genome.fa.s1.2.7.7.80.10.50.1000.125.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  125  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)
37928186--37928228	21	2.0	22	86	4	61	9	25	2	62	1.37
37928279--37928308	16	1.9	16	93	6	53	10	6	0	83	0.81
37930285--37930325	22	2.0	20	85	9	55	58	9	4	26	1.50
37938149--37938247	19	5.3	18	70	23	64	49	5	3	42	1.40
37941367--37941640	41	6.6	40	79	8	217	22	17	24	35	1.95
37941411--37941643	84	2.8	84	94	0	403	20	18	24	37	1.94
37941359--37941687	125	2.6	125	80	8	348	23	17	24	34	1.96
37943659--37943704	16	2.9	16	84	12	51	39	4	0	56	1.19
37945072--37945107	16	2.2	16	100	0	72	38	11	5	44	1.63
37954073--37954099	13	2.1	13	100	0	54	33	0	22	44	1.53
37963737--37963761	8	3.1	8	100	0	50	24	40	12	24	1.88
37968104--37968158	25	2.2	25	100	0	110	23	23	25	27	2.00
37970282--37970455	43	4.1	43	79	4	194	29	26	15	28	1.96
37972285--37972473	97	1.9	97	97	0	360	35	20	16	27	1.94
37977702--37977796	47	2.0	47	97	0	181	33	10	24	31	1.89
37984235--37984321	43	2.0	44	84	2	113	29	27	17	25	1.97
37986997--37987075	38	2.2	37	81	6	90	51	0	7	40	1.30
37987023--37987143	48	2.6	48	86	2	165	51	0	6	42	1.28
38009493--38010883	697	2.0	697	91	0	2239	30	17	21	30	1.96
38011965--38012025	24	2.5	24	81	5	79	18	18	24	39	1.92
38015609--38015704	47	2.0	47	93	0	165	19	32	23	23	1.98
38021860--38022002	41	3.5	41	85	0	160	20	23	23	32	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38027134--38027172	19	2.0	20	90	5	62	30	20	30	17	1.96
38029741--38029818	39	2.0	39	100	0	156	10	20	17	51	1.74
38030370--38030420	23	2.2	23	89	6	77	29	9	19	41	1.84
38030747--38030785	20	2.0	20	90	10	62	15	23	5	56	1.59
38033860--38033910	20	2.5	20	96	0	93	39	15	7	37	1.77
38036889--38037025	40	3.4	41	84	6	165	38	21	19	19	1.93
38037062--38037214	41	3.7	40	84	6	191	23	20	26	29	1.99
38037513--38037549	14	2.6	14	95	0	65	21	0	29	48	1.50
38037598--38037630	14	2.3	15	94	5	59	30	0	33	36	1.58
38037723--38037747	7	3.6	7	100	0	50	16	0	40	44	1.47
38037784--38037871	7	12.4	7	77	7	61	15	0	47	36	1.46
38037782--38037856	14	5.2	15	77	7	75	10	0	50	38	1.37
38037782--38037856	29	2.6	30	79	8	84	10	0	50	38	1.37
38037984--38038023	7	5.6	7	90	3	62	17	0	55	27	1.43
38038527--38038828	122	2.4	126	86	6	434	38	13	13	34	1.84
38039568--38039600	6	5.7	6	96	3	59	15	0	0	84	0.61
38040979--38041014	18	2.0	18	94	0	63	16	25	11	47	1.79
38041842--38042037	43	4.6	43	81	8	188	24	16	28	31	1.96
38041842--38042037	85	2.3	85	80	7	229	24	16	28	31	1.96
38043284--38043311	13	2.2	13	100	0	56	46	0	7	46	1.30
38043430--38043477	12	3.9	12	83	2	51	68	0	2	29	1.01
38043440--38043490	19	2.5	20	90	9	77	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38043445--38043484	13	3.2	13	89	3	55	65	0	0	35	0.93
38043443--38043541	25	4.0	25	73	13	78	63	1	4	31	1.19
38043507--38043569	21	2.9	22	79	11	60	60	0	6	33	1.22
38043487--38043561	22	3.3	22	76	14	64	58	1	8	32	1.35
38043825--38044005	90	2.0	90	94	0	317	32	17	9	39	1.83
38044229--38044299	16	4.4	16	84	7	90	39	4	22	33	1.74
38044230--38044299	32	2.2	33	90	10	110	40	2	22	34	1.69
38044463--38044599	58	2.4	58	80	7	154	51	2	1	43	1.25
38050023--38050071	3	16.3	3	100	0	98	34	0	0	65	0.93
38054190--38054217	14	2.0	14	100	0	56	35	7	14	42	1.73
38068993--38069046	24	2.2	25	80	9	67	44	0	0	55	0.99
38073615--38073657	17	2.4	18	81	18	54	9	30	9	51	1.65
38074611--38074662	18	2.9	18	85	2	61	82	0	11	5	0.82
38074606--38074663	18	3.2	18	74	16	57	82	0	10	6	0.83
38075591--38075644	26	2.1	25	86	3	72	37	24	18	20	1.94
38081315--38081384	6	11.5	6	76	14	63	14	2	5	77	1.07
