genome.fa.s5.2.7.7.80.10.50.1000.42.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: 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  42  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)
11550675--11550701	4	6.8	4	100	0	54	22	0	0	77	0.76
11551335--11551404	3	23.3	3	76	11	63	30	1	5	62	1.27
11551325--11551391	12	5.6	12	77	7	64	26	2	4	65	1.26
11551352--11551404	24	2.2	24	90	6	81	28	1	7	62	1.33
11551754--11551784	2	15.5	2	93	0	53	48	3	0	48	1.17
11554528--11554605	38	2.1	38	100	0	156	24	12	10	52	1.70
11557712--11558062	148	2.3	148	81	7	361	45	9	15	29	1.78
11563558--11563592	17	2.0	18	88	5	54	22	5	0	71	1.07
11563971--11564063	30	3.1	30	89	3	125	29	26	18	25	1.98
11567503--11567541	19	2.1	18	85	4	51	20	2	2	74	1.06
11567546--11567601	18	3.1	19	82	7	71	35	0	3	60	1.14
11575996--11576138	39	3.7	38	78	3	151	15	18	34	32	1.92
11578191--11578572	139	2.7	138	82	6	432	30	23	17	28	1.97
11578191--11578579	70	5.6	69	80	5	376	30	22	17	29	1.97
11578869--11578899	16	1.9	16	100	0	62	38	16	12	32	1.86
11581744--11581786	20	2.2	20	86	0	59	25	11	37	25	1.90
11583028--11583059	16	2.0	16	100	0	64	37	18	12	31	1.88
11591969--11592006	18	2.1	18	95	0	67	23	26	10	39	1.87
11596300--11596353	16	3.4	16	94	0	90	33	0	35	31	1.58
11596332--11596441	45	2.6	43	77	9	120	32	6	29	31	1.82
11596547--11596595	25	2.0	25	84	8	64	46	4	0	48	1.20
11599478--11599707	43	5.4	43	89	1	311	19	17	32	30	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11599478--11599704	85	2.7	85	88	2	321	19	17	33	29	1.95
11600779--11600805	13	2.1	13	100	0	54	48	22	0	29	1.51
11601266--11601659	125	3.1	126	83	4	499	30	15	15	38	1.89
11601715--11601840	34	3.8	33	78	11	150	41	15	0	43	1.46
11603631--11603670	21	1.9	21	84	0	53	27	27	12	32	1.93
11611794--11611869	13	5.8	13	73	1	62	23	7	27	40	1.82
11612452--11612495	22	2.0	21	91	4	70	40	4	13	40	1.65
11620461--11620502	21	2.0	21	86	9	59	59	33	7	0	1.25
11626217--11626569	197	1.8	190	84	4	481	43	9	11	35	1.72
11626639--11626682	18	2.3	19	85	14	56	59	2	6	31	1.36
11629136--11629238	31	3.4	31	77	8	111	52	3	2	40	1.35
11629133--11629248	61	1.9	61	90	0	187	51	3	2	42	1.32
11632449--11632542	25	3.8	25	91	0	125	19	29	21	29	1.97
11639904--11639962	25	2.4	25	82	2	66	18	27	16	37	1.93
11639917--11639985	25	2.8	25	90	0	102	14	28	23	33	1.94
11655644--11655688	5	8.8	5	85	4	63	0	26	0	73	0.84
11662618--11662678	13	5.1	13	70	29	55	59	1	0	39	1.08
11662618--11662679	11	5.0	13	72	20	53	58	1	0	40	1.08
11662704--11662763	23	2.7	23	82	14	81	56	0	1	41	1.09
11669061--11669089	12	2.4	12	100	0	58	51	6	0	41	1.28
11670835--11670865	16	1.9	16	93	0	53	70	9	9	9	1.33
11675857--11675905	18	2.8	17	84	6	71	14	26	40	18	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11682543--11682575	15	2.2	15	89	10	50	57	0	0	42	0.98
11682541--11682581	9	4.9	9	80	14	52	58	0	0	41	0.98
11685837--11685884	18	2.7	17	81	9	60	41	4	16	37	1.68
11686244--11686345	20	5.7	18	73	19	72	49	4	2	43	1.39
11686252--11686386	68	2.0	69	92	1	227	50	3	3	42	1.38
11687952--11688011	29	2.1	29	100	0	120	56	3	16	23	1.55
11688259--11688296	18	2.1	18	95	0	67	36	15	7	39	1.77
11689439--11689496	20	2.9	20	70	10	55	24	27	18	29	1.98
11696542--11696575	18	1.9	17	88	5	50	52	8	20	17	1.71
11697986--11698049	28	2.3	28	97	0	119	37	15	9	37	1.80
11698610--11698723	13	8.7	13	67	9	52	43	4	16	35	1.68
11705289--11705520	125	1.9	124	90	2	376	28	14	25	31	1.94
11707411--11707488	35	2.4	31	80	15	104	16	20	35	26	1.94
11708827--11709560	23	32.4	23	76	19	646	28	2	21	46	1.64
11708886--11708919	17	2.0	17	94	0	59	32	0	20	47	1.51
