genome.fa.s8.2.7.7.80.10.50.1000.21.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  21  of  190  ( 22705 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)
5950628--5950662	13	2.6	14	91	8	56	34	0	0	65	0.93
5951832--5951957	22	5.3	24	81	8	127	15	25	20	38	1.92
5952607--5952699	39	2.5	37	78	7	89	27	27	22	21	1.99
5952858--5952906	23	2.0	26	88	11	77	30	20	0	48	1.50
5952867--5952913	23	2.0	24	87	4	69	34	21	0	44	1.52
5953059--5953117	3	19.7	3	100	0	118	66	0	0	33	0.92
5953999--5954048	3	16.7	3	100	0	100	66	0	0	34	0.92
5954473--5954533	28	2.1	29	82	8	72	24	29	32	13	1.93
5955913--5955967	24	2.3	23	78	6	56	21	7	10	60	1.55
5959436--5959460	13	1.9	13	100	0	50	32	0	0	68	0.90
5963728--5963976	50	4.8	50	84	4	291	20	28	23	27	1.99
5963727--5963976	100	2.4	104	87	5	355	20	28	23	27	1.99
5964071--5964101	13	2.4	13	94	0	53	54	12	0	32	1.38
5964314--5964371	30	1.9	30	85	0	80	31	22	3	43	1.70
5966450--5966499	16	3.1	16	88	0	73	32	0	34	34	1.58
5966715--5966758	16	2.8	16	83	13	56	52	2	0	45	1.13
5966830--5966876	15	3.3	15	82	11	55	53	2	0	44	1.12
5968637--5968663	11	2.5	11	100	0	54	51	18	7	22	1.70
5970140--5970185	15	3.1	15	76	17	51	45	19	10	23	1.82
5976462--5976516	29	1.9	29	92	3	94	30	12	9	47	1.73
5978394--5978428	15	2.4	15	95	4	63	57	5	2	34	1.37
5979097--5979130	7	5.1	7	93	6	54	88	0	0	11	0.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5979848--5980001	44	3.6	44	76	11	131	28	22	21	27	1.99
5979750--5980001	128	2.0	129	81	5	305	28	21	20	29	1.98
5980308--5980727	44	9.7	44	83	5	525	27	25	18	28	1.98
5980314--5980727	214	1.9	214	94	0	729	27	25	19	28	1.98
5980730--5981314	88	6.6	88	89	2	870	21	24	26	27	1.99
5987952--5987991	2	20.0	2	100	0	80	50	0	0	50	1.00
5988235--5988269	15	2.4	15	95	4	63	57	5	2	34	1.37
5988955--5988986	17	1.9	16	93	6	55	87	0	0	12	0.54
5992632--5992668	9	4.1	9	92	0	65	29	10	13	45	1.77
5992691--5992721	9	3.4	9	90	0	53	38	22	12	25	1.90
5993035--5993074	18	2.1	19	86	9	55	57	0	0	42	0.98
6004053--6004079	13	2.1	13	100	0	54	40	22	14	22	1.90
6004443--6004574	67	2.0	67	89	0	201	31	20	9	38	1.84
6007389--6007415	11	2.5	11	100	0	54	22	29	7	40	1.81
6008876--6008925	26	1.9	26	84	8	66	34	6	6	54	1.50
6009458--6009498	20	2.0	21	90	4	66	39	0	0	60	0.96
6010057--6010133	18	3.9	18	70	18	55	3	22	2	71	1.15
6010690--6010836	63	2.3	63	84	0	177	22	20	29	27	1.98
6012325--6012366	17	2.5	17	88	7	59	42	35	16	4	1.69
6013534--6013581	23	2.1	23	84	0	60	33	6	2	58	1.35
6013998--6014039	19	2.2	20	82	4	50	30	7	11	50	1.66
6015609--6015675	11	6.6	11	70	19	56	46	1	0	52	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6018214--6018251	17	2.2	18	86	13	53	60	15	23	0	1.35
6018735--6018785	26	2.0	26	92	0	84	27	19	7	45	1.78
6020512--6020601	35	2.6	35	72	10	85	28	11	7	52	1.65
6020729--6020774	20	2.2	21	84	3	58	26	2	19	52	1.58
6020783--6021323	273	2.0	273	93	0	922	28	13	12	45	1.79
6021971--6022061	42	2.1	43	82	6	105	21	20	24	32	1.98
6023965--6024010	20	2.2	20	85	11	58	23	19	13	43	1.86
6030703--6030727	12	2.1	12	100	0	50	60	16	0	24	1.36
6031630--6031687	19	3.1	19	75	9	64	36	31	18	13	1.90
6031651--6031812	19	8.4	19	68	6	85	30	24	24	21	1.99
6031651--6031812	77	2.1	77	89	0	243	30	24	24	21	1.99
6032375--6032401	2	13.5	2	100	0	54	51	0	0	48	1.00
6034703--6034738	2	18.5	2	94	5	65	50	0	0	50	1.00
6035051--6035087	19	2.0	18	89	5	56	56	5	5	32	1.45
6035583--6035624	11	3.9	11	84	6	59	78	0	16	4	0.91
