genome.fa.s2.2.7.7.80.10.50.1000.146.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: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62769430

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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   

This is table  146  of  206  ( 24623 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)
44594687--44594758	25	2.9	25	82	0	72	19	25	22	33	1.97
44596980--44597023	21	2.1	21	95	0	79	47	25	13	13	1.79
44598251--44598276	6	4.3	6	100	0	52	50	0	34	15	1.45
44600025--44600086	25	2.5	25	86	0	79	22	24	24	29	1.99
44601798--44601867	34	2.1	34	100	0	140	37	5	17	40	1.73
44602015--44602063	3	16.3	3	100	0	98	67	0	0	32	0.91
44604620--44604800	91	2.0	92	86	5	260	37	22	7	33	1.83
44604836--44604916	37	2.2	37	82	12	96	65	0	1	33	1.01
44604858--44604918	19	3.3	19	68	11	54	67	0	0	32	0.91
44604905--44604969	17	3.6	17	76	15	69	66	3	4	26	1.26
44605358--44605542	92	2.0	91	84	2	237	33	7	22	36	1.83
44605629--44605653	13	1.9	13	100	0	50	64	0	0	36	0.94
44608223--44608313	44	2.1	44	87	0	128	27	10	13	48	1.75
44610187--44610380	94	2.1	94	97	0	361	33	12	12	41	1.81
44614144--44614173	6	5.0	6	100	0	60	66	0	33	0	0.92
44617081--44617153	27	2.7	27	87	4	103	17	21	38	21	1.93
44620563--44620624	6	10.3	6	96	0	106	0	37	32	30	1.58
44622058--44622091	3	11.7	3	87	6	52	0	35	2	61	1.11
44622512--44622556	24	1.9	24	82	13	58	44	0	2	53	1.13
44623719--44623909	45	4.4	45	84	7	259	41	20	17	19	1.90
44623728--44623939	45	5.2	39	82	11	203	39	21	19	19	1.92
44623728--44623939	84	2.5	83	87	3	282	39	21	19	19	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44623773--44623939	39	4.2	39	84	11	167	38	22	20	18	1.93
44624922--44624947	11	2.4	11	100	0	52	0	42	7	50	1.31
44626507--44626610	16	6.2	17	75	18	85	63	1	2	31	1.20
44626514--44626609	24	3.8	23	75	22	86	63	1	3	32	1.17
44626507--44626612	8	12.4	9	70	22	70	63	1	2	32	1.20
44626516--44626575	7	7.7	7	76	20	57	61	0	3	35	1.12
44626530--44626611	26	3.1	27	69	27	70	63	1	3	31	1.19
44626686--44626732	3	15.7	3	95	0	85	63	0	2	34	1.06
44627296--44627336	17	2.5	16	81	18	57	80	2	12	4	0.97
44630558--44630606	22	2.3	20	75	6	53	40	8	22	28	1.82
44632023--44632063	13	3.2	13	75	25	50	70	7	7	14	1.31
44635375--44635405	15	2.0	16	93	6	55	35	6	12	45	1.68
44636157--44636198	15	2.8	16	75	14	52	11	30	33	23	1.91
44636155--44636198	17	2.8	17	74	22	51	11	31	31	25	1.91
44639371--44639488	59	2.0	59	98	0	227	38	10	12	38	1.77
44643907--44643931	2	12.5	2	100	0	50	48	0	0	52	1.00
44644400--44644451	15	3.3	15	81	5	59	63	3	0	32	1.12
44644395--44644468	31	2.5	27	76	20	67	68	4	0	27	1.07
44654545--44654603	12	4.8	12	89	4	82	74	8	0	16	1.05
44654545--44654609	18	3.6	18	85	4	85	73	9	0	16	1.07
44654545--44654617	6	12.0	6	91	2	74	73	9	0	16	1.07
44656030--44656069	3	13.3	3	100	0	80	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44656162--44656253	33	2.8	33	78	9	89	69	4	2	23	1.17
44657589--44657637	25	2.0	25	83	0	62	32	6	6	55	1.49
44657685--44657752	25	2.6	27	69	9	68	38	4	2	54	1.36
44662774--44662857	36	2.4	36	78	9	93	70	7	8	14	1.33
44664893--44665219	87	3.8	87	91	2	532	28	22	24	24	1.99
44665516--44665678	44	3.7	44	76	6	143	28	21	23	25	1.99
44665602--44665723	44	2.8	44	81	2	129	30	18	20	31	1.96
44666936--44667105	90	1.9	90	82	4	218	36	15	21	26	1.93
44667271--44667637	114	3.2	114	70	13	295	29	17	24	27	1.98
44667339--44667714	115	3.3	115	73	9	397	27	17	24	30	1.97
44667310--44667656	114	3.0	114	71	10	346	28	18	25	26	1.98
44667265--44667778	229	2.2	228	88	3	789	30	18	22	28	1.97
44667417--44667921	115	4.4	113	72	9	396	30	19	21	29	1.97
44668239--44668287	14	3.4	15	83	8	57	18	0	38	42	1.50