11708831--11708902	27	2.6	28	93	4	128	31	1	19	47	1.58
11708945--11708982	17	2.2	17	95	0	67	28	2	15	52	1.56
11708940--11709028	18	4.4	18	68	26	63	26	2	23	47	1.64
11708862--11709495	109	5.8	106	81	14	546	29	2	22	46	1.65
11708966--11709121	51	3.2	51	84	9	182	28	3	22	45	1.68
11709105--11709142	17	2.2	17	95	0	67	28	2	15	52	1.56
11709350--11709383	17	2.0	17	94	0	59	32	0	20	47	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11709409--11709446	17	2.2	17	95	0	67	28	2	15	52	1.56
11709078--11709469	41	9.2	41	73	18	191	28	2	21	46	1.65
11709175--11709548	86	4.2	88	76	15	270	29	2	21	46	1.64
11708866--11709499	132	4.8	133	79	14	638	28	2	22	46	1.65
11709463--11709565	28	3.9	28	78	12	126	29	2	20	47	1.64
11711698--11711731	15	2.3	15	90	5	52	67	5	0	26	1.13
11711927--11711968	22	1.9	22	90	0	66	33	0	33	33	1.58
11711940--11711996	30	1.9	30	92	0	96	33	0	35	31	1.58
11711918--11712020	52	2.0	51	86	5	145	33	0	33	33	1.58
11711970--11712025	22	2.5	22	91	0	94	37	0	30	32	1.58
11713282--11713323	21	2.0	21	90	0	66	35	7	11	45	1.69
11715748--11715808	10	5.7	10	75	12	59	4	18	3	73	1.14
11715748--11715808	21	2.8	20	80	7	59	4	18	3	73	1.14
11717287--11717340	21	2.5	22	79	8	58	59	3	0	37	1.15
11717502--11717583	21	3.6	21	68	25	51	65	4	3	25	1.29
11717531--11717582	3	17.3	3	82	7	61	67	1	3	26	1.18
11719319--11719445	46	2.8	44	86	4	166	25	22	20	31	1.98
11731829--11731882	21	2.5	22	79	8	58	59	3	0	37	1.15
11732044--11732084	21	2.0	21	81	18	50	65	7	2	24	1.30
11732073--11732123	18	2.8	18	77	11	59	62	1	7	27	1.33
11760205--11760237	13	2.5	13	90	9	50	33	24	0	42	1.55
11760691--11760737	20	2.4	20	76	16	53	46	0	8	44	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11764423--11764721	50	5.8	50	87	2	391	20	29	23	26	1.99
11764816--11764846	13	2.4	13	94	0	53	54	12	0	32	1.38
11765059--11765115	30	1.9	30	88	0	87	31	22	3	42	1.71
11768242--11768274	2	16.5	2	100	0	66	51	0	0	48	1.00
11769213--11769254	20	2.1	20	100	0	84	40	30	9	19	1.83
11770155--11770197	22	2.0	22	82	8	54	67	6	2	23	1.27
11772444--11772481	19	2.0	19	85	10	51	44	0	5	50	1.24
11774334--11774397	30	2.1	30	85	5	85	42	7	6	43	1.58
11787412--11787469	18	3.3	18	69	13	57	58	1	3	36	1.25
11790866--11790898	17	2.0	16	94	5	57	48	0	9	42	1.35
11791139--11791190	20	2.6	20	82	8	61	67	0	5	26	1.13
11791494--11791739	125	2.0	124	87	2	359	31	15	21	31	1.94
11795009--11795211	23	7.9	23	79	13	127	30	1	24	43	1.65
11794973--11795246	28	10.0	28	83	8	275	29	1	24	43	1.64
11797510--11797543	15	2.3	15	90	5	52	67	5	0	26	1.13
11797641--11797684	10	4.3	10	77	5	52	68	0	0	31	0.90
11797740--11797781	22	1.9	22	90	0	66	33	0	33	33	1.58
11797753--11797811	30	2.0	30	89	0	91	35	0	33	30	1.58
11797731--11797833	52	2.0	51	83	9	129	34	0	32	32	1.65
11797783--11797852	22	3.2	21	86	8	95	40	1	28	30	1.65
11799354--11799415	31	2.0	31	100	0	124	29	16	16	38	1.90
11802026--11802084	29	2.0	29	80	6	66	47	8	18	25	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11803068--11803092	8	3.1	8	100	0	50	52	0	0	48	1.00
11805068--11805097	11	2.7	11	100	0	60	56	16	10	16	1.66
11814542--11814619	25	3.2	24	70	5	66	34	19	28	17	1.95
11819120--11819154	16	2.2	16	90	5	54	77	0	2	20	0.90
11819162--11819244	31	2.7	29	78	17	78	62	4	6	26	1.39
11819229--11819260	8	3.9	8	92	8	55	78	0	0	21	0.76
11819225--11819260	17	2.1	17	100	0	72	77	0	0	22	0.76
11820191--11820233	12	3.7	12	82	14	54	81	4	13	0	0.84
11822895--11822988	31	3.0	31	79	3	91	28	20	24	26	1.99
11823081--11823140	31	1.9	31	89	0	93	26	23	28	21	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