genome.fa.s4.2.7.7.80.10.50.1000.175.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  175  of  198  ( 23681 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)
54831418--54831459	22	1.9	22	90	0	66	33	0	33	33	1.58
54831461--54831530	22	3.2	22	83	4	88	41	0	28	30	1.56
54831739--54831891	22	7.0	22	90	0	225	32	14	26	26	1.94
54834701--54834943	128	1.9	130	90	2	391	46	14	16	21	1.83
54835443--54835494	19	2.7	20	82	11	63	48	5	0	46	1.26
54835441--54835483	22	1.9	22	85	4	59	53	4	0	41	1.21
54838706--54838764	31	1.9	30	82	3	73	35	16	11	35	1.86
54841791--54841877	3	29.3	3	95	2	158	31	0	0	68	0.89
54842572--54842610	19	2.1	19	85	4	53	35	7	0	56	1.28
54842914--54842984	37	1.9	37	94	0	124	50	0	8	40	1.33
54842914--54842988	18	4.1	19	84	6	102	53	0	8	38	1.31
54843062--54843139	27	2.9	26	83	7	95	19	29	23	28	1.98
54843205--54843302	28	3.5	28	91	2	153	47	2	11	38	1.51
54852613--54852639	12	2.2	12	100	0	54	66	0	0	33	0.92
54852610--54852673	22	3.2	20	72	12	60	59	0	1	39	1.07
54852609--54852690	29	2.8	29	75	12	78	62	0	2	35	1.09
54854654--54854703	18	2.8	17	77	22	57	18	0	6	76	0.99
54855644--54855678	14	2.5	14	90	0	52	31	20	8	40	1.82
54856304--54856339	12	3.0	12	87	0	54	25	27	36	11	1.90
54860163--54860237	27	2.8	27	80	8	98	25	33	24	17	1.96
54860315--54860342	9	3.1	9	100	0	56	46	0	0	53	1.00
54860792--54860841	20	2.5	20	80	3	57	42	30	6	22	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54862379--54862425	23	2.0	23	87	0	67	46	14	10	27	1.78
54863038--54863087	24	2.0	25	84	3	66	6	20	54	20	1.65
54867035--54867094	24	2.4	25	86	8	79	13	30	23	33	1.93
54867149--54867283	25	5.5	25	77	13	102	17	28	22	31	1.96
54867166--54867259	24	3.8	24	83	8	91	15	29	23	30	1.96
54867149--54867283	49	2.7	49	81	6	148	17	28	22	31	1.96
54868749--54868790	20	2.1	20	82	8	50	64	2	9	23	1.35
54869096--54869127	3	10.7	3	100	0	64	65	0	0	34	0.93
54878663--54878727	31	2.1	30	88	2	94	56	7	4	30	1.48
54879187--54879211	12	2.1	12	100	0	50	64	0	0	36	0.94
54887134--54887222	12	7.4	11	72	15	52	11	12	4	71	1.27
54887128--54887202	39	1.9	39	86	5	107	9	16	2	72	1.22
54887529--54887555	14	1.9	14	100	0	54	70	0	7	22	1.12
54889798--54889840	20	2.1	21	83	12	54	2	20	4	72	1.14
54892560--54892868	46	6.8	46	81	8	283	18	19	15	46	1.84
54892612--54892865	90	2.8	90	80	5	251	17	19	17	45	1.85
54892603--54892867	45	5.8	45	83	4	192	17	19	17	45	1.86
54903388--54903418	16	2.0	16	93	6	55	35	6	12	45	1.68
54903435--54903466	15	2.1	16	88	11	50	12	0	18	68	1.20
54906847--54906885	19	2.1	19	100	0	78	17	41	20	20	1.91
54908125--54908268	73	2.0	74	93	4	247	28	17	17	36	1.92
54909780--54909826	19	2.5	19	86	6	60	27	19	8	44	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54912718--54912795	40	2.0	39	87	2	111	41	17	25	15	1.89
54913955--54914141	88	2.1	88	86	2	250	29	19	21	29	1.97
54914085--54914347	132	2.0	132	81	3	314	31	21	23	24	1.98
54914308--54914413	51	2.1	52	81	1	124	33	15	21	30	1.94
54914616--54915172	44	12.8	43	72	7	187	32	19	19	28	1.96
54914610--54914820	88	2.4	89	81	0	226	34	19	17	27	1.95
54914926--54915748	44	18.7	44	71	10	411	30	20	21	26	1.98
54915056--54915386	183	1.8	179	82	3	421	30	21	20	28	1.98
54915244--54915665	222	1.9	223	82	4	530	31	19	23	25	1.98
54920438--54920582	74	2.0	73	94	4	256	27	18	18	35	1.95
54925597--54925649	22	2.3	23	83	3	63	50	1	3	43	1.30
54925787--54925814	9	3.1	9	100	0	56	32	0	10	57	1.33
54925638--54925844	65	3.1	65	95	2	360	40	4	9	45	1.57
54925909--54925952	21	2.0	23	86	8	65	59	2	0	38	1.10
54927667--54927779	57	2.0	58	89	3	176	49	2	4	43	1.36
