genome.fa.s9.2.7.7.80.10.50.1000.155.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  155  of  226  ( 27023 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)
50391270--50391331	22	2.8	21	83	13	72	64	3	1	30	1.19
50391349--50391389	21	2.0	21	85	0	55	56	4	7	31	1.48
50391397--50391472	28	2.5	28	81	16	73	71	3	5	19	1.22
50391940--50392073	19	6.7	21	79	8	77	40	14	6	38	1.73
50391940--50391997	22	2.6	22	81	7	64	41	17	5	36	1.72
50391976--50392086	19	5.8	19	86	0	168	37	14	9	38	1.78
50391976--50392079	38	2.7	38	96	0	190	38	13	8	39	1.75
50392372--50392478	43	2.4	43	76	6	108	29	26	15	28	1.96
50392415--50392786	132	2.8	132	91	1	604	28	24	18	28	1.98
50394133--50394178	15	3.1	15	81	12	58	4	10	2	82	0.89
50396745--50396791	24	2.0	24	86	0	67	12	25	17	44	1.84
50399180--50399233	26	2.1	26	85	0	72	68	5	1	24	1.21
50399179--50399239	22	2.6	22	82	12	61	65	4	1	27	1.22
50399255--50399295	21	2.0	21	90	0	64	58	4	4	31	1.40
50399849--50399903	23	2.6	21	78	13	60	41	16	7	34	1.76
50399852--50399896	23	2.0	22	86	4	63	40	17	6	35	1.76
50399875--50399985	19	5.8	19	88	0	168	38	13	9	38	1.76
50399875--50399978	38	2.7	38	96	0	190	39	12	8	39	1.74
50406860--50407056	97	2.0	97	98	0	376	28	14	17	39	1.89
50413895--50413978	38	2.2	40	89	4	127	28	7	20	44	1.78
50416044--50416111	34	2.0	34	94	0	118	63	4	13	19	1.46
50416049--50416121	34	2.1	34	90	5	112	64	5	12	17	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50420373--50420408	15	2.4	15	85	0	54	36	19	22	22	1.95
50420680--50420723	19	2.2	20	84	11	56	36	0	4	59	1.18
50420812--50420838	9	3.0	9	100	0	54	33	0	11	55	1.35
50420812--50420850	18	2.2	18	86	9	53	33	2	12	51	1.54
50424981--50425007	2	13.5	2	100	0	54	48	0	0	51	1.00
50428811--50428842	2	16.0	2	100	0	64	50	0	0	50	1.00
50429288--50429349	29	2.2	29	82	2	81	24	12	12	50	1.76
50432969--50433057	29	3.2	29	66	15	78	42	4	13	39	1.64
50432890--50433105	55	3.9	54	93	1	360	44	5	12	37	1.64
50432890--50433105	109	2.0	110	92	3	364	44	5	12	37	1.64
50433107--50433569	64	7.6	64	81	13	571	25	0	29	45	1.57
50433292--50433350	18	3.3	18	63	13	50	23	0	32	44	1.54
50433239--50433323	23	3.4	23	82	17	116	23	0	30	45	1.53
50433512--50433576	18	3.7	18	67	8	53	24	1	27	46	1.62
50433530--50433554	11	2.3	11	100	0	50	16	0	44	40	1.47
50433101--50433546	29	14.8	29	81	13	535	25	0	29	45	1.56
50433101--50433569	93	5.1	90	82	13	518	25	0	28	44	1.57
50433626--50433736	25	4.6	25	69	20	83	45	14	1	37	1.55
50433575--50433738	71	2.3	71	95	0	292	46	14	1	37	1.55
50433845--50433902	21	2.8	21	97	0	107	3	20	29	46	1.67
50434844--50434868	7	3.6	7	100	0	50	60	12	0	28	1.32
50435949--50436013	31	2.2	31	88	5	98	63	1	0	35	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50436101--50436148	22	2.2	22	96	0	87	43	0	31	25	1.55
50436014--50436126	51	2.2	51	91	0	181	40	1	28	29	1.66
50436507--50436610	51	2.0	51	90	0	163	34	11	14	39	1.82
50437102--50437139	14	2.7	14	84	8	51	68	7	0	23	1.16
50446415--50446465	19	2.7	18	85	8	66	31	1	1	64	1.15
50450626--50450688	20	3.1	20	75	20	60	47	1	1	49	1.20
50450626--50450698	11	6.8	11	78	13	64	47	2	1	47	1.24
50453073--50453141	31	2.2	31	84	5	86	31	4	5	57	1.42
50456348--50456386	21	1.9	21	84	5	53	25	0	5	69	1.09
50456555--50456592	14	2.7	15	84	12	53	60	2	0	36	1.11
50459204--50459244	21	2.0	21	85	9	57	26	19	14	39	1.90
50459684--50459727	9	4.9	9	81	10	54	36	9	2	52	1.46
50467093--50467126	16	2.1	16	88	0	50	52	0	0	47	1.00
50478203--50478261	29	2.0	30	86	3	84	54	15	3	27	1.57
50480472--50480528	5	10.6	5	78	14	60	19	19	0	61	1.35
