genome.fa.s1.2.7.7.80.10.50.1000.133.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  133  of  187  ( 22383 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)
40296154--40296192	20	2.1	18	85	9	51	53	0	0	46	1.00
40298151--40298867	158	4.5	158	94	2	1214	23	17	21	36	1.94
40298151--40298867	315	2.3	317	93	3	1218	23	17	21	36	1.94
40300752--40300862	49	2.4	47	80	11	122	29	15	8	46	1.74
40306418--40306450	14	2.3	15	94	5	59	30	0	33	36	1.58
40306551--40306688	70	2.0	70	95	0	249	29	0	22	47	1.51
40306866--40306895	15	2.1	15	93	6	53	20	0	46	33	1.51
40308518--40308626	27	3.7	30	86	7	113	29	29	23	17	1.97
40308549--40308626	27	2.9	27	94	0	138	25	29	26	17	1.98
40308467--40308704	130	1.8	130	95	0	431	29	27	21	21	1.98
40309767--40309800	11	2.8	12	91	8	52	35	8	11	44	1.72
40310198--40310235	2	19.5	2	89	5	60	52	0	2	44	1.14
40310423--40310467	22	2.1	21	88	12	65	80	0	6	13	0.91
40310474--40310540	20	3.2	21	75	14	50	43	7	0	49	1.31
40313185--40313229	19	2.3	19	85	11	56	42	0	4	53	1.21
40313291--40313342	12	4.7	11	77	15	54	48	13	0	38	1.43
40313482--40313555	16	4.5	16	76	6	76	47	22	1	28	1.60
40313531--40313654	61	2.0	62	81	10	148	46	17	0	34	1.54
40313543--40313647	52	2.0	51	82	14	126	46	18	0	34	1.55
40313606--40313630	13	1.9	13	100	0	50	48	16	0	36	1.46
40313619--40313799	9	20.9	9	71	16	107	43	18	1	35	1.60
40313615--40313657	12	4.0	11	80	14	54	46	11	0	41	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40313606--40313681	32	2.3	31	82	15	89	43	14	0	42	1.45
40313674--40313786	25	4.5	25	84	0	145	46	20	1	31	1.61
40313674--40313796	50	2.4	50	87	2	174	44	21	2	31	1.65
40316562--40316810	43	5.8	43	81	3	261	23	20	30	26	1.98
40316879--40316921	22	2.0	22	85	0	59	41	23	20	13	1.88
40324202--40324238	17	2.1	18	90	5	58	37	5	10	45	1.62
40326224--40326249	2	13.0	2	100	0	52	50	0	0	50	1.00
40327017--40327058	20	2.0	21	90	4	68	71	4	4	19	1.22
40330157--40330258	24	4.3	23	69	13	73	30	20	25	23	1.99
40333609--40333663	23	2.2	25	84	9	69	61	14	9	14	1.55
40337218--40337269	24	2.2	24	89	0	77	48	5	30	15	1.68
40341157--40341218	26	2.4	26	86	5	90	38	12	14	33	1.84
40342920--40342949	14	2.2	13	94	5	51	46	6	0	46	1.29
40350577--40350624	18	2.5	20	77	22	57	45	0	12	41	1.42
40350870--40350924	21	2.7	21	85	2	67	47	0	27	25	1.52
40350871--40350924	20	2.7	20	85	2	63	48	0	25	25	1.52
40352273--40352540	126	2.1	126	83	6	337	26	16	18	38	1.92
40352608--40352733	34	3.6	34	84	6	164	46	16	0	36	1.53
40352758--40352867	33	3.4	33	79	15	131	48	24	0	27	1.52
40354146--40354353	99	2.1	99	97	0	389	31	40	14	12	1.84
40365084--40365124	20	2.0	20	85	0	55	14	4	7	73	1.22
40367948--40367972	2	12.5	2	100	0	50	48	0	52	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40368805--40368855	23	2.2	24	93	6	88	37	1	0	60	1.08
40370547--40370571	2	12.5	2	100	0	50	48	0	0	52	1.00
40372652--40372693	22	1.9	22	90	0	66	52	0	4	42	1.22
40376952--40377009	19	3.4	19	68	26	65	39	10	5	44	1.61
40377985--40378025	20	2.1	19	86	4	55	70	0	0	29	0.87
40379348--40379388	21	2.0	21	90	0	64	63	4	0	31	1.15
40381288--40381357	36	1.9	36	88	11	108	10	4	28	57	1.50
40381673--40381898	43	5.3	43	84	6	307	26	29	17	27	1.97
40381674--40381898	85	2.6	85	86	6	312	26	28	17	27	1.97
40384902--40385030	28	4.6	28	91	0	197	32	13	24	30	1.93
40385756--40386285	70	7.5	70	91	1	776	27	11	17	43	1.84
40385853--40386200	47	7.4	45	73	10	180	26	12	17	44	1.83
40385787--40386298	23	21.8	25	71	13	136	27	11	17	42	1.85
40390819--40391204	9	43.2	9	72	13	244	34	1	18	45	1.60
40390820--40391023	25	8.0	26	79	11	142	32	0	22	44	1.57
