genome.fa.s8.2.7.7.80.10.50.1000.131.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  131  of  190  ( 22705 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)
38853115--38853161	18	2.6	18	79	0	58	27	59	4	8	1.45
38853209--38853370	18	8.7	18	68	17	73	24	59	3	12	1.47
38853325--38853410	12	7.2	12	76	10	50	23	59	3	13	1.50
38856423--38856545	36	3.3	37	87	7	187	60	0	3	35	1.19
38857153--38857217	31	2.1	31	88	0	94	43	13	10	32	1.79
38867154--38867188	12	2.8	12	91	4	52	85	2	2	8	0.79
38868045--38868069	11	2.3	11	100	0	50	92	0	8	0	0.40
38868854--38869000	44	3.4	45	81	5	133	30	23	18	27	1.97
38868888--38869003	44	2.6	44	87	0	160	31	25	19	24	1.98
38869010--38869358	132	2.6	132	91	0	565	25	24	19	30	1.98
38874795--38874844	14	3.4	14	75	24	50	74	8	18	0	1.06
38874799--38874844	15	3.1	15	82	14	51	73	8	17	0	1.07
38881203--38881275	25	2.8	26	72	19	62	65	1	1	31	1.09
38881251--38881300	24	2.1	24	88	7	75	62	4	2	32	1.25
38886088--38886114	2	13.5	2	100	0	54	48	0	0	51	1.00
38889452--38889615	50	3.3	50	91	1	249	27	21	26	24	1.99
38889460--38889598	75	1.9	75	83	8	185	26	20	28	25	1.99
38889452--38889615	25	6.6	25	81	10	167	27	21	26	24	1.99
38890711--38890746	13	2.8	13	91	8	56	38	8	5	47	1.57
38892401--38892444	21	2.2	20	91	4	70	22	0	0	77	0.77
38895380--38895420	21	2.0	21	90	9	66	31	12	2	53	1.51
38909169--38909268	21	4.8	21	75	4	94	39	19	23	19	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38909347--38909394	24	2.0	24	95	0	87	22	25	10	41	1.85
38913139--38913385	50	4.8	50	79	7	232	29	22	26	21	1.99
38915068--38915116	21	2.3	21	75	6	55	16	32	22	28	1.95
38919178--38919229	27	1.9	27	84	7	70	36	17	1	44	1.60
38924488--38924544	21	2.7	21	88	0	87	24	43	15	15	1.86
38933033--38933099	31	2.2	31	89	5	100	64	0	1	34	1.03
38933042--38933081	21	1.9	21	84	0	53	62	0	0	37	0.95
38933133--38933183	22	2.3	21	87	9	75	35	0	33	31	1.58
38933136--38933234	52	1.9	52	93	0	171	38	0	31	30	1.58
38933188--38933234	22	2.1	22	92	0	76	40	0	31	27	1.57
38933436--38933502	29	2.3	29	78	0	71	43	17	16	22	1.88
38933580--38933617	16	2.4	16	86	8	51	36	0	18	44	1.50
38934730--38934797	26	2.7	23	70	18	55	26	1	4	67	1.18
38939203--38939246	14	3.1	14	81	18	56	31	6	20	40	1.79
38939268--38939341	31	2.3	32	86	4	96	28	5	16	50	1.67
38939741--38939808	15	4.4	15	71	18	50	41	0	5	52	1.25
38939826--38939876	13	3.6	14	77	15	52	47	1	0	50	1.12
38945613--38945668	19	3.1	18	72	23	55	39	1	3	55	1.28
38945782--38945834	21	2.5	21	90	0	79	30	37	9	22	1.86
38946705--38946733	6	4.8	6	100	0	58	17	0	0	82	0.66
38947420--38947469	21	2.3	22	82	6	75	38	18	8	36	1.80
38950186--38950246	5	12.2	5	96	0	113	39	22	0	37	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38950492--38950577	24	3.6	24	74	13	70	36	22	25	16	1.94
38952031--38952298	134	2.0	134	100	0	536	38	5	18	36	1.76
38959218--38959266	20	2.2	21	82	13	55	63	2	4	30	1.24
38959227--38959267	20	2.0	22	90	9	68	63	2	0	34	1.08
38960603--38960666	30	2.1	32	88	5	96	43	0	4	51	1.22
38960603--38960677	31	2.4	29	83	14	89	44	0	4	52	1.20
38967769--38967818	23	2.2	23	89	7	75	42	0	8	50	1.32
38968728--38968752	13	1.9	13	100	0	50	32	16	16	36	1.90
38968895--38968957	32	1.9	34	83	6	85	53	4	3	38	1.38
38969020--38969081	30	2.1	29	82	11	72	50	3	0	46	1.17
38969251--38969280	13	2.3	13	94	0	51	36	26	0	36	1.57
38969568--38969878	136	2.3	137	92	1	518	28	10	9	51	1.68
38969876--38969902	13	2.1	13	100	0	54	40	0	0	59	0.98
38971098--38971316	51	4.3	51	94	0	375	29	22	14	33	1.94
38973662--38973894	46	5.0	46	93	2	378	27	25	9	37	1.87
