genome.fa.s1.2.7.7.80.10.50.1000.118.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  118  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)
35534229--35534269	19	2.2	19	100	0	82	26	9	34	29	1.88
35536862--35536914	18	2.9	18	77	0	52	15	35	3	45	1.64
35557963--35557987	13	1.9	13	100	0	50	32	4	24	40	1.73
35559098--35559253	43	3.6	42	74	10	136	25	19	25	30	1.98
35562035--35562073	18	2.2	18	100	0	78	33	5	17	43	1.72
35562817--35562968	36	4.3	35	89	5	227	33	0	17	48	1.52
35562847--35562988	9	16.2	9	68	11	55	35	0	17	46	1.54
35562817--35562968	70	2.2	70	92	0	250	33	0	17	48	1.52
35562817--35562988	70	2.5	70	88	1	211	34	0	17	47	1.52
35563078--35563104	13	2.1	13	100	0	54	37	11	0	51	1.37
35563622--35563659	19	2.0	20	89	5	60	68	2	2	26	1.16
35563617--35563673	19	3.1	18	76	14	53	68	1	1	28	1.09
35564048--35564276	72	3.2	72	76	3	237	45	13	6	35	1.68
35564035--35564249	71	3.0	72	72	9	215	45	12	6	34	1.69
35567241--35567307	27	2.5	27	90	0	98	34	16	37	11	1.85
35567463--35567556	41	2.3	40	85	1	116	14	24	19	41	1.89
35581209--35581272	17	3.6	17	72	15	58	29	12	12	45	1.79
35581476--35581569	47	2.0	48	93	2	163	17	18	23	41	1.90
35583085--35583168	42	2.0	42	100	0	168	21	28	19	30	1.97
35586647--35586740	47	2.0	48	87	2	136	20	17	21	41	1.90
35589107--35589453	122	2.8	123	88	2	511	29	15	22	32	1.95
35592528--35592552	10	2.5	10	100	0	50	48	0	8	44	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35592536--35592716	55	3.3	55	93	0	326	43	4	12	39	1.64
35592711--35592950	117	2.1	116	94	3	421	27	0	27	45	1.54
35592929--35592974	17	2.7	18	93	6	78	28	0	17	54	1.43
35592711--35592950	29	8.3	29	93	3	421	27	0	27	45	1.54
35593013--35593127	36	3.2	36	65	11	92	46	15	4	33	1.66
35593045--35593155	25	4.6	25	68	20	83	45	14	2	37	1.59
35592973--35593157	71	2.6	71	94	0	325	44	14	3	37	1.63
35593554--35593599	18	2.6	18	82	0	56	39	8	30	21	1.84
35595346--35595411	31	2.2	30	91	2	105	63	0	0	36	0.95
35595346--35595411	10	6.5	10	72	10	53	63	0	0	36	0.95
35595435--35595523	29	3.3	29	62	20	75	40	0	29	30	1.57
35595412--35595533	51	2.4	51	93	4	201	41	0	29	28	1.56
35595506--35595531	12	2.2	12	100	0	52	38	0	30	30	1.58
35597719--35597746	2	14.0	2	100	0	56	50	0	0	50	1.00
35600684--35600720	17	2.1	18	90	5	58	29	24	0	45	1.53
35601437--35601562	9	14.6	9	90	8	192	78	10	0	11	0.96
35601437--35601562	17	7.3	18	92	7	192	78	10	0	11	0.96
35601443--35601570	19	6.7	19	72	24	85	78	10	0	10	0.98
35601574--35601625	22	2.5	20	81	12	61	76	0	21	1	0.87
35601582--35601619	16	2.4	15	87	12	58	84	0	15	0	0.63
35601583--35601621	11	3.5	11	82	10	53	82	0	17	0	0.68
35602467--35602499	9	3.9	9	84	15	52	75	0	12	12	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35602467--35602499	16	2.1	16	100	0	66	75	0	12	12	1.04
35604235--35605069	88	9.5	88	91	1	1365	26	22	25	25	2.00
35604235--35605069	263	3.2	264	92	1	1365	26	22	25	25	2.00
35606765--35606806	3	14.0	3	100	0	84	33	0	0	66	0.92
35606805--35606838	3	11.3	3	100	0	68	0	0	32	67	0.91
35606886--35606923	2	19.0	2	100	0	76	50	0	0	50	1.00
35610395--35610568	85	2.0	85	95	0	312	16	14	16	51	1.76
35612908--35612954	19	2.6	18	77	9	51	65	6	0	27	1.16
35612959--35613011	21	2.5	21	81	9	63	52	5	1	39	1.36
35612908--35613071	9	17.4	9	71	14	75	59	3	2	34	1.28
35616244--35616284	23	1.9	22	85	14	59	7	26	7	58	1.51
35619236--35619406	84	2.0	84	97	0	324	37	17	23	21	1.94
35622201--35622315	9	12.4	9	70	18	76	66	0	2	29	1.10
35622201--35622315	19	6.2	19	74	11	89	66	0	2	29	1.10
35628895--35628957	31	2.0	32	96	3	119	42	15	9	31	1.79
