genome.fa.s4.2.7.7.80.10.50.1000.163.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  163  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)
51313725--51313857	37	3.4	40	71	11	114	31	23	16	28	1.96
51314791--51314985	41	4.8	41	97	0	363	26	28	20	24	1.99
51315637--51315701	2	33.0	2	83	9	80	46	4	1	47	1.32
51317971--51318144	5	34.8	5	95	0	222	57	8	0	34	1.28
51322170--51322234	20	3.3	19	71	16	53	20	16	7	55	1.65
51322165--51322245	39	2.1	39	92	0	135	20	19	6	53	1.67
51326690--51326766	15	5.0	15	70	20	52	33	7	15	42	1.76
51329960--51330421	224	2.1	224	92	0	780	24	25	26	23	2.00
51331062--51331138	33	2.3	32	82	6	91	25	23	18	32	1.97
51332911--51332961	17	3.4	17	65	30	51	5	29	0	64	1.17
51332911--51332979	28	2.5	28	100	0	138	5	28	0	65	1.16
51342137--51342182	3	15.7	3	78	13	51	39	0	2	58	1.10
51342136--51342182	13	3.7	13	82	2	60	40	0	2	57	1.11
51342187--51342217	2	15.5	2	100	0	62	51	0	0	48	1.00
51342668--51342701	17	1.9	18	88	5	52	41	0	23	35	1.55
51343150--51343219	21	3.4	21	74	7	63	18	18	25	37	1.94
51347862--51347978	49	2.5	48	86	6	161	30	21	17	30	1.96
51348036--51348341	96	3.3	96	69	12	278	31	22	15	30	1.95
51348136--51348386	44	5.6	44	70	15	190	31	24	15	28	1.95
51348000--51348400	181	2.2	181	89	0	624	31	21	16	30	1.95
51348096--51348386	89	3.2	88	73	15	297	31	23	15	28	1.96
51358916--51358985	26	2.7	26	86	0	95	37	14	17	31	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
51366502--51366610	26	4.1	26	85	4	121	22	20	19	37	1.94
51369312--51369496	51	3.6	51	80	3	169	23	17	27	30	1.97
51369312--51369496	101	1.8	102	90	3	302	23	17	27	30	1.97
51369418--51369498	26	3.2	26	62	28	64	23	14	28	33	1.94
51377064--51377103	2	20.0	2	100	0	80	50	0	0	50	1.00
51377514--51377715	49	4.2	47	74	8	140	23	28	15	32	1.96
51377706--51377799	48	1.9	49	82	6	120	18	22	18	41	1.90
51379213--51379265	21	2.5	21	90	0	79	30	37	9	22	1.86
51383404--51383480	5	15.4	5	70	24	56	59	0	1	38	1.06
51383410--51383459	16	3.8	13	78	21	59	60	0	2	38	1.09
51383423--51383499	11	7.6	10	69	22	54	58	0	1	40	1.06
51383443--51383504	20	3.2	18	86	13	88	59	0	0	40	0.97
51384165--51384219	28	1.9	29	85	3	76	50	10	5	32	1.60
51385039--51385113	22	3.4	22	79	18	84	26	26	1	45	1.62
51385039--51385113	34	2.2	34	81	9	91	26	26	1	45	1.62
51385039--51385105	11	5.9	12	76	16	72	25	28	1	44	1.63
51385075--51385172	51	1.9	51	85	8	137	26	23	3	46	1.66
51385388--51385497	22	5.1	22	87	2	152	42	30	0	25	1.61
51385387--51385497	44	2.6	43	86	2	168	42	30	0	26	1.61
51388641--51389183	126	4.3	124	84	3	660	30	22	16	29	1.96
51388641--51389183	250	2.2	250	85	2	734	30	22	16	29	1.96
51394321--51394360	22	2.0	20	85	14	55	55	20	2	22	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
51395017--51395180	43	3.8	43	84	7	217	30	28	21	19	1.97
51396551--51396676	43	2.9	43	81	10	157	31	20	15	32	1.93
51396848--51396880	15	2.2	15	94	0	57	21	12	6	60	1.53
51403443--51403468	7	3.7	7	100	0	52	26	0	0	73	0.84
51403860--51403909	20	2.4	19	81	15	55	62	4	0	34	1.14
51410542--51410572	14	2.2	14	94	0	53	25	25	3	45	1.69
51414088--51414113	6	4.3	6	100	0	52	15	0	0	84	0.62
51414670--51414840	62	2.8	62	79	5	163	48	4	11	36	1.58
51414741--51414855	60	1.9	61	85	7	164	46	3	13	37	1.60
51414773--51414858	29	3.0	27	72	14	73	51	2	11	34	1.51
51416181--51416220	12	3.4	12	83	16	57	40	7	25	27	1.82
51417425--51417450	10	2.6	10	100	0	52	88	0	0	11	0.52
51423309--51423400	23	3.9	23	80	15	107	20	26	21	31	1.98
51426690--51426729	12	3.4	12	83	16	57	40	7	25	27	1.82
51428208--51428237	3	10.0	3	100	0	60	33	0	0	66	0.92
