genome.fa.s4.2.7.7.80.10.50.1000.43.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  43  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)
12858488--12858798	61	5.2	61	67	9	226	50	4	2	42	1.35
12858572--12858623	15	3.6	15	80	12	56	53	1	0	44	1.11
12858456--12858823	120	3.1	119	92	3	578	51	4	1	42	1.32
12858713--12858759	18	2.6	18	90	6	69	57	0	0	42	0.98
12858821--12858859	20	2.0	20	84	0	51	43	2	12	41	1.56
12859133--12859168	12	3.1	12	88	4	56	25	5	2	66	1.27
12859121--12859184	23	2.7	23	72	13	67	29	6	4	59	1.42
12869059--12869092	16	2.1	17	88	5	52	79	2	8	8	1.03
12869308--12869365	6	9.3	6	85	14	82	79	3	1	15	0.95
12872807--12873056	25	10.4	25	80	13	276	22	24	16	36	1.94
12873733--12873757	2	12.5	2	100	0	50	48	0	0	52	1.00
12873766--12873797	16	2.0	16	100	0	64	25	6	18	50	1.70
12882423--12882468	23	2.0	24	82	4	58	32	26	0	41	1.56
12882614--12882693	6	13.3	6	94	0	97	57	6	1	35	1.32
12882948--12882977	14	2.1	14	100	0	60	30	13	6	50	1.67
12883427--12883465	16	2.4	16	86	0	51	20	7	0	71	1.10
12883877--12883919	21	2.0	21	81	0	50	58	6	2	32	1.38
12884007--12884067	24	2.5	23	80	15	61	49	4	0	45	1.23
12884015--12884094	35	2.3	35	85	8	103	50	5	0	45	1.23
12891413--12891445	17	2.0	16	94	5	57	39	36	0	24	1.56
12910880--12910927	25	1.9	25	95	0	87	33	12	22	31	1.91
12917177--12917216	15	2.7	15	100	0	80	22	20	37	20	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12921855--12921894	18	2.3	18	86	4	55	70	2	0	27	1.01
12921877--12921917	15	2.7	15	85	7	57	60	2	0	36	1.10
12949744--12949787	17	2.4	18	85	11	54	29	0	0	70	0.88
12950821--12950845	13	1.9	13	100	0	50	8	0	24	68	1.16
12951818--12951858	2	20.5	2	94	0	73	48	0	2	48	1.14
12951838--12952166	114	2.9	114	93	2	563	40	4	14	40	1.67
12952504--12952643	41	3.4	40	92	2	217	29	17	27	25	1.98
12952620--12952663	16	2.8	16	89	6	63	34	20	22	22	1.97
12962670--12962707	20	1.9	20	88	0	58	60	5	0	34	1.19
12965506--12965739	34	6.9	34	70	8	147	43	14	11	30	1.81
12965508--12965738	68	3.4	67	86	3	286	43	14	11	30	1.81
12965494--12965739	102	2.4	101	77	5	246	43	14	11	30	1.81
12975368--12975412	19	2.4	19	92	0	72	17	17	26	37	1.93
12977981--12978065	41	2.1	41	88	4	127	16	24	20	38	1.92
12979089--12979114	12	2.2	12	100	0	52	65	0	34	0	0.93
12979450--12979487	20	1.9	20	84	10	51	52	0	15	31	1.43
12979996--12980093	40	2.4	39	85	6	108	26	13	25	34	1.93
12980010--12980093	41	2.1	40	90	2	132	26	13	23	36	1.91
12981731--12981770	20	2.0	21	85	5	55	27	15	5	52	1.63
12985675--12985700	3	8.7	3	100	0	52	34	0	0	65	0.93
12996819--12996941	35	3.5	35	82	5	124	39	31	13	15	1.85
12996841--12996943	35	3.0	35	84	4	129	36	31	14	17	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12997870--12997894	10	2.5	10	100	0	50	24	0	8	68	1.16
12999194--12999235	16	2.7	16	81	3	50	45	16	4	33	1.69
13001142--13001179	15	2.7	14	88	11	60	68	5	0	26	1.11
13001396--13001435	18	2.1	18	86	9	53	27	2	10	60	1.42
13004048--13004092	21	2.1	21	83	0	54	15	33	22	28	1.95
13006204--13006241	2	19.0	2	100	0	76	50	0	0	50	1.00
13010348--13010435	27	3.3	26	74	13	81	22	17	15	44	1.86
13010348--13010461	27	4.3	25	78	8	77	23	16	15	43	1.86
13022022--13022069	18	2.7	18	73	20	55	45	2	12	39	1.54
13028510--13028557	18	2.7	18	75	9	53	43	2	14	39	1.57
13032276--13032328	27	1.9	28	92	3	90	43	3	1	50	1.30
13032276--13032328	28	1.9	27	92	3	88	43	3	1	50	1.30
13032354--13032411	30	1.9	30	82	6	73	34	3	1	60	1.24
13032349--13032444	39	2.5	39	83	3	106	29	5	3	62	1.32
13032850--13032932	11	7.8	11	69	20	61	59	0	2	38	1.11
13032869--13032941	31	2.4	31	97	0	137	60	0	2	36	1.11