35629049--35629074	3	8.7	3	100	0	52	69	0	0	30	0.89
35629410--35629445	18	1.9	19	88	5	56	27	5	0	66	1.13
35629429--35629559	48	2.7	47	81	8	149	33	5	0	60	1.25
35629498--35629569	19	3.8	19	76	9	67	33	4	1	61	1.24
35629476--35629569	28	3.4	26	80	11	91	35	4	1	59	1.24
35629470--35629598	48	2.6	48	81	13	124	35	4	0	58	1.24
35629982--35630028	15	3.3	14	80	11	51	36	2	12	48	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35631229--35631868	343	1.9	342	86	2	915	22	25	16	35	1.95
35634197--35634272	36	2.1	38	82	9	95	48	0	2	48	1.15
35636182--35636230	25	2.0	25	84	8	64	48	8	10	32	1.66
35636182--35636232	24	2.1	25	85	3	68	50	7	9	31	1.64
35637215--35637266	16	3.3	16	76	10	54	61	0	23	15	1.33
35637224--35637268	16	2.9	16	80	3	56	62	0	22	15	1.33
35641042--35641078	2	18.5	2	100	0	74	48	0	0	51	1.00
35641593--35641627	12	2.8	12	91	4	52	45	2	0	51	1.16
35642462--35642568	11	10.4	11	70	18	70	39	3	0	57	1.17
35642452--35642602	41	3.6	41	83	8	180	37	2	0	59	1.11
35649486--35649531	19	2.4	18	82	10	56	26	23	10	39	1.88
35658238--35658609	44	8.0	44	70	17	234	33	19	20	26	1.96
35658200--35658610	98	4.3	95	69	18	253	33	19	19	27	1.96
35658103--35658666	142	4.0	142	93	0	941	34	18	20	27	1.96
35660680--35660707	13	2.2	13	100	0	56	57	14	7	21	1.61
35661707--35661737	4	7.8	4	100	0	62	48	0	0	51	1.00
35665422--35665469	23	2.1	23	88	7	71	18	8	35	37	1.81
35674185--35674275	6	15.2	6	97	0	164	48	16	0	35	1.47
35675866--35675899	16	2.1	15	89	10	50	11	2	5	79	1.02
35676277--35676327	20	2.5	20	87	6	68	29	13	15	41	1.86
35678586--35678616	16	1.9	16	93	0	53	54	0	6	38	1.26
35679561--35679744	33	5.6	33	89	2	262	20	8	30	41	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35679561--35679777	33	6.5	33	87	4	258	18	8	32	40	1.82
35684056--35684141	22	3.9	22	90	0	118	27	15	27	29	1.96
35699898--35699958	25	2.4	25	81	10	72	37	3	0	59	1.14
35702774--35702807	16	2.1	16	100	0	68	47	5	17	29	1.71
35706428--35706473	22	2.1	22	91	0	74	39	6	19	34	1.78
35708634--35708693	18	3.5	17	77	13	61	63	5	25	6	1.39
35708650--35708701	15	3.3	15	76	23	61	55	5	28	9	1.55
35719358--35719400	18	2.3	18	88	4	59	30	13	20	34	1.92
35719980--35720032	19	2.9	19	76	15	58	37	1	1	58	1.20
35738342--35738561	30	7.3	30	78	6	187	22	24	13	39	1.90
35738430--35738500	29	2.4	30	90	2	108	16	28	11	43	1.83
35742443--35742477	12	3.0	12	95	4	63	22	0	0	77	0.78
35742430--35742468	20	2.0	20	100	0	78	23	0	0	76	0.78
35747365--35747412	20	2.4	20	100	0	96	12	37	45	4	1.61
35747933--35747973	4	10.0	4	84	5	55	26	0	0	73	0.84
35752888--35752921	13	2.4	14	90	9	52	20	0	0	79	0.73
35754801--35754908	50	2.2	50	96	0	198	25	22	4	48	1.70
35757032--35757137	53	2.0	53	100	0	212	24	18	28	28	1.98
35763007--35763041	17	1.9	19	88	11	56	8	25	0	65	1.21
35763005--35763054	18	2.7	18	81	12	57	8	24	0	68	1.16
35766586--35766677	37	2.5	37	96	0	166	25	8	31	34	1.86
35776349--35776526	51	3.5	50	73	12	157	26	17	25	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35780224--35780256	17	1.9	17	100	0	66	24	9	36	30	1.86
35789000--35789103	52	2.0	52	100	0	208	25	15	3	55	1.57
35789090--35789209	57	2.1	58	88	1	179	24	22	5	47	1.73
35791533--35791628	19	4.9	19	73	19	65	65	1	5	28	1.20
35791542--35791588	21	2.4	19	85	7	58	68	0	4	27	1.08
35791728--35791778	18	2.7	19	74	17	52	19	5	1	72	1.15
35791929--35791978	20	2.5	21	80	9	68	36	2	0	62	1.07
35791943--35792004	19	3.3	19	73	13	65	30	3	0	66	1.08
35793119--35793149	4	7.8	4	100	0	62	22	0	0	77	0.77
35795959--35796066	56	1.9	56	86	0	153	31	25	15	27	1.96

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