genome.fa.s3.2.7.7.80.10.50.1000.20.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  20  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)
5265574--5265686	9	12.6	9	72	10	97	36	0	17	45	1.55
5265583--5265677	27	3.5	27	78	5	120	36	1	16	45	1.55
5265573--5265686	54	2.1	54	95	0	201	36	0	17	44	1.55
5265697--5265721	13	1.9	13	100	0	50	44	8	0	48	1.32
5265966--5265998	17	1.9	17	100	0	66	48	6	15	30	1.69
5266480--5266702	43	5.2	43	86	3	290	31	29	17	21	1.96
5266480--5266707	86	2.7	86	88	4	320	32	29	16	21	1.96
5268423--5268480	22	2.6	22	77	20	59	36	34	0	29	1.58
5268503--5268543	22	1.9	21	85	5	55	36	31	0	31	1.58
5268474--5268551	21	3.7	21	77	6	59	35	38	0	25	1.56
5268892--5269009	41	2.9	41	92	2	193	25	33	20	21	1.97
5270408--5270902	127	4.0	127	87	2	695	23	22	18	35	1.95
5270400--5270898	125	4.0	125	86	2	686	23	21	18	36	1.95
5270408--5270902	252	2.0	246	88	3	740	23	22	18	35	1.95
5271519--5271649	21	6.1	21	74	11	104	51	29	0	19	1.46
5271515--5271649	7	19.0	7	71	5	74	50	30	0	19	1.48
5271675--5271827	41	3.7	41	84	6	141	23	24	16	35	1.94
5273406--5273442	17	2.2	17	95	0	65	35	2	5	56	1.36
5276024--5276089	34	1.9	34	93	6	116	31	12	10	45	1.76
5280258--5280311	5	10.6	5	80	4	54	18	7	0	74	1.05
5281284--5281309	13	2.0	13	100	0	52	38	15	23	23	1.92
5286740--5286768	14	2.1	14	100	0	58	20	6	37	34	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5290884--5290937	2	28.0	2	85	7	76	48	3	0	48	1.19
5291800--5291824	12	2.1	12	100	0	50	68	0	0	32	0.90
5293377--5293428	26	2.0	26	100	0	104	7	11	19	61	1.53
5297942--5298051	33	3.3	33	68	12	89	31	17	24	26	1.97
5297942--5298119	68	2.6	68	86	3	225	30	15	24	28	1.96
5301791--5301953	43	3.8	42	78	4	157	31	25	16	26	1.96
5305600--5305760	33	4.8	32	73	8	133	30	14	25	29	1.95
5305533--5305772	101	2.4	101	92	0	390	30	14	25	30	1.95
5310703--5310778	25	3.0	25	78	3	73	19	23	18	38	1.93
5310713--5310782	25	2.8	25	80	4	79	17	24	20	38	1.93
5310784--5310869	25	3.5	25	74	13	70	19	29	19	31	1.97
5310852--5310932	25	3.3	24	70	11	65	17	27	20	34	1.95
5310875--5310931	25	2.3	25	84	0	69	17	28	19	35	1.94
5314030--5314142	50	2.3	50	80	0	127	29	23	26	21	1.99
5314415--5314453	20	2.0	20	90	10	62	56	5	23	15	1.59
5314704--5314736	17	1.9	17	100	0	66	42	6	27	24	1.78
5319298--5319347	17	2.9	17	96	0	91	44	6	26	24	1.76
5321622--5321901	146	1.9	146	100	0	560	33	13	13	38	1.85
5327868--5327923	22	2.5	23	82	2	69	51	1	1	44	1.22
5327899--5327938	16	2.5	16	91	0	62	47	2	7	42	1.45
5328011--5328047	9	4.1	9	100	0	74	32	0	10	56	1.34
5328144--5328187	24	1.9	24	90	9	74	61	2	0	36	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5342875--5342961	43	2.0	43	95	0	156	25	22	18	33	1.97
5347762--5347804	22	1.9	23	86	13	63	55	0	6	37	1.27
5349073--5349143	13	5.4	12	72	21	54	40	1	1	56	1.17
5356920--5356971	20	2.5	21	75	12	54	61	0	1	36	1.07
5362725--5362753	2	14.5	2	100	0	58	51	48	0	0	1.00
5364306--5364357	3	17.3	3	91	0	86	0	30	0	69	0.89
5369956--5369981	12	2.2	12	100	0	52	38	46	7	7	1.61
5371185--5371229	23	2.0	23	95	0	81	40	22	8	28	1.84
5374976--5375020	6	7.3	6	90	5	72	15	20	0	64	1.29
5375060--5375089	6	5.0	6	91	0	51	13	20	0	66	1.24
5378837--5379027	36	5.0	36	81	12	229	37	13	19	29	1.90
5378801--5378991	82	2.3	82	94	0	328	37	12	20	29	1.89
5383083--5383111	2	15.0	2	92	7	51	48	0	0	51	1.00
5384535--5384587	20	2.7	19	80	8	61	28	5	5	60	1.42
5384526--5384590	20	3.5	17	70	25	51	27	4	4	63	1.34