38973662--38973894	93	2.5	92	93	3	396	27	25	9	37	1.87
38981868--38981914	11	4.4	10	82	12	58	21	29	0	48	1.50
38983619--38983723	30	3.5	30	81	5	124	31	44	15	8	1.76
38983785--38983827	18	2.4	18	88	0	59	18	27	9	44	1.80
38987409--38987696	126	2.3	126	91	0	477	25	19	19	34	1.96
38987769--38987812	7	6.3	7	97	0	70	45	31	0	22	1.53
38987804--38988056	95	2.7	90	77	13	233	38	14	3	43	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38988688--38988777	39	2.2	41	90	3	139	53	4	2	40	1.33
38999394--38999916	44	11.8	44	73	4	291	29	22	16	31	1.96
38999394--38999896	89	5.6	88	79	2	432	28	23	16	32	1.96
38999553--38999884	179	1.9	180	85	2	463	28	23	18	30	1.97
38999527--38999916	45	8.7	43	71	6	231	28	24	17	29	1.97
39001196--39001284	45	2.0	45	93	0	151	13	23	15	47	1.81
39001199--39001296	45	2.2	45	84	1	124	14	25	14	45	1.82
39016583--39016901	135	2.3	137	89	6	472	45	15	7	31	1.74
39026680--39026723	4	11.0	4	100	0	88	25	0	25	50	1.50
39027113--39027174	3	20.7	3	79	0	70	59	4	3	32	1.34
39037531--39037556	7	3.7	7	100	0	52	84	0	0	15	0.62
39040658--39040698	19	2.3	18	87	8	57	39	7	0	53	1.29
39045343--39045388	22	2.3	19	82	14	56	30	15	15	39	1.88
39045891--39045937	23	2.0	23	100	0	94	38	4	17	40	1.69
39061951--39061980	3	10.0	3	100	0	60	33	0	0	66	0.92
39068357--39068391	15	2.4	15	90	4	54	48	0	8	42	1.33
39068619--39068644	9	2.9	9	100	0	52	19	0	0	80	0.71
39070305--39070509	105	2.0	105	93	0	347	28	27	22	21	1.99
39074957--39075032	4	18.5	4	76	20	61	22	2	0	75	0.93
39074976--39075025	5	10.0	5	75	16	50	20	4	0	76	0.95
39074956--39075040	30	2.9	29	86	5	127	23	2	0	74	0.94
39075187--39075246	22	2.7	22	82	5	59	26	46	10	16	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39076970--39077000	9	3.4	9	90	0	53	25	12	22	38	1.90
39084707--39084896	25	7.6	25	68	11	77	37	18	23	20	1.94
39093165--39093256	30	2.9	32	76	12	100	44	1	16	38	1.55
39107889--39107954	31	2.2	30	84	13	82	43	0	0	56	0.99
39115292--39115335	14	3.1	15	87	12	58	43	0	9	47	1.35
39115295--39115336	19	2.3	18	84	8	57	45	0	7	47	1.30
39120991--39121050	26	2.3	26	85	5	77	36	20	20	23	1.95
39132101--39132165	22	2.8	24	80	17	68	64	10	1	23	1.33
39133620--39133652	17	2.0	17	94	5	59	36	0	0	63	0.95
39135339--39135370	2	16.0	2	100	0	64	50	0	0	50	1.00
39138424--39138517	3	31.3	3	76	12	77	31	2	2	63	1.18
39140175--39141001	413	2.0	413	99	0	1636	36	15	19	27	1.92
39142201--39142293	3	31.3	3	73	20	63	32	3	3	61	1.28
39142365--39142456	35	2.6	36	80	8	93	31	4	2	61	1.27
39142376--39142472	52	1.9	50	85	12	135	31	3	1	63	1.16
39142411--39142479	17	4.2	16	82	14	70	34	2	1	60	1.20
39142377--39142470	26	3.8	23	75	24	86	31	3	1	63	1.17
39142411--39142470	7	7.7	7	76	20	57	35	3	0	61	1.12
39144742--39144805	7	8.5	8	74	10	55	14	1	32	51	1.51
39144749--39144811	15	4.3	15	76	11	76	15	1	31	50	1.54
39144752--39144811	14	4.1	14	80	6	66	16	1	30	51	1.54
39145235--39145858	226	2.8	221	90	6	955	34	3	20	42	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39149855--39149952	49	2.0	51	86	8	139	46	3	24	25	1.67
39149914--39149963	11	4.5	11	85	7	66	46	4	28	22	1.70
39150581--39150704	55	2.3	54	80	8	135	62	2	3	32	1.24
39150617--39150708	27	3.3	28	76	17	84	63	3	2	31	1.23
39150608--39150703	19	5.2	19	71	12	65	61	3	3	32	1.27
39150871--39151011	19	7.2	20	71	16	68	28	7	2	61	1.36
39150912--39150989	10	8.3	10	75	9	67	28	3	1	66	1.17
39150866--39151009	56	2.5	57	83	10	179	29	6	2	61	1.34
39150938--39151030	19	4.8	19	77	11	84	29	5	3	62	1.33
39150912--39151009	9	10.4	10	71	19	68	28	4	2	65	1.22

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