genome.fa.s8.2.7.7.80.10.50.1000.182.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  182  of  190  ( 22705 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)
53551854--53551919	29	2.3	29	81	5	80	37	4	0	57	1.19
53551844--53551912	21	3.4	19	75	11	66	39	4	1	55	1.29
53561614--53561663	2	25.0	2	100	0	100	50	0	0	50	1.00
53562941--53562992	21	2.5	20	78	12	59	44	25	17	13	1.85
53563888--53563918	15	2.1	15	93	0	53	77	0	19	3	0.90
53565013--53565123	25	4.6	24	84	6	120	15	21	20	42	1.89
53566168--53566201	17	1.9	18	88	5	52	35	23	0	41	1.55
53566885--53566956	25	3.0	25	79	4	85	33	22	23	20	1.97
53567160--53567229	24	2.8	24	77	12	70	32	15	28	22	1.95
53567012--53568239	410	3.0	410	95	0	2179	35	19	17	27	1.94
53568000--53568047	24	2.0	24	84	8	62	37	16	25	20	1.93
53578423--53578527	52	2.0	52	94	0	183	22	0	32	43	1.60
53578430--53578513	28	3.1	28	65	25	72	21	0	33	45	1.52
53580209--53580239	2	15.5	2	93	0	53	48	3	0	48	1.17
53582037--53582068	5	6.4	5	100	0	64	18	18	0	62	1.33
53593692--53593731	18	2.2	18	86	4	53	12	27	0	60	1.33
53593818--53593866	19	2.5	20	75	21	59	6	16	4	73	1.19
53594790--53594824	12	2.8	13	91	8	63	14	14	5	65	1.44
53598791--53598833	2	21.0	2	95	4	77	48	0	2	48	1.14
53606198--53606241	22	2.0	22	100	0	88	45	9	27	18	1.79
53610312--53610341	2	15.0	2	100	0	60	50	0	0	50	1.00
53626016--53626070	27	2.0	27	83	13	69	25	20	10	43	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53628639--53628677	20	2.0	19	90	5	60	30	0	2	66	1.05
53635535--53635570	17	2.2	16	90	5	54	44	0	0	55	0.99
53638944--53639002	20	2.7	21	82	12	66	30	3	3	62	1.28
53640463--53640507	22	2.0	22	82	0	54	20	13	11	55	1.68
53646867--53646953	40	2.2	40	85	8	115	31	8	20	40	1.82
53647153--53647385	45	5.2	45	85	3	310	21	18	19	40	1.92
53648860--53648902	20	2.2	20	87	8	61	46	0	2	51	1.13
53648855--53648913	20	2.8	20	74	5	55	49	0	1	49	1.11
53658234--53658269	15	2.5	14	86	8	54	44	8	0	47	1.33
53661218--53661244	13	2.1	13	100	0	54	37	0	0	62	0.95
53663520--53663546	6	4.5	6	100	0	54	48	0	14	37	1.45
53664207--53664240	2	17.0	2	100	0	68	50	0	0	50	1.00
53667666--53667697	2	16.0	2	100	0	64	50	0	0	50	1.00
53675649--53675715	25	2.6	25	81	13	66	2	26	4	65	1.26
53675738--53675801	7	8.6	7	77	19	51	53	1	1	43	1.19
53675735--53675798	8	8.4	8	76	13	55	51	1	1	45	1.20
53676322--53676400	39	2.0	39	97	0	149	39	16	17	26	1.91
53678671--53678721	26	2.0	26	88	3	77	56	5	1	35	1.35
53691180--53691238	22	2.6	22	76	10	57	28	0	5	66	1.13
53694071--53694122	18	2.9	18	85	5	70	26	44	13	15	1.84
53694278--53694343	18	3.5	18	87	10	80	36	21	6	36	1.78
53694306--53694364	21	2.8	21	94	0	100	37	20	5	37	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53697038--53697069	3	10.7	3	100	0	64	34	0	0	65	0.93
53699909--53700002	46	2.0	46	97	0	179	35	29	15	19	1.93
53701942--53701985	22	2.0	22	100	0	88	45	9	13	31	1.75
53703354--53703401	12	3.9	12	78	5	60	16	4	16	62	1.48
53729828--53729856	7	4.1	7	100	0	58	27	17	13	41	1.87
53742592--53742636	23	2.0	23	82	8	56	51	2	0	46	1.13
53743184--53743244	29	2.1	28	81	3	68	24	13	18	44	1.85
53744081--53744170	42	2.2	41	78	11	96	18	28	26	25	1.98
53751899--53751955	3	19.0	3	92	0	96	64	1	1	31	1.13
53752711--53752754	20	2.2	20	84	8	54	79	0	13	6	0.92
53753440--53753551	44	2.7	40	74	15	127	24	18	24	33	1.97
53753555--53754243	174	4.0	172	85	4	626	26	23	21	28	1.99
53753570--53754417	303	2.8	304	93	1	1412	26	23	22	28	1.99
53754041--53754462	130	3.2	130	94	0	736	27	23	21	27	1.99
53753565--53754458	46	20.6	42	73	13	394	26	23	22	28	1.99
