genome.fa.s8.2.7.7.80.10.50.1000.183.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  183  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)
53975084--53975129	15	3.2	15	81	9	60	36	34	0	28	1.58
53975382--53975419	14	2.7	15	88	12	62	42	28	0	28	1.56
53974916--53975639	298	2.5	288	87	4	1020	41	26	3	29	1.71
53975631--53975702	23	3.2	23	80	9	69	34	38	1	25	1.65
53975665--53975723	23	2.7	23	79	12	70	33	33	0	32	1.58
53976114--53976395	41	6.9	41	85	4	356	28	28	22	20	1.99
53976114--53976395	82	3.4	82	90	0	413	28	28	22	20	1.99
53976114--53976393	123	2.3	122	87	3	400	28	27	22	20	1.99
53976431--53976524	39	2.4	40	84	7	113	20	19	21	39	1.93
53976531--53976556	12	2.2	12	100	0	52	46	30	15	7	1.74
53976869--53976926	28	2.1	27	90	6	91	34	10	3	51	1.53
53978281--53978337	29	2.0	29	85	0	78	35	12	7	45	1.69
53992597--53992681	28	3.0	28	83	8	93	49	0	1	49	1.08
53992629--53992677	8	6.2	8	90	4	73	44	0	0	55	0.99
53992626--53992683	23	2.6	22	81	10	73	46	0	0	53	1.00
53992684--53992746	11	5.8	10	75	15	54	69	6	20	3	1.24
53993396--53993442	24	2.0	24	84	16	62	31	0	17	51	1.46
53995287--53995328	22	1.9	22	95	0	75	40	11	4	42	1.63
53998597--53998703	29	3.7	29	79	0	115	15	24	19	40	1.91
54002841--54002875	3	11.7	3	100	0	70	34	31	0	34	1.58
54008424--54008502	25	3.2	25	96	0	149	21	18	20	39	1.93
54017184--54017223	20	2.0	20	100	0	80	50	15	20	15	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54018982--54019050	20	3.6	19	80	16	81	36	2	0	60	1.11
54019009--54019047	10	3.9	10	80	12	53	38	0	0	61	0.96
54027555--54027596	22	1.9	22	95	0	75	35	0	2	61	1.09
54030234--54030299	30	2.2	30	81	7	80	33	9	12	45	1.73
54051461--54051500	20	2.0	20	100	0	80	35	10	20	35	1.86
54051483--54051575	47	2.0	47	100	0	186	39	10	21	27	1.87
54053942--54053974	13	2.5	14	90	9	52	69	0	30	0	0.88
54056551--54056605	25	2.2	25	86	0	74	18	27	18	36	1.94
54059625--54059736	42	2.7	42	78	0	116	41	18	24	16	1.90
54079999--54080034	5	7.2	5	87	0	54	36	2	2	58	1.27
54081343--54081375	2	16.5	2	100	0	66	51	0	0	48	1.00
54082451--54082513	8	8.0	8	82	3	74	46	0	22	31	1.52
54104795--54104834	22	2.0	20	85	14	55	50	15	0	35	1.44
54110752--54110784	16	2.0	17	88	5	50	24	3	3	69	1.16
54118191--54118370	93	1.9	93	82	5	213	28	10	15	46	1.78
54118611--54118790	81	2.2	81	82	6	215	23	9	16	50	1.74
54118614--54118790	80	2.2	82	82	7	211	23	9	16	50	1.74
54132146--54132172	14	1.9	14	100	0	54	33	0	0	66	0.92
54145618--54145682	3	21.7	3	100	0	130	33	0	0	66	0.92
54146950--54146994	23	2.0	23	81	0	54	33	4	4	57	1.38
54147252--54147283	15	2.1	15	100	0	64	6	25	6	62	1.42
54168679--54168746	30	2.3	30	89	5	102	50	5	0	44	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54169239--54169280	19	2.2	19	87	8	59	52	9	2	35	1.47
54175474--54175515	20	2.0	22	82	13	54	50	0	0	50	1.00
54178093--54178133	20	2.0	20	100	0	82	24	19	26	29	1.98
54178407--54178461	27	2.1	26	83	10	67	41	3	1	52	1.29
54203435--54203464	2	15.0	2	100	0	60	50	0	0	50	1.00
54208073--54208993	341	2.7	341	91	1	1496	26	22	18	32	1.97
54212783--54212836	27	2.0	27	82	7	65	64	5	3	25	1.32
54217821--54217867	18	2.7	18	77	6	53	65	4	17	12	1.40
54226699--54226737	21	1.9	20	94	5	69	33	7	30	28	1.85
54234217--54234265	23	2.0	23	84	7	62	61	2	0	36	1.08
54236696--54236744	19	2.6	19	80	9	64	61	4	0	34	1.15
54237045--54237078	16	2.0	18	88	11	54	14	0	8	76	1.01
54238825--54239009	91	2.0	91	96	0	343	16	12	10	61	1.57
54239103--54239233	25	5.5	24	77	7	115	32	6	3	57	1.41
54239469--54239514	24	1.9	24	90	0	74	30	8	2	58	1.40
