genome.fa.s2.2.7.7.80.10.50.1000.14.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: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62769430

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   

This is table  14  of  206  ( 24623 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)
4275677--4275819	9	15.7	9	67	17	64	33	2	0	62	1.14
4275678--4275745	10	6.9	10	75	9	59	33	2	1	61	1.20
4275727--4275805	30	2.6	31	76	11	92	36	1	0	62	1.04
4277428--4277473	22	2.1	22	83	0	56	58	10	17	13	1.62
4281747--4281782	13	2.8	13	91	4	56	25	0	0	75	0.81
4283630--4283674	4	11.5	4	85	4	65	24	4	0	71	1.05
4289783--4289890	55	1.9	57	81	9	132	57	11	7	24	1.58
4292020--4292081	25	2.5	24	76	10	61	46	4	0	48	1.23
4292071--4292098	11	2.5	11	100	0	56	35	0	0	64	0.94
4306676--4306704	5	5.8	5	100	0	58	17	0	0	82	0.66
4309279--4309324	15	3.3	14	82	8	58	47	0	10	41	1.38
4311266--4311297	13	2.6	13	90	9	50	43	9	6	40	1.62
4319295--4319337	22	1.9	23	90	4	70	39	25	9	25	1.85
4327906--4327941	16	2.3	15	85	4	54	69	8	2	19	1.27
4328705--4328845	52	2.8	52	90	2	214	52	9	1	36	1.42
4328705--4328857	50	3.0	50	85	7	211	51	8	1	38	1.41
4332859--4332895	18	2.0	18	89	5	56	51	2	2	43	1.30
4339982--4340010	14	2.1	14	93	6	51	62	0	6	31	1.22
4340486--4340525	3	13.7	3	86	5	55	62	0	0	37	0.95
4340478--4340525	15	3.1	15	77	11	51	62	2	0	35	1.07
4341621--4341678	23	2.5	24	77	2	64	65	1	1	31	1.13
4345587--4345675	25	3.5	25	74	13	74	29	22	26	21	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4345681--4345820	73	1.9	73	82	2	174	33	20	25	20	1.97
4345790--4345858	26	2.7	25	75	4	75	36	21	23	18	1.95
4345704--4345864	25	6.5	25	67	18	79	33	19	25	21	1.97
4347396--4347427	10	3.1	11	91	8	50	46	0	0	53	1.00
4354796--4354830	10	3.3	10	85	14	52	51	0	17	31	1.45
4354802--4354826	6	4.2	6	100	0	50	52	0	16	32	1.44
4354796--4354830	16	2.2	16	89	0	52	51	0	17	31	1.45
4362178--4362217	20	2.0	20	95	0	71	32	20	12	35	1.90
4372533--4372608	3	25.3	3	86	0	107	28	2	1	67	1.12
4372762--4372790	12	2.4	12	100	0	58	41	10	0	48	1.37
4378869--4378901	11	2.9	12	86	13	52	66	0	0	33	0.92
4383592--4383882	161	1.8	161	91	1	485	33	9	10	46	1.70
4388049--4388120	23	3.2	22	74	24	69	20	0	2	76	0.91
4388097--4388121	8	3.1	8	100	0	50	16	0	0	84	0.63
4389033--4389089	26	2.2	26	93	0	96	28	12	17	42	1.85
4392179--4392217	19	2.1	19	90	4	62	64	0	0	35	0.94
4396694--4396738	19	2.5	19	82	7	58	64	0	0	35	0.94
4400092--4400119	12	2.3	12	100	0	56	39	14	0	46	1.44
4405446--4405483	19	2.0	20	89	5	60	60	0	5	34	1.19
4405515--4405574	31	1.9	31	90	6	95	66	1	6	25	1.25
4405812--4405875	8	8.4	8	76	20	57	23	0	4	71	1.04
4405812--4405903	23	4.1	21	74	16	78	25	0	6	68	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4419465--4419731	46	5.6	45	89	6	311	32	14	23	29	1.94
4419479--4419731	51	5.2	49	89	4	297	33	14	23	29	1.94
4420822--4420855	18	1.9	17	88	5	50	8	0	44	47	1.34
4422324--4422385	27	2.3	26	81	5	70	67	4	1	25	1.19
4422335--4422388	27	2.0	27	92	0	90	68	0	1	29	1.00
4422748--4422787	10	3.6	12	74	19	50	12	17	0	70	1.18
4422749--4422797	21	2.3	21	96	3	89	8	20	0	71	1.11
4430423--4430465	21	2.0	21	82	8	52	23	34	16	25	1.95
4434280--4434336	28	2.0	28	86	0	78	33	17	7	42	1.76
4435793--4435970	16	11.8	15	65	25	56	37	1	0	60	1.07
4435800--4435899	23	3.9	23	73	26	85	34	1	0	65	1.00
4435832--4435976	9	16.9	9	67	24	73	41	2	0	56	1.11
4435807--4435945	33	4.5	32	73	24	120	37	1	0	61	1.05
4435762--4435936	56	3.0	56	86	10	228	35	2	0	62	1.08
