genome.fa.s8.2.7.7.80.10.50.1000.117.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  117  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)
35422598--35422648	24	2.1	24	82	13	61	76	1	7	13	1.09
35424161--35424202	20	2.1	20	86	8	59	66	4	2	26	1.23
35425531--35425691	44	3.6	44	81	2	171	27	20	20	31	1.97
35425768--35426616	89	9.6	89	87	0	1106	21	24	24	28	1.99
35425771--35426616	444	1.9	444	87	0	1233	21	24	25	28	1.99
35426885--35426941	24	2.4	24	82	5	71	31	24	10	33	1.89
35428429--35428479	21	2.5	21	79	20	63	74	7	1	15	1.13
35434413--35434452	19	2.0	20	85	4	55	30	7	17	45	1.76
35441527--35441933	44	8.9	44	75	10	298	35	18	17	28	1.94
35441522--35441934	95	4.5	89	76	8	264	34	18	17	28	1.94
35441567--35441934	95	3.9	95	78	5	302	35	17	17	29	1.93
35441792--35441934	51	2.9	51	81	7	156	34	17	17	30	1.93
35443516--35443610	4	23.8	4	75	12	61	23	9	0	67	1.19
35448183--35448207	9	2.8	9	100	0	50	68	8	0	24	1.16
35449854--35450019	44	3.8	44	75	7	131	24	27	21	27	1.99
35463293--35463374	12	7.0	12	70	9	62	24	6	3	65	1.31
35467611--35467695	35	2.4	35	96	0	152	40	14	3	42	1.62
35468744--35468790	19	2.6	18	90	9	78	76	6	17	0	0.98
35468744--35468791	18	2.6	19	90	6	73	77	6	16	0	0.97
35468975--35469128	17	8.3	18	71	18	93	38	13	9	38	1.78
35468976--35469163	18	10.2	18	68	17	84	36	13	9	39	1.78
35474846--35474933	6	14.8	6	78	13	85	81	14	3	0	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35474844--35474902	9	6.9	9	76	16	63	81	18	0	0	0.69
35474845--35474936	16	5.7	15	81	15	89	82	14	3	0	0.79
35474844--35474936	33	2.9	31	76	20	86	82	13	3	0	0.78
35474844--35474936	13	7.3	12	77	13	71	82	13	3	0	0.78
35475783--35476551	76	9.9	76	89	4	952	27	15	20	36	1.93
35475801--35476663	76	11.1	75	86	6	381	26	16	20	35	1.94
35476824--35476891	31	2.2	32	86	2	102	29	19	2	48	1.63
35477298--35477366	27	2.6	25	80	14	77	78	4	15	1	0.98
35477302--35477366	17	3.7	17	85	4	85	78	4	15	1	0.99
35478249--35478436	18	10.2	17	70	14	83	36	12	10	40	1.78
35478248--35478378	19	6.8	19	73	12	99	35	12	10	41	1.77
35479769--35479816	7	7.0	7	90	4	80	68	0	16	14	1.21
35479772--35479810	20	2.0	20	100	0	78	66	0	17	15	1.25
35480968--35481275	87	3.5	87	88	2	440	28	24	25	22	1.99
35481022--35481247	44	5.2	44	63	14	117	25	23	25	24	2.00
35481141--35481278	45	3.1	44	71	10	129	28	23	24	22	1.99
35481671--35482074	100	4.0	100	93	0	684	32	25	19	23	1.98
35481701--35482126	50	8.5	50	74	7	364	32	24	19	23	1.98
35483594--35483628	12	2.9	12	82	0	52	25	2	2	68	1.17
35486740--35486775	17	2.1	17	89	0	54	75	8	8	8	1.21
35487556--35487594	20	1.9	20	85	15	53	61	5	0	33	1.18
35487650--35487684	14	2.5	13	90	9	52	20	0	0	80	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35490601--35490885	107	2.6	109	88	6	436	34	20	16	28	1.95
35491524--35491596	35	2.1	34	84	2	92	52	2	9	35	1.49
35493319--35493344	2	13.0	2	100	0	52	50	0	0	50	1.00
35493993--35494035	18	2.4	18	88	0	59	44	18	11	25	1.84
35499114--35499165	25	2.1	25	96	0	95	44	9	26	19	1.81
35500036--35500061	13	2.0	13	100	0	52	23	15	7	53	1.67
35500197--35500244	25	1.9	25	91	0	78	27	12	20	39	1.89
35502588--35502737	41	3.7	41	88	0	219	26	28	18	27	1.98
35503145--35503177	12	2.8	12	90	4	50	51	9	3	36	1.49
35503098--35503405	114	2.7	112	93	3	526	40	13	4	41	1.64
35504382--35504406	13	1.9	13	100	0	50	68	24	0	8	1.16
35506125--35506361	33	7.1	33	70	7	100	30	15	25	28	1.96
35506058--35506361	101	3.0	101	93	0	511	30	15	25	28	1.95
35506355--35506420	25	2.7	25	81	11	66	53	3	21	22	1.60
35508394--35508437	18	2.5	17	85	10	61	25	2	2	70	1.10
