genome.fa.s9.2.7.7.80.10.50.1000.168.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  168  of  226  ( 27023 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)
53586002--53586648	217	3.0	217	93	0	1132	28	19	23	27	1.98
53586221--53586964	390	1.9	390	93	0	1272	28	19	23	28	1.98
53586002--53586904	217	4.2	218	85	5	998	28	19	23	28	1.98
53586438--53586821	173	2.2	173	92	0	633	28	19	24	28	1.98
53586438--53586901	173	2.7	173	87	2	518	28	19	23	28	1.98
53588986--53589043	30	1.9	30	86	6	82	15	10	10	63	1.51
53597137--53597220	30	2.9	30	80	3	100	27	11	21	39	1.88
53597553--53597607	21	2.6	21	85	0	83	29	9	32	29	1.88
53598766--53598802	13	2.7	14	84	16	51	67	8	2	21	1.29
53601039--53601457	44	9.5	44	77	3	403	30	24	15	29	1.96
53601034--53601457	133	3.2	132	79	3	476	29	24	16	29	1.96
53601073--53601545	221	2.1	220	81	3	549	28	24	17	29	1.98
53601436--53602248	88	9.2	88	86	2	934	22	25	24	26	2.00
53601442--53601665	44	5.1	43	65	12	141	23	26	24	25	2.00
53601706--53602252	44	12.4	44	64	8	209	22	24	25	27	2.00
53601732--53602219	43	11.1	43	62	13	170	21	25	25	27	2.00
53601436--53602251	264	3.1	263	85	1	1051	23	25	24	26	2.00
53603519--53603551	14	2.3	15	89	5	50	27	33	12	27	1.92
53627613--53627892	44	6.4	45	79	5	259	27	17	24	30	1.97
53627640--53627891	89	2.9	87	77	4	245	28	17	24	28	1.97
53627883--53628020	44	3.1	44	64	4	107	26	29	23	20	1.99
53627875--53628096	88	2.5	88	91	0	354	29	28	22	19	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53628409--53628566	44	3.7	44	74	5	135	24	21	23	31	1.99
53634942--53634985	22	2.0	22	86	0	61	38	25	4	31	1.76
53638687--53638711	11	2.3	11	100	0	50	24	20	20	36	1.95
53644999--53645147	50	3.0	50	84	0	172	20	28	22	27	1.99
53645122--53645171	24	2.1	24	100	0	100	16	38	20	26	1.92
53653521--53653693	25	7.4	25	80	10	172	19	23	17	39	1.92
53653598--53653635	19	2.0	19	89	0	58	21	28	13	36	1.91
53653629--53653697	22	3.1	22	89	0	111	17	21	17	43	1.88
53655362--53655708	50	6.9	50	82	6	353	28	20	27	23	1.99
53665029--53665120	38	2.4	39	85	5	116	35	8	9	45	1.68
53671826--53671901	33	2.3	33	97	0	143	43	15	5	35	1.70
53674979--53675187	92	2.3	91	86	5	278	45	3	3	46	1.39
53675115--53675162	26	1.9	25	84	16	64	45	0	2	52	1.12
53675241--53675451	66	3.4	63	69	21	192	42	2	6	48	1.44
53675203--53675495	120	2.4	120	94	2	509	43	2	5	49	1.37
53675328--53675385	15	3.9	15	80	13	59	44	0	1	53	1.10
53675457--53675498	15	2.7	16	82	14	52	45	0	2	52	1.13
53675448--53675489	15	2.9	15	82	10	52	47	0	0	52	1.00
53675433--53675671	75	3.1	75	63	16	189	46	3	3	46	1.35
53675432--53675748	157	2.0	157	97	0	598	47	5	3	44	1.41
53675601--53675635	18	2.0	17	88	5	52	45	0	0	54	0.99
53675871--53675906	16	2.2	16	95	0	63	38	33	0	27	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53689875--53689908	17	1.9	18	88	5	52	61	2	0	35	1.11
53694327--53694375	25	2.0	25	95	0	89	59	10	12	18	1.60
53694401--53694431	16	1.9	16	93	0	53	29	3	9	58	1.46
53707460--53707518	30	2.0	30	96	0	109	40	13	10	35	1.78
53708124--53708160	19	1.9	19	88	0	56	67	2	27	2	1.17
53709595--53709631	9	4.1	9	85	0	56	48	13	8	29	1.71
53712452--53712593	27	5.3	27	85	3	169	37	24	19	18	1.94
53712926--53712996	28	2.5	27	81	4	79	23	19	22	33	1.97
53714870--53714898	6	4.8	6	100	0	58	82	0	0	17	0.66
53729193--53729239	24	2.0	24	100	0	94	44	21	17	17	1.86
53729219--53729491	43	6.3	43	81	7	266	28	28	16	25	1.97
53729411--53729504	41	2.3	41	80	10	111	35	22	11	30	1.90
53731043--53731074	5	6.4	5	100	0	64	81	0	0	18	0.70
53731341--53731365	5	5.0	5	100	0	50	20	0	0	80	0.72
53733975--53734020	22	2.1	21	84	4	56	21	2	52	23	1.58
