genome.fa.s6.2.7.7.80.10.50.1000.138.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  138  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)
40395898--40396312	120	3.5	120	90	3	665	42	2	5	48	1.41
40396068--40396235	38	4.3	38	66	21	94	41	3	7	48	1.48
40396269--40396310	15	2.7	16	82	14	52	45	0	2	52	1.13
40396260--40396301	15	2.9	15	82	10	52	47	0	0	52	1.00
40400355--40400387	12	2.8	12	90	0	57	15	39	3	42	1.62
40404515--40404605	40	2.3	40	83	7	121	24	23	8	43	1.81
40405982--40406006	8	3.1	8	100	0	50	48	24	0	28	1.52
40407400--40407519	35	3.3	35	72	15	116	29	22	23	25	1.99
40407366--40407538	75	2.3	75	84	2	222	28	21	24	24	1.99
40416059--40416091	12	2.8	12	90	0	57	15	39	3	42	1.62
40417352--40417405	25	2.2	24	78	12	56	55	0	3	40	1.17
40419436--40419598	80	2.0	80	88	2	238	38	19	12	28	1.89
40425372--40425398	4	6.8	4	100	0	54	77	22	0	0	0.76
40427832--40427871	20	2.0	20	90	0	62	27	10	12	50	1.72
40427817--40427883	34	1.9	35	90	3	109	31	8	13	46	1.74
40427811--40427887	14	5.0	15	71	20	52	33	9	14	42	1.77
40429665--40429709	23	2.0	23	95	0	81	26	15	11	46	1.79
40430703--40430748	18	2.6	18	79	6	58	21	0	43	34	1.53
40431284--40431376	33	2.8	32	82	4	105	17	23	40	18	1.90
40436900--40436924	11	2.3	11	100	0	50	24	32	20	24	1.98
40448372--40448430	13	4.5	13	76	0	64	38	27	8	25	1.84
40448369--40448430	26	2.4	26	83	0	88	37	25	8	29	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40454682--40454726	21	2.1	22	83	4	56	48	2	8	40	1.47
40465065--40465102	17	2.2	17	100	0	76	47	26	10	15	1.78
40465165--40465199	17	2.1	17	94	0	61	65	2	5	25	1.28
40465325--40465394	2	36.5	2	86	13	103	52	1	0	45	1.09
40465518--40465557	2	20.0	2	100	0	80	50	0	0	50	1.00
40465606--40465687	24	3.4	23	71	12	65	65	2	4	26	1.25
40465590--40465693	50	2.1	51	83	3	131	59	2	7	29	1.40
40467354--40467479	28	4.5	28	88	2	182	32	12	25	29	1.93
40468178--40468477	23	12.9	23	76	12	256	27	15	17	39	1.90
40468172--40468470	93	3.2	93	96	0	544	28	15	17	38	1.90
40471673--40471714	19	2.2	20	82	4	50	30	7	11	50	1.66
40474470--40474529	27	2.2	27	90	0	93	25	31	8	35	1.85
40487975--40487999	13	1.9	13	100	0	50	32	4	0	64	1.12
40491082--40491134	18	3.0	18	70	13	56	50	0	7	41	1.30
40496737--40496774	15	2.4	16	82	4	51	28	2	0	68	1.03
40497237--40497282	21	2.1	22	84	8	58	54	2	0	43	1.12
40497581--40497619	20	1.9	21	89	5	62	51	0	0	48	1.00
40500221--40500269	25	2.0	24	84	4	62	48	2	0	48	1.12
40507953--40507988	12	3.2	12	85	14	51	58	0	0	41	0.98
40511232--40511284	22	2.4	22	83	0	70	26	13	3	56	1.54
40512049--40512090	21	2.0	22	90	4	68	57	9	7	26	1.56
40517286--40517335	15	3.4	15	81	13	52	42	8	0	50	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40520112--40520137	2	13.0	2	100	0	52	50	0	0	50	1.00
40521123--40521201	38	2.1	38	97	0	149	48	6	10	35	1.62
40521140--40521206	19	3.5	19	66	28	52	47	2	10	38	1.53
40529302--40529364	20	3.1	20	67	13	56	55	11	9	23	1.64
40541418--40541458	22	2.0	20	85	9	55	48	4	7	39	1.52
40541750--40541798	23	2.1	23	85	7	64	48	8	2	40	1.44
40541837--40541896	23	2.5	24	81	13	70	53	0	0	46	1.00
40541837--40541896	12	5.1	12	78	13	63	53	0	0	46	1.00
40541876--40541921	22	2.3	19	88	11	65	47	4	2	45	1.34
40541913--40541952	19	2.2	19	86	4	55	55	0	2	42	1.13
40541999--40542042	22	2.0	22	86	4	63	47	0	0	52	1.00
40544424--40544583	86	1.9	84	84	7	216	28	28	18	25	1.98
40545873--40545927	23	2.4	23	79	11	67	14	21	21	41	1.89
40548041--40548084	11	3.8	11	80	11	52	34	0	0	65	0.93
40548034--40548082	24	2.1	23	92	3	80	38	0	0	61	0.96
