genome.fa.s11.2.7.7.80.10.50.1000.1.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   207   208   
          209   210   

This is table  1  of  210  ( 25152 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)
1--304	7	43.3	7	90	4	407	44	40	2	12	1.56
304--378	32	2.3	32	90	0	114	38	18	25	17	1.92
544--611	32	2.1	32	83	0	82	36	22	23	17	1.94
311--769	235	2.0	233	92	0	756	35	21	22	19	1.96
2034--2069	17	2.1	17	94	0	63	52	11	5	30	1.59
2988--3035	19	2.5	20	90	6	73	72	8	10	8	1.27
16973--17043	21	3.4	21	100	0	142	40	32	16	9	1.82
18019--18104	45	1.9	44	88	6	129	32	27	5	33	1.81
30427--30457	7	4.4	7	95	0	53	29	45	9	16	1.79
34112--34201	47	1.9	47	88	4	137	34	26	5	33	1.80
35606--35630	11	2.3	11	100	0	50	52	24	16	8	1.70
39351--39584	36	5.6	45	74	22	217	36	14	20	28	1.92
39351--39584	82	2.9	82	91	5	379	36	14	20	28	1.92
42926--42966	4	10.2	4	100	0	82	24	0	26	48	1.51
45866--45910	23	1.9	24	86	4	65	44	2	2	51	1.26
54504--55034	268	2.0	261	96	2	972	29	20	23	26	1.99
70826--70874	6	8.3	6	81	4	64	18	65	0	16	1.28
73894--73924	2	15.5	2	100	0	62	48	0	0	51	1.00
91023--91061	18	2.2	19	90	9	64	0	12	2	84	0.72
94402--94458	26	2.2	26	77	0	60	24	8	26	40	1.84
99197--99253	26	2.2	26	77	0	60	24	8	26	40	1.84
102203--102259	23	2.5	22	88	8	80	22	22	14	40	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
102216--102260	23	2.0	23	100	0	90	22	17	17	42	1.89
103897--103922	5	5.2	5	100	0	52	80	0	0	19	0.71
105077--105262	93	2.0	93	97	0	354	47	19	9	24	1.78
108678--108707	10	2.8	11	95	5	53	13	6	0	80	0.91
121320--121373	2	27.5	2	96	3	101	51	0	0	48	1.00
124161--124204	22	2.0	22	100	0	88	50	0	13	36	1.42
125491--125543	27	2.0	27	96	0	97	66	5	0	28	1.15
136326--136355	4	7.8	4	92	7	53	0	23	0	76	0.78
139126--139189	33	1.9	33	96	0	119	26	15	14	43	1.85
142250--142278	13	2.2	13	100	0	58	44	13	0	41	1.44
143469--143498	14	2.2	14	94	5	53	13	16	0	70	1.18
157149--157173	5	5.0	5	100	0	50	0	20	0	80	0.72
175348--175397	24	2.2	24	79	10	61	36	4	0	60	1.16
175723--175773	3	17.0	3	87	0	66	25	33	1	39	1.67
187840--187873	7	5.0	7	96	3	61	41	0	14	44	1.45
194015--194079	22	3.0	22	93	0	103	33	15	26	24	1.95
202021--202055	15	2.3	15	90	0	52	20	25	17	37	1.94
210101--210133	12	2.8	12	100	0	66	66	9	24	0	1.20
211042--211096	8	6.9	8	80	15	60	21	1	9	67	1.28
211050--211094	23	2.0	23	82	8	56	22	2	6	68	1.24
211286--211358	29	2.5	28	77	16	69	54	10	2	31	1.49
212083--212143	15	4.0	15	73	10	52	47	1	3	47	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
213439--213480	22	1.9	22	85	0	57	54	7	4	33	1.49
234456--234516	31	2.0	31	93	0	104	36	19	9	34	1.85
234866--235103	123	1.9	122	91	4	390	32	16	23	27	1.96
237634--237666	17	2.0	16	94	5	57	39	0	18	42	1.50
237665--238087	29	14.9	29	88	4	587	32	1	22	43	1.61
238367--238422	24	2.3	24	90	0	85	23	17	32	26	1.97
238722--238772	22	2.3	21	83	9	66	33	0	33	33	1.58
242017--242051	4	8.8	4	87	12	54	51	22	2	22	1.61
246623--246674	26	2.0	26	100	0	104	30	34	11	23	1.90
252474--252549	35	2.1	35	85	4	98	13	17	18	51	1.76
256248--256296	25	1.9	26	83	4	64	32	8	20	38	1.82
258596--258879	72	4.0	70	86	5	383	49	11	1	37	1.50
258920--258973	27	2.0	27	100	0	108	25	11	11	51	1.70
259585--259635	23	2.3	22	82	3	57	17	3	9	68	1.33
264850--264914	31	2.1	31	94	0	112	44	12	9	33	1.74