51429701--51429742	23	1.9	21	85	9	57	30	7	2	59	1.37
51431209--51431271	27	2.3	29	86	8	87	61	7	1	28	1.33
51431228--51431281	27	2.0	27	86	10	76	53	9	5	31	1.56
51438018--51438051	17	2.0	17	88	0	50	64	0	0	35	0.94
51437974--51438043	33	2.2	33	87	5	99	64	1	0	34	1.03
51437998--51438063	29	2.2	30	89	5	98	60	1	1	36	1.15
51437975--51438123	41	3.6	40	81	7	156	59	2	2	36	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
51447762--51447813	7	7.0	7	77	18	52	21	1	0	76	0.87
51447759--51447805	17	2.8	17	77	9	51	23	2	0	74	0.93
51449040--51449195	42	3.7	42	80	1	152	46	16	20	16	1.85
51449033--51449209	21	8.4	21	70	9	92	46	15	20	16	1.84
51449049--51449231	84	2.2	84	81	2	206	45	15	21	16	1.84
51451738--51451767	15	1.9	16	93	6	53	73	16	3	6	1.18
51451908--51451941	17	2.0	17	88	0	50	29	17	20	32	1.96
51452622--51452672	27	2.0	27	92	7	88	50	0	5	43	1.26
51453553--51453682	43	3.0	43	78	8	147	21	20	27	30	1.98
51458048--51458102	19	3.0	19	81	5	51	45	3	0	50	1.19
51458326--51458380	3	18.7	3	96	3	103	65	0	0	34	0.93
51458522--51458585	24	2.8	23	76	17	62	48	4	0	46	1.23
51458550--51458614	35	1.9	33	84	6	85	50	4	0	44	1.22
51459899--51459939	17	2.3	18	83	4	57	53	0	0	46	1.00
51460908--51460975	23	2.9	23	97	2	127	25	30	13	30	1.93
51467389--51467447	26	2.3	26	96	0	109	44	5	0	50	1.24
51467499--51467556	27	2.1	27	96	0	107	27	31	29	12	1.92
51467621--51467653	3	11.0	3	93	0	57	69	0	30	0	0.88
51467823--51467874	3	17.3	3	100	0	104	32	0	0	67	0.91
51467877--51467910	3	11.3	3	93	0	59	0	2	32	64	1.08
51468696--51468740	18	2.5	18	88	0	72	28	4	48	17	1.66
51473758--51473784	10	2.7	10	100	0	54	7	0	0	92	0.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
51474444--51474605	24	6.3	26	68	15	81	1	30	1	66	1.07
51474449--51474489	17	2.4	17	79	0	55	0	36	0	63	0.95
51474430--51474580	40	3.9	36	71	21	101	1	27	1	69	1.04
51478833--51478880	24	2.0	24	83	0	60	43	2	27	27	1.66
51479097--51479193	42	2.3	42	81	10	126	27	16	28	26	1.97
51486274--51486333	30	2.0	30	100	0	120	20	16	16	46	1.84
51493620--51493777	78	2.0	78	92	2	264	39	13	12	34	1.82
51498717--51498855	46	3.0	46	97	0	260	43	15	16	24	1.87
51502054--51502092	19	2.0	20	85	14	55	46	0	2	51	1.14
51506109--51506133	1	25.0	1	100	0	50	100	0	0	0	0.00
51506454--51506563	52	2.1	52	98	0	211	14	28	8	49	1.72
51534095--51534128	17	2.0	17	94	0	59	58	0	2	38	1.13
51539514--51539587	29	2.6	29	95	0	130	33	28	12	25	1.92
51546153--51546244	39	2.3	39	81	7	96	32	17	26	23	1.97
51546175--51546265	39	2.3	40	84	5	123	35	19	24	20	1.96
51546296--51546486	41	4.7	41	90	2	303	20	20	29	29	1.98
51546778--51546806	14	2.1	14	100	0	58	20	0	34	44	1.52
51547972--51548014	21	2.0	21	86	9	59	41	39	2	16	1.61
51548898--51548988	46	2.0	46	97	0	173	25	10	7	56	1.60
51552328--51552487	43	3.7	42	84	3	178	25	21	29	23	1.99
51552331--51552493	86	1.9	86	83	2	211	26	20	28	24	1.99
51556493--51556563	35	2.0	35	91	0	115	28	11	15	45	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
51560770--51560861	39	2.3	41	88	3	134	52	8	2	36	1.45
51561491--51561520	11	2.7	11	94	0	51	20	0	3	76	0.92
51569774--51569838	34	1.9	34	93	0	112	24	30	7	36	1.84
51574066--51574128	31	2.0	31	87	0	90	38	9	15	36	1.81
51576882--51576930	5	10.0	5	87	12	75	40	20	0	38	1.53
51582623--51582871	30	8.2	30	89	0	309	33	6	16	43	1.74
51590221--51590259	20	2.0	20	84	0	51	46	5	0	48	1.24
51591269--51591334	13	5.1	13	81	0	69	33	30	6	30	1.82
51595658--51595696	13	2.9	13	84	3	51	79	2	10	7	1.02
51605757--51605805	19	2.7	19	85	14	68	61	4	0	34	1.15

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