35516935--35516981	2	23.5	2	100	0	94	48	0	0	51	1.00
35518960--35519163	108	1.9	110	91	2	340	33	18	18	30	1.94
35519710--35519790	13	6.5	13	73	8	62	60	3	1	34	1.22
35519902--35519959	3	19.3	3	100	0	116	67	0	0	32	0.91
35520597--35520640	20	2.1	22	79	12	56	72	0	4	22	1.02
35526174--35526213	11	3.6	11	96	0	71	20	25	7	47	1.75
35526219--35526262	12	3.8	12	81	3	54	40	0	0	59	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35527362--35527386	7	3.6	7	100	0	50	28	0	12	60	1.32
35528328--35528375	25	1.9	25	95	0	87	45	0	12	41	1.42
35528419--35528730	45	7.0	43	78	10	220	49	24	0	26	1.55
35528418--35528730	68	4.6	66	80	10	305	48	23	0	26	1.55
35528418--35528730	23	13.8	23	75	15	285	48	23	0	26	1.55
35528835--35529382	23	23.9	23	83	7	627	49	24	0	26	1.52
35528922--35529382	228	2.0	227	92	2	766	49	23	0	26	1.52
35529377--35529620	116	2.1	116	94	1	427	38	9	7	44	1.64
35532631--35533003	124	3.0	125	91	1	597	32	22	15	29	1.95
35534138--35534202	2	33.5	2	93	6	116	47	0	0	52	1.00
35538510--35538594	2	43.0	2	95	2	154	48	1	0	50	1.08
35560421--35560502	21	3.9	19	77	15	74	64	4	3	26	1.30
35560932--35560956	11	2.3	11	100	0	50	16	0	0	84	0.63
35562786--35562811	13	2.0	13	100	0	52	46	7	15	30	1.74
35569996--35570040	2	22.5	2	100	0	90	48	0	0	51	1.00
35570265--35570292	5	5.6	5	100	0	56	60	0	0	39	0.97
35570380--35570409	4	7.5	4	100	0	60	26	0	23	50	1.50
35574314--35574387	3	24.7	3	94	0	130	63	0	0	36	0.95
35575244--35575274	4	7.8	4	100	0	62	51	0	0	48	1.00
35575748--35576062	160	2.0	158	88	3	465	32	14	16	36	1.89
35578333--35578375	18	2.4	18	92	0	68	25	53	0	20	1.46
35578384--35578429	24	2.0	23	91	4	74	30	54	0	15	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35578351--35578614	57	4.8	57	76	10	269	27	46	4	21	1.70
35578480--35578586	48	2.2	48	86	0	142	28	47	2	20	1.64
35578351--35578614	105	2.4	105	81	9	289	27	46	4	21	1.70
35579780--35579843	2	32.0	2	96	0	119	0	48	0	51	1.00
35583542--35583588	16	2.8	17	82	17	55	44	0	12	42	1.42
35583542--35583575	17	2.0	17	88	11	52	47	0	11	41	1.40
35585602--35586320	131	5.5	131	89	0	931	25	24	20	30	1.99
35586129--35586313	44	4.2	44	68	8	133	25	23	20	29	1.99
35587544--35587584	7	6.0	7	94	5	75	14	14	0	70	1.16
35587544--35587580	13	2.8	13	95	4	65	13	13	0	72	1.11
35587544--35587584	20	2.0	20	100	0	82	14	14	0	70	1.16
35588500--35588572	27	2.6	28	82	10	87	12	9	8	69	1.35
35588523--35588587	33	2.0	33	81	6	78	10	6	9	73	1.23
35597346--35597403	15	3.8	15	73	13	55	27	0	1	70	0.97
35600934--35601064	18	7.4	18	71	13	94	5	27	8	58	1.49
35600935--35601064	36	3.7	34	77	12	111	5	27	8	58	1.49
35600981--35601037	15	3.4	15	70	25	51	7	26	8	57	1.54
35600937--35601081	69	2.1	70	81	3	166	4	27	8	58	1.49
35600970--35601070	36	2.9	36	85	4	136	4	26	10	57	1.53
35602552--35602596	3	15.0	3	95	0	81	64	0	2	33	1.06
35603243--35603288	23	2.0	23	83	8	58	50	2	0	47	1.13
35607805--35607833	13	2.2	13	100	0	58	44	13	6	34	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35628791--35629196	124	3.3	123	87	3	598	30	19	17	32	1.95
35636027--35636086	30	2.0	30	87	3	86	45	5	20	30	1.72
35636419--35636609	50	3.8	50	89	0	283	25	23	30	20	1.98
35645378--35645417	14	2.7	15	84	11	55	27	2	12	57	1.48
35654173--35654219	3	15.7	3	93	0	76	29	0	34	36	1.58
35654587--35654632	11	4.1	11	78	15	58	28	2	2	67	1.14
35654593--35654636	23	1.9	23	95	0	79	29	2	4	63	1.26
35656083--35656124	13	2.9	15	76	23	54	66	0	0	33	0.92
35656083--35656123	14	2.9	14	80	20	50	68	0	0	31	0.90
35665128--35665190	33	1.9	33	84	12	85	41	0	1	57	1.08

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