53753743--53754559	434	1.9	434	94	1	1431	27	23	21	28	1.99
53754554--53755166	86	7.1	86	90	3	815	24	24	22	28	2.00
53754616--53754744	44	2.9	44	71	13	129	26	24	23	25	2.00
53754756--53755064	43	7.2	43	65	12	195	24	23	22	28	1.99
53754756--53755152	43	9.2	42	63	14	164	24	23	22	28	1.99
53756387--53756411	13	1.9	13	100	0	50	12	8	0	80	0.92
53760868--53760924	3	19.0	3	92	0	96	64	1	1	31	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53765051--53765082	6	5.3	6	100	0	64	31	34	0	34	1.58
53768817--53768882	33	1.9	35	87	6	100	45	18	10	25	1.81
53770544--53770574	2	15.5	2	93	0	53	45	0	3	51	1.17
53776451--53776509	31	1.9	32	86	6	86	28	5	11	54	1.58
53776451--53776524	31	2.4	31	78	17	75	28	5	10	55	1.56
53784044--53784111	31	2.2	31	81	5	75	42	4	10	42	1.58
53805154--53805193	7	5.6	7	85	5	53	30	0	10	60	1.30
53805895--53805938	19	2.5	17	80	20	54	47	6	0	45	1.29
53808750--53808988	96	2.5	95	91	4	374	37	18	2	41	1.63
53808750--53809051	88	3.2	94	86	6	377	38	17	1	42	1.61
53809153--53809274	40	3.0	40	82	7	165	22	24	26	26	2.00
53809472--53809528	18	3.1	19	82	9	73	50	1	0	47	1.11
53809530--53809600	18	4.0	18	71	8	56	66	4	0	29	1.11
53809549--53809603	28	1.9	29	85	3	76	67	5	0	27	1.12
53810004--53810067	21	3.1	21	75	11	60	35	3	4	56	1.36
53810921--53810945	7	3.6	7	100	0	50	28	0	0	72	0.86
53819047--53819105	9	6.9	9	75	11	52	28	5	25	40	1.77
53819060--53819105	18	2.6	18	89	0	65	28	6	28	36	1.82
53822358--53822420	31	2.0	31	87	0	90	53	14	11	20	1.70
53826165--53826212	22	2.2	22	85	7	62	27	0	2	70	0.98
53831701--53831738	14	2.8	13	88	7	58	44	5	10	39	1.61
53834875--53834919	20	2.1	23	88	12	69	13	8	8	68	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53834951--53834993	21	2.0	23	81	9	54	32	11	11	44	1.77
53844920--53844944	12	2.1	12	100	0	50	8	8	24	60	1.52
53847036--53847103	25	2.7	25	77	11	68	45	0	2	51	1.16
53850719--53850846	30	4.2	30	85	7	145	36	3	0	60	1.13
53895989--53896031	21	2.0	21	100	0	86	55	4	13	25	1.58
53903464--53903502	18	2.2	17	86	13	53	33	0	20	46	1.51
53906119--53906193	11	7.0	11	72	14	59	41	4	0	54	1.19
53906516--53906555	20	2.0	21	85	5	55	47	10	2	40	1.50
53908111--53908141	12	2.7	11	90	9	53	0	25	0	74	0.82
53908751--53908798	2	24.0	2	100	0	96	50	0	0	50	1.00
53916451--53916485	13	2.8	13	87	12	56	71	0	0	28	0.86
53916551--53916621	3	23.7	3	97	0	133	64	0	1	33	1.02
53917529--53917557	14	2.0	15	93	6	51	89	0	10	0	0.48
53917528--53917553	11	2.4	11	100	0	52	88	0	11	0	0.52
53949788--53949825	17	2.2	18	85	4	51	42	0	2	55	1.14
53950073--53950114	15	2.9	15	86	6	52	38	7	7	47	1.58
53952217--53952249	17	1.9	17	100	0	66	12	15	18	54	1.71
53952969--53953067	43	2.3	43	84	3	137	27	14	17	41	1.87
53954057--53954091	18	2.0	17	88	5	52	45	0	0	54	0.99
53954324--53954376	16	3.3	16	78	0	61	22	32	7	37	1.82
53955559--53955599	20	2.0	20	95	0	73	36	4	0	58	1.20
53957426--53957485	30	2.0	30	100	0	120	66	13	3	16	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53957806--53957857	23	2.2	23	93	3	86	26	19	7	46	1.77
53958320--53958355	17	2.0	19	89	10	58	77	2	0	19	0.88
53964246--53964285	21	1.9	21	90	10	64	32	2	10	55	1.47
53968826--53968880	19	3.0	18	79	17	60	58	1	3	36	1.26
53969967--53970303	43	7.8	43	88	0	458	25	31	20	23	1.98
53971629--53971673	2	22.5	2	100	0	90	48	0	51	0	1.00
53971866--53971905	20	2.0	20	100	0	80	65	10	0	25	1.24
53975013--53975087	15	5.1	15	77	19	70	38	37	0	24	1.55
53975017--53975137	22	5.6	22	71	16	67	36	37	0	26	1.57
53975088--53975132	14	3.1	14	87	6	63	31	40	0	28	1.57

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