genome.fa.s10.2.7.7.80.10.50.1000.16.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: At_chr6
Parameters: 2 7 7 80 10 50 1000
Length:  56482370

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   

This is table  16  of  172  ( 20562 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)
5086850--5087938	83	13.2	83	94	1	1829	32	20	20	26	1.97
5093747--5093828	36	2.3	36	78	0	92	26	10	26	35	1.90
5094718--5094742	12	2.1	12	100	0	50	44	0	24	32	1.54
5096115--5096176	31	2.0	31	96	0	115	27	16	17	38	1.91
5100896--5100946	25	2.0	25	96	0	93	49	17	3	29	1.65
5101987--5102047	9	6.8	9	90	0	86	24	8	27	39	1.84
5103753--5103784	8	4.0	8	100	0	64	37	0	37	25	1.56
5105237--5105263	2	13.5	2	100	0	54	0	48	0	51	1.00
5112048--5112078	15	2.1	15	93	0	53	64	6	6	22	1.40
5113499--5113553	15	3.9	15	74	13	62	56	9	5	29	1.53
5113504--5113557	27	2.0	27	100	0	108	55	7	3	33	1.45
5117268--5117313	23	2.0	23	87	4	67	26	4	2	67	1.21
5131590--5131639	25	2.0	25	100	0	100	64	0	4	32	1.12
5131868--5131915	26	1.9	24	87	8	69	64	4	0	31	1.12
5131886--5131944	21	2.8	22	82	7	61	67	6	1	23	1.24
5134412--5134437	12	2.2	12	100	0	52	0	23	0	76	0.78
5134760--5134814	9	6.3	9	75	14	53	32	1	0	65	1.03
5136657--5136696	14	2.9	14	84	0	62	40	7	0	52	1.30
5138307--5138357	22	2.3	22	96	0	93	25	49	17	7	1.74
5146087--5146126	14	2.9	14	84	0	62	40	7	0	52	1.30
5147737--5147787	22	2.3	22	96	0	93	25	49	17	7	1.74
5156863--5156899	18	2.1	17	90	5	56	59	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5159543--5159582	14	2.9	14	84	0	53	32	7	17	42	1.77
5160962--5161029	27	2.5	27	79	9	75	51	20	2	25	1.61
5170921--5170967	24	2.0	24	100	0	94	31	17	17	34	1.92
5172808--5172843	13	2.8	14	84	16	51	27	25	0	47	1.52
5172795--5172835	18	2.2	19	87	12	59	29	24	0	46	1.53
5172940--5172997	23	2.5	23	97	0	107	46	41	3	8	1.51
5173499--5173575	15	5.1	15	80	0	100	49	12	2	35	1.55
5173497--5173575	30	2.6	30	100	0	158	49	12	2	35	1.54
5173975--5174013	19	2.1	19	95	0	69	33	5	10	51	1.58
5173978--5174021	19	2.4	19	78	17	56	34	6	9	50	1.61
5183312--5183361	6	7.8	6	78	12	55	76	2	18	4	1.04
5183317--5183373	27	2.1	27	100	0	114	66	3	22	7	1.31
5183329--5183373	15	3.2	15	69	18	51	62	4	24	8	1.43
5185318--5185372	27	2.0	28	85	3	76	43	0	12	43	1.42
5186267--5186333	23	2.8	24	81	4	73	25	22	16	35	1.94
5188979--5189107	43	3.0	42	76	7	134	31	24	15	28	1.96
5191765--5192097	130	2.6	128	83	5	402	28	17	17	37	1.92
5203048--5203080	3	11.0	3	93	0	57	63	0	33	3	1.10
5203888--5204393	44	11.5	44	90	0	798	27	15	30	26	1.96
5207505--5207974	131	3.6	131	95	1	809	25	18	19	35	1.95
5211065--5211118	27	2.0	27	88	0	81	16	25	29	27	1.97
5223814--5223883	27	2.7	25	82	8	70	31	14	5	48	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5223816--5223872	26	2.1	27	80	3	62	29	14	7	49	1.69
5224515--5224653	72	1.9	72	97	0	260	30	15	16	37	1.90
5235812--5236707	172	5.2	169	85	7	1057	27	17	19	35	1.94
5235812--5236826	89	11.8	85	80	11	1002	27	17	19	35	1.94
5235811--5236826	172	5.9	171	83	8	1034	27	17	19	35	1.94
5236402--5236710	164	1.9	159	90	3	483	29	17	19	33	1.95
5236489--5236655	75	2.2	75	86	0	235	29	16	20	34	1.94
5248818--5248856	16	2.6	14	84	11	51	51	0	2	46	1.14
5248818--5248860	15	2.8	16	80	19	56	51	0	2	46	1.13
5249958--5250022	33	2.1	29	83	11	76	44	1	0	53	1.09
5261812--5261906	46	2.1	46	92	4	156	34	12	21	31	1.91
5276003--5276055	3	17.7	3	84	7	72	1	28	1	67	1.11
5276023--5276062	18	2.2	18	86	0	53	2	30	5	62	1.29
5276532--5276562	3	10.3	3	100	0	62	32	35	0	32	1.58