13032841--13032981	71	2.0	71	87	5	205	61	0	2	35	1.11
13032841--13032981	40	3.5	40	71	16	103	61	0	2	35	1.11
13034350--13034396	19	2.4	20	89	3	78	31	8	10	48	1.68
13034397--13034467	36	2.0	36	94	0	124	26	4	18	50	1.65
13036371--13036423	27	2.0	27	96	0	97	33	16	11	37	1.85
13040534--13040563	5	6.0	5	96	0	51	0	0	23	76	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13044560--13044683	49	2.5	49	84	6	144	33	8	25	33	1.85
13052040--13052197	78	2.0	78	93	0	271	22	20	15	40	1.91
13052239--13052565	162	2.0	163	93	0	566	27	14	17	40	1.89
13053756--13053791	2	18.0	2	100	0	72	0	0	50	50	1.00
13063020--13063061	20	2.1	20	90	0	66	54	0	2	42	1.13
13075181--13075221	15	2.7	15	88	0	55	51	2	26	19	1.59
13079950--13079997	17	2.6	18	80	16	53	41	16	0	41	1.48
13080115--13080161	24	2.0	24	83	8	60	48	23	2	25	1.62
13083060--13083316	109	2.3	110	93	2	446	33	20	14	31	1.93
13083630--13083708	31	2.4	33	83	10	92	53	1	6	39	1.35
13083787--13083845	21	2.8	22	84	7	86	59	0	5	35	1.20
13083784--13083845	3	20.7	3	80	6	72	59	0	4	35	1.19
13084651--13084690	17	2.4	17	91	0	62	17	22	50	10	1.76
13086398--13086453	26	2.2	26	84	12	71	62	1	0	35	1.06
13086919--13086961	23	2.0	22	81	9	52	25	0	4	69	1.07
13086977--13087019	14	3.1	14	80	6	52	44	0	0	55	0.99
13087190--13087232	14	3.5	12	82	14	52	32	0	0	67	0.91
13087189--13087231	13	3.3	13	84	12	61	32	0	0	67	0.91
13087509--13087547	17	2.4	17	91	4	62	46	0	0	53	1.00
13092104--13092187	42	2.0	42	88	4	125	46	10	13	29	1.76
13092216--13092246	12	2.6	12	94	0	53	32	9	9	48	1.69
13092391--13092886	248	2.0	248	100	0	992	22	22	13	40	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13097729--13097753	12	2.1	12	100	0	50	24	16	24	36	1.94
13098359--13098845	168	2.9	167	95	1	841	30	8	21	39	1.83
13099260--13099292	15	2.1	16	94	5	59	12	12	24	51	1.73
13111064--13111259	97	2.0	97	92	0	329	34	14	10	40	1.80
13114850--13115134	140	2.0	141	93	1	491	31	12	19	36	1.89
13119954--13120317	185	2.0	186	86	1	516	28	14	21	35	1.93
13126399--13126514	51	2.3	51	78	0	133	33	28	14	23	1.94
13165502--13165798	50	5.8	50	84	3	328	26	22	29	21	1.99
13175633--13175673	21	2.0	21	90	0	64	14	14	19	51	1.77
13177240--13177269	6	4.8	6	95	4	51	53	0	30	16	1.44
13179802--13179862	26	2.3	26	82	0	77	24	16	16	42	1.88
13181946--13182007	22	2.8	22	80	9	72	70	6	0	22	1.09
13181971--13182037	28	2.4	29	82	12	79	70	1	0	28	0.96
13181973--13182068	18	5.2	17	69	18	59	70	2	3	23	1.12
13183190--13183234	23	1.9	24	86	4	65	6	8	46	37	1.61
13184269--13184329	11	5.6	11	72	16	56	57	0	1	40	1.08
13184256--13184345	31	2.8	31	88	6	117	57	0	2	40	1.11
13190313--13190471	45	3.6	44	82	4	167	37	27	13	22	1.92
13190352--13190530	45	4.0	45	81	4	193	36	25	12	25	1.92
13195150--13195277	50	2.6	50	79	7	145	31	21	24	23	1.98
13195150--13195286	49	2.8	50	76	8	147	29	21	24	24	1.99
13197750--13197832	41	2.0	41	90	0	130	48	4	2	44	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13198725--13198782	24	2.5	23	78	15	73	25	0	6	67	1.16
13201024--13201057	16	2.1	16	94	0	59	41	8	32	17	1.80
13201856--13201918	21	3.2	20	74	24	55	42	19	1	36	1.61
13203379--13203467	45	2.0	45	90	0	142	33	23	16	25	1.96
13203477--13203660	51	3.6	50	80	3	217	30	26	17	24	1.97
13203475--13203659	101	1.8	101	89	3	291	31	26	17	24	1.97
13207440--13207486	24	1.9	25	82	4	60	4	27	4	63	1.31
13209213--13209237	6	4.2	6	100	0	50	48	36	0	16	1.46
13220055--13220110	28	2.1	28	83	12	73	51	0	1	46	1.11
13231894--13232013	41	2.9	41	76	4	125	34	25	22	18	1.96

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