genome.fa.s5.2.7.7.80.10.50.1000.176.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   

This is table  176  of  208  ( 24913 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)
53777468--53777503	19	2.0	18	89	10	56	61	0	0	38	0.96
53803583--53803700	59	2.0	59	94	0	209	44	11	13	30	1.78
53806996--53807041	19	2.4	19	82	7	58	71	0	2	26	0.97
53806999--53807044	20	2.4	19	77	3	56	71	0	2	26	0.97
53807000--53807079	29	2.8	29	77	11	74	65	0	2	32	1.06
53807057--53807123	20	3.4	19	77	18	82	65	0	7	26	1.19
53809396--53809437	20	2.1	20	86	8	59	23	11	2	61	1.42
53810008--53810089	19	4.2	19	76	10	76	29	2	2	65	1.18
53810008--53810166	10	16.4	9	69	16	79	28	2	2	66	1.18
53810273--53810450	86	2.1	85	86	4	250	33	8	20	38	1.83
53812427--53812463	3	12.0	3	88	5	56	64	2	0	32	1.07
53814191--53814794	87	7.0	85	75	6	541	27	23	19	29	1.98
53814197--53815016	44	18.8	44	69	10	337	27	22	19	30	1.98
53814180--53814846	174	3.8	173	93	2	1070	27	22	20	29	1.98
53815063--53815322	88	3.0	87	84	3	308	25	23	21	29	1.99
53816108--53816138	16	1.9	16	93	0	53	38	22	6	32	1.80
53816455--53816501	21	2.2	21	85	7	60	23	36	12	27	1.91
53816593--53816632	7	5.2	8	85	14	50	12	12	0	75	1.06
53816584--53816647	22	3.0	21	79	18	71	10	15	0	73	1.09
53816584--53816649	14	4.8	14	76	10	64	10	15	0	74	1.07
53816584--53816626	7	6.1	7	82	15	54	13	13	0	72	1.13
53817572--53817610	7	5.9	7	93	6	64	0	15	0	84	0.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53817574--53817612	6	6.2	6	94	5	60	0	15	0	84	0.62
53817572--53817612	13	3.2	13	86	13	66	0	17	0	82	0.66
53817572--53817621	26	1.9	26	84	8	66	2	18	0	80	0.82
53817572--53817627	26	2.2	26	80	6	60	3	17	1	76	1.01
53817632--53817671	8	4.9	8	87	6	53	10	0	7	82	0.84
53817633--53817674	16	2.7	16	82	17	61	9	0	7	83	0.81
53822905--53822938	16	2.1	16	88	5	50	85	2	0	11	0.71
53822969--53823013	3	14.7	3	86	4	63	62	2	2	33	1.20
53824225--53824269	14	3.2	14	84	6	56	80	6	0	13	0.91
53824660--53824722	31	2.1	30	85	8	83	46	7	14	31	1.73
53827987--53828118	44	3.0	43	88	2	174	40	7	15	35	1.76
53831030--53831275	27	9.1	27	84	4	275	19	17	19	42	1.90
53831030--53831275	54	4.6	54	85	5	304	19	17	19	42	1.90
53831030--53831275	81	3.0	80	84	4	325	19	17	19	42	1.90
53833080--53833109	2	15.0	2	100	0	60	50	0	0	50	1.00
53840305--53840334	8	3.8	8	100	0	60	46	0	26	26	1.53
53840428--53840526	42	2.4	42	89	3	146	25	19	17	38	1.93
53845866--53845912	24	2.0	23	91	4	76	70	2	21	6	1.20
53845880--53845918	17	2.2	18	86	4	53	74	0	15	10	1.07
53849190--53849265	5	15.2	5	100	0	152	60	0	0	39	0.97
53849402--53849433	17	1.9	16	93	6	55	50	6	0	43	1.27
53849384--53849487	44	2.3	44	77	4	111	49	3	10	36	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53849645--53849695	23	2.3	23	80	10	61	33	1	7	56	1.39
53851137--53851178	18	2.6	16	79	17	50	42	0	7	50	1.30
53851144--53851210	20	3.5	19	86	6	82	32	1	8	56	1.39
53855458--53855488	15	2.1	14	94	5	53	29	0	0	70	0.87
53859272--53859331	29	2.1	29	90	0	93	31	15	21	31	1.94
53873028--53873080	27	2.0	27	84	0	70	18	16	18	45	1.86
53883613--53883653	6	6.8	6	97	0	73	34	12	0	53	1.38
53889972--53890049	36	2.2	36	88	0	111	34	29	8	26	1.87
53890752--53890791	22	1.9	21	90	10	64	45	17	0	37	1.49
53892463--53892515	24	2.2	24	86	0	70	37	3	7	50	1.49
53894494--53894546	26	2.0	26	100	0	106	33	11	11	43	1.76
53896877--53896917	16	2.6	16	100	0	82	53	0	0	46	1.00
53908800--53908842	21	2.0	22	81	4	52	23	9	4	62	1.44
53909165--53909268	19	5.5	19	88	0	163	40	8	13	37	1.75
53909172--53909268	38	2.6	38	98	0	185	41	8	12	38	1.73
53913137--53913174	8	4.6	8	87	6	58	89	10	0	0	0.49
