genome.fa.s1.2.7.7.80.10.50.1000.129.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  129  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)
39160213--39160274	26	2.4	26	81	5	72	32	6	25	35	1.82
39160234--39160271	13	2.9	13	100	0	76	23	7	28	39	1.83
39167581--39167748	46	3.6	47	79	4	189	28	16	23	30	1.96
39167565--39167741	92	1.9	92	82	2	221	27	16	23	32	1.96
39178128--39178268	75	1.9	75	87	0	210	36	21	2	38	1.69
39181899--39181946	10	4.6	10	81	5	51	18	2	14	64	1.38
39191132--39191370	50	4.7	50	78	5	142	25	26	19	28	1.99
39192342--39192559	47	4.6	47	90	2	307	39	14	18	27	1.90
39192439--39192666	114	2.0	115	90	2	361	38	14	19	28	1.90
39192545--39192822	46	6.0	46	91	0	448	37	15	20	26	1.92
39192383--39192719	160	2.1	161	91	1	550	37	14	20	27	1.91
39192450--39192697	114	2.2	114	87	2	318	37	14	20	27	1.92
39192383--39192765	160	2.4	160	88	2	500	38	14	19	27	1.91
39193644--39193767	43	2.9	43	82	11	139	29	29	19	21	1.98
39194012--39194036	8	3.1	8	100	0	50	24	36	12	28	1.91
39200643--39200860	47	4.6	47	91	2	325	39	14	18	27	1.89
39200740--39200967	114	2.0	115	91	2	370	38	14	19	28	1.91
39200846--39201123	46	6.0	46	90	0	430	36	15	20	27	1.93
39200684--39201020	160	2.1	161	92	1	559	37	14	19	27	1.91
39207128--39207248	50	2.4	49	80	2	116	28	19	20	31	1.97
39207130--39207269	25	5.6	25	75	5	95	27	20	20	31	1.97
39213165--39213217	23	2.3	23	83	9	63	15	11	7	66	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39214610--39214643	17	2.0	17	88	0	50	58	5	2	32	1.37
39214853--39214887	18	1.9	18	94	0	61	28	17	17	37	1.92
39218025--39218065	18	2.2	19	91	4	66	34	12	0	53	1.38
39223204--39223254	24	2.1	24	85	3	66	29	0	1	68	1.00
39229746--39229993	94	2.6	94	81	0	289	32	18	26	22	1.97
39229916--39229978	27	2.4	27	86	2	83	31	20	31	15	1.94
39231817--39231871	29	2.0	29	86	13	80	16	14	9	60	1.59
39240085--39240123	21	1.9	21	89	5	62	61	5	2	30	1.31
39247176--39247249	39	1.9	38	86	8	105	36	29	12	21	1.90
39251578--39251677	40	2.5	40	86	0	137	42	22	25	11	1.86
39251578--39251687	20	5.5	20	84	0	112	43	20	25	10	1.83
39251560--39251695	40	3.4	39	74	10	105	41	19	26	11	1.86
39252619--39252755	69	2.0	70	92	1	231	32	6	5	54	1.50
39262104--39262284	57	3.1	58	89	4	269	27	20	6	45	1.76
39264213--39264315	40	2.6	39	83	9	127	28	22	18	31	1.97
39264224--39264403	40	4.5	40	83	2	184	28	24	16	30	1.97
39264221--39264370	80	1.9	80	85	0	210	28	24	17	29	1.97
39270119--39270268	74	2.0	74	89	0	228	30	22	14	33	1.93
39270644--39270682	19	2.2	18	86	9	53	79	7	5	7	1.05
39277933--39277999	22	3.1	21	71	12	55	2	26	2	67	1.20
39281330--39281365	18	2.0	18	88	0	54	33	5	5	55	1.46
39283905--39283943	19	2.1	19	95	0	69	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39283905--39283937	10	3.4	10	91	8	59	63	0	0	36	0.95
39283905--39283943	9	4.1	9	87	9	51	61	0	0	38	0.96
39286378--39286435	30	1.9	30	89	0	89	27	31	29	12	1.92
39289018--39289049	13	2.4	14	94	5	57	46	9	0	43	1.35
39293714--39293763	25	2.0	25	92	0	82	54	10	4	32	1.52
39302504--39302566	32	2.0	32	100	0	126	38	9	7	44	1.66
39308731--39308783	6	8.8	6	97	0	97	49	16	1	32	1.57
39311247--39311295	2	24.5	2	100	0	98	0	48	0	51	1.00
39314394--39314782	81	4.7	83	80	10	350	45	10	11	32	1.74
39314479--39314950	166	2.9	167	81	5	437	44	9	12	32	1.75
39314456--39314950	81	5.9	86	79	12	419	45	9	12	32	1.75
39315557--39315605	20	2.5	20	89	0	71	57	10	4	28	1.50
39320497--39320562	21	3.2	21	74	16	57	42	13	27	16	1.86
39320497--39320582	42	2.1	41	84	2	109	43	13	24	18	1.87
39325533--39325661	67	1.9	67	91	0	213	20	17	33	28	1.95
