genome.fa.s3.2.7.7.80.10.50.1000.23.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  23  of  150  ( 17918 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)
6018212--6018261	25	2.0	25	100	0	100	28	28	4	40	1.74
6025955--6026022	31	2.2	31	83	0	91	47	16	8	27	1.76
6027535--6027560	7	3.7	7	100	0	52	42	0	0	57	0.98
6035829--6035888	29	2.0	30	81	9	70	48	0	5	46	1.24
6039942--6039966	13	1.9	13	100	0	50	0	0	8	92	0.40
6042518--6042561	19	2.3	20	84	11	65	61	0	2	36	1.09
6042525--6042560	18	1.9	19	94	5	65	61	0	2	36	1.11
6043568--6043608	3	13.7	3	100	0	82	68	0	0	31	0.90
6049758--6049819	3	20.7	3	100	0	124	67	0	0	32	0.91
6052465--6052521	27	2.1	27	86	0	78	29	21	22	26	1.99
6053761--6053793	15	2.2	15	100	0	66	42	15	18	24	1.88
6056242--6056269	12	2.3	12	100	0	56	75	0	0	25	0.81
6056434--6056489	26	2.2	26	81	12	73	39	0	0	60	0.97
6056432--6056478	23	2.0	25	83	8	62	40	0	0	59	0.97
6056432--6056488	25	2.2	25	85	14	73	38	0	0	61	0.96
6057804--6057847	20	2.2	20	84	8	54	63	4	0	31	1.14
6059166--6059200	2	17.5	2	100	0	70	51	0	0	48	1.00
6065721--6066127	138	2.9	138	89	0	627	30	23	23	22	1.99
6068823--6068856	11	2.9	12	86	8	52	85	0	11	2	0.71
6068824--6068858	18	1.9	18	88	0	52	85	0	11	2	0.69
6069692--6069729	14	2.8	14	81	18	53	21	0	0	78	0.74
6073308--6073390	2	41.5	2	97	0	157	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6074896--6074933	2	19.0	2	94	0	67	50	2	0	47	1.15
6074899--6074961	18	3.5	18	82	6	74	47	7	0	44	1.32
6079006--6079078	19	3.9	19	74	10	62	80	10	5	2	0.97
6079001--6079078	31	2.5	31	80	17	90	78	11	6	3	1.07
6079020--6079077	25	2.4	23	83	13	73	81	8	6	3	0.98
6079018--6079066	13	3.9	12	76	7	53	81	8	6	4	0.97
6079591--6079628	15	2.7	14	88	8	51	65	0	21	13	1.26
6079582--6079626	22	2.0	23	83	12	58	64	0	20	15	1.29
6080915--6081054	45	3.2	45	65	4	122	30	20	25	24	1.98
6080883--6081086	88	2.3	88	93	0	336	25	22	27	25	2.00
6081078--6081794	100	7.2	100	90	0	1096	30	22	24	22	1.99
6083613--6083646	2	17.0	2	100	0	68	50	0	0	50	1.00
6083629--6083686	28	2.0	29	83	3	73	39	8	0	51	1.33
6086702--6086755	20	2.6	20	85	5	63	62	0	1	35	1.06
6086804--6086842	20	2.0	20	89	0	60	28	17	17	35	1.94
6086993--6087076	28	2.9	27	77	10	78	60	2	0	36	1.10
6087208--6087272	26	2.5	26	82	9	96	27	0	4	67	1.10
6087217--6087265	13	4.1	12	76	23	50	28	0	2	69	1.00
6088994--6089071	18	4.2	18	66	16	52	42	0	2	55	1.13
6093864--6093898	17	2.0	18	88	5	54	40	2	0	57	1.14
6095377--6095435	29	2.1	29	81	15	70	25	3	16	54	1.58
6097503--6097527	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6099248--6099626	125	3.0	125	89	3	564	30	16	21	32	1.95
6102790--6103007	116	1.9	116	96	0	400	42	9	9	38	1.70
6103012--6103055	22	2.1	21	87	8	63	31	0	22	45	1.53
6103038--6103390	29	12.3	29	90	5	556	26	0	27	45	1.58
6103066--6103120	23	2.4	21	100	0	74	27	0	25	47	1.52
6103038--6103390	88	4.1	87	92	3	556	26	0	27	45	1.58
6103038--6103390	117	3.1	115	91	5	563	26	0	27	45	1.58
6103416--6103501	43	2.0	45	88	4	131	50	11	0	38	1.39
6105514--6105700	94	2.0	94	94	0	329	43	16	5	34	1.71
6105914--6105946	10	3.0	11	86	13	50	45	0	36	18	1.49
6109726--6109791	13	4.6	14	75	17	64	57	1	0	40	1.08
6109726--6109791	29	2.3	29	81	5	80	57	1	0	40	1.08
6109755--6109791	16	2.3	17	86	13	60	62	0	0	37	0.96
6110719--6111020	107	2.8	107	96	0	550	31	20	20	27	1.98
6112002--6112044	3	14.7	3	90	4	70	69	2	0	27	1.00
6112636--6112669	2	17.0	2	87	0	50	52	2	0	44	1.16
