genome.fa.s4.2.7.7.80.10.50.1000.173.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  173  of  198  ( 23681 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)
54175748--54175936	101	1.9	101	80	8	224	27	6	5	60	1.44
54177525--54177555	14	2.2	14	94	0	53	48	12	0	38	1.42
54179484--54179515	12	2.6	13	85	14	50	56	6	0	37	1.25
54189007--54189092	43	2.0	43	100	0	172	23	18	23	34	1.96
54202215--54202258	16	2.7	16	83	16	63	56	0	0	43	0.99
54205112--54205146	17	2.1	17	89	10	54	57	8	0	34	1.29
54205280--54205313	15	2.4	14	86	13	52	50	0	17	32	1.47
54206987--54207387	44	8.9	44	77	9	335	29	19	17	33	1.95
54206980--54207387	133	3.0	132	76	7	338	28	19	17	33	1.95
54206954--54207387	177	2.4	180	81	5	491	28	19	17	33	1.95
54207341--54207669	51	6.6	51	74	10	293	26	19	18	35	1.95
54207314--54207633	147	2.2	146	80	7	355	27	19	19	33	1.96
54207641--54207690	21	2.4	21	89	0	73	22	22	12	44	1.85
54207662--54207853	102	1.9	102	89	2	296	31	19	15	33	1.93
54207763--54207897	44	3.1	43	75	6	137	27	20	18	34	1.96
54214227--54214280	28	1.9	28	84	0	72	22	11	18	48	1.79
54219605--54219639	17	2.1	17	89	10	54	57	8	0	34	1.29
54219820--54219864	3	15.3	3	82	13	58	68	2	0	28	1.01
54225009--54225044	18	2.0	18	94	0	63	33	19	5	41	1.75
54227092--54227116	3	8.3	3	100	0	50	0	68	0	32	0.90
54230124--54230202	23	3.2	24	75	21	76	49	0	1	49	1.09
54230239--54230282	18	2.5	17	85	3	52	56	2	0	40	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54230922--54230955	12	2.8	12	86	0	50	76	2	0	20	0.92
54235167--54235207	19	2.1	20	86	13	59	70	9	0	19	1.14
54235166--54235241	31	2.6	29	78	16	75	64	11	2	21	1.38
54237304--54237448	71	2.0	71	82	0	173	28	13	9	47	1.75
54247123--54247179	3	20.0	3	75	13	50	31	3	0	64	1.10
54248203--54248367	51	3.3	50	92	0	267	28	24	14	32	1.95
54251998--54252044	24	2.0	24	87	8	69	31	10	0	57	1.33
54251998--54252035	12	3.2	12	82	10	51	34	10	0	55	1.34
54256738--54256787	22	2.3	22	82	3	66	44	2	0	54	1.11
54265159--54265196	19	2.0	19	94	0	67	63	7	0	28	1.23
54272878--54272927	25	2.0	25	92	0	82	22	14	18	46	1.84
54276958--54277147	4	47.5	4	100	0	380	24	0	25	50	1.50
54277686--54277860	30	5.9	29	75	8	140	32	23	4	40	1.73
54277684--54277817	59	2.2	60	81	5	164	34	21	3	40	1.71
54278400--54278429	14	2.1	15	93	6	53	60	0	40	0	0.97
54279815--54280057	42	5.8	42	87	4	332	27	23	19	29	1.98
54279815--54280054	85	2.9	85	90	4	355	27	22	19	30	1.98
54282105--54282167	17	3.6	17	78	17	67	33	12	7	46	1.71
54282111--54282204	18	5.3	18	71	11	59	41	10	6	41	1.65
54282230--54282522	18	16.6	18	77	12	261	30	13	9	46	1.76
54282230--54282522	53	5.5	53	78	11	273	30	13	9	46	1.76
54282230--54282522	35	8.3	36	77	12	261	30	13	9	46	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54284955--54284991	3	12.3	3	100	0	74	32	0	0	67	0.91
54290926--54291112	9	20.9	9	71	12	109	34	0	18	45	1.54
54290928--54291059	55	2.3	59	83	10	166	34	0	19	45	1.56
54290926--54291118	36	5.7	34	72	15	125	35	0	18	46	1.53
54291461--54291658	28	6.3	29	64	22	80	51	12	3	33	1.55
54291508--54291701	38	5.7	37	69	23	165	50	14	2	32	1.56
54291482--54291694	66	3.2	66	95	0	363	50	13	2	33	1.56
54294249--54294558	124	2.5	124	87	2	433	28	19	16	35	1.94
54294249--54294577	126	2.6	123	85	2	408	28	20	16	35	1.94
54294677--54294722	21	2.1	22	84	11	60	47	0	4	47	1.21
54294928--54294973	21	2.1	22	84	11	60	47	0	4	47	1.21
54294521--54295022	251	2.0	251	97	0	952	35	10	14	39	1.80
54295544--54295591	21	2.3	21	85	3	71	37	37	4	20	1.72
54295731--54295780	21	2.4	21	75	0	55	44	36	0	20	1.52
54295858--54295898	14	2.9	14	81	3	55	56	26	0	17	1.41
