genome.fa.s8.2.7.7.80.10.50.1000.41.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  41  of  190  ( 22705 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)
11454458--11454542	44	1.9	44	92	0	143	14	16	18	50	1.78
11455394--11455429	16	2.2	16	90	5	54	0	2	11	86	0.68
11458126--11458168	22	2.0	22	85	0	59	23	18	16	41	1.89
11458836--11458869	16	2.1	16	94	0	59	14	5	8	70	1.31
11461475--11461500	10	2.6	10	100	0	52	30	0	7	61	1.24
11466438--11466466	4	7.2	4	100	0	58	75	0	0	24	0.80
11466490--11466520	16	1.9	16	100	0	62	12	9	6	70	1.31
11468130--11468258	68	1.9	70	83	6	174	41	3	3	50	1.39
11483353--11483382	10	3.0	10	95	0	51	33	10	0	56	1.32
11483359--11483402	17	2.6	17	78	3	54	36	6	2	54	1.40
11485898--11486252	187	1.9	185	83	5	464	39	8	7	44	1.65
11506088--11506272	36	5.0	37	84	4	221	34	18	15	31	1.92
11506088--11506285	73	2.7	73	80	3	227	33	18	15	32	1.92
11506215--11506291	39	2.0	39	84	0	100	38	19	10	31	1.85
11507745--11507790	24	1.9	24	95	0	83	13	45	4	36	1.63
11509397--11509436	20	2.0	20	90	0	62	50	12	10	27	1.72
11514905--11514957	23	2.3	23	87	3	72	35	18	24	20	1.95
11523757--11524143	194	2.0	193	96	0	720	27	8	22	41	1.83
11524950--11524990	21	2.0	21	95	0	73	29	12	9	48	1.72
11525112--11525183	22	3.3	22	90	0	108	27	15	30	26	1.96
11525823--11525911	23	3.9	23	79	1	90	37	20	21	21	1.95
11528686--11528746	30	2.0	30	100	0	122	29	9	9	50	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11537731--11537801	35	2.0	35	94	0	124	28	22	12	36	1.91
11543897--11543936	13	2.9	14	88	3	55	72	7	2	17	1.19
11544582--11544619	14	2.8	13	88	11	58	10	0	2	86	0.66
11544581--11544622	19	2.2	20	91	4	68	14	0	2	83	0.75
11550253--11550425	28	6.0	28	68	15	104	57	2	13	26	1.48
11550339--11550409	22	3.2	21	80	9	79	56	2	15	25	1.53
11550338--11550407	5	12.7	6	75	10	53	55	2	17	24	1.55
11550570--11550689	11	10.5	11	68	17	57	58	3	11	26	1.49
11550570--11550631	17	3.7	17	81	8	65	53	1	12	32	1.49
11550615--11550807	60	3.2	60	69	12	160	61	4	9	23	1.46
11550622--11550696	23	3.1	24	75	5	71	65	4	10	20	1.40
11550903--11550962	11	5.3	11	75	15	59	55	1	13	30	1.48
11550903--11550962	23	2.6	23	79	10	68	55	1	13	30	1.48
11553228--11553541	89	3.5	89	84	4	384	61	12	3	22	1.46
11553434--11553506	32	2.2	32	80	7	85	65	13	1	19	1.33
11554106--11554277	58	3.0	56	80	4	200	36	15	15	32	1.90
11583999--11584065	32	2.1	32	86	5	91	29	2	11	55	1.51
11584504--11584557	20	2.7	20	85	5	65	27	5	3	62	1.34
11584509--11584564	20	2.8	21	83	5	62	26	7	3	62	1.38
11584532--11584595	29	2.2	29	86	13	87	26	7	1	64	1.30
11584606--11584654	21	2.3	22	82	10	66	38	2	2	57	1.22
11584601--11584654	10	5.2	11	71	10	51	37	1	1	59	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11584601--11584704	20	5.2	19	74	10	73	34	4	0	59	1.25
11586957--11586992	16	2.2	17	90	5	56	75	11	5	8	1.19
11587042--11587100	22	2.7	22	91	0	91	35	15	25	23	1.94
11595697--11595736	18	2.2	19	86	4	55	67	0	2	30	1.04
11601710--11601775	31	2.1	31	97	0	123	33	16	6	43	1.73
11605844--11605906	31	2.0	31	81	6	74	74	9	12	3	1.17
11609747--11609786	20	2.0	20	100	0	80	35	20	20	25	1.96
11620174--11620232	29	2.1	29	81	9	68	28	3	3	64	1.26
11624313--11624406	13	7.2	13	70	11	75	55	8	5	30	1.52
11624308--11624406	40	2.5	39	83	4	110	55	8	6	30	1.53
11627245--11627287	18	2.3	18	88	11	61	20	0	27	51	1.48
11629443--11629490	18	2.8	17	73	17	53	35	8	29	27	1.86
11632530--11632594	29	2.2	30	81	10	80	56	3	3	36	1.30
11632574--11632630	15	4.1	15	71	17	50	57	0	0	42	0.98
11632578--11632633	26	2.2	26	86	0	76	60	0	0	39	0.97
11632575--11632649	26	2.9	26	71	9	73	60	1	0	38	1.06