5384918--5384944	13	2.1	13	100	0	54	14	37	14	33	1.88
5384969--5384998	6	5.0	6	100	0	60	16	0	16	66	1.25
5388016--5388040	13	1.9	13	100	0	50	32	0	20	48	1.50
5392024--5392083	16	3.8	16	78	8	59	70	0	5	25	1.08
5392834--5392881	24	2.0	24	88	8	71	12	14	8	64	1.49
5392847--5392883	12	3.1	12	96	0	65	10	16	8	64	1.47
5394949--5394975	13	2.1	13	100	0	54	11	0	14	74	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5402173--5402212	20	2.0	20	95	0	71	30	12	25	32	1.92
5405687--5405731	16	2.8	17	74	12	51	46	2	8	42	1.47
5405837--5405869	14	2.5	13	90	9	50	57	0	0	42	0.98
5406677--5406724	24	2.0	24	88	8	71	12	14	8	64	1.49
5406690--5406726	12	3.1	12	96	0	65	10	16	8	64	1.47
5407212--5407282	10	6.7	10	73	12	52	63	1	2	32	1.18
5407212--5407269	11	5.1	11	76	13	55	63	0	3	32	1.11
5407215--5407264	25	2.1	24	88	7	75	70	0	4	26	1.05
5410088--5410136	15	3.3	15	78	16	57	63	2	2	32	1.17
5410088--5410141	7	7.2	8	78	19	55	62	1	1	33	1.16
5410069--5410141	34	2.2	34	79	15	82	63	2	2	31	1.23
5411710--5411797	44	2.0	44	84	2	113	25	27	19	28	1.99
5423399--5423461	3	21.7	3	74	18	53	63	3	3	30	1.25
5423414--5423465	15	3.5	15	80	15	63	63	1	1	32	1.16
5432665--5432726	28	2.1	28	88	5	88	41	1	4	51	1.33
5433373--5433408	18	2.1	18	89	5	56	41	0	25	33	1.55
5445572--5445742	86	2.0	86	90	0	270	36	5	11	46	1.63
5446459--5446525	33	2.0	33	100	0	134	32	19	29	17	1.95
5447588--5447626	2	19.5	2	89	0	60	43	2	2	51	1.29
5451723--5451778	27	2.1	27	100	0	112	32	3	10	53	1.53
5462224--5462388	21	8.0	21	69	12	90	16	21	19	42	1.89
5462245--5462423	81	2.2	80	85	2	232	16	21	20	40	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5467444--5467496	25	2.2	24	86	3	70	39	22	20	16	1.92
5473782--5473876	25	3.9	25	75	8	88	37	23	22	16	1.93
5473853--5473978	64	2.0	64	80	0	144	34	20	20	24	1.97
5490465--5490614	81	1.9	81	87	2	221	33	22	17	26	1.96
5492784--5492810	13	2.1	13	100	0	54	48	0	22	29	1.51
5497497--5497561	27	2.4	27	94	0	112	40	3	4	52	1.38
5497638--5497709	33	2.0	33	84	12	90	45	6	16	30	1.74
5504691--5504751	21	3.0	20	85	4	86	68	0	4	26	1.09
5504688--5504756	10	6.6	10	71	14	50	66	0	4	28	1.10
5505031--5505084	21	2.6	21	85	14	76	22	5	1	70	1.18
5505039--5505084	20	2.2	20	88	11	67	19	4	2	73	1.10
5505037--5505075	10	3.8	10	82	3	51	20	2	2	74	1.06
5505031--5505084	11	5.1	11	77	8	58	22	5	1	70	1.18
5507367--5507631	43	6.3	43	89	3	394	25	24	18	30	1.98
5507367--5507631	83	3.1	82	86	4	359	25	24	18	30	1.98
5507367--5507631	126	2.1	127	91	2	426	25	24	18	30	1.98
5507975--5508110	66	2.1	66	94	0	236	13	26	18	41	1.88
5513572--5513733	9	18.4	9	73	12	113	32	0	17	49	1.52
5513585--5513663	16	4.8	17	76	16	58	36	0	18	44	1.51
5513581--5513671	25	3.6	25	93	0	155	35	0	18	46	1.50
5513729--5513769	12	3.4	12	82	0	55	24	2	21	51	1.60
5513721--5513769	24	2.0	24	88	0	71	28	2	18	51	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5514024--5514080	9	6.7	9	76	9	57	43	1	12	42	1.52
5513999--5514057	16	3.9	16	73	13	61	38	0	11	49	1.40
5517381--5517557	41	4.3	41	85	1	203	37	28	18	15	1.91
5518378--5518458	32	2.6	32	78	5	96	50	0	2	46	1.14
5520214--5520348	42	3.2	42	87	0	189	22	22	37	17	1.94
5523180--5523240	29	2.1	29	81	9	70	55	6	9	27	1.57
5524496--5524621	43	2.9	43	75	9	130	19	20	28	30	1.97
5531528--5531638	40	2.8	40	82	5	127	36	25	19	18	1.95
5531704--5532022	41	7.8	40	82	2	341	24	20	25	29	1.99
5531705--5532022	123	2.6	121	84	3	402	24	20	25	29	1.99

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