genome.fa.s5.2.7.7.80.10.50.1000.135.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  135  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)
41439352--41439407	21	2.6	22	78	13	55	78	3	14	3	1.02
41440747--41440993	51	4.8	51	83	0	305	30	18	22	28	1.97
41440975--41441018	21	2.1	21	86	0	61	43	6	29	20	1.78
41441094--41441200	51	2.1	51	83	0	133	33	16	20	28	1.95
41441205--41441356	51	3.0	51	84	0	205	28	17	26	26	1.98
41440898--41441304	209	1.9	210	89	0	636	29	16	24	28	1.97
41441094--41441322	122	1.9	122	85	0	314	31	16	24	27	1.96
41441318--41441391	36	2.1	36	94	0	130	25	20	22	31	1.98
41441360--41441709	143	2.4	143	86	0	468	31	17	22	28	1.97
41441578--41441927	180	1.9	179	87	0	511	30	17	22	29	1.97
41442388--41442534	22	6.7	22	90	0	213	33	14	25	26	1.94
41442548--41442582	17	2.1	17	88	0	52	42	5	0	51	1.25
41442592--41442674	43	1.9	43	87	4	123	36	7	2	54	1.41
41444263--41444293	5	6.2	5	100	0	62	61	19	0	19	1.35
41445723--41445756	17	2.0	17	100	0	68	41	11	29	17	1.85
41446500--41446559	27	2.2	27	87	0	93	38	35	3	23	1.71
41446486--41447042	43	12.8	45	81	6	495	42	29	1	26	1.62
41446486--41447042	22	25.7	22	83	5	629	42	29	1	26	1.62
41446486--41447042	86	6.4	86	83	6	655	42	29	1	26	1.62
41447136--41447304	37	4.4	38	65	16	107	43	9	6	40	1.63
41447042--41447321	115	2.4	114	97	0	524	42	8	7	41	1.63
41450343--41450807	125	3.7	125	89	2	670	29	23	16	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41451872--41451919	25	1.9	25	100	0	96	20	22	18	37	1.94
41452630--41452688	30	1.9	31	89	3	93	47	1	20	30	1.60
41456459--41456496	16	2.4	16	82	4	51	60	5	0	34	1.19
41456748--41456795	3	16.0	3	84	0	60	60	4	4	31	1.35
41461070--41461179	41	2.7	41	81	1	141	20	29	17	32	1.96
41462046--41462075	12	2.5	12	94	0	51	23	40	30	6	1.80
41464510--41464861	126	2.8	124	88	4	546	28	15	22	33	1.94
41468076--41468454	23	14.9	23	69	24	164	27	0	25	45	1.57
41468047--41468306	29	9.4	29	73	20	211	27	0	26	46	1.53
41468078--41468380	74	3.9	75	79	17	318	26	0	26	46	1.56
41468261--41468337	22	3.5	22	73	18	79	27	1	23	48	1.59
41468316--41468567	29	9.2	29	68	22	136	26	0	29	44	1.58
41468115--41468481	103	3.6	103	78	14	354	27	0	26	45	1.58
41468474--41468515	6	6.7	6	91	8	66	14	0	52	33	1.42
41468474--41468515	13	3.3	13	96	3	77	14	0	52	33	1.42
41468474--41468513	19	2.0	20	95	4	73	15	0	55	30	1.41
41468419--41468575	84	1.9	85	91	1	262	25	0	31	42	1.55
41468506--41468594	23	3.6	23	73	16	88	26	0	26	46	1.53
41468419--41468590	29	6.2	28	69	18	110	25	0	31	42	1.55
41468590--41468702	25	4.7	25	70	12	94	41	12	0	45	1.48
41468599--41468709	35	3.2	35	64	14	93	44	12	0	42	1.48
41468670--41468755	43	2.0	45	90	4	140	50	12	0	37	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41469861--41469885	7	3.6	7	100	0	50	60	12	0	28	1.32
41471053--41471109	22	2.5	22	94	2	96	38	0	35	26	1.57
41471261--41471368	42	2.6	42	89	0	162	17	29	27	25	1.97
41473709--41473741	6	5.3	6	92	7	57	15	0	69	15	1.19
41477244--41477275	15	2.1	15	94	5	55	21	0	3	75	0.95
41480495--41480520	12	2.2	12	100	0	52	23	53	0	23	1.46
41480922--41480949	14	2.0	14	100	0	56	35	21	28	14	1.92
41482933--41482975	16	2.5	19	79	20	51	37	4	6	51	1.50
41491411--41491525	51	2.3	51	96	0	212	27	30	0	41	1.56
41491548--41491591	10	4.4	10	82	0	52	27	0	0	72	0.85
41491526--41491584	31	1.9	31	92	0	100	32	0	0	67	0.91
41492673--41492697	7	3.6	7	100	0	50	28	0	12	60	1.32
41493768--41493836	25	2.7	25	81	2	84	47	2	10	39	1.52
41493832--41493880	18	2.7	17	81	12	53	48	20	0	30	1.50
41493854--41493977	29	4.3	29	89	4	196	45	31	0	22	1.58
