genome.fa.s1.2.7.7.80.10.50.1000.35.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  35  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)
11081114--11081138	6	4.2	6	100	0	50	84	0	0	16	0.63
11082731--11082761	7	4.4	7	95	0	53	32	0	3	64	1.09
11084122--11084207	40	2.1	41	93	2	147	55	11	10	22	1.65
11084450--11084480	16	1.9	16	93	0	53	67	0	29	3	1.06
11084467--11084497	11	2.7	12	90	10	55	74	0	16	9	1.07
11096114--11096278	86	1.9	87	93	1	287	25	12	20	42	1.86
11101252--11101282	15	2.1	15	100	0	62	41	6	32	19	1.77
11112864--11112922	29	2.0	29	93	0	100	33	20	32	13	1.91
11115924--11115961	20	1.9	20	88	0	58	52	2	7	36	1.45
11115932--11116013	25	3.5	24	72	8	78	48	3	7	40	1.48
11116723--11116763	19	2.1	19	86	9	55	78	7	4	9	1.10
11117729--11119168	132	10.9	132	91	1	2079	27	24	19	28	1.98
11118432--11119154	44	16.4	45	64	12	146	27	24	19	28	1.99
11120470--11120511	7	6.0	7	79	20	52	14	16	0	69	1.20
11121446--11121486	20	2.0	20	86	9	57	63	4	17	14	1.47
11127482--11127541	21	2.8	21	78	17	61	50	8	3	38	1.49
11130791--11130821	2	15.5	2	100	0	62	48	0	0	51	1.00
11137468--11137715	42	5.9	42	80	4	221	29	20	20	29	1.97
11138031--11138080	21	2.4	21	82	0	64	2	46	18	34	1.60
11143801--11143938	25	5.3	25	88	7	195	34	0	18	46	1.50
11143700--11143919	9	24.8	9	66	31	104	35	0	20	44	1.52
11143753--11143892	45	3.0	43	84	13	172	33	0	20	45	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11143801--11143938	53	2.6	51	92	5	215	34	0	18	46	1.50
11143975--11144125	74	2.1	74	98	1	295	41	6	1	50	1.37
11144272--11144316	13	3.5	13	87	0	72	51	2	6	40	1.41
11144272--11144330	26	2.4	25	86	8	77	50	3	6	38	1.45
11144288--11144427	40	3.5	40	94	0	235	45	2	9	42	1.51
11144361--11144568	57	3.6	57	89	3	337	40	2	11	45	1.53
11144401--11144559	17	8.6	17	74	21	133	38	2	12	45	1.56
11144361--11144568	115	1.8	114	93	1	362	40	2	11	45	1.53
11145999--11146068	15	4.9	15	79	13	94	41	20	0	38	1.52
11145999--11146068	26	2.5	27	86	9	88	41	20	0	38	1.52
11146474--11146826	84	4.1	83	83	7	395	30	18	19	31	1.95
11146543--11146841	84	3.5	84	88	4	447	30	18	19	31	1.96
11148268--11148401	40	3.3	40	88	1	196	21	30	15	32	1.95
11150653--11150880	117	2.0	117	81	7	272	41	9	4	45	1.56
11158640--11158680	20	2.0	20	85	0	55	12	9	21	56	1.65
11166613--11166670	27	2.1	27	83	6	71	58	0	3	37	1.15
11188956--11189048	42	2.2	43	96	1	170	36	27	8	26	1.86
11201849--11201879	7	4.6	7	96	4	55	64	12	9	12	1.50
11203462--11203823	18	20.5	17	69	17	170	44	10	12	32	1.76
11203458--11203823	35	10.4	34	74	8	243	44	10	12	32	1.76
11203600--11203823	105	2.1	104	86	5	317	41	11	13	33	1.80
11203523--11203832	71	4.4	66	79	10	210	42	10	12	35	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11203515--11203914	53	7.4	56	73	14	251	43	9	13	34	1.75
11203847--11203914	17	3.7	18	72	25	61	42	4	16	36	1.68
11204013--11204062	17	2.9	17	80	14	66	46	10	14	30	1.77
11204744--11204894	29	5.2	29	75	7	110	41	5	19	33	1.76
11207898--11207981	11	7.9	11	72	15	61	58	0	3	38	1.16
11207883--11207970	23	4.1	23	75	14	98	62	1	3	32	1.19
11226705--11226732	2	14.0	2	100	0	56	50	0	50	0	1.00
11231817--11231885	31	2.3	30	79	2	75	39	13	13	34	1.83
11234321--11234449	30	4.3	31	90	4	160	60	0	3	36	1.12
11234323--11234409	41	2.1	42	87	6	124	59	0	3	36	1.14
11234323--11234379	11	5.4	11	74	18	50	61	0	1	36	1.07
11234345--11234449	30	3.5	29	93	3	165	60	0	3	36	1.15
11238056--11238129	20	4.0	20	73	20	79	28	9	13	48	1.73
11238041--11238141	34	2.9	34	95	1	175	30	8	13	46	1.74
11238036--11238145	14	6.9	15	68	23	57	30	9	15	44	1.77
