genome.fa.s5.2.7.7.80.10.50.1000.15.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   207   208   

This is table  15  of  208  ( 24913 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)
4595726--4595844	54	2.2	55	92	4	206	40	5	15	39	1.69
4601050--4601083	6	5.7	6	89	0	50	35	35	0	29	1.58
4601831--4601879	22	2.3	20	80	13	53	32	8	8	51	1.61
4602475--4602526	3	17.3	3	100	0	104	34	0	0	65	0.93
4603495--4603548	28	1.9	28	85	7	74	53	9	9	27	1.63
4610864--4610898	6	5.8	6	100	0	70	14	0	0	85	0.59
4615201--4615237	3	12.0	3	94	5	65	67	0	0	32	0.91
4616768--4616853	44	2.0	41	86	8	120	29	20	13	36	1.92
4616837--4617430	45	13.3	44	72	7	376	27	24	18	29	1.98
4616815--4617074	89	2.9	89	79	4	290	28	25	17	28	1.98
4616926--4617224	135	2.2	135	88	1	431	27	24	18	30	1.98
4617033--4617792	89	8.6	89	78	8	668	27	23	18	30	1.98
4617202--4617785	44	13.2	44	71	8	209	28	23	18	29	1.98
4617548--4617785	44	5.4	44	79	3	253	30	21	18	28	1.97
4619033--4619169	52	2.8	48	84	11	163	13	24	17	44	1.84
4623904--4623929	2	13.0	2	100	0	52	50	0	0	50	1.00
4633887--4633971	31	2.8	30	74	11	84	41	14	10	34	1.80
4636106--4636135	14	2.1	14	93	0	51	0	26	0	73	0.84
4648347--4648397	23	2.2	23	82	10	59	50	1	0	47	1.12
4648742--4648815	39	1.9	38	84	10	98	58	21	4	16	1.55
4650065--4650134	4	17.8	4	72	8	54	25	7	1	65	1.26
4656303--4656979	90	7.4	90	76	8	485	33	17	19	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4656303--4657155	44	18.6	45	71	9	415	33	18	19	28	1.95
4656529--4657062	133	3.9	133	74	10	351	34	17	19	29	1.94
4656854--4657058	89	2.3	86	78	8	196	33	18	19	29	1.95
4658713--4658803	4	22.8	4	69	10	53	23	8	1	67	1.25
4658725--4658788	14	4.8	13	77	12	67	21	9	1	67	1.28
4658740--4658802	27	2.4	26	85	12	85	25	7	1	65	1.29
4660555--4660597	20	2.2	20	91	4	70	44	0	4	51	1.22
4660555--4660606	19	2.7	19	78	3	59	40	0	3	55	1.18
4660516--4660607	19	4.3	20	68	20	53	40	0	3	56	1.15
4664667--4664770	52	2.0	52	98	0	199	32	18	17	31	1.94
4666140--4666165	2	13.0	2	100	0	52	50	0	0	50	1.00
4667707--4667746	2	20.0	2	100	0	80	50	0	0	50	1.00
4672133--4672875	114	6.5	114	92	0	1202	34	19	20	25	1.96
4673433--4673468	14	2.6	14	95	0	63	8	0	47	44	1.33
4675600--4675633	14	2.5	13	90	4	50	79	0	0	20	0.73
4675939--4675980	19	2.4	18	84	11	52	35	4	16	42	1.69
4675949--4675985	19	1.9	19	100	0	74	32	5	18	43	1.73
4676374--4676446	21	3.3	21	67	23	60	28	4	6	60	1.41
4677169--4677590	9	49.3	9	66	16	139	43	17	1	37	1.59
4677170--4677431	25	10.4	25	76	7	181	44	19	0	35	1.56
4677253--4677330	41	1.9	41	94	0	138	42	15	2	39	1.61
4677309--4677590	41	6.7	42	74	14	149	43	15	1	38	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4677174--4677448	16	17.1	16	65	17	83	44	18	1	35	1.58
4677294--4677601	25	11.9	25	71	10	217	43	15	1	39	1.57
4677253--4677601	184	1.9	183	86	2	502	43	15	2	39	1.58
4692100--4692193	44	2.1	44	86	3	127	31	21	20	26	1.98
4691858--4692291	142	3.1	143	94	1	748	34	17	19	28	1.95
4692144--4692342	98	2.0	98	90	1	310	33	16	20	30	1.94
4695496--4695607	9	13.2	9	72	19	82	44	19	2	33	1.65
4695517--4695594	16	5.3	16	75	22	64	47	20	1	30	1.58
4695531--4695602	25	3.0	23	82	11	90	47	19	0	33	1.50
4695494--4695602	41	2.6	41	81	9	132	46	19	1	32	1.60
4696750--4696802	21	2.5	21	84	6	63	30	13	47	9	1.74
4697200--4697317	44	2.7	44	74	11	100	32	17	26	23	1.97
4697290--4697495	43	4.8	43	80	5	191	24	19	21	33	1.97
4697368--4697494	45	2.9	45	90	2	195	25	22	18	33	1.97
4698389--4698421	14	2.3	15	89	5	50	45	6	15	33	1.70