39339746--39339770	13	1.9	13	100	0	50	32	4	24	40	1.73
39341903--39341932	13	2.3	13	94	0	51	10	0	23	66	1.21
39341902--39341935	13	2.5	13	85	4	50	8	0	26	64	1.22
39344088--39344131	21	2.2	20	83	4	52	47	15	18	18	1.83
39345627--39345672	24	2.0	23	82	4	56	60	13	0	26	1.32
39345918--39345943	5	5.2	5	100	0	52	38	19	19	23	1.93
39346449--39346500	16	3.0	16	76	23	52	46	0	28	25	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39346447--39346536	35	2.7	33	83	10	103	46	0	30	23	1.52
39346587--39346645	30	2.0	29	83	6	73	38	0	38	22	1.54
39346942--39346969	9	3.1	9	100	0	56	46	21	10	21	1.81
39352713--39352750	15	2.4	16	87	12	53	65	0	5	28	1.14
39352724--39352772	25	2.1	23	85	14	66	65	0	4	30	1.11
39352768--39352821	19	2.8	18	88	8	72	59	0	3	37	1.15
39352935--39352996	29	2.2	27	85	5	79	38	4	3	53	1.39
39353381--39353429	18	2.8	17	82	17	64	40	2	0	57	1.10
39357520--39357569	21	2.4	21	78	15	68	40	10	2	48	1.48
39357655--39357774	41	2.9	40	83	2	132	30	22	18	29	1.97
39365826--39366060	50	4.6	50	84	3	272	27	23	27	21	1.99
39365825--39366070	100	2.4	105	86	5	349	27	23	27	21	1.99
39367747--39367809	20	3.1	21	80	11	69	41	19	28	11	1.85
39373846--39373905	19	2.9	21	83	11	63	20	3	3	73	1.12
39374018--39374056	14	2.8	14	88	0	60	35	10	23	30	1.88
39374632--39374667	18	1.9	18	88	5	54	58	2	0	38	1.13
39374783--39374808	9	2.9	9	100	0	52	42	0	0	57	0.98
39378927--39378998	25	2.9	26	87	8	89	18	19	26	36	1.94
39379016--39379399	188	2.0	188	93	0	651	33	10	24	32	1.89
39379524--39379553	15	2.0	15	100	0	60	33	20	26	20	1.97
39379820--39379861	20	2.2	19	83	12	50	59	4	19	16	1.54
39383647--39383675	2	14.5	2	100	0	58	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39384699--39384818	23	5.3	23	75	4	127	32	26	16	24	1.96
39384699--39384818	46	2.7	46	86	2	154	32	26	16	24	1.96
39385044--39385082	18	2.2	17	86	13	53	46	20	0	33	1.51
39402159--39402192	16	2.1	16	88	5	50	8	0	14	76	1.01
39409604--39409815	29	7.2	29	76	3	201	24	26	12	37	1.90
39409604--39409815	59	3.6	58	84	3	255	24	26	12	37	1.90
39415502--39415720	111	2.0	111	99	0	429	37	21	12	28	1.90
39417504--39417568	32	2.0	32	93	0	112	35	12	10	41	1.78
39417955--39418239	29	9.8	29	77	4	252	21	24	13	40	1.89
39418012--39418269	87	3.0	86	80	5	252	22	24	12	39	1.89
39417943--39418245	59	5.2	58	78	5	290	23	24	13	38	1.91
39422186--39422352	43	3.9	43	83	5	196	32	25	17	23	1.97
39422186--39422352	85	2.0	86	83	5	214	32	25	17	23	1.97
39422235--39422411	83	2.1	81	80	12	196	31	24	17	25	1.97
39426382--39426428	14	3.2	14	78	18	51	65	21	4	8	1.37
39427066--39427109	14	3.1	14	86	0	61	34	45	0	20	1.51
39427059--39427112	21	2.5	21	74	14	56	35	46	0	18	1.50
39427163--39427215	14	3.8	14	74	0	52	47	26	0	26	1.53
39427536--39427616	41	2.0	41	87	0	117	27	29	18	24	1.98
39428250--39428315	20	3.3	19	73	12	53	42	12	31	13	1.81
39435168--39435229	25	2.5	25	89	0	88	30	24	20	24	1.99
39435152--39435274	50	2.5	49	77	5	122	32	21	22	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39445658--39445704	22	2.0	24	84	12	62	42	12	8	36	1.74
39450606--39450650	13	3.5	13	93	0	81	20	8	15	55	1.66
39451855--39451890	17	2.1	18	89	5	56	22	13	22	41	1.89
39454257--39454291	16	2.2	16	94	0	61	22	0	31	45	1.53
39460158--39460231	37	2.0	37	100	0	148	40	8	18	32	1.80
39467202--39467235	13	2.6	13	100	0	68	29	0	0	70	0.87
39467423--39467477	21	2.8	20	75	8	67	23	3	5	67	1.28
39468354--39468420	33	2.0	33	86	11	93	49	0	1	49	1.10
39471386--39471411	13	2.0	13	100	0	52	30	23	7	38	1.83
39486301--39486339	2	20.0	2	84	5	53	48	2	2	46	1.29

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