genome.fa.s1.2.7.7.80.10.50.1000.52.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  52  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)
15446805--15446853	19	2.6	18	83	6	53	63	0	4	32	1.13
15449567--15449623	29	2.0	29	93	3	98	38	0	8	52	1.33
15449576--15449642	29	2.3	29	87	2	91	43	0	10	46	1.38
15449752--15449800	14	3.6	14	78	15	50	36	10	0	53	1.35
15449764--15449800	7	5.4	7	90	9	51	37	13	0	48	1.43
15449752--15449800	20	2.5	20	86	6	64	36	10	0	53	1.35
15450284--15450312	14	2.0	15	93	6	51	48	6	0	44	1.29
15477618--15477767	58	2.5	62	81	7	170	40	14	15	30	1.86
15484492--15484542	16	3.1	16	86	10	68	27	0	3	68	1.07
15488122--15488371	126	2.0	126	95	0	446	38	14	18	28	1.90
15495381--15495422	18	2.2	20	80	16	54	42	2	7	47	1.43
15495612--15495702	28	3.1	27	74	22	94	41	7	3	47	1.48
15495572--15495702	60	2.2	60	91	0	208	43	9	3	44	1.51
15495595--15495690	28	3.2	30	73	22	103	42	7	2	47	1.42
15497032--15497057	13	2.0	13	100	0	52	30	7	15	46	1.74
15499756--15499876	60	2.0	60	90	0	188	26	38	4	30	1.75
15501659--15501684	13	2.0	13	100	0	52	30	7	15	46	1.74
15504933--15504958	11	2.4	11	100	0	52	15	7	0	76	0.99
15508764--15508872	52	2.1	52	98	0	209	53	10	13	22	1.70
15509258--15509307	24	2.1	24	81	7	57	64	8	0	28	1.22
15517496--15517547	22	2.3	22	80	9	61	36	1	3	57	1.28
15520503--15520562	6	10.0	6	76	7	50	45	1	33	20	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15522354--15522423	30	2.3	30	95	0	122	42	4	4	48	1.42
15530462--15530715	124	2.1	123	88	2	375	31	16	21	31	1.95
15534049--15534075	10	2.7	10	100	0	54	51	0	7	40	1.30
15534097--15534131	18	1.9	18	94	0	61	51	2	8	37	1.47
15534059--15534240	55	3.3	55	90	5	253	46	4	9	38	1.59
15534277--15534447	18	10.4	17	68	20	105	26	0	27	45	1.54
15534243--15534335	31	3.1	31	96	3	172	22	0	31	46	1.52
15534289--15534461	53	3.4	52	85	11	259	27	0	28	44	1.55
15534277--15534476	46	4.1	48	87	10	300	26	0	28	45	1.54
15534238--15534331	29	3.2	29	95	4	170	23	0	31	44	1.54
15534277--15534476	99	2.1	95	94	3	346	26	0	28	45	1.54
15534354--15534447	35	2.7	35	73	8	109	26	0	27	45	1.54
15540535--15540585	15	3.3	15	76	10	57	68	0	5	25	1.12
15540629--15540676	3	16.0	3	100	0	96	66	0	0	33	0.92
15542393--15542467	29	2.5	29	84	4	96	48	14	12	25	1.78
15544040--15544096	23	2.5	23	91	0	87	12	21	38	28	1.89
15545231--15545273	21	2.0	21	90	0	68	53	11	11	23	1.69
15545941--15546043	20	5.2	19	70	19	59	62	4	0	33	1.17
15545942--15546004	20	3.2	20	79	2	74	60	6	0	33	1.22
15545940--15546040	41	2.5	41	82	7	109	61	4	0	33	1.18
15549039--15549249	34	6.1	34	79	2	206	40	13	21	24	1.89
15549056--15549249	69	2.8	68	80	1	208	40	14	21	23	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15549061--15549249	103	1.8	103	94	0	333	40	15	20	23	1.90
15549486--15549523	14	2.8	13	88	7	58	36	13	2	47	1.56
15552179--15552214	3	12.0	3	100	0	72	66	0	33	0	0.92
15562595--15562676	33	2.5	33	85	0	101	20	26	19	32	1.97
15574572--15574686	37	3.1	37	71	12	117	52	0	6	40	1.32
15574565--15574724	75	2.1	75	77	2	178	51	1	6	40	1.35
15575211--15575254	21	2.1	21	83	8	54	61	2	0	36	1.09
15575205--15575255	20	2.5	21	72	15	52	58	3	0	37	1.16
15588321--15588353	2	16.5	2	100	0	66	51	0	0	48	1.00
15588931--15589490	280	2.0	281	90	1	883	38	11	13	36	1.81
15590046--15590261	90	2.4	90	86	2	272	31	13	25	29	1.94
15600957--15601033	23	3.3	23	79	0	100	31	16	20	31	1.95
15601132--15601211	28	2.9	28	76	0	88	20	20	30	30	1.97
15601311--15601435	30	4.1	30	79	5	110	24	18	28	29	1.98
15613891--15613968	39	2.0	39	100	0	156	33	10	10	46	1.72