53734186--53734557	149	2.5	150	89	3	570	33	13	13	39	1.84
53735584--53735637	21	2.5	21	77	14	56	33	46	0	20	1.51
53735594--53735634	14	2.9	14	85	0	55	29	48	0	21	1.50
53735661--53735693	14	2.3	15	94	5	59	36	33	0	30	1.58
53736099--53736377	41	6.9	41	87	2	323	30	30	21	18	1.97
53758379--53758433	28	1.9	29	82	10	69	36	14	10	38	1.81
53765480--53765576	49	1.9	51	87	8	146	25	13	26	34	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53769699--53769727	11	2.5	12	88	11	51	37	0	34	27	1.57
53776758--53776795	16	2.4	16	100	0	76	34	5	26	34	1.79
53780191--53780232	18	2.4	18	88	4	59	14	45	26	14	1.83
53789058--53789110	21	2.5	21	87	3	70	37	5	35	20	1.77
53789077--53789112	18	2.0	18	88	0	54	36	5	36	22	1.78
53810590--53810957	189	1.9	189	89	2	569	33	14	24	27	1.94
53812746--53812846	50	2.0	50	100	0	202	29	11	17	40	1.86
53813869--53813989	61	2.0	61	85	6	165	38	8	14	38	1.75
53824091--53824125	17	2.1	17	100	0	70	40	22	5	31	1.78
53828669--53828750	10	8.3	9	73	18	58	34	2	1	62	1.16
53828671--53828709	19	2.1	18	85	4	51	35	2	2	58	1.25
53828668--53828754	20	4.2	21	73	11	65	33	2	1	63	1.15
53829027--53829057	16	1.9	16	93	0	53	58	0	9	32	1.31
53829908--53829968	25	2.6	23	73	23	63	49	0	13	37	1.42
53852914--53852961	25	1.9	25	91	0	78	31	22	29	16	1.96
53853768--53853803	18	2.0	18	100	0	72	33	5	11	50	1.61
53865726--53865750	11	2.3	11	100	0	50	76	0	8	16	1.02
53881429--53881472	5	8.6	5	85	5	61	75	2	22	0	0.92
53894984--53895008	12	2.1	12	100	0	50	24	36	24	16	1.94
53895171--53895273	9	11.4	9	83	4	118	43	23	6	26	1.78
53895379--53895422	18	2.4	18	88	0	61	13	2	43	40	1.57
53897301--53897341	22	1.9	22	85	5	57	73	4	0	21	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53899410--53899434	12	2.1	12	100	0	50	24	0	16	60	1.36
53911302--53911340	6	6.7	6	88	11	55	17	0	10	71	1.12
53911302--53911349	18	2.6	18	83	3	60	18	2	8	70	1.22
53911302--53911389	6	14.3	6	75	9	52	18	4	6	70	1.27
53911766--53911804	19	2.1	19	85	0	51	30	30	7	30	1.85
53912421--53912539	59	2.0	59	100	0	238	31	10	23	34	1.88
53915665--53915735	36	2.0	36	85	0	97	43	14	18	23	1.86
53916621--53916691	37	2.0	35	83	10	90	54	5	2	36	1.38
53925261--53925303	22	2.0	22	85	0	59	53	9	0	37	1.33
53928068--53928102	17	1.9	19	88	11	56	20	22	0	57	1.41
53931735--53931893	20	7.8	20	70	12	81	33	6	14	45	1.72
53935506--53935551	23	2.0	23	95	0	83	39	4	19	36	1.72
53937677--53937736	19	3.0	20	72	20	61	35	3	6	55	1.43
53942120--53942152	13	2.5	13	95	0	57	36	15	9	39	1.79
53946544--53946719	45	4.0	45	84	1	230	33	23	15	27	1.95
53963971--53964007	18	2.1	18	100	0	74	43	27	0	29	1.55
53973034--53973145	14	7.7	15	69	16	76	43	9	3	42	1.55
53973048--53973145	29	3.4	29	90	1	144	43	11	4	40	1.59
53973034--53973150	57	2.0	58	85	1	155	43	10	3	42	1.55
53973034--53973150	29	4.1	29	84	2	137	43	10	3	42	1.55
53985699--53985733	18	1.9	18	88	0	52	25	14	28	31	1.95
53986457--53986536	34	2.4	34	91	2	126	23	23	15	37	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53988708--53988761	26	2.0	28	82	13	69	59	1	0	38	1.08
53991290--53991318	12	2.4	12	100	0	58	41	6	27	24	1.80
54002991--54003119	49	2.6	50	86	2	170	25	21	22	30	1.99
54002991--54003129	25	5.6	25	82	1	163	26	22	21	29	1.99
54004230--54004268	20	2.0	20	90	10	62	12	5	30	51	1.62
54004708--54004820	42	2.7	42	87	0	145	19	23	37	20	1.95
54006874--54006914	21	2.0	21	90	0	64	24	26	17	31	1.97
54020564--54020607	18	2.4	18	84	3	61	18	6	11	63	1.48
54024599--54024673	36	2.1	36	100	0	150	44	10	17	28	1.82
54028171--54028234	18	3.5	19	77	12	62	34	1	0	64	1.03

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226