6036777--6036975	45	4.5	45	76	6	165	26	24	18	30	1.98
6036775--6036978	89	2.3	88	85	3	257	26	24	18	30	1.98
6038261--6038309	13	3.6	14	81	13	57	14	20	2	63	1.40
6038271--6038313	7	6.1	7	84	10	52	13	18	2	65	1.38
6038271--6038312	15	2.9	15	82	13	52	14	19	2	64	1.39
6041160--6041201	19	2.2	19	83	8	50	40	9	21	28	1.84
6044644--6044791	43	3.4	43	89	0	215	31	23	17	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6044901--6045009	31	3.5	31	91	2	166	45	15	8	30	1.75
6049226--6049296	6	12.3	6	79	8	76	76	5	0	18	0.98
6049226--6049296	23	3.1	24	76	8	76	76	5	0	18	0.98
6049226--6049295	29	2.4	29	78	2	88	75	5	0	18	0.99
6051124--6051153	15	1.9	16	93	6	53	83	3	13	0	0.77
6055115--6055149	15	2.4	15	95	4	63	34	2	5	57	1.37
6055162--6055186	13	1.9	13	100	0	50	32	0	0	68	0.90
6058263--6058327	32	2.1	32	97	2	123	47	12	9	30	1.72
6059090--6059144	16	3.6	15	75	15	51	67	0	3	29	1.08
6063830--6063883	22	2.5	22	93	3	92	18	16	27	37	1.93
6064275--6064357	26	3.1	26	79	16	96	18	15	31	34	1.92
6068664--6068707	23	1.9	23	86	9	63	29	0	0	70	0.88
6068671--6068708	17	2.3	17	86	13	53	28	0	0	71	0.87
6068764--6068822	27	2.2	27	81	6	66	45	1	5	47	1.34
6068799--6068838	17	2.4	17	88	12	57	50	2	0	47	1.14
6069848--6069884	17	2.2	17	95	0	65	24	2	21	51	1.61
6071111--6071250	46	3.0	46	96	0	253	35	7	26	30	1.85
6072163--6072213	23	2.2	23	82	6	59	49	1	21	27	1.60
6078378--6078410	17	1.9	17	88	11	50	39	0	3	57	1.14
6078612--6078701	8	10.4	8	69	19	56	35	1	15	47	1.53
6078602--6078675	27	2.8	27	95	2	132	35	0	13	51	1.41
6078861--6078904	16	2.8	16	82	0	61	56	2	2	38	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6078937--6079018	38	2.2	38	97	0	155	39	2	3	54	1.31
6079396--6079462	27	2.5	27	97	0	125	11	32	23	31	1.91
6084116--6084142	2	13.5	2	100	0	54	51	0	0	48	1.00
6085603--6085635	16	2.0	17	88	5	50	15	42	0	42	1.46
6089160--6089196	18	2.1	18	94	0	65	48	5	8	37	1.56
6093321--6093352	15	2.2	15	94	5	57	65	0	0	34	0.93
6093829--6093879	20	2.8	17	75	16	57	43	1	3	50	1.31
6099212--6099279	34	2.0	34	83	11	86	27	23	27	20	1.99
6102046--6102144	17	5.8	17	69	25	59	53	5	2	39	1.34
6105326--6105358	14	2.4	14	94	0	57	54	12	0	33	1.37
6107673--6107728	27	2.0	29	82	10	71	41	12	8	37	1.74
6120294--6120318	6	4.2	6	100	0	50	36	0	16	48	1.46
6121675--6121725	2	25.5	2	83	0	66	43	49	7	0	1.32
6123425--6123464	9	4.4	9	90	0	62	40	25	10	25	1.86
6123425--6123464	18	2.2	18	100	0	80	40	25	10	25	1.86
6123630--6123746	39	3.0	39	93	1	200	17	2	28	51	1.59
6123728--6123777	17	2.8	17	87	6	64	12	0	42	46	1.41
6124390--6124426	9	4.1	9	92	0	65	45	13	10	29	1.77
6125460--6125496	5	7.4	5	87	0	56	21	13	18	45	1.84
6125460--6125496	10	3.7	10	96	0	65	21	13	18	45	1.84
6126866--6126915	19	2.7	20	78	12	61	68	2	0	30	1.01
6126866--6126915	9	5.4	9	76	19	50	68	2	0	30	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6131225--6131485	124	2.1	125	91	1	427	30	16	22	30	1.96
6132473--6132516	18	2.4	19	76	3	54	20	6	4	68	1.31
6138040--6138076	16	2.2	17	90	9	58	75	0	16	8	1.02
6143008--6143032	5	5.0	5	100	0	50	20	20	0	60	1.37
6144105--6144135	2	15.5	2	100	0	62	51	0	0	48	1.00
6144702--6144745	2	22.0	2	95	0	79	50	2	0	47	1.13
6148490--6148539	26	1.9	26	91	0	82	26	0	14	60	1.34
6151171--6151211	18	2.3	18	82	0	55	63	4	14	17	1.47
6152620--6152829	113	1.9	113	86	0	303	33	22	10	33	1.89
6155037--6155079	13	3.3	13	78	9	52	48	0	6	44	1.29

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