genome.fa.s4.2.7.7.80.10.50.1000.1.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  1  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)
5--462	7	64.1	7	88	6	559	41	43	0	13	1.50
281--333	16	3.4	16	72	15	56	30	52	0	16	1.44
456--579	32	3.9	32	83	8	144	40	16	25	17	1.90
456--579	64	1.9	64	83	6	162	40	16	25	17	1.90
701--782	31	2.6	31	73	7	78	29	23	19	28	1.98
5462--5554	46	2.0	46	100	0	186	10	24	19	45	1.82
7870--8031	79	2.0	80	97	1	308	32	17	13	36	1.89
10010--10061	26	2.0	26	81	7	61	26	11	5	55	1.58
10538--10600	25	2.5	26	82	7	76	68	7	7	15	1.38
10744--10819	7	10.3	7	82	10	71	32	57	6	2	1.38
10744--10819	30	2.5	30	93	0	125	32	57	6	2	1.38
10813--10860	21	2.2	22	88	3	71	41	39	10	8	1.69
17997--18061	31	2.1	31	100	0	130	36	29	12	21	1.90
18425--18505	31	2.6	31	90	0	126	39	11	12	37	1.78
28346--28397	15	3.3	15	71	10	50	30	7	3	57	1.45
28422--28461	20	2.0	20	100	0	80	55	0	15	30	1.41
29758--29798	21	2.0	21	90	9	66	48	21	17	12	1.79
30684--30767	40	2.1	40	100	0	168	38	38	11	11	1.79
40227--40288	31	2.0	30	87	3	88	25	11	12	50	1.74
40880--40940	13	4.7	13	87	0	86	40	22	8	27	1.82
40875--40940	26	2.5	26	92	0	105	39	21	7	31	1.81
43972--44009	17	2.2	18	86	9	53	31	10	2	55	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
51571--51600	6	5.0	6	100	0	60	33	16	16	33	1.92
65228--65292	35	1.9	34	84	6	87	29	15	30	24	1.96
74516--74546	2	15.5	2	100	0	62	51	0	0	48	1.00
80306--80336	2	15.5	2	100	0	62	51	0	0	48	1.00
89060--89173	56	2.0	56	100	0	228	21	14	10	53	1.71
89265--89290	2	13.0	2	100	0	52	50	0	0	50	1.00
99054--99089	19	1.9	19	88	5	56	5	38	0	55	1.23
105180--105206	12	2.2	12	100	0	54	44	0	14	40	1.46
105474--105521	17	2.8	17	75	12	53	37	16	2	43	1.60
113129--113189	18	3.6	18	75	20	76	39	4	3	52	1.39
118686--118710	13	1.9	13	100	0	50	60	0	0	40	0.97
121349--121376	14	2.0	14	100	0	56	42	14	28	14	1.84
141459--141512	28	1.9	28	96	0	99	42	3	18	35	1.68
145424--145457	2	17.0	2	100	0	68	50	0	50	0	1.00
148992--149024	15	2.1	16	88	5	50	39	0	0	60	0.97
158518--158552	6	5.8	6	89	0	52	8	34	20	37	1.83
158518--158552	18	1.9	18	94	0	61	8	34	20	37	1.83
163126--163174	18	2.7	18	83	0	62	32	4	30	32	1.77
178927--178961	15	2.2	16	90	5	54	57	2	0	40	1.14
183270--183324	27	2.0	27	100	0	110	25	25	7	41	1.81
187354--187882	269	2.0	269	84	3	697	37	9	15	38	1.80
195919--195955	18	2.1	18	89	0	56	40	0	2	56	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
196360--196405	22	2.1	22	95	0	83	45	4	19	30	1.70
203466--203527	30	2.0	30	81	3	70	58	6	1	33	1.34
203587--203619	3	11.0	3	100	0	66	33	0	0	66	0.92
204168--204227	31	1.9	31	86	6	86	38	8	13	40	1.75
207131--207191	28	2.2	27	82	8	70	54	0	1	44	1.10
208554--208667	60	1.9	59	83	1	147	37	10	12	39	1.77
214376--214430	23	2.4	23	100	0	110	43	3	9	43	1.53
221045--221086	21	2.0	21	100	0	84	33	9	28	28	1.88
244114--244156	15	2.9	15	92	0	68	39	16	39	4	1.69
251252--251284	18	1.9	17	88	11	50	48	0	15	36	1.45
252566--252728	46	3.6	46	92	1	258	33	15	22	28	1.95
257635--257719	31	3.0	27	75	18	82	45	7	11	35	1.68
258045--258089	23	2.0	22	83	12	56	48	2	2	46	1.26
261692--261731	14	2.9	14	84	0	53	32	7	17	42	1.77
263631--263656	13	2.0	13	100	0	52	46	15	15	23	1.83
278071--278153	33	2.4	34	78	17	82	37	1	1	60	1.12
