genome.fa.s1.2.7.7.80.10.50.1000.42.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  42  of  187  ( 22383 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)
12891153--12891204	24	2.2	24	89	0	77	55	9	1	32	1.43
12893121--12893172	24	2.2	24	89	0	77	55	9	1	32	1.43
12894420--12894484	29	2.2	29	86	5	87	32	1	9	56	1.40
12894598--12894668	27	2.7	27	91	2	108	54	4	0	40	1.20
12898358--12898396	14	2.8	14	84	0	51	35	12	23	28	1.91
12903473--12903530	27	2.1	27	100	0	116	10	13	36	39	1.79
12903518--12903588	26	2.7	26	82	0	79	23	15	26	33	1.95
12905059--12905258	43	4.7	43	79	7	178	27	17	24	31	1.97
12910889--12910920	15	2.0	17	88	11	50	75	0	0	25	0.81
12913190--12913229	20	2.0	20	90	0	62	27	10	12	50	1.72
12913175--12913241	34	1.9	35	90	3	109	31	8	13	46	1.74
12913999--12914057	29	2.1	27	84	9	75	27	13	15	44	1.84
12914282--12914438	52	3.0	52	94	0	269	22	11	28	36	1.89
12914516--12914609	28	3.3	28	91	4	152	30	0	23	45	1.53
12915778--12915809	7	4.6	7	100	0	64	59	12	0	28	1.34
12916745--12916801	25	2.3	25	80	14	64	63	5	0	31	1.17
12916898--12916956	29	2.0	29	90	6	93	55	1	0	42	1.09
12916987--12917092	52	2.1	51	85	1	140	33	1	31	33	1.69
12917045--12917113	22	3.1	22	87	0	102	39	1	27	31	1.66
12917392--12917446	29	1.9	29	85	3	76	40	18	14	27	1.89
12918407--12918460	26	2.1	25	82	3	63	48	3	0	48	1.19
12922468--12922508	7	5.9	7	94	0	73	17	29	12	41	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12925041--12925082	2	21.0	2	100	0	84	50	0	0	50	1.00
12927322--12927397	22	3.4	23	83	8	86	26	30	1	42	1.64
12927316--12927395	33	2.4	33	83	10	99	26	30	1	42	1.63
12927316--12927397	11	7.3	11	73	23	73	26	29	1	42	1.63
12928625--12928650	7	3.7	7	100	0	52	26	0	15	57	1.38
12929301--12929340	18	2.2	18	95	0	71	22	30	7	40	1.81
12929596--12929644	21	2.3	21	82	0	62	34	34	26	4	1.76
12931568--12931636	24	2.8	25	77	18	83	52	10	4	33	1.55
12932499--12932523	13	1.9	13	100	0	50	80	0	20	0	0.72
12933234--12933478	44	5.6	43	66	8	134	25	25	22	26	2.00
12933205--12933455	88	2.9	88	93	0	430	23	26	23	25	2.00
12933450--12933675	44	5.1	43	82	7	109	24	25	21	28	1.99
12933487--12933814	44	7.5	44	84	4	437	22	25	21	29	1.99
12935085--12935118	16	2.1	17	89	10	54	11	5	0	82	0.83
12935113--12935217	48	2.1	51	82	6	128	14	20	15	49	1.79
12939791--12939859	24	2.8	25	77	18	83	52	10	4	33	1.55
12940711--12940735	13	1.9	13	100	0	50	80	0	20	0	0.72
12943359--12943728	125	3.0	124	83	3	508	30	21	17	30	1.96
12946357--12946398	3	14.3	3	95	5	77	69	0	0	30	0.89
12948069--12948653	44	13.3	44	67	10	275	27	23	19	28	1.98
12948025--12948653	132	4.8	132	93	0	1044	27	23	19	28	1.98
12950229--12950372	50	2.9	50	86	1	198	26	23	29	20	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12952080--12952104	13	1.9	13	100	0	50	56	8	24	12	1.62
12952473--12952520	20	2.3	21	89	10	73	14	16	0	68	1.21
12952473--12952520	13	3.5	14	86	11	64	14	16	0	68	1.21
12952473--12952520	7	7.0	7	81	13	64	14	16	0	68	1.21
12953449--12953477	14	2.1	14	100	0	58	72	0	20	6	1.07
12953761--12954455	349	2.0	348	98	0	1345	25	21	22	31	1.98
12955694--12955735	19	2.2	19	83	8	50	40	9	21	28	1.84
12955766--12955791	13	2.0	13	100	0	52	46	15	7	30	1.74
12964162--12964218	22	2.6	22	91	0	87	22	26	15	35	1.94
12965248--12965278	2	15.5	2	93	0	53	54	0	45	0	0.99
12965037--12965385	171	2.0	173	91	2	567	38	8	25	27	1.85
12981918--12981942	13	1.9	13	100	0	50	40	0	8	52	1.31
12994270--12994311	6	7.0	6	86	0	57	2	38	28	30	1.70
12996019--12996044	7	3.7	7	100	0	52	61	0	0	38	0.96
12996519--12996576	18	3.2	19	76	9	68	53	0	0	46	1.00
