genome.fa.s1.2.7.7.80.10.50.1000.126.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  126  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)
38241156--38241219	30	2.1	30	100	0	128	35	14	6	43	1.70
38241447--38241639	50	3.7	50	80	4	197	23	26	23	26	2.00
38244123--38244164	7	5.9	7	86	5	57	9	4	2	83	0.88
38244117--38244163	22	2.1	22	88	4	67	8	6	2	82	0.90
38246110--38246157	18	2.7	17	77	6	51	22	2	6	68	1.23
38246206--38246233	3	9.3	3	100	0	56	35	32	0	32	1.58
38247533--38247751	45	4.9	45	84	1	269	35	19	21	23	1.96
38247717--38247838	47	2.7	46	80	8	124	43	19	20	16	1.88
38260657--38260809	22	7.0	22	90	0	225	26	26	14	32	1.94
38267261--38267329	34	2.0	34	97	0	129	39	5	13	42	1.68
38283010--38283078	6	12.0	6	83	11	83	66	1	1	30	1.09
38283010--38283080	36	2.0	34	89	5	106	66	1	2	29	1.15
38287263--38287303	20	2.0	21	85	4	57	43	9	14	31	1.78
38291622--38292252	340	1.9	341	85	3	887	34	15	20	30	1.93
38295550--38295591	22	2.0	22	86	13	63	45	2	0	52	1.13
38296273--38296332	25	2.4	25	81	10	61	36	0	6	56	1.26
38297203--38297233	3	10.3	3	92	0	53	64	0	32	3	1.09
38302896--38303020	51	2.4	52	84	6	166	27	14	30	28	1.95
38305503--38305578	30	2.5	30	84	0	98	27	25	9	38	1.86
38305563--38305752	60	3.2	60	77	4	195	18	26	16	38	1.92
38305490--38305752	120	2.2	119	84	3	341	20	26	15	36	1.93
38305563--38305784	30	7.4	30	78	5	157	18	26	16	38	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38310365--38310405	18	2.3	18	95	4	75	9	17	12	60	1.57
38311273--38311301	14	2.0	15	93	6	51	20	6	6	65	1.40
38314158--38314201	20	2.2	20	91	0	70	31	22	9	36	1.86
38316433--38316544	6	18.0	6	71	10	64	69	1	23	5	1.18
38316433--38316544	25	4.2	25	76	19	95	69	1	23	5	1.18
38316452--38316599	45	3.5	42	76	13	108	64	1	24	9	1.31
38321304--38321334	14	2.2	14	94	0	53	25	6	0	67	1.14
38327303--38327336	17	2.0	17	94	0	59	2	11	5	79	1.02
38333170--38333303	30	4.5	30	79	3	126	24	20	12	41	1.87
38339962--38339990	8	3.6	8	100	0	58	75	0	0	24	0.80
38343617--38343851	54	4.4	54	85	2	301	41	20	14	22	1.89
38343617--38343852	81	2.9	80	86	3	312	41	20	14	22	1.89
38343617--38343851	27	8.7	27	85	6	271	41	20	14	22	1.89
38344042--38344091	26	1.9	26	91	0	82	14	26	24	36	1.93
38345982--38346026	22	2.0	22	86	0	63	20	28	17	33	1.95
38351268--38351301	16	2.2	15	89	5	50	44	0	0	55	0.99
38354630--38354716	45	1.9	45	95	0	156	39	10	17	33	1.83
38356819--38356845	12	2.2	12	100	0	54	33	7	18	40	1.78
38358067--38358105	15	2.8	13	82	14	51	43	5	12	38	1.65
38358359--38358500	35	4.1	35	81	1	169	19	23	17	39	1.92
38358364--38358490	35	3.7	34	84	2	173	19	25	18	36	1.95
38361300--38361344	20	2.1	22	84	12	58	13	11	8	66	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38365846--38366115	29	9.3	29	82	3	283	37	13	27	22	1.92
38365831--38366115	87	3.3	87	80	4	326	37	12	27	22	1.91
38366229--38366267	20	2.0	20	100	0	78	38	5	20	35	1.75
38369792--38369838	20	2.3	20	85	7	60	27	29	17	25	1.97
38371358--38371386	14	2.1	14	93	6	51	75	6	3	13	1.13
38371379--38371440	12	4.8	13	78	18	58	77	1	17	3	0.98
38371379--38371436	27	2.2	26	82	11	66	79	1	15	3	0.95
38372483--38372529	15	3.1	15	84	9	60	70	0	17	12	1.17
38372542--38372602	18	3.1	18	75	15	50	63	1	22	11	1.36
38374464--38374510	20	2.3	20	85	7	60	27	29	17	25	1.97
38375862--38376036	30	5.9	30	77	4	124	20	26	13	38	1.90
38375912--38375993	29	2.8	29	90	0	137	14	26	15	42	1.86
38375983--38376054	30	2.4	30	88	0	99	22	27	12	37	1.90
38389956--38389990	18	1.9	18	94	0	61	48	8	14	28	1.73
38404740--38404897	63	2.5	63	87	0	226	23	25	17	33	1.96
38407486--38407601	26	4.4	27	81	5	121	43	23	17	15	1.87