40549105--40549521	207	2.0	207	98	0	798	40	8	20	29	1.83
40551615--40551824	105	2.0	105	98	0	402	29	10	15	44	1.80
40554145--40554214	35	2.0	35	83	5	88	62	2	0	34	1.10
40554650--40554700	23	2.2	23	92	0	84	27	9	21	41	1.84
40557318--40557370	2	26.5	2	96	0	97	50	47	0	1	1.12
40558900--40559178	139	2.0	139	96	2	515	38	1	18	41	1.57
40559853--40559927	31	2.4	30	82	6	87	33	8	4	54	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40563933--40563971	19	2.0	20	90	5	62	46	30	0	23	1.53
40567502--40567526	3	8.3	3	100	0	50	0	32	0	68	0.90
40571062--40571162	42	2.4	42	81	5	105	23	13	21	40	1.89
40576428--40576457	15	2.0	15	100	0	60	46	13	13	26	1.80
40577451--40577487	9	4.1	9	92	0	65	29	10	13	45	1.77
40578665--40578717	17	2.9	18	80	11	63	43	5	15	35	1.70
40578908--40578941	17	2.1	16	89	10	52	47	11	0	41	1.40
40578922--40578963	22	1.9	21	85	9	57	40	9	2	47	1.49
40581780--40581830	25	2.2	25	89	10	81	33	0	1	64	1.05
40591322--40591365	17	2.6	16	76	13	52	15	54	0	29	1.42
40612820--40612862	21	2.0	21	90	0	68	27	25	11	34	1.91
40618286--40618311	13	2.0	13	100	0	52	46	0	7	46	1.31
40634921--40634993	21	3.7	21	77	12	75	47	0	1	50	1.09
40637740--40637805	22	3.0	22	93	0	105	30	16	27	25	1.97
40638137--40638245	31	3.3	31	78	21	130	49	28	2	19	1.62
40638130--40638277	39	4.0	38	83	12	202	50	27	2	18	1.61
40638137--40638277	70	2.0	69	94	4	248	51	26	2	19	1.61
40638413--40638475	17	3.5	17	69	12	54	34	3	12	49	1.57
40638410--40638484	37	2.0	37	94	0	132	36	4	14	45	1.64
40638483--40638513	9	3.4	9	95	0	53	25	9	22	41	1.84
40638842--40638866	12	2.1	12	100	0	50	60	0	8	32	1.26
40639677--40639768	44	2.2	41	86	7	123	13	17	18	51	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40640997--40641038	16	2.6	15	88	11	57	0	9	4	85	0.72
40641000--40641038	15	2.4	16	87	8	53	0	7	5	87	0.68
40643705--40643767	20	3.2	20	68	17	60	22	25	1	50	1.58
40643702--40643780	38	2.1	38	97	0	149	18	26	2	51	1.59
40643720--40643777	18	3.1	18	72	18	64	17	25	3	53	1.59
40643720--40643781	20	3.2	20	66	25	60	16	25	3	54	1.56
40644290--40644329	20	2.1	19	90	4	62	25	2	27	45	1.66
40645361--40645406	23	2.0	23	87	4	67	34	0	2	63	1.07
40647827--40647952	62	2.0	62	95	0	225	28	7	20	43	1.78
40654055--40654090	2	18.0	2	100	0	72	50	0	0	50	1.00
40665180--40665268	39	2.3	39	81	13	94	42	3	5	48	1.43
40673569--40673658	16	6.1	14	74	13	65	34	1	2	62	1.15
40673581--40673612	7	4.6	7	100	0	64	40	0	0	59	0.97
40673569--40673651	23	3.6	23	75	6	78	34	1	2	61	1.17
40676658--40676716	16	3.4	16	78	17	73	38	20	8	32	1.83
40676670--40676734	20	3.5	20	78	18	86	40	16	9	33	1.81
40676656--40676734	36	2.2	35	95	4	149	39	17	8	34	1.81
40676866--40676953	25	3.6	25	70	1	70	31	21	20	26	1.98
40678964--40679013	20	2.6	19	78	6	55	60	10	0	30	1.30
40678969--40679027	19	3.1	19	82	2	64	54	10	0	35	1.34
40683954--40683994	19	2.0	20	86	9	57	36	0	0	63	0.95
40684189--40684240	26	2.0	26	85	7	70	59	3	0	36	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40684496--40684529	15	2.2	16	89	5	52	50	5	0	44	1.26
40685148--40685189	8	5.1	8	81	13	50	33	2	0	64	1.07
40698371--40698420	26	1.9	26	95	0	91	32	20	18	30	1.96
40699993--40700022	6	5.0	6	95	0	51	16	3	66	13	1.37
40706453--40706481	8	3.6	8	100	0	58	24	0	0	75	0.80
40709183--40709827	322	2.0	322	100	0	1290	35	11	19	33	1.87
40716622--40716652	2	15.5	2	100	0	62	51	0	0	48	1.00
40716997--40717146	41	3.6	41	93	0	237	24	22	28	24	2.00
40728152--40728185	17	2.0	17	88	11	52	38	5	8	47	1.59
40729167--40729203	9	4.1	9	85	0	56	48	13	8	29	1.71

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