12999272--12999307	13	2.7	13	86	4	54	33	2	0	63	1.08
12999900--12999934	2	17.5	2	100	0	70	51	0	48	0	1.00
13002604--13002654	26	2.0	26	84	7	68	25	5	5	62	1.41
13003371--13003418	23	2.1	23	84	0	60	37	4	4	54	1.39
13007657--13007796	42	3.3	42	77	5	133	44	17	20	17	1.87
13010036--13010063	14	2.0	14	100	0	56	50	7	21	21	1.72
13015898--13015947	27	2.0	25	85	14	68	42	12	4	42	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13018029--13018186	28	5.7	28	84	3	167	20	15	8	55	1.67
13018029--13018186	56	2.8	55	81	4	192	20	15	8	55	1.67
13018043--13018200	84	1.9	84	81	2	192	20	16	10	52	1.73
13018496--13018633	69	2.0	69	97	0	258	41	15	12	31	1.84
13022140--13022164	2	12.5	2	100	0	50	52	0	0	48	1.00
13027396--13027435	2	20.0	2	100	0	80	50	50	0	0	1.00
13027958--13027986	12	2.3	13	94	5	51	24	0	3	72	1.00
13032544--13032600	23	2.3	26	85	11	75	45	5	7	42	1.53
13049335--13049360	13	2.0	13	100	0	52	15	15	0	69	1.20
13050560--13050595	15	2.5	14	86	8	54	44	8	0	47	1.33
13052768--13053048	135	2.1	136	86	2	386	26	23	18	32	1.97
13054190--13054251	25	2.5	25	80	17	76	45	0	0	54	0.99
13054165--13054239	14	5.2	14	71	26	59	44	0	2	53	1.14
13054193--13054248	14	4.2	14	78	21	59	46	0	0	53	1.00
13054193--13054250	12	4.8	12	80	15	50	44	0	0	55	0.99
13069090--13069214	20	5.9	21	71	18	89	52	2	3	41	1.30
13069120--13069228	31	3.3	31	72	22	114	56	2	2	37	1.28
13069083--13069240	68	2.3	68	98	0	307	53	2	2	41	1.28
13069082--13069255	37	4.9	35	71	20	128	54	2	2	40	1.28
13070866--13070963	41	2.4	40	86	8	135	29	22	18	29	1.97
13071185--13071304	37	3.2	37	70	17	111	38	20	5	36	1.74
13074236--13074272	9	4.1	9	92	0	65	29	10	13	45	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13077487--13077535	25	2.0	25	84	8	64	28	14	4	53	1.59
13083079--13083106	2	14.0	2	100	0	56	50	0	0	50	1.00
13083186--13083219	2	17.0	2	93	0	59	47	0	2	50	1.16
13083342--13083370	3	9.7	3	100	0	58	68	0	0	31	0.89
13084052--13084088	12	3.2	12	88	3	58	78	0	5	16	0.93
13084052--13084084	6	5.7	6	85	7	50	81	0	3	15	0.80
13084051--13084106	27	2.3	23	81	12	58	76	0	8	14	1.00
13084836--13085630	132	6.0	132	94	1	1292	26	23	18	32	1.97
13085615--13085989	46	8.2	46	89	0	570	29	26	16	27	1.97
13087212--13087275	8	8.0	8	93	6	112	12	12	0	75	1.06
13087203--13087275	16	4.7	15	91	6	103	10	13	0	75	1.05
13087278--13087305	12	2.3	12	100	0	56	0	0	14	85	0.59
13088095--13088128	7	5.0	7	85	7	52	0	14	0	85	0.60
13088098--13088128	10	3.1	10	90	0	53	0	16	0	83	0.64
13088095--13088137	20	2.2	20	91	0	68	2	16	0	81	0.79
13088100--13088143	20	2.2	20	83	0	52	4	18	2	75	1.09
13088141--13088167	14	1.9	14	100	0	54	11	0	7	81	0.87
13093003--13093042	2	20.0	2	100	0	80	50	0	0	50	1.00
13093122--13093157	2	18.5	2	88	5	56	47	0	2	50	1.15
13097186--13097337	46	3.4	46	94	2	256	28	22	15	34	1.94
13109454--13109566	37	3.1	37	88	1	174	31	6	15	46	1.71
13109574--13109610	9	3.8	10	83	16	51	21	5	29	43	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13109574--13109611	20	1.9	20	94	0	67	21	5	28	44	1.73
13109703--13109780	29	2.8	27	75	16	77	30	11	25	32	1.91
13110646--13110776	37	3.0	42	70	19	101	51	9	4	33	1.55
13110646--13110776	42	3.1	42	74	10	124	51	9	4	33	1.55
13111867--13111926	23	2.6	24	73	26	58	43	10	0	46	1.37
13125091--13125119	4	7.2	4	100	0	58	27	0	72	0	0.85
13126340--13126401	2	30.5	2	96	3	115	50	1	0	48	1.10
13132659--13132707	25	2.0	25	84	8	64	12	18	20	48	1.79
13133214--13133362	67	2.2	67	93	0	262	52	7	10	30	1.62
13133337--13133362	12	2.2	12	100	0	52	57	11	7	23	1.59

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