genome.fa.s1.2.7.7.80.10.50.1000.98.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  98  of  187  ( 22383 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)
29098952--29099004	26	1.9	29	85	11	76	56	1	0	41	1.10
29099184--29099267	39	2.2	39	82	8	100	41	4	5	47	1.49
29099196--29099278	39	2.1	40	93	2	141	36	7	4	51	1.51
29099926--29099959	14	2.4	14	85	0	50	44	2	0	52	1.16
29103008--29103044	9	4.1	9	92	0	65	29	10	13	45	1.77
29106653--29107042	165	2.4	165	86	5	540	29	12	14	43	1.82
29107196--29108092	164	5.5	164	86	2	1124	28	14	15	41	1.87
29108511--29109369	164	5.2	164	76	7	684	28	12	18	40	1.88
29108657--29109369	338	2.2	323	82	5	822	28	12	17	40	1.87
29112994--29113044	23	2.2	23	89	0	75	41	23	9	25	1.85
29115474--29115521	22	2.2	21	85	10	62	43	31	0	25	1.55
29115758--29115813	28	2.0	28	100	0	112	50	0	0	50	1.00
29119760--29119815	28	2.0	28	100	0	112	42	7	3	46	1.48
29121083--29121121	20	2.0	20	85	10	53	33	0	0	66	0.92
29123497--29123523	12	2.2	12	100	0	54	51	7	33	7	1.58
29127446--29127601	42	3.7	43	81	8	187	27	16	27	28	1.97
29128259--29128326	34	2.0	34	100	0	136	44	5	17	32	1.73
29134040--29134067	6	4.7	6	100	0	56	17	0	28	53	1.44
29134542--29134573	3	11.0	3	93	6	57	68	0	31	0	0.90
29135591--29135662	21	3.5	21	83	3	85	33	31	11	23	1.90
29135693--29135746	21	2.6	20	77	16	56	29	5	25	38	1.79
29135821--29135860	21	1.9	21	84	0	53	55	5	5	35	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29142354--29142415	29	2.1	29	93	0	106	17	20	11	50	1.77
29142941--29142999	26	2.3	26	82	11	68	28	1	13	55	1.48
29143055--29143375	83	3.5	92	77	16	333	27	1	14	56	1.47
29143291--29143315	11	2.3	11	100	0	50	48	0	0	52	1.00
29143193--29143391	103	2.0	103	85	4	278	30	1	13	55	1.44
29145801--29146121	49	6.6	49	87	3	427	43	10	10	35	1.73
29145864--29145941	25	3.2	25	65	23	65	43	12	11	32	1.79
29148981--29149016	17	2.1	17	89	0	54	11	19	0	69	1.18
29149081--29149154	27	2.7	27	82	0	94	21	25	31	21	1.98
29151975--29152000	13	2.0	13	100	0	52	38	7	7	46	1.61
29156549--29156594	14	3.3	14	93	0	74	26	26	2	45	1.65
29157867--29157975	41	2.6	39	75	13	96	51	2	2	43	1.30
29160311--29160336	13	2.0	13	100	0	52	38	15	7	38	1.76
29165952--29165991	16	2.4	16	87	4	53	42	17	0	40	1.49
29171602--29171999	42	9.3	42	87	3	476	34	20	19	25	1.96
29171620--29171999	169	2.2	169	85	4	505	35	20	19	25	1.96
29172473--29172536	12	5.6	12	71	17	64	1	40	18	39	1.60
29172500--29172568	21	3.3	21	93	0	111	1	40	20	37	1.61
29178036--29178340	9	35.0	9	67	14	104	30	3	19	46	1.68
29178067--29178132	25	2.6	25	75	0	69	34	4	16	43	1.68
29178139--29178208	16	4.8	16	68	22	64	27	4	22	45	1.71
29178141--29178188	25	1.9	25	86	0	69	27	4	25	43	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29178193--29178329	37	3.7	37	98	0	256	29	2	18	49	1.62
29181973--29182017	21	2.1	21	83	0	54	42	40	0	17	1.50
29182229--29182403	96	1.8	96	92	0	296	28	20	22	29	1.98
29183697--29183731	18	1.9	18	88	11	54	48	5	0	45	1.26
29194375--29194435	30	2.0	30	87	6	88	34	11	0	54	1.37
29194424--29194458	2	17.5	2	100	0	70	48	0	0	51	1.00
29198975--29199022	20	2.4	20	82	0	60	12	25	22	39	1.89
29202668--29202808	33	4.3	33	75	10	119	27	2	46	22	1.66
29202671--29202800	66	2.0	66	80	8	149	29	3	43	23	1.69
29202915--29203018	51	2.0	51	92	0	172	28	8	27	34	1.87
29203891--29203919	14	2.1	14	100	0	58	6	0	6	86	0.72
29208280--29208390	37	3.0	34	75	16	98	42	2	3	51	1.33
29217749--29217814	20	3.2	21	70	10	64	13	27	22	36	1.92
29229960--29230033	25	2.9	25	84	6	87	43	9	14	32	1.78
29237327--29237351	1	25.0	1	100	0	50	0	0	0	100	0.00
