genome.fa.s7.2.7.7.80.10.50.1000.13.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  13  of  204  ( 24458 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)
5090164--5090203	20	2.0	20	85	5	53	20	7	7	65	1.43
5090233--5090286	12	4.2	13	81	13	51	31	1	0	66	1.02
5090313--5090375	31	2.1	31	82	5	76	42	6	1	49	1.37
5090547--5090668	51	2.4	52	81	6	135	31	5	5	56	1.46
5094798--5094823	2	13.0	2	100	0	52	50	0	0	50	1.00
5096234--5096290	30	1.9	30	100	0	114	33	10	10	45	1.73
5097845--5097877	16	2.1	16	100	0	66	30	18	6	45	1.73
5108196--5108259	26	2.5	25	82	7	74	50	1	3	45	1.27
5108597--5108706	31	3.5	33	75	8	95	50	3	0	45	1.25
5108658--5108705	16	3.1	14	82	14	51	60	2	2	35	1.20
5109543--5109591	23	2.2	21	82	17	55	26	0	8	65	1.20
5111525--5111556	12	2.6	13	85	14	50	37	0	6	56	1.25
5113216--5113457	123	2.0	120	88	2	358	31	9	22	36	1.87
5113747--5113789	13	3.3	13	80	0	50	30	9	25	34	1.87
5114431--5114549	51	2.3	51	92	0	193	28	23	14	33	1.94
5116257--5116291	2	17.5	2	100	0	70	51	0	0	48	1.00
5138544--5138785	81	3.0	81	94	0	412	37	5	23	32	1.79
5144501--5144563	29	2.1	31	94	5	112	26	26	6	39	1.80
5147178--5147203	8	3.2	8	100	0	52	38	0	0	61	0.96
5148152--5148310	25	6.6	25	83	8	190	21	25	16	36	1.94
5151429--5151488	30	2.0	31	86	3	86	28	18	5	48	1.69
5154645--5154671	1	27.0	1	100	0	54	100	0	0	0	0.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5164136--5164163	14	2.0	14	100	0	56	78	7	7	7	1.09
5172287--5172325	19	2.0	20	90	5	62	58	2	0	38	1.12
5172890--5172924	17	1.9	19	88	11	56	14	5	20	60	1.54
5184830--5184862	15	2.4	14	90	10	50	57	6	0	36	1.23
5184959--5184999	21	2.0	22	90	9	68	51	7	7	34	1.58
5186645--5186718	21	3.6	21	72	7	62	40	20	24	14	1.90
5186641--5186762	41	2.9	41	82	9	149	43	19	21	15	1.88
5186692--5186757	21	3.1	21	68	12	55	45	19	19	15	1.85
5190364--5190411	25	2.0	24	91	4	78	43	14	4	37	1.65
5194352--5194397	23	2.0	23	95	0	83	21	15	10	52	1.73
5199192--5199216	6	4.2	6	100	0	50	84	0	0	16	0.63
5220034--5220076	23	1.9	23	90	4	70	41	13	4	39	1.66
5225166--5225210	23	2.0	23	86	4	65	46	15	4	33	1.66
5225163--5225218	22	2.5	22	83	8	69	44	16	3	35	1.65
5225176--5225218	23	1.9	23	90	4	70	41	13	4	39	1.66
5234736--5234794	26	2.3	26	100	0	118	45	20	25	8	1.79
5237995--5238124	27	4.8	27	93	1	208	18	22	37	21	1.94
5238186--5238232	18	2.5	20	79	10	62	63	2	34	0	1.06
5238182--5238235	22	2.4	23	84	12	76	64	1	33	0	1.04
5241549--5241605	6	9.5	6	100	0	114	0	33	31	35	1.58
5243229--5243270	16	2.7	15	85	7	57	57	2	2	38	1.25
5243307--5243389	38	2.2	39	95	2	150	38	2	3	55	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5243803--5244039	22	11.0	22	71	18	162	55	13	0	30	1.41
5243800--5244039	41	5.6	42	71	20	144	55	13	0	30	1.42
5243790--5243906	49	2.4	49	88	0	180	53	13	0	31	1.46
5243790--5243906	22	4.7	25	77	20	111	53	13	0	31	1.46
5244467--5244518	28	2.0	25	82	14	61	46	1	0	51	1.12
5245489--5245545	15	3.7	15	76	6	51	38	8	3	49	1.51
5247382--5247433	21	2.5	20	76	17	52	34	0	5	59	1.21
5247831--5247883	19	2.7	21	75	22	60	64	0	1	33	1.05
5247836--5247882	17	2.5	19	83	10	53	68	0	2	29	1.02
5247929--5247968	16	2.6	15	82	17	55	67	0	0	32	0.91
5247923--5247977	17	3.2	17	77	12	58	65	0	0	34	0.93
5248468--5248539	22	3.4	21	75	21	71	31	0	2	65	1.07
5248450--5248496	16	2.9	16	81	12	60	36	0	0	63	0.94
5248461--5248496	17	2.2	17	90	5	56	33	0	0	66	0.92
5248464--5248530	21	3.3	19	73	20	64	35	0	1	62	1.04