11632678--11632724	2	23.5	2	100	0	94	51	0	0	48	1.00
11633820--11633860	20	2.0	21	85	4	57	60	0	2	36	1.10
11635649--11635856	44	4.7	44	76	9	165	27	26	19	26	1.99
11637296--11637336	18	2.3	18	86	0	55	9	12	0	78	0.98
11641069--11641137	30	2.3	30	87	2	95	27	17	21	33	1.96
11641083--11641144	30	2.1	30	100	0	124	22	19	16	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11654716--11654742	2	13.5	2	100	0	54	48	0	0	51	1.00
11654875--11654960	3	28.0	3	82	4	100	66	2	3	27	1.20
11656434--11656520	44	2.0	44	84	4	113	29	24	16	29	1.96
11656836--11657059	43	5.2	43	64	17	113	27	24	21	27	1.99
11656722--11657116	87	4.6	87	84	2	519	25	24	21	28	1.99
11658723--11658769	17	2.7	17	80	3	58	12	2	14	70	1.26
11658723--11658773	6	8.8	6	82	8	61	11	1	13	72	1.20
11658724--11658767	23	2.0	22	90	4	70	9	2	13	75	1.14
11658724--11658790	29	2.3	29	85	7	91	7	4	10	77	1.10
11663928--11664005	3	26.0	3	97	0	147	65	0	1	33	1.01
11672584--11672687	42	2.5	42	85	6	122	15	23	18	43	1.87
11672603--11672667	21	3.1	22	72	12	57	18	24	16	40	1.91
11672620--11672687	21	3.2	21	75	8	66	16	20	17	45	1.85
11673408--11673432	13	1.9	13	100	0	50	32	4	24	40	1.73
11674664--11674758	30	3.2	29	86	5	118	31	24	4	40	1.74
11674664--11674793	60	2.2	58	79	5	134	30	22	5	42	1.76
11674678--11674794	30	3.9	30	85	2	137	28	23	5	43	1.75
11675337--11675393	13	4.7	12	81	14	64	75	0	24	0	0.80
11675335--11675394	12	4.9	12	77	22	63	75	0	25	0	0.81
11675332--11675394	26	2.5	24	85	15	74	74	0	25	0	0.82
11676164--11676212	17	2.8	17	73	14	55	32	16	10	40	1.82
11676297--11676515	18	12.4	18	76	12	168	29	14	10	44	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11676270--11676515	35	6.9	36	77	6	218	29	14	12	44	1.81
11676263--11676512	53	4.7	53	78	8	217	30	14	12	44	1.81
11687567--11687607	21	2.0	20	90	4	64	82	7	9	0	0.83
11688451--11688888	78	5.7	75	88	5	607	27	16	20	35	1.94
11688451--11688898	152	2.9	152	90	4	667	27	16	20	35	1.94
11688451--11688911	228	2.0	228	89	3	703	27	16	20	35	1.94
11689200--11689300	30	3.4	28	82	9	85	30	25	4	38	1.77
11689200--11689329	60	2.2	59	80	4	136	29	24	6	40	1.79
11689224--11689330	30	3.6	30	87	1	135	28	22	5	43	1.75
11689872--11689914	12	3.7	11	80	20	52	74	0	25	0	0.82
11689865--11689921	29	2.0	29	85	0	78	73	0	24	1	0.92
11690691--11690739	17	2.8	17	73	14	55	32	16	10	40	1.82
11690789--11690982	52	3.6	54	80	11	170	30	14	11	42	1.82
11690796--11691041	35	6.9	36	75	9	186	29	14	11	44	1.80
11690838--11691041	18	11.6	18	73	12	165	29	14	10	45	1.78
11690789--11691041	53	4.8	54	78	10	236	31	13	11	43	1.80
11691012--11691080	34	2.0	35	86	5	97	37	7	8	46	1.63
11692069--11692201	41	3.2	41	89	2	151	24	16	27	31	1.96
11692108--11692201	41	2.3	41	94	0	161	23	15	28	31	1.96
11694712--11694740	15	1.9	15	100	0	58	51	0	6	41	1.28
11696266--11696291	3	8.7	3	100	0	52	34	30	0	34	1.58
11696928--11696978	23	2.2	23	89	0	75	54	23	5	15	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11698125--11698250	10	13.7	9	70	19	82	60	3	2	33	1.28
11698148--11698215	19	3.6	19	78	5	66	60	5	1	32	1.30
11698282--11698341	18	3.3	18	80	13	77	66	1	1	30	1.11
11698651--11698742	19	4.8	19	94	0	166	36	8	16	38	1.79
11698651--11698765	38	2.9	38	93	5	185	36	7	16	39	1.78
11700841--11700878	19	2.0	20	89	5	60	71	2	2	23	1.12
11705596--11705661	26	2.5	26	100	0	132	16	18	12	53	1.73
11707559--11707598	20	2.0	20	100	0	80	30	10	15	45	1.78
11707544--11707608	34	1.9	33	81	9	78	36	9	12	41	1.75
11707696--11707734	20	2.0	20	94	0	69	48	2	0	48	1.15

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