54928896--54928933	16	2.5	16	87	8	53	68	2	0	28	1.03
54931568--54931605	15	2.5	15	87	12	51	50	2	2	44	1.30
54931613--54931641	14	2.0	15	93	6	51	37	0	0	62	0.96
54931803--54931879	30	2.5	30	85	10	95	40	0	7	51	1.31
54947095--54947154	2	30.0	2	100	0	120	50	0	0	50	1.00
54947278--54947317	2	20.0	2	100	0	80	50	0	0	50	1.00
54952126--54952153	9	3.1	9	100	0	56	57	10	0	32	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54952096--54952233	68	2.1	66	94	2	240	44	8	5	41	1.57
54952226--54952267	16	2.6	16	92	0	66	42	4	2	50	1.36
54952241--54952301	22	2.7	22	87	2	77	47	1	1	49	1.21
54954380--54954408	15	1.9	15	100	0	58	41	0	17	41	1.49
54957989--54958038	3	16.7	3	100	0	100	66	0	0	34	0.92
54960998--54962158	397	2.9	393	88	3	1738	27	24	18	28	1.98
54960998--54962158	132	8.8	132	92	1	1701	27	24	18	28	1.98
54963749--54963789	7	5.9	7	86	11	57	12	17	0	70	1.16
54963747--54963789	21	2.1	20	91	4	68	13	18	0	67	1.23
54963753--54963801	21	2.3	22	75	10	57	14	20	0	65	1.27
54964733--54964771	19	2.1	19	90	0	60	66	7	12	12	1.43
54965927--54965960	17	2.0	17	88	0	50	50	11	20	17	1.77
54966178--54966219	21	2.0	21	95	0	75	30	9	11	47	1.72
54966539--54966584	2	22.5	2	95	4	83	50	0	2	47	1.13
54966858--54966960	41	2.5	41	85	0	125	26	20	27	26	1.99
54973355--54973388	17	2.0	17	88	0	50	50	11	20	17	1.77
54973606--54973647	21	2.0	21	90	0	66	30	11	11	45	1.77
54974259--54974361	41	2.5	41	85	0	125	26	20	27	26	1.99
54978742--54978784	14	3.1	14	77	12	52	72	2	9	16	1.21
54981080--54981121	15	2.8	15	78	10	50	52	0	2	45	1.13
54989078--54989105	3	9.3	3	100	0	56	67	0	0	32	0.91
54989929--54989975	18	2.7	17	83	6	58	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54989929--54989983	24	2.3	24	81	9	67	47	0	0	52	1.00
54995162--54995233	22	3.3	22	94	0	117	25	27	16	30	1.97
55001590--55001634	23	2.0	23	91	8	74	33	4	17	44	1.69
55001949--55001973	13	1.9	13	100	0	50	60	24	0	16	1.36
55006173--55006254	26	3.2	26	75	8	87	53	1	0	45	1.08
55006187--55006261	26	2.9	26	78	7	98	54	0	0	45	0.99
55020740--55020799	28	2.1	28	96	0	111	53	5	28	13	1.60
55024495--55024533	19	2.1	19	100	0	78	38	5	0	56	1.22
55025538--55025602	33	1.9	33	82	14	80	41	13	4	40	1.66
55028619--55028652	18	1.9	18	88	5	52	35	0	2	61	1.11
55028645--55028678	12	2.9	12	95	4	61	64	0	0	35	0.94
55035051--55035080	14	2.1	14	93	0	51	40	0	0	60	0.97
55040097--55040123	2	13.5	2	100	0	54	51	0	48	0	1.00
55043376--55043428	2	26.5	2	100	0	106	49	0	0	50	1.00
55048137--55048201	27	2.4	27	86	2	94	38	4	0	56	1.20
55050680--55050758	31	2.6	31	81	2	97	46	11	12	29	1.77
55054118--55054160	18	2.5	17	78	17	52	30	2	6	60	1.35
55055495--55055546	26	2.0	26	88	7	79	42	5	0	51	1.25
55056932--55056990	30	2.0	30	90	3	93	45	3	10	40	1.54
55060438--55060497	3	20.0	3	100	0	120	66	0	0	33	0.92
55083290--55083335	23	2.0	23	91	0	74	39	10	6	43	1.66
55083402--55083525	40	3.1	40	79	4	126	37	18	20	24	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55083463--55083538	39	1.9	39	84	5	100	36	14	21	27	1.92
55083572--55083649	41	1.9	41	89	5	122	19	21	29	29	1.98
55084155--55084264	17	5.8	20	77	17	85	21	1	43	32	1.63
55084174--55084263	17	5.0	17	79	11	90	22	2	45	30	1.64
55084155--55084246	39	2.4	38	85	1	121	22	2	42	32	1.66
55084940--55085050	7	14.9	7	69	11	60	18	1	45	35	1.60
55084939--55085010	21	3.6	21	76	14	89	18	2	43	36	1.64
55084960--55085029	17	3.9	17	71	20	61	20	1	44	34	1.60
55084939--55085032	38	2.5	38	87	6	145	19	2	42	36	1.63
55085403--55085443	18	2.3	18	82	0	55	75	2	2	19	1.03

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