genome.fa.s16.2.7.7.80.10.50.1000.20.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: D03
Parameters: 2 7 7 80 10 50 1000
Length:  53248092

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   

This is table  20  of  175  ( 20966 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)
5366006--5366038	17	2.0	17	88	5	50	33	12	3	51	1.54
5366991--5367135	67	2.2	67	96	0	263	42	10	11	35	1.76
5367428--5367653	43	5.0	42	79	14	229	27	25	18	28	1.98
5367447--5367548	52	2.0	52	96	0	186	24	26	18	30	1.98
5368005--5368140	66	2.1	66	90	0	209	14	25	18	41	1.88
5373515--5373636	9	13.4	9	85	1	172	31	1	18	48	1.58
5373515--5373653	27	5.1	27	82	1	152	30	1	18	49	1.56
5373821--5373995	39	4.5	39	89	9	243	59	0	2	37	1.12
5373827--5373995	86	2.1	78	86	8	230	60	0	2	36	1.12
5373821--5373948	11	12.9	11	73	20	81	57	0	2	39	1.11
5374194--5374249	9	6.2	9	85	8	78	32	1	19	46	1.61
5374303--5374372	12	6.0	12	80	6	81	31	2	17	48	1.61
5374649--5374706	29	2.0	29	100	0	116	41	3	24	31	1.71
5378733--5378778	21	2.1	21	84	11	58	56	23	0	19	1.42
5378802--5378871	16	4.4	16	67	16	56	50	21	1	27	1.57
5378805--5378880	23	3.3	23	73	23	86	48	22	1	27	1.58
5379309--5379461	41	3.7	40	90	5	234	39	28	16	15	1.89
5379282--5379470	82	2.3	82	83	7	249	38	29	17	14	1.89
5382434--5382486	27	2.0	28	85	7	74	64	1	1	32	1.15
5400225--5400286	12	5.0	13	75	9	58	85	0	12	1	0.67
5401226--5401279	24	2.2	24	83	6	65	37	11	20	31	1.88
5401552--5401775	45	5.0	45	78	1	198	30	20	22	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5401552--5401778	90	2.5	88	77	4	240	30	21	22	25	1.99
5401715--5401855	76	1.9	76	86	3	203	35	19	20	24	1.96
5401817--5402116	44	6.8	44	72	11	163	29	25	23	21	1.99
5401795--5402118	89	3.7	89	86	1	438	29	25	23	21	1.99
5402281--5402703	44	9.7	43	70	13	186	30	20	20	28	1.98
5402275--5402645	129	2.8	129	84	4	424	30	21	19	28	1.98
5403347--5403371	11	2.3	11	100	0	50	44	16	16	24	1.86
5404397--5404421	13	1.9	13	100	0	50	28	0	16	56	1.41
5407345--5407372	14	2.0	14	100	0	56	28	35	28	7	1.84
5408882--5408923	20	2.0	21	86	4	59	38	11	0	50	1.40
5409539--5409674	73	1.9	73	87	6	204	30	19	15	34	1.93
5417903--5417945	22	2.0	22	86	9	61	41	0	2	55	1.12
5418431--5418460	13	2.4	13	94	5	53	0	26	0	73	0.84
5421297--5421377	33	2.6	30	81	13	92	40	1	2	55	1.21
5434197--5434303	50	2.1	50	82	0	133	25	21	31	21	1.98
5434593--5434631	12	3.2	12	85	7	53	53	7	23	15	1.67
5436987--5437143	64	2.5	64	84	0	197	23	29	22	24	1.99
5455263--5455300	20	1.9	20	89	10	60	42	13	5	39	1.66
5458871--5458923	24	2.2	24	89	0	79	52	7	3	35	1.48
5461129--5461214	40	2.3	36	80	13	93	32	5	9	52	1.57
5463511--5463561	3	17.0	3	95	0	93	33	1	0	64	1.05
5468496--5468530	7	5.0	7	86	13	54	68	0	17	14	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5468496--5468538	21	2.0	21	86	8	61	67	0	16	16	1.24
5469695--5470245	89	6.2	89	91	0	861	29	19	23	26	1.98
5470230--5470591	132	2.7	132	93	0	607	28	17	24	29	1.98
5472079--5472108	3	10.0	3	92	0	51	33	0	3	63	1.11
5475467--5475513	24	1.9	25	83	12	62	23	4	8	63	1.40
5475188--5476268	325	3.4	322	92	3	1780	30	11	7	50	1.66
5476168--5476365	98	2.0	98	83	7	251	27	13	6	52	1.65
5476026--5476597	258	2.2	257	83	3	700	30	11	6	51	1.65
5480547--5480588	19	2.2	19	83	8	50	28	21	9	40	1.84
5482476--5482516	20	2.0	20	90	9	66	14	14	4	65	1.42
5483446--5483487	7	6.0	7	81	18	52	69	0	16	14	1.20
5483446--5483487	21	2.0	21	86	9	59	69	0	16	14	1.20
5484788--5485588	44	18.1	44	79	3	659	31	13	23	32	1.93
5484777--5485588	88	9.2	88	88	3	902	31	13	23	32	1.93