50480464--50480511	22	2.1	23	92	3	80	16	14	0	68	1.21
50480472--50480528	27	2.1	27	90	6	89	19	19	0	61	1.35
50480472--50480528	11	5.3	10	80	14	60	19	19	0	61	1.35
50480475--50480528	22	2.5	22	87	0	72	20	20	0	59	1.38
50480535--50480609	18	4.1	17	79	14	78	20	12	2	65	1.37
50481077--50481152	5	14.6	5	75	9	64	19	19	1	59	1.45
50481148--50481336	21	8.2	21	67	23	89	24	13	0	62	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50481140--50481405	94	2.8	89	85	9	327	23	15	0	61	1.34
50481142--50481435	48	6.1	48	85	8	386	23	15	0	60	1.34
50481143--50481435	95	3.1	97	87	7	404	23	15	0	60	1.35
50481142--50481419	22	11.7	22	70	21	138	24	14	0	61	1.34
50481169--50481442	73	3.8	72	71	16	217	24	14	0	60	1.34
50481348--50481430	25	3.2	25	68	15	62	20	19	0	60	1.37
50484529--50484560	16	2.0	16	100	0	64	25	6	6	62	1.42
50484553--50484796	122	2.0	123	82	7	300	31	20	16	32	1.94
50484808--50485110	107	2.8	106	85	5	374	33	20	17	29	1.95
50491717--50491770	22	2.6	21	85	8	74	38	1	1	57	1.20
50492626--50492658	17	2.0	17	94	5	59	60	0	0	39	0.97
50493003--50493090	44	2.0	46	80	17	105	30	7	4	56	1.48
50495159--50495250	36	2.6	34	77	12	89	58	5	4	31	1.40
50499144--50499178	16	2.1	16	94	5	61	80	0	20	0	0.72
50501374--50501427	25	2.2	25	86	6	74	42	0	1	55	1.10
50506326--50506355	15	2.0	15	93	0	51	90	0	0	10	0.47
50506813--50506873	17	3.5	18	76	12	65	60	1	1	36	1.16
50509634--50509672	6	6.3	6	82	5	51	38	2	0	58	1.12
50512577--50512739	82	2.0	81	83	4	202	30	19	17	32	1.95
50517694--50517749	19	2.9	19	78	5	67	7	16	25	51	1.69
50519471--50519591	64	1.9	63	83	5	154	23	31	22	22	1.98
50520755--50521056	128	2.4	128	98	0	595	18	30	22	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50520755--50521057	64	4.7	64	93	0	525	18	30	22	29	1.97
50525495--50525594	49	2.0	49	100	0	200	51	8	17	24	1.72
50529559--50529609	21	2.4	21	96	0	93	47	5	17	29	1.71
50533062--50533101	6	6.3	6	86	11	53	82	0	17	0	0.67
50533062--50533101	13	3.2	12	89	7	53	82	0	17	0	0.67
50533062--50533101	20	2.1	19	90	4	62	82	0	17	0	0.67
50533476--50533687	64	3.3	64	85	0	289	28	27	19	23	1.98
50535877--50535909	14	2.4	14	94	0	57	36	0	3	60	1.12
50536376--50536417	21	2.0	21	95	0	75	50	0	21	28	1.49
50536687--50536750	3	21.3	3	100	0	128	34	0	0	65	0.93
50543904--50543949	23	2.0	23	95	0	83	43	10	8	36	1.71
50544040--50544064	2	12.5	2	100	0	50	52	0	0	48	1.00
50544547--50544898	162	2.2	162	93	0	605	27	20	16	35	1.94
50545675--50545723	21	2.3	22	82	3	55	75	6	0	18	1.00
50549653--50549697	19	2.4	19	88	7	65	60	0	2	37	1.09
50551063--50551112	16	3.2	16	82	2	57	32	6	0	62	1.20
50553098--50553252	43	3.6	42	79	4	150	23	15	27	33	1.95
50553098--50553247	42	3.5	42	79	6	133	24	16	26	33	1.95
50554507--50554563	2	28.5	2	100	0	114	50	0	0	49	1.00
50554735--50554765	2	15.5	2	100	0	62	48	0	0	51	1.00
50556234--50556292	15	3.9	15	82	14	61	77	0	1	20	0.85
50556245--50556292	5	9.6	5	88	6	71	81	0	0	18	0.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50556253--50556309	27	2.1	27	84	12	73	78	3	0	17	0.88
50556198--50556293	11	9.1	11	75	4	56	73	2	3	20	1.07
50556222--50556296	11	7.3	10	70	20	57	76	0	4	20	0.95
50556234--50556299	20	3.3	19	79	12	62	77	0	1	21	0.85
50556245--50556299	16	3.1	17	77	17	58	80	0	0	20	0.72
50556953--50557035	3	27.7	3	97	0	157	68	0	31	0	0.90
50557240--50557722	89	5.4	89	81	2	416	28	19	17	34	1.95
50557240--50557721	45	10.9	44	80	3	437	28	19	17	34	1.95
50559273--50559297	13	1.9	13	100	0	50	32	4	24	40	1.73
50563317--50563346	16	1.9	15	93	6	51	30	23	0	46	1.52

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226