genome.fa.s6.2.7.7.80.10.50.1000.23.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  23  of  168  ( 20060 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)
5882141--5882229	18	4.8	18	71	14	74	38	2	12	47	1.54
5882154--5882232	22	3.8	22	71	21	64	37	2	12	46	1.55
5885066--5885147	15	5.5	15	72	13	62	32	43	1	21	1.61
5886078--5886145	15	4.9	14	71	16	52	41	35	0	23	1.55
5886081--5886118	15	2.5	15	86	0	58	36	42	0	21	1.53
5886704--5886982	41	6.8	41	76	8	203	34	25	23	16	1.95
5886745--5886982	82	2.9	81	80	7	257	34	25	23	15	1.95
5887062--5887137	40	1.9	40	83	5	100	18	30	23	27	1.98
5892184--5892261	38	2.1	38	95	0	138	44	15	24	15	1.85
5904130--5904215	25	3.1	27	77	19	97	60	4	2	32	1.30
5909449--5909504	5	11.0	5	79	11	60	76	5	0	17	0.96
5910367--5910407	21	1.9	22	85	5	57	24	19	0	56	1.42
5912613--5912824	76	2.8	76	83	0	253	34	21	19	24	1.96
5913764--5914197	106	4.1	106	90	1	647	34	16	17	32	1.92
5914338--5914367	15	2.0	15	100	0	60	60	0	0	40	0.97
5914617--5914701	3	28.7	3	71	19	63	62	7	1	29	1.29
5915422--5915450	14	2.1	14	93	6	51	6	3	6	82	0.93
5915973--5916064	9	10.2	9	84	4	123	26	8	22	42	1.82
5916305--5916351	17	2.7	18	86	6	69	2	0	25	72	0.96
5917076--5917237	45	3.6	44	83	6	166	26	21	22	29	1.99
5917353--5917648	128	2.3	129	86	3	400	28	19	22	30	1.98
5917458--5917647	44	4.5	41	72	10	141	27	19	24	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5917718--5918669	50	19.1	50	73	2	676	25	19	21	33	1.97
5917735--5918669	100	9.4	100	85	1	1162	25	19	21	33	1.97
5918667--5919117	132	3.4	132	85	5	628	26	24	19	28	1.99
5919758--5919804	19	2.5	19	86	6	60	44	10	19	25	1.82
5921307--5921742	106	4.1	106	91	1	658	33	16	17	31	1.93
5921968--5921999	15	2.1	15	100	0	64	53	0	0	46	1.00
5921959--5921997	15	2.4	16	91	8	62	53	0	0	46	1.00
5922149--5922251	3	34.7	3	76	16	99	63	5	0	30	1.24
5922984--5923012	14	2.1	14	93	6	51	6	3	6	82	0.93
5926627--5927068	144	3.1	143	83	4	559	32	15	23	28	1.95
5932683--5932716	6	5.5	6	89	3	50	14	20	29	35	1.93
5936478--5936547	17	4.1	17	98	0	122	42	2	28	25	1.69
5939756--5939804	24	2.0	24	84	7	64	34	6	2	57	1.35
5943706--5943752	18	2.6	18	93	0	76	29	21	19	29	1.97
5953698--5953742	22	2.0	22	91	0	72	11	22	22	44	1.84
5953830--5954140	43	7.3	42	85	1	345	26	29	19	25	1.99
5953830--5954140	129	2.4	128	83	2	390	26	29	19	25	1.99
5953830--5954136	86	3.6	85	83	2	391	26	29	19	25	1.99
5959046--5959089	21	2.2	20	87	4	61	68	4	6	20	1.31
5960422--5960461	19	2.0	21	85	9	57	20	7	17	55	1.66
5963498--5963661	46	3.6	46	81	0	157	29	25	17	28	1.97
5969204--5969251	15	3.1	15	90	6	69	47	6	0	45	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5973533--5973563	16	2.0	16	93	6	55	16	6	6	70	1.29
5974417--5974475	17	3.4	17	77	11	57	13	20	30	35	1.91
5976661--5976704	18	2.4	19	77	11	56	25	25	13	36	1.92
5980386--5980463	32	2.5	30	84	10	104	37	2	0	60	1.11
5982903--5983079	88	2.0	88	100	0	354	40	9	20	29	1.83
5983827--5983851	2	12.5	2	100	0	50	52	0	0	48	1.00
5984567--5984648	29	2.8	30	80	10	96	51	20	19	8	1.73
5989282--5989336	21	2.5	22	76	8	58	70	10	12	5	1.31
5989284--5989337	22	2.5	21	80	14	56	70	11	12	5	1.32
5990003--5990064	31	2.1	30	87	6	90	51	8	0	40	1.31
5990003--5990067	29	2.2	28	84	10	78	50	7	0	41	1.31
6006128--6006161	2	17.0	2	100	0	68	50	0	0	50	1.00
6007028--6007099	37	2.0	36	89	8	110	41	12	22	23	1.88
6009756--6009792	15	2.4	15	90	4	56	24	13	35	27	1.93
6010250--6010332	30	2.8	30	77	3	78	18	13	27	40	1.87