38407480--38407601	53	2.3	53	77	5	140	43	22	17	17	1.88
38407487--38407590	27	3.9	27	86	6	142	46	22	17	14	1.84
38408716--38408756	18	2.3	18	87	8	57	43	9	26	19	1.82
38416000--38416039	18	2.2	18	91	8	64	72	2	20	5	1.15
38417794--38417865	33	2.1	34	87	2	101	38	6	13	40	1.72
38418954--38418978	12	2.1	12	100	0	50	44	16	8	32	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38420978--38421131	27	5.7	27	80	4	150	44	19	14	20	1.86
38420978--38421131	81	1.9	81	81	2	184	44	19	14	20	1.86
38424126--38424378	27	9.4	27	84	5	273	43	18	16	21	1.88
38424583--38424663	26	3.1	26	83	3	110	19	23	24	32	1.98
38424765--38424915	28	5.4	28	82	7	182	23	23	23	30	1.99
38424765--38424909	56	2.6	56	85	0	209	23	23	23	29	1.99
38424765--38424947	56	3.2	56	81	3	150	22	23	23	30	1.99
38431555--38431611	16	3.6	16	71	19	57	29	15	7	47	1.72
38431547--38431607	16	3.8	16	75	12	54	31	16	8	44	1.77
38433050--38433091	20	2.1	20	90	0	66	50	0	2	47	1.14
38441314--38441345	17	1.9	16	93	6	55	28	37	18	15	1.92
38449308--38449394	43	2.0	43	97	0	165	37	24	6	31	1.82
38450491--38450749	138	1.9	138	83	4	335	34	22	21	21	1.97
38451944--38451988	20	2.2	20	84	7	56	51	11	6	31	1.63
38451954--38451998	20	2.3	19	85	7	63	44	13	13	28	1.81
38456411--38456513	19	5.3	19	70	13	75	14	34	17	33	1.90
38456393--38456528	39	3.5	39	83	3	166	14	33	19	32	1.92
38460422--38460478	20	2.8	20	73	5	53	38	21	29	10	1.87
38468084--38468130	14	3.4	14	76	5	51	44	0	23	31	1.54
38468084--38468139	27	2.1	27	96	0	103	42	0	23	33	1.54
38469621--38469672	20	2.6	20	84	0	68	44	13	7	34	1.72
38472649--38472788	54	2.6	53	83	6	156	40	20	20	19	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38472649--38472797	27	5.5	28	75	9	121	40	19	19	20	1.91
38472838--38472920	24	3.5	23	85	4	103	24	8	21	45	1.79
38473065--38473267	32	6.4	32	88	0	291	20	20	20	38	1.94
38473258--38473313	29	1.9	29	81	0	67	19	19	16	44	1.87
38473948--38473980	18	1.9	17	88	11	50	42	12	15	30	1.83
38477814--38477893	27	3.0	27	84	10	87	35	16	18	30	1.93
38477829--38477894	27	2.4	27	87	9	91	31	18	18	31	1.95
38481566--38481616	19	2.6	19	81	3	57	45	13	5	35	1.68
38482890--38482928	16	2.6	15	84	11	53	46	28	5	20	1.72
38487760--38487872	42	2.7	42	87	2	156	22	34	23	20	1.97
38490376--38490422	24	1.9	25	95	4	87	44	23	4	27	1.72
38499227--38499344	61	1.9	61	96	0	218	17	17	27	36	1.93
38507531--38507578	24	2.0	24	100	0	96	33	16	25	25	1.96
38509485--38509622	41	3.2	42	79	17	156	39	19	2	38	1.67
38509485--38509551	21	3.2	21	70	18	68	40	20	2	35	1.68
38509501--38509607	50	2.1	50	96	0	196	39	17	2	40	1.65
38509542--38509566	9	2.8	9	100	0	50	36	12	0	52	1.39
38509560--38509629	22	3.3	22	65	25	60	38	18	2	40	1.66
38511116--38511204	45	2.0	45	88	0	133	32	23	17	25	1.97
38511211--38511402	51	3.8	50	83	4	233	30	27	17	25	1.97
38511213--38511398	101	1.8	102	87	6	279	30	26	17	25	1.97
38513018--38513052	18	2.0	17	88	5	52	31	17	22	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38515223--38515376	50	3.0	50	87	5	191	25	21	29	23	1.99
38515279--38515407	50	2.6	50	84	0	141	26	24	28	20	1.99
38515665--38515703	20	2.0	20	90	10	62	56	5	23	15	1.59
38518949--38518988	18	2.2	18	91	8	64	72	2	20	5	1.15
38520755--38520826	33	2.1	34	89	2	110	38	8	13	38	1.75
38535198--38535249	21	2.8	18	78	18	61	53	7	7	30	1.57
38535209--38535252	21	2.1	21	95	0	79	54	9	6	29	1.58
38535540--38535566	13	2.1	13	100	0	54	55	14	0	29	1.40
38536775--38536841	28	2.4	28	85	2	91	34	22	20	22	1.97
38536940--38536990	26	2.0	24	88	7	75	37	17	21	23	1.94

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