5276564--5276591	3	9.3	3	100	0	56	64	0	35	0	0.94
5279763--5279793	6	5.2	6	100	0	62	64	0	19	16	1.29
5287630--5287682	23	2.4	22	76	20	56	9	18	1	69	1.25
5290025--5290056	4	8.0	4	100	0	64	75	0	0	25	0.81
5290956--5290999	22	2.0	22	86	0	61	50	2	0	47	1.13
5291078--5291148	15	4.6	15	72	16	56	49	1	1	47	1.18
5291606--5291644	14	2.8	13	84	7	51	33	17	7	41	1.79
5292071--5292120	20	2.5	20	83	6	57	8	34	22	36	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5299662--5299713	15	3.0	18	75	25	58	34	3	0	61	1.14
5299663--5299731	29	2.4	29	72	13	70	37	1	0	60	1.06
5299681--5299732	25	2.1	25	92	3	88	36	1	0	61	1.07
5301875--5301902	13	2.2	13	100	0	56	7	25	14	53	1.66
5314434--5314510	38	2.0	38	90	5	120	42	0	16	40	1.49
5314706--5314731	5	5.2	5	100	0	52	19	0	19	61	1.35
5324952--5324983	5	6.6	5	92	7	57	81	0	0	18	0.70
5329383--5329414	5	6.6	5	92	7	57	81	0	0	18	0.70
5329384--5329414	9	3.3	9	95	4	53	80	0	0	19	0.71
5334532--5334622	3	29.0	3	76	12	85	31	5	3	59	1.36
5334755--5334803	20	2.3	22	82	10	57	34	10	2	53	1.47
5336188--5336226	20	1.9	21	84	5	53	28	5	5	61	1.39
5339919--5339961	15	2.9	14	80	10	50	67	4	0	27	1.10
5343236--5343276	21	2.0	21	85	0	55	21	29	19	29	1.98
5347984--5348049	34	1.9	35	81	3	80	22	13	4	59	1.53
5348026--5348168	3	47.0	3	65	15	53	32	5	4	58	1.41
5348069--5348168	24	4.2	24	78	7	89	33	3	5	59	1.34
5349458--5349503	12	3.6	12	78	16	56	65	0	0	34	0.93
5349458--5349520	27	2.4	26	79	10	74	60	0	3	36	1.13
5351393--5351883	85	5.7	85	92	1	793	25	24	21	28	1.99
5352934--5352980	21	2.2	21	84	0	58	27	38	8	25	1.85
5356574--5356622	19	2.5	20	80	6	57	42	12	18	26	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5358941--5358986	12	3.6	12	78	16	56	65	0	0	34	0.93
5358941--5359003	27	2.4	26	79	10	74	60	0	3	36	1.13
5359529--5359653	63	2.0	63	96	0	232	16	49	25	8	1.73
5359592--5359754	82	2.0	82	97	0	308	15	44	28	11	1.81
5362574--5362652	37	2.1	37	90	4	124	31	12	11	44	1.78
5369935--5369996	31	2.0	31	100	0	124	32	35	9	22	1.87
5372958--5373015	29	2.0	29	80	9	66	53	10	8	27	1.64
5390634--5390763	53	2.4	53	82	3	145	25	23	17	33	1.96
5391023--5391238	104	2.1	104	85	0	299	30	27	9	32	1.88
5391404--5391446	21	2.0	21	90	0	68	30	23	4	41	1.74
5394078--5394437	46	7.8	46	91	0	506	40	13	24	22	1.90
5401107--5401143	18	2.0	19	94	5	67	43	0	16	40	1.48
5401222--5401409	101	1.9	101	88	0	286	31	16	23	28	1.96
5401365--5401427	33	1.9	33	84	12	85	30	14	25	30	1.95
5401215--5401429	101	2.1	100	83	3	279	31	15	24	28	1.96
5404344--5404504	35	4.7	34	70	8	112	29	17	25	27	1.97
5404344--5404602	101	2.6	100	85	3	317	30	18	25	25	1.98
5404477--5404553	33	2.3	32	78	10	84	32	16	24	25	1.96
5408059--5408100	21	2.0	21	90	9	68	47	23	2	26	1.64
5408138--5408200	23	2.7	23	75	25	62	46	1	3	49	1.27
5420387--5420560	40	4.3	40	88	0	249	36	22	20	20	1.95
5437587--5437637	25	2.0	25	85	7	68	47	3	1	47	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5438672--5438939	136	2.0	136	93	0	455	31	19	12	36	1.89
5446076--5446150	10	7.8	9	70	18	53	32	1	2	64	1.16
5450582--5450620	21	1.9	20	84	5	51	48	2	5	43	1.38
5451327--5451474	70	2.1	70	87	5	210	56	9	8	25	1.60
5452825--5452902	40	2.0	40	100	0	156	33	14	14	38	1.86
5455349--5455434	24	3.8	24	77	14	69	46	0	1	52	1.08
5455590--5455682	44	2.1	46	83	4	118	34	25	6	33	1.82
5455664--5455734	16	4.4	16	87	3	99	29	26	5	38	1.79
5456453--5456543	10	9.6	9	69	22	53	54	2	3	39	1.29
5456490--5456591	19	5.2	20	71	15	70	59	2	3	33	1.30

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