genome.fa.s4.2.7.7.80.10.50.1000.154.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  154  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)
48768528--48768588	32	1.9	32	93	0	104	50	1	1	45	1.21
48770969--48771047	40	2.0	40	100	0	158	12	16	2	68	1.32
48775248--48775285	18	2.0	18	90	10	58	76	5	0	18	0.97
48776360--48776421	18	3.7	17	75	18	67	51	1	1	45	1.20
48776373--48776420	14	3.1	14	73	21	51	50	2	2	45	1.25
48776360--48776420	32	1.9	32	93	0	104	50	1	1	45	1.21
48779405--48779477	5	14.6	5	76	20	64	38	0	4	57	1.18
48779433--48779475	19	2.3	19	92	8	70	41	0	0	58	0.98
48779487--48779528	15	2.7	15	88	3	57	73	2	19	4	1.12
48779920--48779953	17	2.0	17	94	0	59	38	11	14	35	1.83
48782857--48782935	40	2.0	40	100	0	158	12	16	2	68	1.32
48788145--48788348	88	2.3	90	84	5	256	37	20	8	33	1.84
48788354--48788414	28	2.2	28	82	11	72	59	0	3	37	1.14
48788360--48788438	26	3.1	25	75	13	79	58	0	3	37	1.16
48790259--48790299	16	2.5	17	84	15	59	26	14	4	53	1.61
48796270--48796306	18	2.1	18	94	0	65	48	8	10	32	1.67
48796502--48796541	19	2.0	21	85	9	57	22	27	0	50	1.50
48808795--48808854	24	2.4	25	81	10	70	36	25	20	18	1.94
48818484--48818536	27	2.0	26	92	3	88	32	32	18	16	1.94
48818415--48818610	102	1.9	102	93	0	338	32	28	18	20	1.96
48818517--48818651	42	3.4	42	75	17	162	31	27	18	22	1.97
48818557--48818711	33	4.6	33	74	20	126	32	26	21	19	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48818517--48818686	75	2.3	75	92	0	295	32	27	18	20	1.96
48818376--48818716	177	1.9	177	92	0	565	31	27	20	21	1.98
48822979--48823050	21	3.4	21	66	0	54	44	15	22	18	1.86
48822985--48823097	42	2.7	42	84	2	138	42	16	22	18	1.89
48829998--48830040	20	2.1	21	82	4	52	48	13	18	18	1.80
48832406--48832459	27	2.0	27	100	0	108	33	7	14	44	1.73
48837291--48837385	47	2.0	49	83	4	122	35	25	8	30	1.86
48841509--48841969	19	23.3	19	66	24	151	30	0	12	56	1.40
48841552--48841934	61	6.4	60	71	16	257	29	0	12	57	1.38
48841613--48841820	101	2.1	99	93	1	362	29	0	12	57	1.40
48841746--48841932	46	4.2	46	66	26	139	28	0	13	57	1.37
48841792--48841875	27	3.1	27	94	1	150	30	0	11	57	1.35
48841789--48841855	8	7.6	8	72	18	53	28	0	13	58	1.36
48841709--48841954	134	1.8	135	94	1	440	28	0	13	57	1.39
48841843--48842035	100	1.9	102	95	2	354	29	0	12	57	1.36
48841705--48841990	134	2.1	133	88	5	416	30	0	12	56	1.38
48842545--48842581	16	2.4	16	90	4	58	32	2	5	59	1.34
48843121--48843179	23	2.6	22	89	5	82	49	0	1	49	1.11
48843156--48843211	16	3.5	16	92	0	94	50	1	5	42	1.35
48843259--48843309	16	2.8	19	70	27	56	39	1	7	50	1.42
48847679--48847710	10	3.2	10	90	0	55	53	0	6	40	1.26
48848645--48848689	18	2.5	18	100	0	90	8	35	44	11	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48849554--48849620	14	5.1	13	78	8	55	38	0	2	58	1.14
48849564--48849626	5	12.4	5	75	21	60	42	0	0	57	0.99
48850033--48850071	16	2.4	16	100	0	78	30	10	12	46	1.75
48850962--48850986	13	1.9	13	100	0	50	56	0	0	44	0.99
48852330--48852370	19	2.2	19	86	0	55	60	2	9	26	1.40
48856567--48856638	36	2.0	36	91	5	119	22	18	19	40	1.92
48856603--48856797	45	4.3	45	85	1	248	21	17	18	43	1.89
48862072--48862155	24	3.3	24	77	14	71	53	3	3	39	1.36
48863614--48863734	44	2.7	44	82	8	156	25	25	20	28	1.99
48863614--48863813	44	4.6	45	74	11	150	26	23	21	29	1.99
48875552--48875590	15	2.6	15	80	15	53	58	7	7	25	1.52
48877495--48877615	44	2.7	44	82	8	156	25	25	20	28	1.99
48877495--48877694	44	4.6	45	74	11	150	26	23	21	29	1.99
48885488--48885609	23	5.3	23	87	0	181	20	21	27	31	1.98
48885490--48885609	46	2.6	46	93	0	204	20	21	27	30	1.98
48892250--48892288	15	2.6	15	80	15	53	58	7	7	25	1.52