38091550--38091613	21	3.0	22	80	11	62	59	0	4	35	1.18
38091573--38091620	14	3.1	17	69	25	52	62	0	2	35	1.07
38093469--38093538	25	2.8	25	86	0	86	21	25	21	31	1.98
38093505--38093574	25	2.8	25	84	2	97	24	22	21	31	1.98
38096065--38096089	5	5.0	5	100	0	50	0	20	0	80	0.72
38096119--38096237	24	4.9	23	71	20	57	9	14	1	74	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38096152--38096211	9	7.4	8	78	12	52	11	6	1	80	0.98
38096143--38096205	10	6.1	11	78	15	55	9	7	1	80	0.95
38096171--38096204	6	5.8	6	86	6	52	11	2	0	85	0.71
38096169--38096205	11	3.3	11	88	7	56	10	2	0	86	0.67
38096134--38096235	32	3.2	32	77	12	93	9	13	0	75	1.09
38097276--38098723	724	2.0	723	94	0	2556	24	23	19	32	1.97
38099041--38099075	17	2.0	18	88	5	54	25	14	0	60	1.35
38101365--38101534	32	5.4	32	84	1	209	40	20	18	20	1.91
38101365--38101534	64	2.7	64	87	1	236	40	20	18	20	1.91
38101710--38101763	24	2.2	24	93	0	90	44	25	11	18	1.83
38101809--38101901	27	3.5	27	91	1	152	23	25	18	32	1.97
38101807--38102034	54	4.2	54	76	5	183	21	20	18	39	1.93
38101835--38102038	27	7.6	27	78	4	151	21	19	18	40	1.91
38101970--38102053	27	3.1	27	86	3	89	20	19	19	41	1.90
38102715--38102782	31	2.3	31	94	5	122	36	35	0	27	1.58
38112382--38112443	27	2.3	27	77	0	70	35	19	12	32	1.90
38112733--38112797	34	2.0	32	90	6	103	32	23	24	20	1.98
38118366--38118390	8	3.1	8	100	0	50	28	0	24	48	1.52
38118366--38118398	15	2.1	16	88	5	50	30	0	24	45	1.53
38124874--38125584	357	2.0	355	95	1	1271	28	15	18	37	1.92
38130522--38130564	22	2.0	22	86	9	61	32	18	34	13	1.90
38134574--38134618	22	2.0	22	86	0	63	35	17	37	8	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38140380--38140453	29	2.5	29	82	4	85	25	14	13	45	1.82
38141823--38141899	29	2.6	29	83	4	82	48	11	12	27	1.76
38141981--38142035	26	2.1	26	100	0	110	38	7	14	40	1.74
38147674--38147716	5	8.4	5	84	5	59	18	4	2	74	1.10
38152018--38152077	20	3.1	19	77	13	68	25	28	11	35	1.91
38160647--38161113	50	9.3	50	72	0	342	27	19	25	26	1.99
38160651--38161159	100	5.1	100	91	0	802	27	20	24	26	1.99
38160701--38161159	50	9.2	50	71	0	324	28	20	24	27	1.99
38162686--38162725	3	13.3	3	100	0	80	32	0	0	67	0.91
38163315--38163350	5	7.2	5	87	0	54	19	2	2	75	1.06
38164269--38164599	137	2.4	137	87	1	466	29	26	14	29	1.95
38171090--38171119	16	1.9	16	93	6	53	50	20	0	30	1.49
38173478--38173589	39	2.9	39	83	0	152	16	32	16	33	1.92
38173504--38173568	20	3.3	20	66	12	53	16	40	13	29	1.88
38177774--38177831	13	4.9	13	75	25	58	43	15	0	41	1.47
38177775--38177831	23	2.5	23	91	5	89	43	15	0	40	1.47
38181110--38181254	50	2.9	49	84	4	182	26	23	28	21	1.99
38181068--38181254	100	1.8	102	81	6	234	26	21	28	23	1.99
38181505--38181553	20	2.5	20	78	15	57	57	6	26	10	1.55
38186129--38186210	42	2.0	42	81	13	98	17	8	2	71	1.21
38191317--38191453	50	2.8	50	77	6	145	32	21	22	23	1.98
38191654--38191702	20	2.5	20	81	15	66	57	6	24	12	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38208445--38208505	26	2.3	26	86	5	79	40	6	19	32	1.77
38212740--38212777	20	1.9	20	88	0	58	44	31	5	18	1.72
38214938--38214967	13	2.3	13	94	0	51	50	3	0	46	1.18
38217980--38218015	11	3.2	11	92	4	54	11	0	5	83	0.80
38226005--38226033	12	2.3	13	94	5	51	20	6	6	65	1.40
38232385--38232514	50	2.6	50	79	4	163	25	23	28	23	1.99
38239947--38240073	50	2.4	49	81	12	130	27	21	27	23	1.99
38239988--38240123	50	2.7	50	83	2	148	27	25	27	19	1.99
38240334--38240376	20	2.2	20	87	8	61	53	2	25	18	1.56
38241120--38241164	20	2.3	21	81	14	60	13	24	6	55	1.62

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