genome.fa.s1.2.7.7.80.10.50.1000.160.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  160  of  187  ( 22383 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)
47315592--47315791	91	2.2	91	84	6	262	32	7	21	39	1.81
47316346--47316389	18	2.3	20	88	7	65	50	4	2	43	1.35
47316502--47316533	10	2.8	12	81	18	50	28	0	0	71	0.86
47319268--47319293	3	8.7	3	100	0	52	69	0	0	30	0.89
47319407--47319443	19	2.0	19	89	5	58	35	0	8	56	1.29
47319412--47319455	19	2.2	21	84	11	58	34	0	9	56	1.31
47320332--47320378	19	2.5	20	82	10	62	42	14	6	36	1.72
47322460--47322516	10	5.7	10	79	8	53	38	0	0	61	0.96
47322618--47322850	94	2.5	91	79	4	245	38	18	11	30	1.87
47323594--47323620	6	4.5	6	100	0	54	85	14	0	0	0.61
47330661--47330695	16	2.3	16	90	9	56	57	0	5	37	1.23
47330696--47330752	19	3.0	19	68	0	51	59	3	3	33	1.31
47330890--47331043	84	1.9	81	84	9	204	34	5	2	57	1.35
47330979--47331034	19	2.9	19	84	7	78	26	3	1	67	1.16
47330942--47331034	37	2.5	38	80	5	100	33	3	2	61	1.24
47331115--47331318	87	2.3	87	78	5	223	33	9	18	39	1.82
47331711--47331746	18	2.1	18	90	10	58	61	0	0	38	0.96
47331959--47332007	20	2.5	20	83	6	64	18	8	2	71	1.21
47335318--47335355	19	2.0	19	100	0	76	36	21	15	26	1.93
47339203--47339484	141	2.0	141	83	2	361	35	13	20	30	1.91
47341350--47341393	17	2.5	18	85	7	63	45	4	20	29	1.71
47344970--47345169	49	4.1	50	79	10	225	17	26	20	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47344977--47345188	25	8.6	25	76	10	172	18	25	20	34	1.96
47345027--47345188	73	2.2	74	80	7	170	18	25	21	34	1.96
47345099--47345200	50	2.1	49	85	5	134	22	23	19	34	1.97
47346407--47346506	39	2.6	39	88	0	155	25	12	29	34	1.91
47348647--47348677	13	2.4	13	100	0	62	45	0	0	54	0.99
47350665--47350694	14	2.1	14	100	0	60	30	6	6	56	1.51
47354767--47354811	23	2.0	23	95	0	81	37	8	26	26	1.86
47355407--47355431	8	3.1	8	100	0	50	76	0	0	24	0.80
47360873--47360955	9	9.2	9	69	21	50	42	0	1	56	1.07
47360906--47360955	17	3.0	16	80	8	55	44	0	0	56	0.99
47372451--47372512	27	2.2	27	85	5	79	53	3	0	43	1.17
47374269--47374317	22	2.3	22	80	20	59	30	2	16	51	1.56
47376213--47376275	25	2.6	23	81	16	74	15	6	3	74	1.15
47376212--47376275	24	2.6	24	77	22	71	15	6	3	75	1.14
47376239--47376315	4	18.5	4	72	15	50	16	5	3	74	1.16
47376340--47376420	35	2.3	35	85	10	112	37	0	0	62	0.95
47376376--47376420	12	3.8	12	77	16	58	35	0	0	64	0.94
47376330--47376436	57	1.9	56	88	9	164	37	0	1	60	1.07
47376375--47376434	21	2.9	22	88	11	83	36	0	0	63	0.95
47376674--47376728	18	3.0	18	81	2	56	52	0	5	41	1.24
47376715--47376761	14	3.4	14	81	0	58	68	0	0	31	0.90
47376732--47376756	7	3.6	7	100	0	50	84	0	0	16	0.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47379390--47379522	30	4.4	30	79	6	135	22	22	24	30	1.99
47379390--47379503	60	1.9	60	87	0	165	23	22	24	28	1.99
47382345--47382498	82	1.9	82	87	4	231	57	5	3	33	1.37
47382430--47382464	7	4.7	7	89	10	52	71	0	0	28	0.86
47382561--47382587	14	1.9	14	100	0	54	51	0	0	48	1.00
47382562--47382595	14	2.5	14	90	4	52	55	0	0	44	0.99
47382575--47382618	21	2.0	23	91	8	74	59	0	0	40	0.98
47382679--47382731	23	2.2	24	86	6	72	75	3	5	15	1.13
47396674--47396708	2	17.5	2	100	0	70	48	0	0	51	1.00
47397066--47397118	22	2.4	23	78	6	65	39	3	9	47	1.54
47399282--47399308	3	9.0	3	100	0	54	66	0	0	33	0.92
47408463--47408489	2	13.5	2	100	0	54	48	0	51	0	1.00
47411233--47411284	25	2.1	24	85	3	68	21	25	19	34	1.96
47411252--47411299	25	1.9	25	82	0	60	20	25	20	33	1.97
47415701--47415743	19	2.2	20	80	12	54	27	0	4	67	1.10