6014863--6014897	8	4.4	8	86	13	54	11	0	0	88	0.51
6014863--6014892	9	3.4	9	95	4	53	10	0	0	90	0.47
6014863--6014897	16	2.1	16	94	5	61	11	0	0	88	0.51
6015145--6015466	109	3.0	109	90	0	504	31	16	18	33	1.93
6019547--6019649	9	10.4	9	71	15	71	56	0	1	40	1.17
6019543--6019649	31	3.5	31	83	12	141	56	0	1	41	1.17
6019551--6019648	50	2.0	49	82	6	117	57	1	2	39	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6022078--6022136	31	1.9	31	92	0	100	42	5	10	42	1.60
6022788--6022844	28	1.9	31	83	16	77	63	1	1	33	1.15
6027620--6027655	18	2.0	18	94	0	63	33	19	11	36	1.87
6032721--6032770	20	2.6	19	93	3	82	56	12	0	32	1.36
6032706--6032754	10	5.0	10	77	20	50	61	10	0	28	1.29
6036409--6036608	109	1.9	106	93	3	346	37	7	16	40	1.75
6041127--6041172	23	2.0	23	100	0	92	39	21	13	26	1.90
6051818--6051874	15	3.8	15	92	0	96	12	12	12	63	1.53
6051807--6051871	30	2.2	30	86	5	87	12	13	13	60	1.60
6052337--6052397	29	2.1	28	82	8	70	39	11	19	29	1.87
6052516--6052578	32	2.0	30	81	6	72	19	0	23	57	1.41
6052580--6052661	29	2.8	29	85	5	103	36	4	25	32	1.77
6062273--6062334	25	2.5	25	91	0	97	19	22	11	46	1.81
6064461--6064591	67	2.0	66	92	1	217	25	33	20	19	1.97
6073322--6073364	15	2.8	14	78	21	50	67	0	2	30	1.03
6078841--6078878	20	1.9	20	100	0	76	34	7	15	42	1.76
6079723--6079780	7	7.8	8	88	9	63	36	0	0	63	0.94
6085531--6085559	2	14.5	2	100	0	58	48	0	0	51	1.00
6087914--6087944	15	2.0	16	93	6	55	70	12	0	16	1.16
6091366--6091401	18	2.0	18	100	0	72	33	27	11	27	1.91
6095137--6095289	22	7.0	22	90	0	225	32	14	26	26	1.94
6095418--6095446	2	14.5	2	100	0	58	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6096071--6096098	14	2.0	14	100	0	56	57	0	14	28	1.38
6096981--6097025	22	2.2	19	84	11	54	66	4	4	24	1.29
6097626--6097674	21	2.4	21	79	3	55	57	2	2	38	1.22
6102708--6102745	15	2.6	15	83	4	51	44	15	7	31	1.75
6102712--6102779	34	2.0	35	85	2	93	44	13	7	35	1.71
6105719--6105788	3	23.3	3	97	0	131	31	0	1	67	1.00
6106037--6106097	32	1.9	32	82	0	77	36	11	3	49	1.55
6122885--6122930	15	2.8	17	80	9	51	58	2	2	36	1.22
6123595--6123681	19	4.6	19	94	0	147	41	5	11	41	1.65
6123596--6123681	38	2.3	38	97	0	163	40	5	11	41	1.65
6123622--6123704	19	4.0	22	81	12	70	39	4	15	39	1.69
6123670--6123714	23	2.0	23	82	4	56	35	4	15	44	1.67
6124002--6124048	21	2.2	21	85	7	60	27	8	0	63	1.23
6129425--6129467	7	6.1	7	86	0	50	30	37	2	30	1.70
6129432--6129548	7	16.7	7	82	0	99	23	29	6	40	1.80
6131621--6131663	21	2.0	21	100	0	86	18	25	18	37	1.94
6138045--6138089	12	3.5	14	82	14	53	28	0	0	71	0.87
6138051--6138089	12	3.4	11	89	10	60	28	0	0	71	0.86
6146475--6146561	30	2.8	30	77	5	93	52	12	11	22	1.71
6149429--6149505	40	1.9	39	84	7	102	38	6	3	50	1.47
6149444--6149511	17	3.9	18	69	16	54	38	5	5	50	1.51
6154000--6154179	20	9.0	20	64	7	69	35	14	30	20	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6153983--6154221	40	6.0	40	88	0	334	35	15	29	19	1.93
6160976--6161264	40	7.2	40	83	0	335	37	19	25	17	1.93
6164904--6164942	2	20.0	2	94	5	71	48	0	0	51	1.00
6176485--6176515	2	15.5	2	100	0	62	48	0	0	51	1.00
6177324--6177374	25	2.0	26	84	3	68	37	11	11	39	1.79
6177483--6177522	21	1.9	21	89	0	62	55	0	0	45	0.99
6180205--6180245	14	2.9	14	85	0	55	31	0	0	68	0.90
6192461--6192514	23	2.3	24	78	15	60	42	25	3	27	1.72
6213528--6213582	28	2.0	27	82	3	65	45	5	16	32	1.70
6215007--6215568	44	12.9	45	70	15	276	27	23	19	29	1.98

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