48892590--48892622	18	1.9	17	88	11	50	60	3	6	30	1.36
48893401--48893462	32	1.9	32	100	0	124	35	22	11	30	1.89
48895837--48896086	130	1.9	130	84	3	333	34	20	14	31	1.92
48897395--48897465	25	2.9	25	82	2	81	33	21	25	19	1.97
48897461--48897589	25	5.2	26	68	18	87	34	21	24	20	1.97
48905218--48905279	25	2.5	25	89	0	97	32	17	29	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48905237--48905287	25	2.0	25	85	7	68	31	17	25	25	1.97
48905342--48905420	26	3.2	26	77	12	76	35	21	25	17	1.95
48905300--48905420	48	2.5	48	80	9	129	35	21	24	18	1.95
48906137--48906170	17	1.9	18	88	5	52	41	23	0	35	1.55
48906410--48906571	44	3.5	44	85	11	234	30	24	14	30	1.94
48906454--48906566	51	2.2	51	96	0	208	30	24	13	31	1.93
48908841--48908874	5	6.4	5	93	6	50	38	20	0	41	1.53
48911362--48911419	26	2.2	26	78	6	64	37	0	5	56	1.21
48913477--48913558	40	2.0	40	95	0	146	31	25	12	30	1.92
48920156--48920313	42	3.7	43	86	2	192	28	15	23	32	1.95
48920160--48920313	43	3.6	43	86	2	193	28	15	23	32	1.95
48924791--48924831	19	2.1	20	86	4	57	39	7	14	39	1.74
48933606--48933776	85	2.0	84	87	3	245	27	16	24	31	1.96
48933606--48933776	42	4.0	42	89	3	229	27	16	24	31	1.96
48937662--48937729	32	2.2	32	91	2	111	32	16	20	30	1.94
48941022--48941061	17	2.2	19	86	8	57	65	2	0	32	1.06
48960845--48960872	12	2.3	12	100	0	56	14	46	17	21	1.84
48961785--48962008	101	2.2	101	86	0	313	26	22	16	34	1.95
48964975--48965046	34	2.1	34	94	0	126	34	19	18	27	1.95
48967996--48968206	117	1.8	117	90	0	341	22	10	23	43	1.84
48968810--48968885	33	2.3	32	84	4	89	26	0	50	23	1.50
48969053--48969154	50	2.0	51	86	1	143	30	8	25	35	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48970455--48970550	31	3.1	31	95	3	174	31	9	13	45	1.75
48971097--48971143	22	2.2	22	84	3	60	82	8	8	0	0.83
48976751--48976846	31	3.1	31	95	3	174	31	9	13	45	1.75
48979874--48979915	16	2.6	16	92	3	66	28	0	30	40	1.57
48982947--48982973	5	5.4	5	100	0	54	22	18	18	40	1.91
48983826--48983852	7	3.9	7	100	0	54	0	11	0	88	0.50
48988083--48988177	46	2.1	46	100	0	190	40	16	4	38	1.68
48988369--48988473	36	2.7	40	81	8	119	38	22	14	24	1.92
48989360--48989398	21	1.9	20	84	5	51	0	28	0	71	0.86
48989727--48989761	13	2.7	13	100	0	70	45	0	0	54	0.99
48997176--48997219	23	1.9	23	90	0	70	61	4	2	31	1.28
48997180--48997222	11	3.8	11	80	17	52	65	2	2	30	1.18
49003188--49003461	123	2.2	124	94	1	480	31	15	20	33	1.93
49006658--49006968	29	10.9	29	88	5	481	29	0	25	45	1.54
49009225--49009280	25	2.3	25	80	14	64	62	5	0	32	1.18
49009371--49009423	10	5.1	10	77	6	52	67	0	0	32	0.91
49009377--49009423	21	2.2	21	88	0	67	65	0	0	34	0.93
49009371--49009439	31	2.2	33	94	5	124	63	0	0	36	0.94
49009473--49009544	22	3.3	22	96	3	128	36	0	34	29	1.58
49012254--49012285	2	16.0	2	100	0	64	50	0	0	50	1.00
49026065--49026134	28	2.5	28	86	2	97	12	35	27	24	1.92
49034455--49034515	28	2.2	27	82	8	70	63	4	11	19	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49034671--49034716	13	3.5	13	73	26	51	26	19	41	13	1.88
49034663--49034728	27	2.4	27	100	0	132	25	22	40	10	1.86
49035039--49035329	22	13.0	21	68	24	125	30	1	12	55	1.44
49035039--49035411	27	16.4	20	71	21	117	30	0	13	54	1.45
49035063--49035119	19	2.9	19	86	2	78	33	0	14	52	1.41
49035164--49035356	27	7.8	26	78	17	223	31	1	13	54	1.46
49035160--49035399	49	5.0	49	88	6	321	30	0	15	53	1.48
49035162--49035351	97	2.0	97	95	0	344	30	1	13	55	1.45
49035278--49035335	22	2.9	19	71	14	53	34	1	12	51	1.49
49035278--49035356	19	4.6	19	69	23	66	34	1	12	51	1.48

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