6115905--6115947	22	2.0	22	86	9	61	60	11	9	18	1.57
6115913--6115991	22	3.6	22	77	0	77	64	11	10	13	1.50
6126384--6126452	35	2.0	35	97	0	129	27	7	14	50	1.69
6128554--6128586	12	2.8	12	95	0	57	45	3	0	51	1.16
6128566--6128623	18	3.1	19	73	16	66	39	1	0	58	1.08
6128613--6128652	21	1.9	21	89	0	62	37	2	0	60	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6128612--6128659	21	2.2	20	79	13	51	33	2	4	60	1.27
6129494--6129530	11	3.4	11	84	0	56	40	0	16	43	1.48
6133508--6133549	21	2.0	20	82	13	50	42	4	4	47	1.45
6134008--6134052	3	15.0	3	100	0	90	66	0	0	33	0.92
6134305--6134351	25	1.9	24	86	4	67	61	2	2	34	1.20
6137350--6137382	12	2.8	12	90	4	50	51	9	3	36	1.49
6137287--6137488	112	1.8	110	94	2	359	39	14	4	41	1.67
6137991--6138015	13	1.9	13	100	0	50	68	24	0	8	1.16
6143707--6143856	41	3.7	41	88	0	219	24	26	19	30	1.98
6144328--6144360	12	2.8	12	90	4	50	51	9	3	36	1.49
6144316--6144584	110	2.4	114	92	3	456	41	14	4	40	1.64
6145087--6145111	13	1.9	13	100	0	50	68	24	0	8	1.16
6147803--6147845	22	2.0	22	90	0	68	11	20	25	41	1.86
6148004--6148128	43	2.9	42	80	7	135	22	19	24	33	1.97
6148139--6148294	43	3.6	44	75	3	156	26	32	19	21	1.97
6148600--6148711	21	5.3	21	82	0	116	4	42	16	35	1.69
6148600--6148701	42	2.4	42	86	0	132	3	43	16	36	1.67
6148683--6148829	66	2.2	66	86	4	199	13	28	18	39	1.89
6148722--6148852	66	2.0	66	87	3	192	15	24	19	41	1.89
6154529--6154874	31	11.4	31	78	13	351	38	2	11	47	1.52
6154597--6154766	56	3.0	56	100	0	340	39	1	10	48	1.48
6154694--6154881	22	8.6	22	68	20	94	39	1	10	47	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6154709--6154862	34	4.7	34	83	9	212	40	1	10	47	1.49
6154553--6154862	90	3.4	91	82	11	343	39	1	10	48	1.49
6155253--6155299	2	23.5	2	80	8	51	46	4	4	44	1.42
6155474--6155526	24	2.2	24	93	0	88	49	1	5	43	1.37
6156130--6156197	33	2.1	33	94	0	118	35	29	2	32	1.73
6156419--6156458	15	2.8	14	85	7	53	37	2	35	25	1.69
6156433--6156489	23	2.4	22	80	13	60	36	1	42	19	1.62
6156452--6156505	23	2.3	23	84	6	65	38	1	38	20	1.63
6157843--6157986	41	3.5	41	96	0	243	31	28	25	14	1.95
6157900--6157973	24	3.4	24	63	25	65	28	29	25	16	1.97
6159787--6159845	27	2.2	27	93	0	100	18	32	25	23	1.97
6160553--6160615	27	2.3	27	94	0	108	20	26	31	20	1.98
6171649--6171717	26	2.7	26	95	4	122	44	8	0	46	1.34
6171784--6171877	27	3.5	27	89	2	136	26	28	27	17	1.97
6171966--6172000	12	3.1	12	92	8	56	60	0	34	5	1.21
6172022--6172060	19	2.0	21	85	10	55	23	0	10	66	1.22
6172405--6172435	12	2.6	12	94	0	53	19	0	19	61	1.35
6172982--6173035	18	3.0	18	94	0	90	38	14	37	9	1.79
6178061--6178112	21	2.5	21	93	0	86	9	38	0	51	1.35
6178823--6179024	21	9.5	21	69	17	98	0	32	0	67	0.91
6178834--6178936	39	2.9	33	73	25	93	0	32	0	67	0.90
6178818--6179006	38	5.0	37	76	14	154	0	31	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6178876--6179025	4	37.0	4	72	16	96	0	33	0	66	0.92
6178843--6178981	44	3.3	43	79	15	175	0	30	0	69	0.89
6178862--6178977	29	4.2	28	76	14	93	0	31	0	68	0.90
6178819--6178981	82	2.0	78	87	8	229	0	29	0	70	0.87
6178819--6179026	70	2.8	72	77	18	182	0	32	0	67	0.91
6178947--6179034	20	4.3	22	74	20	84	0	40	0	59	0.98
6178842--6179025	82	2.3	82	84	8	234	0	33	0	66	0.92
6178823--6179028	77	2.9	71	73	14	183	0	33	0	66	0.92
6201086--6201143	23	2.5	24	80	11	75	51	1	0	46	1.11
6204221--6204361	72	2.0	72	91	2	230	41	14	15	28	1.87

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