genome.fa.s8.2.7.7.80.10.50.1000.40.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  40  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)
11164587--11164665	8	9.0	8	73	17	59	65	0	6	27	1.16
11164596--11164744	29	5.2	28	73	9	113	61	1	5	32	1.27
11164686--11164725	20	2.0	20	85	5	53	52	0	5	42	1.23
11164711--11164759	18	2.7	18	78	12	55	67	0	2	30	1.02
11165021--11165096	36	2.1	35	88	7	109	28	7	2	60	1.38
11167526--11167560	7	5.0	7	100	0	70	42	0	0	57	0.99
11167526--11167569	21	2.0	21	91	4	70	40	0	0	59	0.98
11174068--11174254	50	3.6	50	79	7	187	25	28	18	27	1.98
11176470--11176553	43	2.0	43	95	0	150	25	21	20	33	1.97
11178915--11178944	2	15.0	2	100	0	60	0	50	0	50	1.00
11180171--11180417	52	4.8	52	77	3	192	39	16	13	30	1.87
11181826--11181882	26	2.2	26	87	6	80	42	8	14	35	1.76
11185235--11185276	22	1.9	22	85	9	59	59	21	0	19	1.38
11186004--11186044	21	2.1	19	86	9	55	39	4	14	41	1.67
11206758--11206830	37	1.9	39	81	10	89	60	4	5	30	1.38
11212985--11213025	20	2.1	19	86	4	55	53	0	24	21	1.46
11226053--11226293	29	8.3	29	81	3	164	24	17	21	36	1.95
11226053--11226307	58	4.4	57	78	5	194	25	17	21	36	1.94
11226105--11226308	87	2.4	86	80	4	223	26	18	20	34	1.96
11228005--11228051	19	2.4	19	86	10	60	23	4	0	72	1.02
11235769--11235795	7	3.9	7	100	0	54	14	0	0	85	0.61
11243828--11243863	3	12.3	3	94	5	65	0	30	0	69	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11246206--11246249	17	2.5	18	78	14	56	34	2	2	61	1.21
11246209--11246241	16	1.9	17	88	11	50	33	3	3	60	1.27
11257089--11257174	37	2.2	38	85	6	111	29	27	1	41	1.63
11258904--11258963	28	2.1	28	90	0	93	18	30	16	35	1.93
11262283--11262312	4	7.5	4	100	0	60	50	23	0	26	1.50
11268689--11268782	25	3.8	24	73	10	73	23	25	20	30	1.98
11268681--11268808	49	2.6	49	82	1	139	25	24	21	28	1.99
11268769--11268827	25	2.4	24	83	11	66	30	22	22	25	1.99
11291332--11291394	20	3.0	20	84	6	81	42	22	25	9	1.83
11294306--11294353	3	15.7	3	78	4	51	60	2	6	31	1.33
11294306--11294343	15	2.5	15	86	0	58	60	2	7	28	1.38
11295861--11296746	51	18.2	49	77	9	825	30	23	16	30	1.96
11295861--11296746	148	6.1	139	77	10	751	30	23	16	30	1.96
11295854--11296746	97	9.2	97	83	5	1007	30	23	16	30	1.96
11296752--11297376	44	13.9	44	72	13	332	29	23	18	28	1.97
11296910--11297374	89	5.3	88	73	13	233	30	23	18	27	1.98
11297048--11297373	132	2.5	132	82	7	385	30	22	18	28	1.97
11296897--11297327	221	1.9	222	81	6	516	29	23	17	28	1.97
11297704--11297761	24	2.4	24	97	0	107	25	29	12	32	1.92
11298664--11298789	43	2.9	44	85	1	164	17	21	17	43	1.88
11298666--11298792	44	2.9	43	85	1	164	17	22	17	43	1.88
11300701--11300732	16	2.0	16	93	0	55	25	15	0	59	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11300950--11301086	51	2.7	51	80	3	161	31	26	17	24	1.97
11304658--11304707	3	16.3	3	80	12	57	64	2	4	30	1.23
11305885--11305955	19	3.5	20	79	20	78	67	1	4	26	1.17
11305929--11305965	17	2.2	16	90	4	56	70	0	0	29	0.88
11306027--11306097	31	2.3	30	85	9	90	66	0	5	28	1.14
11306027--11306075	11	4.6	11	78	16	59	69	0	8	22	1.14
11306027--11306097	19	3.5	20	76	7	63	66	0	5	28	1.14
11307737--11307791	29	1.9	27	85	10	74	27	27	20	25	1.99
11309403--11309482	25	3.2	25	79	8	83	13	27	21	37	1.91
11309413--11309569	25	6.3	23	76	10	98	16	22	22	37	1.93
11309562--11309666	48	2.2	49	83	8	126	17	23	20	38	1.93
11309563--11309654	24	3.8	24	77	11	89	16	22	20	40	1.91
11309624--11309679	25	2.2	25	83	0	67	16	25	19	39	1.91
11309562--11309680	48	2.4	48	78	10	125	16	23	21	37	1.93
11309643--11309697	25	2.2	25	87	6	76	21	21	21	34	1.97
