50.1000.99.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  99  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)
31765804--31765830	3	9.0	3	100	0	54	66	0	0	33	0.92
31766009--31766052	23	2.0	22	90	4	70	56	2	6	34	1.38
31766470--31766502	15	2.1	16	94	5	59	60	0	9	30	1.27
31766757--31766814	22	2.7	21	76	10	53	43	17	5	34	1.71
31768923--31769046	27	4.7	27	79	3	126	39	13	22	24	1.90
31768923--31769036	54	2.1	53	85	1	147	42	13	22	21	1.88
31771237--31771287	25	2.0	25	85	7	68	21	3	15	58	1.53
31774864--31774894	15	2.1	15	93	0	53	22	9	32	35	1.87
31774868--31774910	21	2.0	21	95	0	77	20	9	34	34	1.85
31775174--31775216	16	2.6	16	85	3	50	18	2	4	74	1.10
31775214--31775247	15	2.3	15	90	10	52	8	0	14	76	1.01
31789306--31789372	29	2.6	25	80	19	91	29	2	0	67	1.06
31790097--31790144	24	1.9	25	83	8	62	60	4	0	35	1.16
31791886--31791931	23	2.0	23	100	0	92	34	30	0	34	1.58
31803804--31804918	152	7.3	151	85	5	1431	30	9	6	52	1.60
31803804--31804918	303	3.6	304	86	5	1543	30	9	6	52	1.60
31804942--31804976	18	1.9	18	88	0	52	68	2	0	28	1.04
31808019--31808056	18	2.0	20	90	10	62	21	26	0	52	1.47
31808201--31808262	9	7.0	9	73	21	51	35	3	1	59	1.23
31808202--31808262	17	3.5	17	70	24	54	36	3	1	59	1.24
31818541--31818588	19	2.7	18	81	15	55	31	0	31	37	1.58
31825148--31825188	22	2.0	21	86	13	59	31	4	24	39	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31826282--31826526	75	3.3	75	97	0	463	25	12	23	38	1.89
31827978--31828138	83	1.9	83	93	0	277	22	22	16	38	1.93
31833865--31833940	38	2.0	38	84	0	98	27	11	10	50	1.72
31834913--31835007	18	5.3	18	72	20	58	60	1	2	36	1.16
31836765--31836972	43	4.8	43	84	2	267	26	27	18	27	1.98
31838371--31838455	40	2.1	40	84	4	109	49	14	5	30	1.66
31838428--31838592	86	1.9	86	87	0	240	43	15	9	32	1.78
31838374--31838851	259	1.9	252	81	5	584	44	15	8	32	1.76
31841548--31841595	19	2.5	18	86	6	51	16	2	4	77	1.03
31841976--31842046	21	3.4	21	82	3	81	32	43	0	23	1.54
31842000--31842032	14	2.4	14	94	0	57	30	51	0	18	1.46
31842029--31842085	14	4.0	15	72	17	50	42	31	0	26	1.56
31842473--31842828	41	8.9	41	80	5	350	29	27	20	22	1.98
31842549--31842701	76	2.0	76	85	0	207	30	27	19	22	1.98
31842476--31842828	117	2.9	116	79	9	332	29	27	20	22	1.98
31842903--31842989	40	2.2	40	85	0	111	22	19	20	36	1.95
31846051--31846084	17	1.9	17	88	5	50	58	5	0	35	1.22
31846196--31846307	9	12.4	9	69	16	54	61	1	1	34	1.17
31846197--31846288	27	3.4	26	75	11	62	58	2	2	36	1.22
31846270--31846307	17	2.2	19	86	13	55	71	2	0	26	1.00
31848398--31848438	23	1.9	21	85	14	57	65	0	0	34	0.93
31848423--31848465	14	3.0	14	80	6	50	58	2	2	37	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31856928--31856953	7	3.7	7	100	0	52	84	0	0	15	0.62
31861451--31861558	32	3.5	32	74	7	123	28	15	29	25	1.96
31861417--31861587	61	2.8	60	89	1	252	34	14	25	26	1.93
31861418--31861587	29	5.7	29	68	12	101	34	14	25	25	1.93
31864324--31864399	36	2.1	37	82	2	91	15	11	40	31	1.84
31867283--31867323	20	2.0	20	85	0	55	36	17	29	17	1.92
31867293--31867357	20	3.2	20	82	8	87	32	15	33	18	1.92
31871333--31871500	27	6.2	27	82	6	162	44	19	14	22	1.86
31871328--31871505	81	2.2	81	80	5	207	43	18	15	22	1.87
31874025--31874049	11	2.3	11	100	0	50	0	24	0	76	0.80
31878802--31878844	22	2.0	22	90	0	68	27	23	16	32	1.96
31879385--31879428	18	2.4	18	84	0	61	50	20	2	27	1.60
31894382--31894458	32	2.5	31	80	4	82	23	18	29	28	1.97
31902936--31903031	30	3.4	28	84	9	124	27	21	26	25	2.00
31903378--31903615	27	8.8	27	80	3	246	18	20	18	43	1.89
31905970--31906001	12	2.6	13	85	14	50	37	0	6	56	1.25