40390827--40391024	34	5.6	34	77	14	143	32	0	21	45	1.56
40390819--40391259	18	26.6	18	70	19	250	35	1	17	45	1.58
40390996--40391122	48	2.6	48	91	3	193	37	3	13	45	1.62
40391041--40391259	66	3.4	66	86	5	313	37	2	14	45	1.57
40391111--40391252	48	3.0	48	81	8	139	37	0	14	47	1.50
40391174--40391281	48	2.2	48	87	6	148	38	0	12	47	1.49
40391384--40391442	30	1.9	31	93	3	102	42	5	11	40	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40396565--40396655	45	2.0	45	93	0	155	26	16	21	35	1.95
40398294--40398338	23	2.0	23	82	8	56	33	0	42	24	1.55
40398808--40398854	21	2.2	22	81	11	62	57	17	0	25	1.40
40398877--40398939	7	9.1	7	77	3	56	44	39	0	15	1.47
40399025--40399162	7	18.9	7	70	12	64	36	36	3	22	1.72
40399197--40399239	13	3.2	13	83	6	59	55	30	0	13	1.39
40399327--40399372	23	2.0	24	87	8	69	39	28	8	23	1.84
40399830--40400181	168	2.1	165	83	3	438	26	21	19	32	1.97
40402806--40402977	44	3.9	44	85	0	218	40	9	25	25	1.86
40403063--40403201	73	1.9	73	86	0	197	35	12	23	28	1.91
40403210--40403270	27	2.3	27	88	5	88	42	19	21	16	1.89
40406025--40406076	28	1.9	27	84	7	70	38	21	1	38	1.64
40406235--40406415	57	3.1	57	85	1	227	28	19	6	45	1.76
40409342--40409369	14	2.0	14	100	0	56	42	14	0	42	1.45
40414288--40414319	12	2.7	12	90	0	55	28	0	0	71	0.86
40414439--40414531	30	3.1	30	93	0	159	56	15	4	23	1.56
40416198--40416243	22	2.1	22	88	8	67	30	19	28	21	1.98
40416440--40416477	13	3.0	13	92	3	60	44	23	2	28	1.67
40425380--40425533	49	3.1	48	77	8	150	35	17	23	23	1.95
40427941--40428001	18	3.4	18	76	0	68	42	19	8	29	1.80
40427939--40428019	36	2.2	36	84	4	101	44	19	7	28	1.78
40428015--40428052	17	2.2	18	85	4	51	50	15	7	26	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40432845--40432929	40	2.1	41	86	6	120	58	7	1	32	1.32
40435143--40435189	20	2.4	19	82	10	58	23	23	2	51	1.59
40438379--40438416	18	2.1	18	100	0	76	36	5	21	36	1.76
40441187--40441292	41	2.6	41	89	5	153	18	15	41	24	1.89
40441201--40441263	19	3.2	19	67	20	56	19	12	41	26	1.87
40442147--40442184	7	5.6	7	93	6	69	0	0	26	73	0.83
40445667--40445737	31	2.3	31	85	2	90	32	7	16	43	1.75
40445860--40445976	43	2.8	43	84	2	148	25	17	29	27	1.98
40449563--40449587	12	2.1	12	100	0	50	48	8	0	44	1.32
40454805--40454878	11	6.6	11	70	14	53	58	1	0	40	1.07
40454844--40454887	13	3.8	13	72	27	53	68	0	0	31	0.90
40454848--40454929	21	3.8	21	78	10	85	60	1	3	34	1.22
40454789--40454898	57	1.9	58	83	8	147	59	1	1	37	1.19
40461308--40461357	3	16.7	3	95	0	91	34	2	0	64	1.05
40463425--40463482	27	2.1	27	100	0	116	31	3	18	46	1.66
40465548--40465801	126	2.0	126	99	0	499	39	16	20	23	1.92
40466630--40466819	6	31.7	6	84	4	141	20	8	14	56	1.65
40466630--40466823	12	15.7	12	80	6	172	20	8	14	56	1.65
40466630--40466823	18	10.4	18	81	6	199	20	8	14	56	1.65
40467086--40467200	59	2.0	58	94	1	203	23	8	21	46	1.79
40470592--40470671	40	2.0	40	97	0	151	36	12	18	32	1.89
40472013--40472092	35	2.2	36	93	2	135	48	22	11	17	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40474694--40474718	5	5.0	5	100	0	50	40	0	60	0	0.97
40494326--40494394	22	3.1	21	78	17	61	65	1	8	24	1.30
40497400--40497441	20	2.0	21	90	4	68	30	0	4	64	1.14
40499413--40499503	25	3.6	25	75	8	78	34	19	28	17	1.95
40499411--40499509	50	2.0	50	84	7	130	36	19	26	18	1.94
40499845--40499886	21	2.0	21	85	0	57	42	19	0	38	1.51
40506531--40506707	25	7.2	25	75	8	141	33	19	28	18	1.95
40506531--40506699	75	2.3	74	80	8	191	33	19	28	18	1.95
40508457--40508488	15	2.1	15	94	0	55	31	0	21	46	1.52
40508675--40508746	28	2.7	27	81	12	69	44	0	4	51	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