genome.fa.s9.2.7.7.80.10.50.1000.145.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  145  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)
48075099--48075137	19	2.1	19	100	0	78	25	5	33	35	1.78
48078156--48078261	29	3.7	29	85	3	133	33	23	1	40	1.66
48078168--48078285	57	2.1	57	87	4	166	32	22	1	44	1.63
48078168--48078268	28	3.6	28	84	6	123	31	24	1	41	1.66
48078771--48078801	11	2.8	11	100	0	62	83	6	9	0	0.79
48078758--48078833	17	4.5	17	73	17	59	77	2	19	0	0.88
48078760--48078835	39	2.0	38	84	7	100	78	2	18	0	0.86
48078759--48078835	18	4.2	17	74	22	68	79	2	18	0	0.85
48083210--48083262	14	3.7	14	73	14	54	13	0	37	49	1.42
48083203--48083245	20	2.2	20	87	8	61	13	0	39	46	1.44
48083309--48083486	93	1.9	93	87	3	261	41	3	15	39	1.66
48083525--48083942	126	3.3	126	87	0	584	32	17	20	29	1.95
48088070--48088127	26	2.2	26	84	0	71	41	18	15	24	1.89
48089415--48089472	26	2.2	26	90	0	89	44	18	12	24	1.84
48090367--48090405	6	6.8	6	82	11	55	12	0	2	84	0.72
48090359--48090407	22	2.2	22	88	0	80	14	0	2	83	0.73
48090359--48090399	16	2.7	15	96	3	73	12	0	2	85	0.70
48091002--48091063	3	20.3	3	80	9	72	27	3	0	69	1.04
48091477--48091520	23	1.9	23	82	17	56	25	11	2	61	1.41
48091491--48091537	19	2.5	19	80	10	60	23	10	6	59	1.53
48096287--48096371	43	2.0	44	86	9	122	45	3	4	45	1.41
48096983--48097026	8	5.1	8	79	15	52	29	0	0	70	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48096968--48097027	10	6.4	9	75	9	50	31	0	0	68	0.90
48097045--48097102	25	2.3	26	82	8	66	29	1	5	63	1.25
48099420--48099575	58	2.7	57	72	19	135	46	7	4	41	1.53
48099590--48099674	30	2.8	29	76	20	100	44	7	5	42	1.55
48099590--48099691	34	3.2	33	80	15	117	48	6	5	39	1.54
48107022--48107050	9	3.2	9	100	0	58	41	0	0	58	0.98
48110828--48111204	44	8.4	44	72	10	152	27	20	19	32	1.97
48110828--48112238	227	6.3	226	81	6	1272	28	20	19	31	1.97
48111054--48111575	263	2.0	263	91	1	850	28	20	19	31	1.97
48110846--48111807	490	2.0	490	90	1	1518	27	20	19	31	1.97
48111358--48112282	409	2.3	409	87	1	1316	28	21	19	30	1.97
48111435--48112012	138	4.2	138	70	13	320	29	20	19	30	1.97
48111611--48112055	182	2.4	182	90	1	669	28	20	19	30	1.97
48111333--48112309	44	21.6	44	68	15	336	27	21	19	31	1.98
48113737--48113798	8	8.0	8	76	16	51	3	1	11	83	0.82
48113740--48113796	6	9.8	6	75	21	50	3	1	10	84	0.82
48113739--48113797	7	8.9	7	76	14	54	3	1	10	84	0.80
48120896--48120935	15	3.0	13	83	16	55	60	2	0	37	1.11
48122918--48122951	3	11.3	3	87	0	50	58	2	2	35	1.28
48122918--48122973	15	3.7	15	79	9	60	57	3	8	30	1.47
48127897--48127933	6	6.2	6	100	0	74	32	0	0	67	0.91
48128583--48128608	5	5.2	5	100	0	52	42	19	19	19	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48129621--48129657	9	4.1	9	85	0	56	29	8	13	48	1.71
48130917--48130956	20	2.0	20	95	0	71	25	7	5	62	1.42
48145957--48146037	26	3.2	25	74	10	76	25	18	13	41	1.87
48146139--48146182	23	1.9	23	95	0	79	11	20	25	43	1.85
48147328--48147383	26	2.2	26	83	0	67	26	17	16	39	1.91
48153931--48154003	32	2.3	32	97	0	137	45	0	2	52	1.15
48156400--48156450	21	2.5	20	82	17	54	54	27	3	13	1.56
48157442--48157482	18	2.3	19	83	12	59	24	9	0	65	1.22
48157505--48157557	3	17.7	3	86	0	70	32	3	1	62	1.24
48157547--48157661	34	3.2	33	64	27	79	29	7	6	56	1.52
48157583--48157706	43	3.1	43	68	27	135	27	7	8	56	1.56
48157550--48157706	77	2.0	77	100	0	314	28	7	7	56	1.55
48160109--48160146	13	2.8	13	85	14	51	39	0	0	60	0.97
48161093--48161131	18	2.2	18	85	0	51	30	33	0	35	1.58
48174073--48174315	46	5.3	46	86	2	328	41	17	13	27	1.87