15618540--15618597	22	2.6	22	81	7	64	41	17	5	36	1.72
15618576--15618650	19	3.8	19	93	6	132	36	16	10	37	1.83
15627052--15627209	43	3.7	43	79	8	151	27	17	25	29	1.98
15627089--15627201	42	2.7	42	79	10	115	29	16	24	29	1.97
15631184--15631239	2	28.0	2	96	0	103	51	0	0	48	1.00
15633343--15633560	47	4.6	47	84	4	262	37	23	15	23	1.93
15633336--15633560	94	2.4	94	86	0	297	36	24	15	23	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15634230--15634308	20	3.9	20	88	1	95	37	24	29	8	1.85
15634259--15634318	20	2.9	21	87	2	68	35	21	33	10	1.87
15652557--15652594	15	2.5	15	84	16	51	47	0	5	47	1.24
15652914--15652969	29	1.9	29	100	0	112	33	3	28	33	1.75
15653383--15653407	13	1.9	13	100	0	50	40	0	20	40	1.52
15662972--15663012	18	2.2	19	87	12	59	36	0	0	63	0.95
15670968--15671063	46	2.1	46	81	11	110	37	5	2	55	1.34
15671037--15671105	14	4.7	14	71	16	50	46	1	0	52	1.09
15682172--15682220	25	1.9	26	91	4	82	14	16	10	59	1.61
15683104--15683631	44	12.1	44	70	13	290	30	19	23	26	1.98
15683108--15683622	45	11.8	45	71	12	324	30	19	22	26	1.98
15683076--15683395	173	1.8	174	80	7	391	29	20	23	26	1.99
15683108--15683633	219	2.4	218	86	3	711	31	19	23	26	1.98
15687298--15687383	43	2.0	43	100	0	172	46	23	11	18	1.82
15700428--15700539	25	4.5	24	75	7	91	21	19	21	37	1.94
15702829--15702912	37	2.3	37	89	0	132	40	33	11	14	1.82
15705287--15705422	72	1.9	71	90	1	218	34	17	17	30	1.93
15708457--15708509	25	2.1	25	96	0	97	30	15	30	24	1.95
15709066--15709099	15	2.4	14	90	9	52	47	2	11	38	1.55
15713751--15713803	26	2.1	26	85	3	72	33	3	0	62	1.13
15715277--15715331	18	3.1	18	83	0	74	52	0	0	47	1.00
15715394--15715444	21	2.7	18	85	11	66	17	5	9	66	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15718593--15718645	25	2.1	26	86	10	74	67	1	1	28	1.11
15722721--15722758	14	2.7	14	88	8	51	18	15	0	65	1.27
15725543--15725600	3	19.3	3	82	7	73	32	0	3	63	1.11
15725720--15725822	29	3.6	29	74	12	88	34	5	1	57	1.34
15739934--15740009	30	2.7	28	80	9	82	34	6	3	55	1.44
15746514--15746551	16	2.4	16	90	0	58	34	2	34	28	1.71
15746840--15747006	38	4.2	38	66	19	108	49	6	2	41	1.42
15746860--15747044	43	4.6	41	66	20	102	50	4	2	42	1.34
15746903--15746937	17	2.1	16	89	5	52	60	0	0	40	0.97
15746765--15747059	119	2.5	120	94	2	522	49	5	2	43	1.37
15747041--15747372	47	7.3	46	68	19	178	47	3	3	45	1.35
15747075--15747372	91	3.3	91	95	0	515	47	3	3	45	1.35
15750557--15750582	6	4.3	6	100	0	52	50	0	0	50	1.00
15751368--15751392	13	1.9	13	100	0	50	20	16	8	56	1.65
15751357--15751463	53	2.1	51	84	7	135	34	12	5	47	1.64
15752011--15752073	23	2.7	24	76	14	78	50	22	9	17	1.74
15752040--15752085	22	2.1	22	84	8	58	58	19	4	17	1.55
15765034--15765090	26	2.2	26	81	6	62	29	1	1	66	1.12
15765136--15765180	20	2.3	20	88	3	65	28	0	4	66	1.11
15769845--15769908	9	7.2	9	92	3	94	21	10	28	39	1.87
15782880--15782925	23	2.0	22	87	4	65	45	4	8	41	1.55
15790256--15790489	44	5.5	44	78	6	212	29	19	21	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15790252--15790408	85	1.8	85	90	0	251	28	19	22	29	1.98
15790249--15790489	129	1.9	129	90	1	385	28	20	21	29	1.98
15805135--15805185	23	2.2	23	92	0	84	27	9	21	41	1.84
15805656--15805692	2	18.5	2	88	0	56	51	0	0	48	1.00
15805981--15806014	2	17.0	2	100	0	68	50	0	0	50	1.00
15806950--15806980	13	2.4	13	94	0	53	6	0	38	54	1.26
15808198--15808266	28	2.4	30	87	7	115	52	2	0	44	1.16
15841097--15841123	2	13.5	2	100	0	54	48	0	0	51	1.00
15841246--15841319	27	2.8	27	73	8	71	62	2	6	28	1.35
15843152--15843183	15	2.1	15	100	0	64	43	0	0	56	0.99

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