53913134--53913179	17	2.6	17	90	10	67	86	13	0	0	0.56
53913134--53913179	6	8.0	6	86	13	62	86	13	0	0	0.56
53913136--53913179	11	4.0	11	91	5	63	88	11	0	0	0.51
53915019--53915200	44	4.1	45	66	9	97	29	17	24	29	1.97
53914799--53915566	132	5.8	132	92	0	1243	29	17	23	28	1.97
53915893--53916003	19	5.8	19	89	0	177	39	9	13	37	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53915900--53916003	38	2.7	38	98	0	199	40	8	12	38	1.74
53917793--53917849	20	2.8	20	81	7	62	71	1	14	12	1.21
53930396--53930472	31	2.5	31	97	0	145	31	36	11	20	1.89
53934500--53935031	263	2.0	263	95	0	965	25	22	15	37	1.93
53941424--53941448	12	2.1	12	100	0	50	16	40	16	28	1.89
53949019--53949083	30	2.2	30	83	5	78	21	23	27	27	1.99
53952225--53952258	16	2.1	17	88	5	52	67	2	11	17	1.34
53952357--53952400	23	1.9	23	86	9	63	65	6	13	13	1.44
53952398--53952446	15	3.5	13	80	20	55	69	2	4	24	1.17
53953435--53953492	20	2.7	21	78	10	55	60	1	6	31	1.33
53956212--53956291	25	3.2	25	81	0	97	38	17	27	16	1.91
53958410--53958460	16	3.4	16	78	15	72	31	19	3	45	1.69
53960682--53961443	379	2.0	379	95	1	1359	35	17	13	33	1.89
53965415--53965481	29	2.4	27	90	9	116	46	16	17	19	1.85
53965652--53965729	26	2.8	28	82	5	88	21	15	21	41	1.90
53965842--53965895	28	2.0	28	88	3	83	25	27	20	25	1.99
53968178--53968215	16	2.4	16	100	0	76	13	39	28	18	1.88
53972927--53973009	26	3.2	26	84	1	87	19	21	22	36	1.95
53987530--53987815	129	2.2	128	88	3	416	25	39	0	34	1.61
53991542--53991571	2	15.0	2	100	0	60	50	0	0	50	1.00
53994233--53994282	2	25.0	2	95	0	91	2	50	0	48	1.12
53994851--53994881	4	7.8	4	100	0	62	25	0	48	25	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53999683--53999749	29	2.2	30	81	5	82	46	10	4	38	1.59
54000358--54000408	19	2.6	19	76	17	52	60	3	0	35	1.15
54005687--54006077	131	3.0	131	77	2	392	39	11	10	38	1.75
54005687--54006076	130	3.0	129	78	3	395	39	11	10	38	1.75
54007546--54007596	20	2.5	19	78	15	57	78	3	9	7	1.07
54011440--54011520	24	3.2	24	71	21	85	40	4	16	38	1.70
54011439--54011542	51	2.0	51	100	0	208	40	3	13	42	1.62
54011455--54011539	24	3.4	23	72	21	82	43	2	11	42	1.54
54011566--54011609	3	15.7	3	78	21	51	34	0	0	65	0.93
54011566--54011612	15	3.1	16	87	9	71	34	0	0	65	0.93
54012415--54012487	37	2.0	37	89	2	112	45	0	23	31	1.53
54020809--54020900	41	2.2	41	88	0	130	30	20	19	29	1.97
54024386--54024429	13	3.4	13	81	9	54	72	4	2	20	1.13
54024372--54024416	21	2.0	23	83	8	58	66	6	8	17	1.40
54024458--54024489	13	2.4	14	90	10	50	62	0	12	25	1.30
54024864--54024911	5	9.8	5	93	6	73	62	0	14	22	1.32
54027382--54027432	18	2.8	18	80	11	59	72	3	0	23	1.01
54036801--54036887	42	2.0	44	86	4	124	25	22	2	49	1.62
54049609--54049646	20	1.9	20	88	0	58	42	0	10	47	1.38
54050096--54050160	33	1.9	34	87	9	98	35	0	3	61	1.12
54056820--54056877	26	2.2	27	87	3	82	29	29	18	22	1.98
54063296--54063643	50	6.9	50	83	4	353	27	21	29	22	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54063296--54063643	99	3.5	99	80	5	360	27	21	29	22	1.99
54071008--54071062	25	2.3	24	84	6	67	61	10	9	18	1.54
54079637--54079690	28	1.9	28	100	0	108	42	14	16	25	1.87
54088326--54088386	28	2.2	27	80	13	70	45	11	14	27	1.80
54088340--54088393	28	1.9	28	100	0	108	40	14	16	27	1.88
54105991--54106086	50	1.9	50	86	0	138	3	21	23	51	1.63
54105973--54106089	25	5.0	24	76	13	118	3	22	23	50	1.64
54106066--54106104	19	2.1	19	90	9	62	0	23	23	53	1.46
54106935--54107006	24	3.0	24	100	0	144	20	25	16	37	1.93
54107461--54107548	28	3.1	28	83	3	104	40	3	15	39	1.64

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   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208