5484804--5485619	89	9.2	89	88	1	910	31	13	23	31	1.93
5485607--5485682	37	2.1	37	82	5	91	32	19	21	26	1.97
5489103--5489132	16	1.9	15	93	6	51	26	3	0	70	1.03
5488895--5489787	164	5.5	160	71	16	669	29	11	7	51	1.66
5488861--5489896	323	3.2	323	94	1	1817	29	12	7	50	1.68
5489704--5490112	216	1.9	216	90	3	662	27	13	7	51	1.68
5490497--5490638	24	6.0	24	76	13	134	0	30	0	68	0.95
5490515--5490638	10	12.6	10	77	13	84	0	29	0	69	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5490515--5490637	14	8.4	14	75	15	106	0	29	0	69	0.94
5490522--5490637	4	30.0	4	75	20	81	0	28	0	70	0.93
5492892--5492924	16	2.1	16	88	11	50	18	6	6	69	1.30
5495479--5495562	24	3.5	24	83	4	98	40	9	22	27	1.85
5495524--5495601	25	3.1	24	81	7	84	34	16	15	33	1.90
5495571--5495924	60	6.0	60	84	5	418	34	17	15	32	1.91
5495571--5495924	121	3.0	118	84	8	468	34	17	15	32	1.91
5495553--5495942	181	2.1	183	79	9	447	34	17	15	32	1.91
5498243--5498593	112	3.1	115	85	6	478	31	18	15	34	1.93
5498242--5498641	112	3.6	111	84	8	476	33	18	15	33	1.92
5502055--5502125	35	2.0	35	97	0	133	23	11	32	32	1.90
5507559--5507603	17	2.6	17	96	0	81	31	0	15	53	1.43
5512938--5513017	23	3.4	23	69	20	58	37	8	5	48	1.56
5512954--5513021	27	2.5	26	76	9	73	39	7	4	48	1.51
5517472--5517702	43	5.4	43	73	4	171	29	25	17	27	1.98
5517418--5517629	42	5.1	43	78	4	202	28	27	17	26	1.98
5517463--5517683	85	2.6	84	77	5	203	30	25	17	26	1.97
5518027--5518076	21	2.4	21	86	0	73	0	44	18	38	1.50
5522713--5522792	40	2.0	40	95	0	142	37	22	10	30	1.87
5522980--5523009	15	2.0	15	93	0	51	26	36	0	36	1.57
5523510--5523550	20	2.0	20	100	0	82	24	24	9	41	1.85
5523758--5523870	9	12.6	9	74	7	104	36	0	17	46	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5523767--5523861	27	3.5	27	80	11	131	36	0	16	46	1.48
5523757--5523871	54	2.1	54	96	0	212	37	0	17	45	1.49
5524647--5524839	43	4.5	43	86	7	234	33	29	14	22	1.94
5524643--5524806	86	1.9	85	90	3	258	31	29	15	23	1.95
5526578--5526616	15	2.5	15	87	4	51	38	46	0	15	1.46
5526597--5526637	21	1.9	22	85	5	57	39	39	0	21	1.54
5526633--5526670	14	2.7	15	80	12	53	39	31	2	26	1.70
5526901--5526944	21	2.0	22	86	4	63	36	43	0	20	1.52
5526859--5526985	57	2.2	59	83	8	154	37	34	0	27	1.63
5526937--5526977	22	1.9	21	85	5	55	36	31	0	31	1.58
5526908--5526985	21	3.7	21	77	6	59	37	37	0	25	1.56
5526447--5527051	306	2.0	303	90	3	961	41	27	2	28	1.67
5528795--5529552	121	6.1	123	83	4	918	24	22	17	36	1.95
5528787--5529561	371	2.1	370	88	2	1144	24	22	17	36	1.95
5530416--5530554	15	9.6	15	77	6	99	52	32	0	15	1.43
5530412--5530582	7	24.0	7	73	7	85	50	31	0	18	1.47
5530608--5530732	41	3.0	41	89	1	169	24	25	15	34	1.94
5532440--5532469	12	2.6	11	90	10	51	60	0	0	40	0.97
5532495--5532531	17	2.2	17	95	0	65	35	2	5	56	1.36
5535117--5535182	34	1.9	34	90	0	105	33	9	9	48	1.66
5539162--5539243	41	2.0	41	100	0	164	29	14	14	41	1.86
5542724--5542752	14	2.1	14	100	0	58	20	6	37	34	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5544929--5544967	19	2.1	18	85	4	51	30	23	7	38	1.83
5546656--5546711	28	2.0	28	89	6	87	53	7	0	39	1.28
5546740--5546797	27	2.2	26	90	3	89	24	27	27	20	1.99
5547297--5547357	19	3.3	19	76	4	70	42	9	0	47	1.36
5547305--5547357	18	2.9	18	75	11	54	41	9	0	49	1.35
5547842--5547898	27	2.2	26	90	3	87	21	26	28	24	1.99
5547879--5547918	20	2.0	20	95	0	71	17	25	37	20	1.94
5554694--5554740	19	2.5	19	96	0	85	21	17	8	53	1.70
5555236--5555270	18	1.9	18	88	0	52	31	5	0	62	1.18
5560572--5560608	18	2.0	20	84	10	51	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