54297298--54297525	43	5.3	41	77	10	206	31	29	17	21	1.96
54297321--54297529	86	2.4	87	86	4	300	31	29	17	21	1.96
54300465--54300502	2	19.0	2	100	0	76	50	0	0	50	1.00
54302535--54302567	14	2.4	14	94	0	57	0	9	24	66	1.20
54302611--54302683	23	3.1	23	94	2	119	27	5	6	60	1.45
54303439--54303559	61	2.0	63	86	3	174	50	17	0	31	1.52
54304075--54304309	41	5.7	41	89	2	355	28	31	20	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54304075--54304306	123	1.9	123	92	0	392	28	30	21	20	1.98
54312791--54312832	19	2.3	19	84	16	61	71	4	0	23	1.05
54319057--54319105	26	1.9	25	84	12	64	42	2	30	24	1.66
54320596--54320645	26	1.9	26	83	0	64	32	4	8	56	1.47
54326711--54326753	19	2.1	22	87	12	65	55	0	0	44	0.99
54326825--54326921	33	2.8	35	72	20	89	50	1	3	45	1.24
54327394--54327453	24	2.5	24	86	5	77	61	1	0	36	1.06
54329039--54329086	22	2.3	21	80	20	57	43	14	22	18	1.87
54329316--54329381	31	2.2	30	84	13	82	46	0	0	53	1.00
54329435--54329491	15	3.5	15	71	17	51	49	1	1	47	1.22
54342353--54342406	23	2.4	23	84	9	67	53	3	3	38	1.36
54342383--54342420	16	2.4	16	90	0	58	47	5	5	42	1.48
54345254--54345349	45	2.1	45	92	3	158	36	12	13	37	1.83
54346786--54346817	10	3.2	10	90	0	55	53	0	6	40	1.26
54347541--54347578	7	5.4	7	93	0	58	68	13	0	18	1.21
54348380--54348496	42	2.7	43	77	5	112	26	16	24	32	1.96
54350355--54350411	28	2.0	28	83	12	73	36	22	0	40	1.55
54353603--54353650	21	2.3	20	85	3	60	35	18	4	41	1.70
54354402--54354438	19	1.9	19	88	0	56	43	0	18	37	1.51
54354574--54354638	5	13.2	5	75	15	64	38	0	3	58	1.14
54358050--54358114	21	3.1	21	81	0	94	16	21	24	36	1.94
54365694--54365740	21	2.3	20	88	3	67	36	19	4	40	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54369028--54369071	12	3.6	12	81	3	52	45	9	2	43	1.48
54369289--54369339	19	2.7	19	79	11	68	23	3	7	64	1.37
54377367--54377479	60	1.9	60	81	3	138	39	6	16	37	1.74
54377357--54377490	60	2.2	59	77	3	135	39	5	14	40	1.69
54378166--54378206	22	1.9	21	90	5	64	60	0	2	36	1.10
54385384--54385425	22	2.0	21	81	9	50	50	0	2	47	1.14
54387651--54387715	18	3.6	18	77	8	60	29	29	26	15	1.96
54391138--54391175	19	2.0	19	90	10	60	39	0	5	55	1.23
54401041--54401205	82	2.0	82	96	0	303	42	2	10	44	1.51
54404296--54404387	48	1.9	48	95	0	166	33	5	11	48	1.63
54405006--54405040	14	2.5	14	95	0	61	40	5	20	34	1.76
54406352--54406397	2	23.5	2	95	4	85	52	0	0	47	1.00
54406921--54406988	31	2.2	31	84	5	84	64	10	0	25	1.24
54407133--54407171	6	6.2	6	88	11	60	0	46	0	53	1.00
54420750--54420812	32	2.0	31	84	3	81	41	1	7	49	1.42
54428530--54428577	20	2.4	20	79	6	53	56	6	16	20	1.62
54435573--54435604	16	2.0	16	93	0	55	37	21	25	15	1.93
54447216--54447252	16	2.3	16	95	0	65	32	10	8	48	1.67
54447216--54447261	16	3.1	15	82	14	51	30	8	8	52	1.62
54450233--54450284	21	2.5	21	96	0	95	26	7	28	36	1.84
54454316--54454340	1	25.0	1	100	0	50	0	0	0	100	0.00
54455546--54455609	19	3.4	18	80	6	65	62	0	1	35	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54455834--54455890	19	3.0	18	75	10	60	24	5	0	70	1.08
54455875--54455952	30	2.6	29	84	11	95	23	5	0	71	1.05
54466654--54466704	13	3.9	13	84	0	75	35	27	5	31	1.81
54469018--54469103	43	2.0	44	93	2	147	52	4	18	24	1.64
54476262--54476306	2	22.5	2	100	0	90	48	0	0	51	1.00
54484421--54484459	20	2.0	20	85	5	53	41	0	5	53	1.23
54484932--54484974	21	1.9	21	86	13	59	46	11	2	39	1.53
54486592--54486628	2	18.5	2	100	0	74	48	0	0	51	1.00
54489382--54489432	25	2.0	25	96	0	93	41	1	3	52	1.31
54498789--54498828	21	1.9	21	94	0	71	37	7	15	40	1.75

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