267634--267937	112	2.8	113	80	6	322	49	16	9	24	1.75
271545--271631	25	3.5	25	98	0	165	42	5	18	33	1.74
272473--272515	21	2.0	22	86	4	61	48	4	0	46	1.22
287272--287351	21	4.0	21	76	12	78	36	7	13	42	1.73
300955--300985	4	7.8	4	92	0	53	22	0	3	74	0.96
304883--304917	18	1.9	18	88	11	54	60	0	5	34	1.21
316721--316771	15	3.4	15	75	20	61	15	41	25	17	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
316715--316785	30	2.4	30	100	0	142	18	33	29	18	1.95
316715--316785	15	4.8	14	70	23	56	18	33	29	18	1.95
325903--325974	34	2.1	34	82	5	83	44	2	15	37	1.61
326574--326636	30	2.0	30	84	12	81	44	1	1	52	1.20
342716--342749	15	2.4	14	95	5	59	50	0	50	0	1.00
342701--342756	27	2.1	27	86	6	78	53	0	46	0	1.00
342702--342756	12	4.5	12	77	16	51	54	0	45	0	0.99
355772--355810	15	2.4	16	87	8	53	35	0	0	64	0.94
355766--355816	24	2.1	24	81	0	66	45	0	0	54	0.99
355800--355874	30	2.5	30	82	2	87	46	2	2	48	1.30
358953--358991	2	20.0	2	94	5	71	51	0	0	48	1.00
377623--377747	60	2.1	60	83	3	153	44	18	10	26	1.82
380513--380548	18	1.9	19	94	5	65	44	0	27	27	1.55
408550--408656	18	6.1	18	64	13	53	32	2	0	64	1.08
408572--408668	11	9.4	11	71	20	59	35	4	0	60	1.16
408651--408689	20	2.0	20	89	0	60	38	2	0	58	1.12
408650--408707	20	2.8	20	80	17	57	41	1	3	53	1.28
408710--408751	16	2.6	16	84	0	57	19	47	23	9	1.78
409207--409271	23	3.1	20	77	16	69	49	9	4	36	1.56
416597--416627	16	1.9	16	93	0	53	35	0	9	54	1.33
417524--417563	20	2.0	21	85	5	55	60	7	0	32	1.25
423773--423813	21	1.9	21	85	5	55	19	0	4	75	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
423786--423824	15	2.6	15	87	0	60	25	2	2	69	1.14
425105--425158	25	2.2	25	83	6	65	57	0	3	38	1.17
430529--430572	21	2.0	22	82	8	54	43	2	4	50	1.35
437764--437810	22	2.1	22	84	4	58	12	0	23	63	1.28
445256--445283	14	2.0	14	100	0	56	42	7	7	42	1.59
453646--453699	2	27.5	2	94	3	92	53	0	0	46	1.00
455254--455383	41	3.2	41	86	4	156	29	19	22	29	1.98
455570--455594	13	1.9	13	100	0	50	24	8	20	48	1.76
455606--455672	2	33.5	2	96	0	125	52	0	0	47	1.00
458022--458063	20	2.1	20	90	0	66	40	9	16	33	1.81
458072--458102	15	2.1	15	100	0	62	22	12	25	38	1.90
462741--462782	20	2.1	20	90	0	66	40	9	16	33	1.81
462791--462821	15	2.1	15	100	0	62	22	12	25	38	1.90
470182--470213	9	3.6	9	100	0	64	12	0	9	78	0.97
470264--470315	23	2.3	23	90	6	79	34	13	9	42	1.77
470264--470379	59	2.0	59	92	0	196	29	15	10	44	1.79
471803--471847	23	2.0	23	83	12	58	53	11	4	31	1.56
474347--474435	44	2.0	44	100	0	178	38	13	17	30	1.89
483716--483759	24	1.9	24	90	9	74	38	0	0	61	0.96
483856--483883	9	3.1	9	100	0	56	57	10	0	32	1.33
483826--484035	68	3.1	68	97	1	388	45	9	4	40	1.57
483924--483951	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)
484024--484065	16	2.6	16	92	0	66	42	7	2	47	1.43
484039--484093	22	2.5	22	84	0	74	43	1	1	52	1.22
484078--484106	6	4.8	6	100	0	58	34	0	0	65	0.93
494589--494634	2	23.0	2	100	0	92	50	0	0	50	1.00
504169--504230	30	2.1	30	93	0	106	12	17	51	17	1.76
509275--509326	26	2.0	27	88	3	79	61	3	19	15	1.48
517625--517666	19	2.3	19	84	12	52	73	2	4	19	1.12
528177--528207	6	5.2	6	100	0	62	19	0	16	64	1.29
531242--531270	3	9.7	3	100	0	58	65	0	0	34	0.93
536358--536448	45	2.0	45	100	0	182	36	13	15	35	1.86

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   207   208   
          209   210