4435860--4435945	23	3.8	23	71	20	65	38	1	0	60	1.04
4436240--4436279	20	2.0	20	90	0	62	27	10	12	50	1.72
4436225--4436291	34	1.9	35	84	3	91	34	8	10	46	1.70
4437996--4438152	11	15.5	11	69	22	55	35	3	0	61	1.12
4437987--4438163	38	4.5	39	86	9	245	35	2	0	61	1.11
4438058--4438128	9	7.8	9	73	14	56	38	0	0	61	0.96
4438838--4438879	23	1.9	23	85	9	61	28	2	16	52	1.56
4449714--4449780	30	2.3	29	85	10	91	17	13	19	49	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4449785--4449903	40	2.9	40	80	12	111	20	26	32	20	1.97
4455538--4455564	14	1.9	14	100	0	54	22	0	7	70	1.12
4459634--4459789	30	5.2	30	68	12	97	32	19	4	43	1.71
4459681--4459757	29	2.6	28	85	8	91	35	16	2	45	1.62
4460322--4460366	6	7.7	6	97	2	83	86	13	0	0	0.57
4461235--4461767	157	3.4	152	84	10	671	28	16	19	35	1.94
4461235--4461775	79	6.9	78	81	8	596	28	16	19	34	1.94
4461235--4461768	76	6.8	77	82	7	583	28	16	19	35	1.94
4461235--4461780	237	2.3	234	84	5	708	28	16	20	34	1.94
4461264--4461811	77	7.0	78	78	10	291	28	16	20	34	1.94
4461932--4462051	30	4.0	30	79	4	118	32	20	5	41	1.76
4461941--4462072	30	4.4	29	77	11	108	35	18	4	40	1.72
4461941--4462116	59	3.0	59	72	12	146	33	19	5	40	1.75
4462608--4462656	20	2.5	19	86	3	71	81	6	12	0	0.86
4462612--4462681	32	2.2	31	85	12	97	81	4	14	0	0.84
4462776--4462881	21	4.9	20	75	22	92	71	0	27	0	0.92
4462777--4462880	25	4.1	26	80	7	90	72	0	26	0	0.91
4462781--4462880	7	13.9	7	73	17	64	72	0	27	1	0.92
4462778--4462867	46	2.0	46	89	8	139	71	0	27	1	0.94
4463011--4463044	14	2.4	14	90	0	50	58	17	17	5	1.57
4463146--4463211	13	5.2	12	81	13	78	80	0	19	0	0.72
4463146--4463211	26	2.5	27	88	11	93	80	0	19	0	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4463332--4463356	9	2.8	9	100	0	50	20	12	12	56	1.67
4463521--4463561	19	2.2	19	86	8	57	39	12	12	36	1.80
4463518--4463618	18	5.4	19	68	16	59	31	13	10	43	1.79
4463750--4463785	18	1.9	19	88	5	56	38	13	13	33	1.85
4463809--4463866	19	3.2	19	80	14	68	43	8	5	43	1.57
4466235--4466308	29	2.5	29	82	4	85	25	14	13	45	1.82
4467214--4467254	20	2.1	19	95	4	73	48	0	0	51	1.00
4475038--4475079	18	2.3	18	87	0	57	54	9	7	28	1.59
4476775--4476829	27	2.0	27	100	0	110	34	14	18	32	1.91
4480144--4480198	27	2.0	27	100	0	110	30	14	21	32	1.93
4480149--4480206	27	2.1	27	87	6	82	32	12	22	32	1.91
4484397--4484425	15	1.9	15	100	0	58	31	6	20	41	1.79
4485281--4485307	13	2.1	13	100	0	54	14	7	14	62	1.51
4490116--4490280	83	1.9	86	79	9	187	33	6	10	48	1.64
4498476--4498506	16	1.9	16	100	0	62	54	0	0	45	0.99
4498994--4499041	22	2.2	22	100	0	96	29	31	0	39	1.57
4499013--4499124	51	2.2	51	95	0	197	29	29	0	41	1.57
4499125--4499181	29	2.0	29	89	6	89	36	0	0	63	0.95
4500272--4500296	7	3.6	7	100	0	50	28	0	12	60	1.32
4500947--4500981	18	1.9	18	88	0	52	25	34	8	31	1.86
4501385--4501570	25	7.7	25	64	22	85	38	3	14	44	1.62
4501383--4501567	71	2.6	71	95	0	334	37	3	14	44	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4501570--4501750	29	6.2	29	94	1	310	45	29	0	23	1.57
4501570--4501750	86	2.1	87	93	2	310	45	29	0	23	1.57
4501748--4501927	55	3.2	55	96	3	317	40	11	5	43	1.63
4505020--4505368	123	2.8	124	95	1	621	32	22	15	29	1.95
4507546--4507592	15	3.0	15	82	11	58	46	0	2	51	1.13
4507549--4507592	17	2.8	15	80	12	52	50	0	2	47	1.13
4507647--4507685	20	2.0	20	89	0	60	38	2	10	48	1.51
4508589--4508618	16	1.9	15	93	6	51	73	0	0	26	0.84
4533163--4533212	25	1.9	26	84	8	66	44	2	2	52	1.24
4534484--4534593	40	2.8	38	82	8	130	29	20	22	27	1.99

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