29242950--29242989	19	2.2	19	86	8	57	32	22	2	42	1.67
29244179--29244214	16	2.2	16	100	0	72	50	5	5	38	1.49
29245711--29246163	85	5.3	86	73	8	262	26	20	21	31	1.98
29245794--29246297	129	3.9	129	88	1	760	25	21	22	30	1.98
29246400--29246655	129	2.0	129	82	3	318	27	20	21	30	1.98
29246617--29246937	100	3.2	100	88	0	462	25	21	21	31	1.98
29246701--29246875	49	3.5	49	75	3	188	24	20	22	32	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29246646--29246926	51	5.6	51	73	3	219	24	22	21	30	1.99
29246992--29247725	46	16.0	46	90	0	1049	30	27	15	26	1.96
29248097--29248152	24	2.3	24	78	6	69	26	21	16	35	1.94
29248618--29248920	97	3.0	97	80	12	362	47	9	16	26	1.77
29248709--29248911	108	1.9	106	88	4	309	47	9	16	25	1.77
29254034--29254073	11	3.5	11	84	15	55	57	0	0	42	0.98
29254092--29254123	16	2.0	16	93	0	55	78	0	3	18	0.89
29263715--29263747	4	8.2	4	100	0	66	75	0	24	0	0.80
29264606--29264666	23	2.6	22	75	12	59	40	6	1	50	1.38
29266342--29266396	20	2.8	20	82	0	65	49	10	7	32	1.65
29271312--29271371	23	2.6	23	83	2	66	53	8	0	38	1.31
29274799--29274831	8	4.1	8	88	11	50	90	0	9	0	0.44
29274802--29274831	9	3.4	9	90	9	53	90	0	10	0	0.47
29278607--29278634	12	2.3	12	100	0	56	92	0	7	0	0.37
29278838--29278862	10	2.5	10	100	0	50	32	0	0	68	0.90
29280636--29280699	20	3.2	20	88	2	74	34	28	26	10	1.90
29280645--29280699	20	2.7	20	91	2	83	34	23	29	12	1.92
29286179--29286231	26	2.0	26	85	7	72	47	13	9	30	1.74
29291454--29291493	14	2.9	13	88	7	53	60	20	12	7	1.56
29291776--29291813	20	1.9	20	94	0	67	23	23	28	23	1.99
29291779--29291823	20	2.2	20	84	0	54	26	24	26	22	2.00
29294940--29294977	13	2.7	15	80	16	53	42	2	7	47	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29294940--29294983	15	3.1	15	80	12	56	45	2	6	45	1.42
29297523--29297610	30	2.9	30	76	6	97	22	36	27	13	1.92
29302238--29302310	4	19.8	4	83	13	79	24	1	0	73	0.90
29302259--29302301	3	13.7	3	83	9	50	25	2	0	72	0.97
29302246--29302309	23	2.7	23	83	11	85	25	1	0	73	0.92
29302398--29302436	19	2.0	19	90	5	60	10	2	5	82	0.93
29304087--29304127	21	2.0	21	90	0	64	14	2	4	78	1.03
29304072--29304144	27	2.7	27	83	8	78	13	4	5	76	1.11
29304092--29304145	15	3.9	14	77	18	58	14	1	5	77	1.03
29304080--29304145	6	10.0	6	74	18	51	13	3	6	77	1.08
29316356--29316432	26	3.0	26	82	0	82	33	28	24	12	1.93
29316605--29316758	27	5.7	27	82	6	170	18	16	20	44	1.87
29316596--29316758	54	3.0	54	84	1	193	19	15	21	42	1.88
29316605--29316757	81	1.9	81	86	5	220	18	16	19	44	1.87
29316714--29316801	43	2.0	43	86	0	122	20	18	17	44	1.87
29316688--29316827	70	2.0	70	81	2	165	22	17	16	44	1.87
29317343--29317380	18	2.1	19	85	5	51	73	2	21	2	1.07
29323067--29323105	20	2.0	20	89	0	60	30	12	12	43	1.81
29324007--29324177	27	6.3	27	84	2	193	23	14	16	45	1.85
29324007--29324177	81	2.1	82	85	4	231	23	14	16	45	1.85
29325035--29325074	18	2.2	19	86	8	57	70	2	25	2	1.13
29336355--29336505	50	3.0	49	72	14	146	23	24	23	29	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29336673--29336791	46	2.6	46	89	0	166	29	19	21	30	1.97
29336524--29336925	221	1.8	221	90	0	651	29	20	18	31	1.96
29345156--29345185	14	2.1	14	93	0	51	40	0	16	43	1.48
29346545--29347580	130	8.0	130	92	0	1671	25	20	22	31	1.98
29347594--29347835	50	4.9	50	71	2	173	29	22	19	28	1.98
29347594--29347858	100	2.7	100	86	0	361	29	23	20	27	1.98
29348155--29348211	24	2.4	24	81	0	69	29	24	14	31	1.94
29353801--29353831	16	1.9	16	93	0	53	48	3	9	38	1.52
29360231--29360324	39	2.4	38	87	1	125	52	8	3	36	1.48
29364690--29364791	37	2.7	37	75	17	102	34	0	3	61	1.14

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