47415814--47415891	40	2.0	40	100	0	156	17	24	10	47	1.79
47417628--47417831	52	3.9	54	80	10	219	28	21	18	31	1.97
47417599--47417831	52	4.5	50	76	10	166	28	22	20	29	1.98
47417717--47417852	52	2.6	50	80	9	148	27	23	18	30	1.97
47418864--47418925	25	2.4	27	92	7	103	43	9	0	46	1.36
47419090--47419228	4	34.0	4	70	20	76	69	0	29	0	0.93
47419093--47419145	27	1.9	28	88	3	81	71	0	26	1	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47419095--47419295	41	5.1	40	76	11	170	69	0	29	0	0.92
47419176--47419268	3	32.3	3	73	14	54	67	0	32	0	0.91
47419095--47419295	78	2.6	76	87	9	282	69	0	29	0	0.92
47420318--47420352	17	2.1	17	94	0	61	77	5	14	2	1.07
47421245--47421313	27	2.7	27	82	10	83	43	0	23	33	1.54
47422615--47422670	27	2.1	27	96	0	103	42	14	33	8	1.77
47427015--47427043	10	2.7	11	89	10	51	0	27	0	72	0.85
47427205--47427265	27	2.3	27	94	0	104	52	0	6	40	1.27
47427754--47427810	30	1.9	30	88	0	87	12	8	8	70	1.35
47427954--47428019	34	1.9	34	87	6	98	31	7	15	45	1.74
47433405--47433444	15	2.6	15	92	4	62	50	0	5	45	1.23
47436955--47437003	2	24.0	2	95	4	89	48	2	0	48	1.12
47437919--47438047	43	3.0	42	75	17	138	31	26	18	23	1.97
47439155--47439179	13	1.9	13	100	0	50	40	24	4	32	1.73
47440713--47440895	51	3.6	50	76	4	206	24	16	27	31	1.97
47440905--47440999	45	2.1	45	92	0	163	26	18	24	30	1.98
47444222--47444272	24	2.2	24	86	13	72	74	1	3	19	1.07
47444278--47444355	29	2.7	29	82	9	88	30	21	5	42	1.75
47444916--47444950	19	1.9	18	88	11	54	65	0	31	2	1.07
47445053--47445087	17	2.1	16	89	10	52	80	0	11	8	0.92
47445059--47445086	13	2.2	13	100	0	56	85	0	7	7	0.73
47457661--47457849	93	2.0	93	100	0	378	28	22	11	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47459021--47459076	27	2.1	27	96	0	103	46	16	12	25	1.81
47461906--47462423	76	6.7	77	88	0	718	25	19	20	33	1.96
47462951--47463051	30	3.4	30	83	4	125	28	18	4	47	1.70
47463763--47463850	6	14.8	6	81	7	108	79	1	19	0	0.79
47467936--47467987	11	4.9	11	79	13	56	30	0	3	65	1.10
47467930--47468154	10	22.9	9	68	21	82	35	1	4	58	1.26
47467936--47467995	30	2.0	30	93	6	104	31	0	5	63	1.16
47468078--47468118	17	2.5	17	80	11	50	36	0	4	58	1.20
47473257--47473296	8	4.9	8	90	3	53	67	0	0	32	0.91
47476473--47476528	29	1.9	29	85	7	78	25	16	19	39	1.91
47485487--47485530	14	3.1	14	83	0	52	45	27	4	22	1.72
47485625--47485682	29	2.0	29	100	0	116	55	6	6	31	1.53
47486189--47486219	16	1.9	16	93	0	53	67	6	0	25	1.14
47486373--47486407	13	2.8	12	87	8	52	20	0	5	74	1.02
47488524--47488567	14	3.1	14	83	0	52	45	27	4	22	1.72
47488870--47488902	7	4.7	7	100	0	66	45	0	24	30	1.53
47490138--47490168	13	2.3	14	94	5	55	83	6	3	6	0.88
47490938--47490971	5	6.6	5	86	6	50	79	0	5	14	0.91
47490938--47490972	16	2.2	16	89	0	52	80	0	5	14	0.89
47490938--47490987	26	1.9	26	88	8	75	76	0	8	16	1.02
47491935--47491965	15	2.1	15	100	0	62	45	19	16	19	1.86
47497302--47497337	16	2.2	16	95	0	63	52	5	2	38	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47500707--47500765	31	1.9	31	83	13	77	38	10	15	35	1.81
47504491--47504529	18	2.1	18	85	4	51	58	12	2	25	1.47
47506361--47506399	16	2.4	16	87	8	53	48	2	25	23	1.63
47506471--47506549	36	2.1	38	81	9	101	48	0	22	29	1.51
47506743--47506805	23	2.9	22	88	9	94	19	20	23	36	1.95
47508842--47508876	17	2.1	17	89	10	54	60	2	2	34	1.26
47509839--47509884	2	23.0	2	100	0	92	50	0	0	50	1.00
47521960--47521990	16	1.9	16	100	0	62	25	19	16	38	1.92
47522133--47522215	41	2.0	41	97	0	157	44	19	18	18	1.87
47527522--47527552	14	2.2	14	100	0	62	48	0	12	38	1.42

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