11317258--11317288	9	3.4	9	90	0	53	25	12	22	38	1.90
11317745--11317783	20	2.0	20	90	5	62	23	25	0	51	1.49
11317746--11317791	20	2.3	20	85	7	58	21	32	0	45	1.52
11318395--11318420	5	5.2	5	100	0	52	19	19	19	42	1.90
11323787--11323912	27	4.7	26	77	8	92	25	22	33	19	1.97
11326597--11326647	26	2.0	26	88	0	75	23	25	13	37	1.92
11331323--11331367	22	2.0	22	100	0	90	35	24	22	17	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11333574--11333606	17	1.9	17	88	11	50	66	30	3	0	1.06
11353433--11353484	27	1.9	27	88	0	77	32	17	13	36	1.89
11369603--11369640	20	2.0	20	85	15	53	34	7	15	42	1.76
11380726--11380769	12	3.7	12	76	11	54	38	0	40	20	1.53
11380726--11380775	12	4.0	13	75	15	52	38	0	40	22	1.54
11381441--11381533	27	3.5	27	80	10	93	43	22	16	18	1.88
11381462--11381739	27	10.4	27	80	5	260	37	19	18	24	1.94
11381486--11381739	107	2.4	108	85	4	318	36	19	20	24	1.95
11381510--11381737	80	2.8	82	86	3	295	36	18	20	25	1.95
11381462--11381760	80	3.7	80	80	5	284	37	19	19	24	1.94
11381784--11381850	23	2.9	23	88	2	89	19	5	25	49	1.71
11381785--11381866	24	3.5	24	86	5	96	20	6	24	48	1.72
11381930--11381992	27	2.4	26	76	10	65	25	25	14	34	1.94
11381992--11382047	26	2.2	26	80	6	60	16	21	28	33	1.95
11382038--11382125	32	2.8	32	87	3	124	21	21	21	35	1.96
11382035--11382208	32	5.5	32	78	7	104	21	20	20	37	1.95
11382258--11382310	26	2.0	26	88	0	79	18	28	20	32	1.97
11388796--11388844	21	2.3	21	83	13	57	22	0	12	65	1.26
11389796--11389841	23	2.0	23	83	8	58	28	2	19	50	1.60
11390944--11390979	14	2.6	14	86	0	54	19	38	16	25	1.92
11391036--11391088	28	1.9	27	84	3	70	37	16	20	24	1.93
11394685--11394731	3	15.7	3	100	0	94	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11398569--11398880	43	7.3	43	73	5	193	38	17	19	24	1.93
11398646--11398757	42	2.7	42	78	0	125	38	15	19	26	1.91
11405409--11405435	14	1.9	14	100	0	54	59	0	7	33	1.25
11405409--11405442	14	2.4	14	90	0	50	58	5	5	29	1.45
11408583--11408646	28	2.3	30	76	13	73	53	7	7	31	1.58
11409590--11409619	14	2.2	14	94	5	53	33	6	20	40	1.78
11409603--11409642	20	2.0	20	95	0	71	30	12	15	42	1.83
11409589--11409652	34	1.9	32	84	12	85	34	9	15	40	1.80
11409740--11409778	20	2.0	20	94	0	69	48	2	0	48	1.15
11411033--11411097	32	2.0	32	96	0	121	52	16	3	27	1.59
11411036--11411105	32	2.4	29	86	11	90	54	17	2	25	1.57
11413344--11413377	2	17.0	2	87	0	50	47	2	0	50	1.16
11420097--11420132	19	1.9	18	94	5	63	30	19	0	50	1.48
11421051--11421108	29	2.0	29	80	12	66	41	25	1	31	1.66
11421326--11421366	22	1.9	21	95	5	73	12	4	7	75	1.16
11421505--11421574	31	2.3	30	80	11	79	52	4	1	41	1.30
11421633--11421689	29	2.0	29	86	6	80	50	3	0	45	1.18
11426915--11426962	25	1.9	25	95	0	87	27	10	4	58	1.49
11427630--11427665	19	1.9	18	94	5	63	30	19	0	50	1.48
11428589--11428646	29	2.0	29	80	12	66	41	25	1	31	1.66
11428925--11428963	18	2.2	17	86	4	51	48	5	0	46	1.24
11429049--11429111	33	2.0	31	87	12	92	50	6	0	42	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11433867--11433918	24	2.2	24	85	0	68	38	3	7	50	1.50
11436180--11436398	51	4.3	52	80	3	223	31	28	15	25	1.95
11444570--11444664	31	3.1	31	98	0	181	40	22	13	24	1.90
11446957--11447144	51	3.7	49	82	4	223	30	26	20	23	1.98
11449741--11449828	46	1.9	46	84	9	117	38	17	21	22	1.93
11450056--11450185	32	4.1	32	84	6	156	39	20	19	20	1.93
11450363--11450405	11	3.7	11	76	11	50	51	27	6	13	1.67
11450353--11450431	24	3.4	24	82	8	101	48	25	7	18	1.75
11450495--11450862	27	13.7	27	84	4	415	23	20	18	38	1.94
11452776--11453294	264	2.0	263	92	0	876	27	23	18	30	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