48174073--48174315	91	2.7	92	86	1	328	41	17	13	27	1.87
48174632--48174669	18	2.1	18	100	0	76	47	15	15	21	1.82
48186010--48186057	19	2.4	21	83	10	66	45	14	0	39	1.45
48186205--48186601	193	2.1	190	84	6	507	48	5	3	43	1.40
48186642--48186678	15	2.2	18	81	18	53	59	0	2	37	1.12
48186648--48186697	15	3.2	16	83	8	59	66	0	2	32	1.03
48187037--48187143	50	2.1	50	98	0	205	27	10	22	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48188216--48188293	31	2.5	31	83	2	95	46	3	19	30	1.68
48194417--48194527	40	2.8	39	86	4	150	34	18	26	21	1.96
48198897--48199038	27	5.3	27	77	0	140	46	21	14	17	1.84
48198905--48199038	54	2.5	54	85	7	191	46	20	14	17	1.84
48198897--48199050	81	1.9	81	80	0	182	44	22	14	19	1.86
48199204--48199257	26	2.1	26	92	0	90	14	18	27	38	1.90
48199333--48199410	28	2.8	28	84	0	111	26	25	23	24	2.00
48201704--48201750	16	2.9	16	87	12	62	10	6	0	82	0.82
48201723--48201772	8	6.4	8	86	2	66	2	20	0	78	0.86
48201708--48201748	21	2.0	21	85	0	55	9	7	0	82	0.83
48202476--48202599	29	4.2	28	73	8	70	44	4	13	37	1.63
48202803--48203922	75	14.8	75	87	3	1484	33	20	18	27	1.96
48202802--48203922	378	3.0	376	88	3	1553	33	20	18	27	1.96
48204777--48204806	13	2.3	13	94	0	51	0	3	10	86	0.67
48216054--48216104	7	6.9	7	80	10	57	1	19	0	78	0.85
48216052--48216107	16	3.6	16	72	18	55	1	19	0	78	0.84
48216044--48216107	23	2.7	24	80	9	78	1	18	1	78	0.92
48216296--48216334	12	3.3	12	82	3	53	0	25	0	74	0.82
48216292--48216335	19	2.4	18	80	3	52	0	25	0	75	0.81
48222776--48222835	29	2.1	29	87	6	86	38	30	21	10	1.86
48223997--48224136	71	1.9	72	81	2	165	24	19	27	29	1.98
48226123--48226164	22	1.9	22	90	9	68	21	35	0	42	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48236147--48236229	42	2.0	43	90	2	132	33	21	21	22	1.97
48236152--48236291	43	3.3	43	80	6	142	30	23	20	25	1.98
48254413--48254461	20	2.4	21	83	6	57	59	4	2	34	1.28
48254377--48254450	29	2.6	28	75	12	69	63	2	1	32	1.17
48256725--48256769	18	2.5	17	79	10	54	57	2	2	37	1.23
48258957--48258989	16	2.1	16	100	0	66	51	24	0	24	1.48
48262163--48262196	16	2.2	16	94	5	61	47	14	11	26	1.79
48262129--48262282	75	2.1	75	96	0	281	45	6	17	30	1.74
48266368--48266651	147	1.9	147	95	0	514	37	10	10	41	1.75
48266662--48266687	11	2.4	11	100	0	52	46	0	7	46	1.31
48267838--48267864	14	1.9	14	100	0	54	22	7	11	59	1.56
48271605--48271699	14	6.8	14	67	7	50	45	17	1	35	1.56
48271649--48271733	28	3.0	28	76	6	100	45	21	0	32	1.52
48271619--48271733	56	2.1	56	89	0	176	44	18	0	36	1.56
48271747--48271786	20	2.1	19	85	4	53	75	5	5	15	1.15
48272439--48272484	24	1.9	24	81	0	56	63	4	0	32	1.14
48272716--48272778	3	21.0	3	100	0	126	66	0	0	33	0.92
48273414--48273455	2	21.0	2	87	0	57	50	2	0	47	1.14
48273859--48274185	76	4.3	76	82	3	349	38	21	12	27	1.90
48285450--48285476	9	3.0	9	100	0	54	44	11	22	22	1.84
48295286--48295316	16	1.9	16	93	0	53	48	9	6	35	1.62
48295497--48295562	20	3.4	20	78	17	77	34	1	7	56	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48295984--48296024	17	2.3	18	88	12	59	60	0	2	36	1.10
48314890--48314950	22	2.8	20	79	16	68	39	11	8	40	1.71
48314913--48314948	11	3.3	11	100	0	72	38	8	8	44	1.65
48319095--48319158	13	4.9	13	83	7	85	39	23	6	31	1.79
48319763--48319829	2	35.0	2	82	8	86	52	0	0	47	1.00
48324996--48325047	23	2.3	23	86	0	77	26	26	13	32	1.94
48327677--48327721	21	2.1	22	84	12	58	73	6	4	15	1.21
48329497--48329548	23	2.3	23	96	0	95	42	7	3	46	1.51
48334000--48334044	18	2.5	18	82	7	56	40	17	4	37	1.70
48337745--48337790	24	1.9	24	82	8	58	50	6	6	36	1.54

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