41493975--41494211	55	4.3	55	83	5	316	37	11	5	45	1.62
41494084--41494118	18	1.9	18	94	0	61	31	11	2	54	1.51
41494195--41494219	10	2.5	10	100	0	50	44	8	0	48	1.32
41497334--41497666	123	2.7	123	93	1	551	31	22	16	29	1.96
41500050--41500102	16	3.3	15	79	12	52	56	3	0	39	1.17
41500060--41500095	17	2.2	16	90	5	54	61	0	0	38	0.96
41501345--41501385	3	13.7	3	100	0	82	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41503165--41503333	87	1.9	87	90	2	268	35	21	14	28	1.93
41507153--41507196	23	1.9	23	85	0	61	29	2	6	61	1.34
41508530--41508564	2	17.5	2	100	0	70	51	0	0	48	1.00
41510126--41510172	16	2.8	17	70	9	51	31	2	2	63	1.18
41518196--41518302	50	2.1	50	82	3	126	25	22	27	25	2.00
41518370--41518653	50	5.7	50	69	3	205	28	21	25	24	1.99
41518429--41518702	50	5.5	49	69	3	217	30	21	23	24	1.99
41518379--41518707	99	3.3	99	94	2	579	29	22	23	24	1.99
41521181--41521231	27	2.0	27	81	11	63	37	3	3	54	1.37
41521194--41521264	29	2.5	28	80	10	83	33	1	4	60	1.25
41525129--41525161	15	2.2	15	94	0	57	48	24	12	15	1.78
41529497--41529542	24	1.9	24	90	0	74	60	4	6	28	1.40
41530241--41530275	15	2.3	15	85	0	52	62	11	2	22	1.41
41532487--41533174	44	15.7	44	72	14	380	27	23	20	28	1.99
41532579--41532993	128	3.2	128	71	12	412	28	22	20	28	1.99
41532363--41532824	217	2.1	216	90	1	726	28	23	19	28	1.98
41532665--41533171	89	5.8	89	75	12	356	26	24	20	28	1.99
41532407--41533082	261	2.6	260	87	3	925	27	23	19	28	1.99
41532399--41533082	217	3.1	219	82	5	655	27	23	19	28	1.99
41539967--41540010	20	2.2	20	100	0	88	18	25	15	40	1.90
41544327--41544375	25	2.0	25	87	0	71	59	8	16	16	1.60
41547164--41547246	39	2.1	40	95	2	150	51	21	6	20	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41549272--41549340	33	2.1	33	100	0	138	40	14	15	28	1.87
41555681--41556002	175	1.8	173	88	2	493	30	14	28	25	1.95
41558690--41558747	22	2.6	22	81	7	64	39	22	5	32	1.76
41562035--41562074	19	2.2	19	86	8	57	55	17	5	22	1.61
41564176--41564206	2	15.5	2	100	0	62	51	0	0	48	1.00
41564850--41564952	54	1.9	54	88	4	154	32	17	8	41	1.80
41564779--41565084	135	2.3	135	87	3	447	33	15	9	41	1.79
41564978--41565084	54	2.0	54	96	0	196	30	16	9	42	1.80
41567923--41567956	5	6.8	5	87	12	52	79	0	0	20	0.73
41575784--41576041	86	3.0	87	84	1	349	31	16	16	35	1.91
41576530--41576567	19	2.0	20	89	5	60	50	5	13	31	1.63
41576551--41576622	27	2.6	28	77	2	83	51	11	16	20	1.75
41581528--41581568	2	20.5	2	100	0	82	51	48	0	0	1.00
41583386--41583418	13	2.3	15	90	10	52	51	24	6	18	1.68
41583518--41583556	11	3.5	11	82	10	53	76	5	0	17	0.96
41583519--41583554	16	2.2	16	90	0	54	77	5	0	16	0.94
41585487--41585547	23	2.7	24	82	7	65	57	0	1	40	1.08
41585498--41585535	20	1.9	20	89	10	60	60	0	0	39	0.97
41585502--41585545	20	2.1	21	83	4	54	63	0	2	34	1.07
41588998--41589035	14	2.7	14	87	0	58	34	7	18	39	1.80
41589019--41589058	20	2.0	20	95	0	71	27	10	15	47	1.77
41589004--41589070	34	1.9	35	90	3	109	31	8	16	43	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41589144--41589287	74	2.0	71	93	5	245	33	4	6	56	1.44
41589172--41589290	34	3.2	38	64	13	102	33	4	5	56	1.43
41589360--41589422	34	1.9	32	93	6	108	41	4	9	44	1.58
41591872--41591908	19	1.9	19	94	0	65	51	10	37	0	1.37
41600449--41600536	38	2.3	38	98	0	167	20	10	39	29	1.85
41601692--41601805	58	1.9	59	91	1	185	37	2	9	50	1.49
41605987--41606015	2	14.5	2	100	0	58	48	0	0	51	1.00
41608187--41608239	23	2.2	24	83	3	63	33	5	3	56	1.41
41615242--41615341	44	2.3	44	92	0	173	26	24	25	25	2.00
41615325--41615597	128	2.1	129	87	2	399	29	21	23	25	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   207   208