4699005--4699065	20	3.2	20	77	11	74	54	0	0	45	1.00
4698986--4699067	34	2.3	36	80	16	91	54	0	0	45	0.99
4702354--4702401	17	2.8	16	81	9	51	25	2	16	56	1.51
4703313--4703337	13	1.9	13	100	0	50	56	0	4	40	1.18
4715139--4715172	12	2.9	11	91	4	50	20	2	0	76	0.92
4716756--4716791	17	2.1	17	90	10	56	63	0	5	30	1.17
4717580--4717604	7	3.6	7	100	0	50	44	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4721950--4722050	40	2.5	40	80	3	105	38	20	15	24	1.92
4722120--4722400	41	6.9	41	87	3	370	17	19	30	31	1.95
4725207--4725471	43	6.2	42	88	2	361	20	18	33	27	1.96
4725207--4725478	128	2.1	129	90	2	422	20	17	32	29	1.95
4728740--4728792	3	17.7	3	100	0	106	66	0	33	0	0.92
4736070--4736102	2	16.5	2	100	0	66	51	0	0	48	1.00
4736075--4736125	16	3.2	16	83	5	50	49	5	3	41	1.45
4736113--4736155	21	2.1	21	83	8	54	46	11	9	32	1.72
4736194--4736231	2	19.0	2	100	0	76	50	0	0	50	1.00
4737805--4737861	18	3.0	18	68	22	53	38	3	19	38	1.69
4740795--4740835	19	2.2	19	86	4	57	68	0	9	21	1.18
4740824--4740915	28	3.3	29	70	17	86	53	1	14	31	1.48
4740898--4740936	19	2.1	19	90	0	60	48	0	23	28	1.51
4740978--4741029	19	2.6	21	81	9	63	59	0	11	28	1.32
4747866--4747913	21	2.2	22	77	3	53	22	16	2	58	1.49
4764014--4764147	31	4.5	31	74	16	104	43	11	17	27	1.84
4766883--4766916	2	17.0	2	100	0	68	50	0	0	50	1.00
4778363--4778404	19	2.3	19	88	8	61	30	9	0	59	1.29
4778364--4778413	18	2.8	18	82	14	59	38	10	0	52	1.35
4778859--4778934	31	2.4	30	77	16	75	61	1	2	34	1.18
4783863--4784034	81	2.1	81	100	0	344	33	20	8	37	1.83
4789816--4789909	30	3.1	30	82	1	116	27	20	6	45	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4789831--4789911	15	5.3	15	66	18	51	27	17	6	49	1.70
4794240--4794312	33	2.2	32	83	9	85	38	8	1	52	1.40
4794321--4794361	16	2.6	16	92	0	64	34	7	2	56	1.40
4798217--4798265	14	3.4	14	73	15	55	38	2	0	59	1.09
4804003--4804062	18	3.1	19	71	15	59	38	3	0	58	1.15
4804001--4804118	40	3.0	37	73	17	121	37	3	2	56	1.29
4804698--4804761	20	3.2	20	68	18	51	39	3	0	57	1.14
4804720--4804761	17	2.5	17	76	11	50	38	4	0	57	1.20
4803552--4805628	696	3.0	693	91	3	3295	28	14	25	31	1.95
4806215--4806285	36	2.0	36	100	0	142	22	14	22	40	1.89
4811052--4811076	2	12.5	2	100	0	50	48	0	0	52	1.00
4818675--4818703	2	14.5	2	100	0	58	51	0	0	48	1.00
4819487--4819537	17	3.1	17	77	2	50	43	0	0	56	0.99
4821136--4821181	22	2.1	21	84	11	58	65	0	0	34	0.93
4821529--4821579	23	2.2	23	89	0	75	41	0	7	50	1.31
4826254--4826352	36	3.0	32	71	16	83	25	33	17	24	1.96
4828178--4828206	15	1.9	15	100	0	58	37	6	6	48	1.57
4830124--4830153	8	3.6	8	95	4	51	83	3	0	13	0.77
4832790--4832847	30	1.9	30	86	6	82	15	31	32	20	1.94
4834667--4834758	6	15.0	6	70	13	62	71	4	4	19	1.20
4842115--4842190	40	1.9	40	89	5	118	19	34	30	15	1.93
4842814--4842853	21	1.9	21	89	0	62	20	12	17	50	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4843845--4843906	28	2.2	28	78	16	65	61	4	0	33	1.17
4844092--4844227	68	2.0	68	98	0	263	48	9	19	22	1.77
4846635--4846682	22	2.2	21	79	13	53	37	2	6	54	1.38
4848150--4848182	6	5.5	6	100	0	66	0	15	0	84	0.61
4855422--4855599	89	2.0	89	97	0	338	14	11	24	49	1.76
4856966--4857033	24	2.8	25	76	8	70	23	13	19	44	1.85
4860658--4860710	3	17.7	3	77	14	56	73	1	24	0	0.93
4860664--4860718	13	4.2	13	86	6	67	76	1	21	0	0.88
4860657--4860720	6	10.5	6	83	9	58	76	1	21	0	0.87
4860657--4860720	33	2.0	33	87	9	96	76	1	21	0	0.87

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   207   208