54240962--54241000	20	2.0	20	84	0	51	58	2	0	38	1.12
54241192--54241271	36	2.2	36	82	8	92	48	5	0	46	1.24
54243229--54243287	24	2.5	24	86	5	84	11	35	23	28	1.91
54243417--54243487	21	3.2	21	69	18	54	18	19	21	40	1.91
54243390--54243517	45	2.8	45	78	2	123	17	25	17	39	1.92
54277167--54277208	3	14.0	3	90	9	68	69	0	30	0	0.89
54280739--54280805	34	1.9	35	87	3	100	31	8	14	44	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54293082--54293124	16	2.7	16	82	7	52	41	0	4	53	1.21
54294983--54295037	29	1.9	29	82	10	69	43	3	14	38	1.63
54303824--54304065	108	2.2	108	85	1	315	17	18	19	44	1.87
54304124--54304209	36	2.4	35	83	9	102	13	20	24	40	1.89
54311381--54311418	17	2.2	18	85	4	51	26	0	7	65	1.19
54311408--54311467	25	2.4	24	81	13	68	38	0	3	58	1.15
54327388--54327431	21	2.1	21	86	0	61	22	4	6	65	1.35
54336313--54336339	13	2.1	13	100	0	54	40	7	7	44	1.60
54344516--54344561	9	5.1	9	91	0	74	45	13	13	28	1.80
54377652--54377728	39	2.0	39	84	5	102	40	16	23	19	1.91
54382304--54382340	19	1.9	19	94	0	65	70	8	10	10	1.35
54383706--54383756	3	17.0	3	100	0	102	66	0	0	33	0.92
54385295--54385321	4	6.8	4	100	0	54	77	0	0	22	0.76
54393130--54393192	31	2.0	31	100	0	126	19	38	9	33	1.84
54395426--54395478	19	2.9	18	75	10	54	66	7	3	22	1.34
54399270--54399316	25	1.9	25	82	4	60	17	6	21	55	1.64
54400819--54400859	3	13.7	3	86	0	55	4	36	24	34	1.77
54400816--54400861	21	2.2	21	92	0	74	8	34	21	34	1.84
54401669--54401729	22	2.6	24	67	17	56	55	3	1	39	1.26
54401949--54401995	6	7.2	6	84	15	58	19	0	0	80	0.70
54402439--54402480	22	1.9	22	85	0	57	23	2	2	71	1.10
54402928--54403032	52	2.0	52	100	0	210	13	20	17	48	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54405235--54405260	3	8.7	3	100	0	52	34	30	0	34	1.58
54418035--54418072	20	1.9	20	89	10	60	50	15	15	18	1.79
54422230--54422385	25	6.3	25	68	18	85	17	23	19	39	1.93
54424112--54424152	8	5.0	8	88	5	64	41	0	0	58	0.98
54424178--54424257	30	2.6	30	75	13	83	62	5	30	2	1.29
54431386--54431457	28	2.7	28	69	14	71	48	0	8	43	1.33
54436994--54437104	46	2.4	46	93	1	188	30	20	17	31	1.95
54436981--54437214	37	5.6	45	83	11	234	28	21	14	35	1.93
54439320--54439414	25	3.8	25	91	0	154	22	22	16	38	1.93
54440515--54440611	10	9.8	10	70	25	55	35	2	0	62	1.07
54440516--54440601	30	3.0	28	83	11	111	37	2	0	60	1.10
54440515--54440653	40	3.5	39	79	14	131	35	2	0	62	1.07
54440539--54440665	40	3.1	40	92	5	184	35	2	0	61	1.14
54440617--54440678	32	1.9	32	83	0	79	29	1	4	64	1.23
54441433--54441465	15	2.2	15	100	0	66	42	24	21	12	1.86
54444039--54444095	28	2.1	26	84	12	71	43	3	0	52	1.18
54446256--54446298	17	2.8	16	80	20	56	41	0	2	55	1.12
54450299--54450331	6	5.5	6	92	0	57	3	33	36	27	1.72
54455960--54455984	2	12.5	2	100	0	50	0	48	0	52	1.00
54455984--54456012	2	14.5	2	100	0	58	48	0	0	51	1.00
54468027--54468074	24	2.0	24	91	0	78	33	43	2	20	1.64
54471030--54471081	8	6.6	8	78	10	54	61	0	36	1	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54472193--54472246	27	2.0	27	85	7	74	33	5	27	33	1.80
54474863--54475042	64	2.9	63	79	12	210	48	10	8	31	1.68
54477696--54477975	85	3.2	85	67	16	251	58	15	1	24	1.45
54477641--54478009	181	2.0	181	98	0	713	57	14	1	26	1.45
54478154--54478217	27	2.4	27	89	0	92	12	26	42	18	1.86
54481800--54481854	24	2.3	24	83	0	65	16	27	25	30	1.96
54482237--54482281	15	2.8	17	80	12	60	55	0	11	33	1.35
54487075--54487117	20	2.3	19	80	11	52	79	4	4	11	1.04
54487400--54487515	60	1.9	60	85	0	160	40	5	16	37	1.71
54487777--54487872	30	3.2	30	95	2	167	35	6	16	41	1.74

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