31908158--31908694	102	5.3	102	91	2	848	20	19	27	31	1.97
31909560--31909754	49	4.0	49	90	0	282	23	13	29	33	1.93
31909920--31909981	27	2.3	27	97	2	117	25	6	25	41	1.79
31911491--31911522	12	2.6	13	85	14	50	37	0	6	56	1.25
31917385--31917430	23	2.0	23	87	8	67	32	6	23	36	1.81
31922434--31922528	28	3.4	28	85	5	104	30	21	23	25	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31922633--31922707	26	2.9	26	85	0	105	38	24	22	14	1.92
31931035--31931114	28	2.9	28	86	3	81	38	10	25	26	1.87
31931063--31931140	28	2.8	28	86	2	102	39	12	20	26	1.89
31931371--31931457	27	3.2	27	75	3	77	37	11	24	26	1.89
31945500--31945600	49	2.1	49	86	3	141	31	8	13	45	1.75
31947207--31947608	203	2.0	206	87	4	582	36	13	19	31	1.90
31960041--31960080	18	2.2	19	90	4	64	25	25	0	50	1.50
31962800--31962825	2	13.0	2	100	0	52	50	0	0	50	1.00
31962895--31962940	23	2.0	23	84	12	60	23	2	30	43	1.66
31979531--31979565	15	2.3	15	100	0	70	57	5	11	25	1.56
31981890--31982076	51	3.7	50	78	7	182	30	16	22	29	1.96
31985948--31986073	17	6.7	17	67	19	63	37	0	0	61	1.01
31985977--31986083	11	10.4	11	77	14	79	36	1	0	61	1.07
31985959--31986092	40	3.3	40	89	4	216	34	1	0	64	1.03
31986066--31986105	21	1.9	21	89	0	62	37	2	0	60	1.11
31986065--31986123	22	2.8	21	80	14	59	40	1	3	54	1.27
31989590--31989720	50	2.6	51	86	3	176	28	16	24	31	1.96
31999270--31999300	15	2.1	15	93	0	53	41	19	9	29	1.83
32010927--32011235	57	5.5	57	82	6	317	26	15	22	35	1.94
32010935--32011235	28	10.6	28	80	6	304	25	16	22	35	1.94
32011152--32011271	57	2.1	57	84	3	152	30	14	16	38	1.88
32012563--32012686	50	2.5	50	82	0	140	26	22	28	22	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32022095--32022125	16	1.9	16	93	0	53	61	22	0	16	1.34
32034710--32034749	20	2.1	20	90	9	66	35	10	0	55	1.34
32036006--32036053	3	16.3	3	95	4	89	31	0	0	68	0.90
32036520--32036563	20	2.2	20	87	0	61	34	2	2	61	1.21
32036520--32036563	22	2.1	20	83	8	52	34	2	2	61	1.21
32040878--32040907	13	2.2	14	94	5	53	80	0	20	0	0.72
32042170--32042438	100	2.7	100	91	1	423	27	21	24	26	1.99
32042183--32042454	50	5.4	50	71	3	206	29	19	25	25	1.99
32042448--32043749	132	9.9	132	90	3	1797	28	19	23	27	1.98
32042634--32042941	45	6.9	45	65	11	132	28	21	24	25	1.99
32044734--32044770	16	2.2	17	86	13	51	2	18	0	78	0.87
32045373--32045417	3	15.3	3	95	4	83	31	0	0	68	0.89
32045884--32045927	20	2.2	20	87	0	61	34	2	2	61	1.21
32045884--32045927	22	2.1	20	83	8	52	34	2	2	61	1.21
32055061--32055092	16	2.1	15	94	5	55	43	25	6	25	1.77
32088335--32088388	17	3.2	17	89	0	72	18	27	35	18	1.94
32090778--32090819	20	2.0	21	90	4	68	54	4	0	40	1.21
32090778--32090826	20	2.4	20	86	10	64	53	4	0	42	1.20
32091531--32091574	15	2.9	15	80	9	54	61	2	0	36	1.09
32092241--32092302	19	3.4	19	78	14	76	32	0	0	67	0.91
32092244--32092302	9	6.4	9	82	9	75	32	0	0	67	0.91
32094674--32094775	47	2.2	47	92	1	170	55	7	5	30	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32094690--32094764	24	3.2	24	62	17	57	52	9	6	32	1.60
32111474--32111531	3	19.3	3	81	0	62	56	1	6	34	1.36
32111474--32111531	21	2.8	21	86	0	89	56	1	6	34	1.36
32113106--32113525	44	9.7	44	73	9	306	28	25	18	27	1.98
32113070--32113295	85	2.7	86	74	11	207	29	26	17	26	1.97
32113105--32113354	129	1.9	129	90	1	403	29	25	18	26	1.98
32113516--32113790	128	2.1	128	91	1	444	24	22	21	31	1.98
32114230--32114262	17	1.9	17	100	0	66	18	36	18	27	1.94
32115011--32115043	17	2.0	17	88	5	50	18	18	0	63	1.31
32121190--32121265	3	25.3	3	86	0	107	59	0	5	35	1.20

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