11238228--11238266	20	2.0	20	94	0	69	48	2	0	48	1.15
11240552--11240577	11	2.4	11	100	0	52	61	15	0	23	1.33
11240765--11240814	25	2.0	25	84	0	64	58	2	34	6	1.34
11240874--11240925	24	2.2	24	82	0	59	42	0	55	1	1.10
11241274--11241350	37	2.1	37	92	0	127	33	15	16	33	1.91
11250559--11250605	17	2.8	17	79	20	62	55	6	2	36	1.37
11250866--11250925	30	2.0	31	86	3	86	40	0	40	20	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11251219--11251248	9	3.3	9	90	0	51	36	23	13	26	1.92
11251788--11251835	18	2.6	19	80	9	55	72	4	4	18	1.17
11251917--11251946	2	15.5	2	93	6	53	50	0	0	50	1.00
11252209--11252285	3	25.7	3	100	0	154	66	0	0	33	0.92
11252214--11252311	15	6.5	16	90	4	64	64	1	2	32	1.12
11254712--11254767	3	18.7	3	100	0	112	33	0	32	33	1.58
11255648--11255752	40	2.7	40	77	5	106	32	18	27	21	1.97
11255810--11256065	41	6.2	41	85	0	298	14	22	25	37	1.92
11255810--11256062	123	2.1	123	84	1	328	14	22	24	37	1.92
11255830--11256128	41	7.3	41	81	4	124	16	23	23	35	1.95
11255871--11256128	123	2.1	123	78	2	268	17	23	23	36	1.95
11256642--11256679	15	2.5	15	86	0	58	21	0	42	36	1.53
11256943--11256969	14	1.9	14	100	0	54	37	3	14	44	1.63
11257122--11257152	2	16.0	2	93	6	55	51	0	0	48	1.00
11257406--11257436	2	15.5	2	100	0	62	51	0	0	48	1.00
11257991--11258062	37	1.9	37	83	13	94	19	1	43	36	1.60
11261470--11261514	22	2.0	22	95	0	81	46	11	0	42	1.39
11261437--11262047	31	20.7	30	79	12	503	46	10	2	40	1.51
11261744--11261813	22	3.0	22	89	6	95	44	10	1	44	1.46
11261728--11261806	25	3.3	25	92	5	128	43	10	2	44	1.51
11261824--11261958	22	6.1	22	69	22	86	47	11	1	40	1.48
11261970--11262014	22	2.0	22	95	0	81	46	11	0	42	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11261508--11262047	56	9.3	57	87	7	461	46	10	2	40	1.52
11262035--11262136	9	12.3	9	66	21	53	44	16	0	38	1.55
11261992--11262067	34	2.2	33	81	9	82	43	13	1	42	1.52
11262014--11262100	41	2.1	42	78	8	88	41	13	2	42	1.57
11262047--11262125	34	2.3	34	82	0	95	44	13	1	40	1.52
11267867--11267993	66	1.9	66	90	6	204	40	18	25	14	1.89
11267869--11268013	66	2.2	66	86	7	197	42	17	27	13	1.86
11267996--11268056	21	2.9	21	82	0	68	36	19	40	3	1.68
11268004--11268096	21	4.4	21	83	2	107	37	16	41	4	1.68
11268453--11268701	43	5.8	43	76	10	181	26	16	28	29	1.96
11268453--11268709	85	3.0	82	73	17	227	25	16	28	29	1.97
11268479--11268743	128	2.1	128	82	5	313	27	17	27	27	1.98
11268727--11268827	43	2.4	42	83	1	112	29	29	20	19	1.97
11282266--11282494	42	5.5	41	85	3	298	28	22	19	28	1.98
11282277--11282494	83	2.6	82	86	4	294	29	21	19	29	1.98
11282223--11282510	125	2.3	126	85	4	406	28	23	20	28	1.99
11284067--11284102	8	4.4	8	86	6	54	8	2	0	88	0.59
11284067--11284102	17	2.1	17	94	0	63	8	2	0	88	0.59
11286312--11286411	4	25.0	4	100	0	200	50	25	0	25	1.50
11288322--11288375	6	9.3	6	80	4	58	14	3	31	50	1.61
11289138--11289181	2	22.0	2	100	0	88	50	0	0	50	1.00
11295279--11295421	58	2.5	58	89	2	218	27	18	13	41	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11313315--11313378	32	2.0	32	93	0	110	31	12	12	43	1.80
11314049--11314095	18	2.6	18	80	12	60	63	4	2	29	1.25
11315720--11315763	16	2.8	16	85	0	61	22	13	18	45	1.84
11323460--11323498	3	13.0	3	100	0	78	33	0	0	66	0.92
11335944--11335982	2	19.5	2	100	0	78	51	0	0	48	1.00
11340925--11340976	27	1.9	27	84	7	70	42	17	1	38	1.60
11341550--11341582	16	2.1	16	88	5	50	45	9	12	33	1.73
11350442--11350489	25	2.0	24	84	8	62	39	6	2	52	1.39
11353058--11353105	15	3.1	15	74	14	53	54	8	8	29	1.60
11355772--11355840	28	2.5	27	86	9	86	47	4	1	46	1.31

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