44668239--44668278	15	2.7	15	92	3	64	17	0	37	45	1.49
44669458--44669551	44	2.1	44	84	3	118	22	34	8	35	1.84
44671284--44671366	35	2.4	34	90	4	139	34	4	3	56	1.38
44671492--44671529	19	2.0	19	94	0	67	44	0	0	55	0.99
44671534--44671734	24	9.3	22	65	23	65	48	18	1	31	1.59
44671561--44671597	19	2.1	18	85	14	51	48	13	2	35	1.57
44671651--44671735	24	4.0	21	75	14	68	52	18	1	27	1.52
44671658--44671726	24	3.0	24	87	8	92	53	17	1	27	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44671741--44671884	34	4.5	33	66	17	86	52	18	2	26	1.56
44671682--44671996	95	3.3	95	86	4	402	52	16	3	27	1.59
44671665--44671909	12	20.8	12	65	17	86	53	17	1	27	1.54
44671970--44671996	12	2.2	12	100	0	54	51	14	0	33	1.43
44671981--44672047	19	3.7	19	79	18	88	50	17	1	29	1.55
44671981--44672090	9	12.4	9	72	18	72	47	20	2	30	1.64
44672012--44672048	16	2.3	16	95	0	65	51	16	5	27	1.66
44672016--44672081	25	2.6	25	80	0	78	45	21	4	28	1.71
44677623--44677712	21	4.3	21	85	0	108	36	18	41	3	1.68
44677697--44677736	12	3.3	12	85	0	53	40	12	40	7	1.71
44678168--44678501	42	7.9	41	80	6	296	23	20	20	34	1.97
44678170--44678501	43	7.8	42	80	6	323	23	21	21	34	1.97
44678170--44678494	128	2.6	127	82	3	377	24	21	20	33	1.97
44678170--44678509	85	4.0	84	85	6	413	23	20	20	35	1.96
44679813--44679853	20	2.0	21	85	4	57	24	0	63	12	1.28
44680426--44680543	60	2.0	60	89	0	182	38	19	11	30	1.86
44683490--44683527	19	2.0	20	89	5	60	76	0	2	21	0.91
44683479--44683528	19	2.7	18	81	9	55	72	2	2	24	1.06
44684302--44684348	19	2.8	17	78	15	53	42	4	2	51	1.33
44684386--44684422	16	2.3	16	86	13	58	40	0	0	59	0.97
44684417--44684489	31	2.2	33	83	16	89	53	0	1	45	1.09
44684434--44684484	20	2.5	20	83	0	57	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44689078--44689113	2	18.0	2	100	0	72	50	0	0	50	1.00
44689447--44689582	42	3.3	41	78	3	128	28	27	18	25	1.98
44690644--44690833	43	4.4	43	87	2	258	31	25	19	23	1.98
44691205--44691264	30	2.0	30	96	0	111	35	25	6	33	1.82
44695450--44695522	7	10.6	7	84	12	80	27	45	0	27	1.54
44695459--44695500	13	3.2	13	93	6	75	28	40	0	30	1.57
44695697--44695740	7	6.4	7	84	5	54	36	45	2	15	1.59
44695699--44695737	13	2.9	13	88	3	51	38	46	2	12	1.56
44695642--44695828	88	2.1	90	82	6	231	41	28	2	26	1.69
44695884--44695916	14	2.3	15	94	5	59	36	33	0	30	1.58
44696274--44696468	41	4.8	41	85	2	275	28	27	20	24	1.99
44697737--44697762	3	8.7	3	100	0	52	34	0	30	34	1.58
44703339--44703394	21	2.7	21	83	5	60	32	46	0	21	1.52
44703347--44703426	7	11.4	7	82	0	70	37	45	0	17	1.49
44703477--44703516	7	5.9	7	88	2	55	30	47	2	20	1.63
44703616--44703648	14	2.3	15	94	5	59	36	33	0	30	1.58
44704043--44704153	41	2.7	41	90	2	170	30	29	18	20	1.97
44704486--44704511	2	13.0	2	100	0	52	50	0	0	50	1.00
44712677--44712703	14	1.9	14	100	0	54	74	0	3	22	0.98
44713472--44713541	19	3.7	19	74	18	74	60	5	0	34	1.21
44713523--44713567	16	2.6	18	75	10	58	55	4	0	40	1.20
44713603--44713627	10	2.5	10	100	0	50	56	8	0	36	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44714864--44714988	51	2.4	53	81	6	157	28	32	12	26	1.93
44715210--44715240	2	15.5	2	93	0	53	48	0	0	51	1.00
44723356--44723398	10	4.2	10	85	5	59	65	0	2	32	1.06
44723355--44723395	21	2.0	21	95	0	73	70	0	2	26	0.99
44723719--44723762	15	2.8	15	78	21	54	27	0	4	68	1.09
44723726--44723761	15	2.5	15	90	4	56	30	0	2	66	1.06
44724513--44724593	6	14.0	6	76	13	64	17	1	6	75	1.07
44724509--44724589	5	14.6	5	75	20	56	17	1	6	75	1.07
44724652--44724689	12	3.3	12	78	14	53	18	13	0	68	1.21
44731079--44731227	41	3.6	41	83	7	203	35	26	17	20	1.95

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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206