5259469--5259551	27	3.1	27	75	3	78	22	32	24	20	1.98
5277675--5277723	22	2.4	21	80	10	57	36	0	0	63	0.95
5277920--5277976	15	3.5	15	73	17	60	49	5	0	45	1.24
5283111--5283224	49	2.3	50	94	4	198	29	7	13	49	1.70
5285751--5286407	331	2.0	331	94	0	1163	27	22	14	35	1.94
5289521--5289572	3	17.3	3	95	0	95	32	30	0	36	1.58
5298727--5298782	20	2.8	20	77	2	58	48	0	1	50	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5298750--5298788	11	3.4	11	80	13	51	51	0	2	46	1.14
5298727--5298778	21	2.5	20	76	11	52	48	0	1	50	1.12
5298768--5298808	14	2.6	16	88	11	59	48	0	0	51	1.00
5299073--5299132	16	3.5	17	74	12	52	75	10	13	1	1.13
5299144--5299174	13	2.3	14	94	5	55	80	0	19	0	0.71
5299139--5299180	17	2.5	17	76	0	57	69	0	30	0	0.89
5299808--5299893	3	28.7	3	95	0	154	33	1	1	63	1.09
5304832--5304913	31	2.7	31	83	3	87	52	15	1	30	1.51
5304880--5304922	22	1.9	23	85	4	61	48	4	4	41	1.44
5316057--5316314	132	2.0	132	85	3	349	29	17	21	31	1.96
5316189--5316524	150	2.2	150	83	3	399	28	18	19	33	1.96
5317117--5317149	2	16.5	2	100	0	66	51	0	0	48	1.00
5321046--5321097	25	2.2	24	89	6	79	55	0	7	36	1.29
5326373--5326433	18	3.4	18	68	14	54	54	3	0	42	1.17
5328359--5328556	98	2.0	98	99	1	387	31	13	20	34	1.91
5336878--5336942	33	2.0	33	82	11	80	43	1	4	50	1.32
5345221--5345255	2	17.5	2	100	0	70	51	0	0	48	1.00
5347490--5347530	13	3.0	14	82	7	57	31	0	2	65	1.05
5347490--5347535	13	3.5	13	84	3	56	36	0	2	60	1.09
5353371--5353395	6	4.2	6	100	0	50	16	0	0	84	0.63
5357201--5357270	35	2.0	35	97	0	131	27	22	15	34	1.95
5357571--5357845	136	2.0	136	97	0	523	26	22	16	34	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5363611--5363660	25	2.0	25	92	0	82	4	36	4	56	1.37
5365900--5365932	12	2.8	12	90	4	50	42	33	18	6	1.75
5366579--5366631	21	2.5	21	84	0	70	30	33	9	26	1.88
5371494--5371687	96	2.0	96	87	0	280	23	15	36	24	1.94
5375669--5375705	17	2.2	16	90	4	56	13	8	5	72	1.24
5376158--5376227	32	2.2	33	84	7	90	22	5	0	71	1.07
5378162--5378215	25	2.1	25	82	3	63	44	9	3	42	1.54
5381141--5381258	58	2.0	58	100	0	236	32	15	13	38	1.86
5381836--5381869	17	2.0	17	94	0	59	44	0	2	52	1.16
5383497--5383541	19	2.5	19	85	7	58	57	6	2	33	1.37
5384791--5384840	11	4.5	11	82	9	57	12	10	16	62	1.55
5384802--5384852	22	2.3	22	83	6	59	9	11	17	60	1.57
5386031--5386128	28	3.5	28	94	5	164	38	13	0	47	1.42
5386703--5386763	19	3.3	18	76	4	59	42	8	0	49	1.32
5386711--5386763	18	2.9	18	75	11	54	41	9	0	49	1.35
5387254--5387310	27	2.2	26	90	3	87	15	24	31	28	1.96
5387349--5387422	29	2.5	30	95	4	134	48	0	12	39	1.41
5387655--5387718	31	2.1	29	85	5	83	35	15	7	40	1.76
5398695--5398771	29	2.6	28	79	8	82	24	11	15	48	1.79
5400420--5400456	3	12.3	3	100	0	74	67	0	0	32	0.91
5409782--5409811	14	2.1	14	100	0	60	36	30	13	20	1.90
5413375--5413407	2	16.5	2	100	0	66	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5415773--5415817	20	2.3	19	88	7	63	40	13	4	42	1.64
5415895--5415959	20	3.2	20	83	10	80	50	6	9	33	1.59
5416296--5416329	17	2.0	17	88	0	50	47	0	0	52	1.00
5416619--5416651	5	6.4	5	93	6	57	57	0	0	42	0.98
5442205--5442501	126	2.4	126	91	0	488	32	19	20	26	1.97
5443931--5443975	23	2.0	24	91	8	76	48	4	4	42	1.43
5443977--5444057	11	7.4	11	80	9	94	40	0	34	24	1.56
5445975--5446030	20	2.9	19	73	23	55	46	3	0	50	1.19
5449996--5450152	41	3.8	42	88	3	223	33	28	19	19	1.96
5450082--5450151	16	3.8	16	71	28	59	32	25	22	18	1.97

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