283481--283516	16	2.1	16	90	10	54	44	0	0	55	0.99
291569--291603	18	1.9	18	88	0	52	62	0	5	31	1.18
301131--301210	39	2.1	39	95	0	142	38	2	22	36	1.68
304775--304852	17	4.5	17	67	17	61	58	2	1	37	1.20
304761--304878	53	2.2	54	92	1	193	55	4	2	37	1.33
304794--304877	27	3.1	27	68	13	82	55	4	3	35	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
305896--305930	16	2.2	16	94	0	61	54	0	2	42	1.15
307008--307033	5	5.2	5	100	0	52	19	61	19	0	1.35
317574--317612	20	2.0	20	85	10	53	38	7	12	41	1.72
318091--318547	231	2.0	231	91	1	736	36	15	10	37	1.82
318490--318737	118	2.1	117	92	2	408	39	8	12	39	1.74
322437--322486	26	1.9	26	91	0	82	50	10	6	34	1.60
326992--327046	17	3.4	17	67	10	51	63	0	0	36	0.95
327038--327113	11	7.5	11	74	21	53	55	1	3	39	1.27
326992--327120	38	3.6	37	85	11	171	58	0	2	37	1.16
338348--338405	29	2.0	29	86	6	82	32	6	20	39	1.79
338650--338694	2	23.5	2	91	8	76	48	0	0	51	1.00
341508--341567	20	3.0	20	76	16	61	50	1	1	46	1.21
361060--361088	12	2.3	13	94	5	51	62	0	3	34	1.12
366242--366269	2	14.0	2	100	0	56	50	0	0	50	1.00
386518--386561	20	2.2	20	96	4	81	38	4	0	56	1.20
400375--400415	21	2.0	21	85	0	55	56	24	12	7	1.61
404035--404059	10	2.5	10	100	0	50	20	24	0	56	1.43
404728--404768	21	1.9	21	85	5	55	0	46	0	53	1.00
407025--407050	7	3.7	7	100	0	52	57	11	15	15	1.65
412055--412153	28	3.5	27	86	6	135	38	11	1	49	1.45
412232--412325	27	3.5	27	94	0	152	27	29	26	15	1.96
412353--412409	29	2.0	29	93	3	98	68	3	17	10	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
412467--412505	19	2.0	21	85	10	55	25	0	7	66	1.18
412551--412585	3	11.3	3	87	6	52	31	0	5	62	1.18
412584--412615	3	10.7	3	100	0	64	0	0	31	68	0.90
412613--412648	19	1.9	18	88	5	54	25	2	11	61	1.43
412612--412652	19	2.3	18	80	15	50	24	4	9	60	1.47
412708--412806	26	3.0	36	63	27	92	36	1	12	50	1.46
413372--413416	18	2.5	18	77	0	54	28	8	46	15	1.76
414922--414993	22	3.3	22	94	0	117	30	16	27	25	1.97
417389--417503	39	3.0	38	77	14	128	0	33	0	66	0.92
417419--417539	8	14.5	8	67	20	52	0	33	0	66	0.92
417418--417534	23	5.2	23	67	23	72	0	32	0	67	0.91
417399--417539	58	2.6	57	78	16	131	0	34	0	65	0.93
417388--417539	44	3.5	45	76	15	142	0	32	0	67	0.91
417397--417537	18	7.6	18	74	21	89	0	33	0	66	0.92
417429--417509	33	2.4	34	82	9	105	0	33	0	66	0.92
417421--417522	37	2.7	37	80	15	111	0	34	0	65	0.93
417385--417505	40	3.1	39	80	14	151	0	32	0	67	0.91
417573--417639	27	2.5	27	95	0	116	14	26	29	28	1.96
417707--417777	28	2.5	29	93	2	117	47	1	12	38	1.50
437424--437463	21	1.9	21	89	0	62	55	15	0	30	1.41
441980--442040	26	2.2	28	85	8	81	72	16	3	8	1.23
450473--450507	18	1.9	18	94	0	61	71	2	0	25	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
450479--450517	18	2.2	18	85	0	51	71	5	0	23	1.05
458233--458266	12	2.8	12	90	0	50	5	41	20	32	1.76
463722--463749	2	14.0	2	100	0	56	50	0	0	50	1.00
464731--464793	25	2.6	25	78	12	60	30	22	25	22	1.99
467099--467164	30	2.2	30	88	0	96	22	31	25	19	1.98
468697--468743	5	9.2	5	81	4	58	38	17	0	44	1.48
475371--475558	25	7.5	25	69	11	98	34	20	23	21	1.97
475452--475558	26	4.2	26	73	12	105	38	18	20	22	1.94
475443--475546	51	2.0	52	90	1	165	36	20	21	22	1.95
475452--475558	51	2.1	51	85	3	144	38	18	20	22	1.94

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