genome.fa.s3.2.7.7.80.10.50.1000.16.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  16  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)
4357827--4357865	16	2.4	16	82	0	51	79	2	2	15	0.95
4362054--4362084	16	1.9	16	93	0	53	61	0	3	35	1.12
4368722--4368941	110	2.0	110	97	0	413	39	11	6	41	1.68
4368907--4368968	32	1.9	32	84	12	83	45	3	0	51	1.17
4368917--4368968	14	3.2	17	76	20	58	46	1	0	51	1.12
4374484--4374550	29	2.3	29	94	5	118	49	16	2	31	1.61
4374571--4374633	18	3.4	18	72	22	51	57	6	0	36	1.24
4378358--4378452	6	15.8	6	100	0	190	33	0	16	49	1.46
4382959--4383029	26	2.8	25	72	19	67	56	0	11	32	1.35
4382925--4383025	52	1.9	52	89	0	157	53	0	12	33	1.39
4383133--4383173	20	2.0	20	100	0	82	29	9	29	31	1.89
4383899--4383967	36	1.9	36	93	0	120	36	17	5	40	1.74
4385716--4385764	22	2.2	22	82	7	64	61	10	8	20	1.53
4388232--4388302	28	2.5	29	75	9	74	57	8	0	33	1.29
4389073--4389153	30	2.7	30	82	3	92	41	2	4	50	1.37
4391591--4391661	36	2.0	36	94	0	124	50	8	22	18	1.73
4394580--4394621	21	2.0	21	85	0	57	42	7	9	40	1.65
4395905--4395957	19	3.0	17	78	10	61	35	9	18	35	1.84
4395928--4395976	22	2.2	22	78	7	55	36	6	16	40	1.73
4396147--4396185	19	2.0	21	85	10	55	15	10	5	69	1.34
4396408--4396450	3	14.3	3	85	9	61	32	0	0	67	0.91
4396392--4396449	15	3.7	15	76	13	55	31	0	1	67	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4396478--4396540	31	2.1	31	85	5	85	42	4	1	50	1.32
4396517--4396609	47	2.0	48	81	10	111	34	8	2	54	1.43
4401122--4401308	41	4.6	41	91	0	284	27	20	29	21	1.98
4401613--4401682	35	2.0	35	85	0	95	40	10	15	34	1.81
4405553--4405581	6	4.8	6	100	0	58	34	17	17	31	1.93
4406222--4406260	19	2.0	20	90	9	64	38	0	2	58	1.12
4408023--4408077	25	2.2	26	78	15	62	23	7	16	52	1.68
4409175--4409462	46	6.4	46	77	9	252	32	4	25	37	1.76
4409189--4409449	23	11.6	23	74	9	207	33	3	25	37	1.73
4410974--4411035	28	2.2	28	91	0	97	32	27	20	19	1.97
4411141--4411217	26	3.0	26	84	0	100	38	23	22	15	1.92
4411392--4411669	27	10.3	27	84	3	299	16	16	20	46	1.85
4412307--4412367	34	1.9	32	83	12	81	49	14	26	9	1.75
4421158--4421193	15	2.4	15	90	0	54	30	16	0	52	1.44
4422881--4422929	22	2.1	23	92	7	82	30	20	4	44	1.70
4425489--4425545	23	2.4	23	91	2	96	54	8	0	36	1.32
4430208--4430423	86	2.5	86	86	2	283	30	16	22	30	1.96
4430213--4430433	43	5.1	44	80	4	238	29	16	22	31	1.96
4432642--4432871	37	6.0	37	88	8	320	25	21	15	37	1.93
4432788--4433161	46	7.6	46	75	16	304	28	22	14	35	1.93
4432835--4433155	46	6.2	52	85	9	378	27	23	14	34	1.93
4432877--4433003	59	2.2	58	94	2	218	25	24	12	37	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4436275--4436371	49	2.0	50	91	2	160	32	28	14	23	1.94
4439438--4439476	20	2.0	20	100	0	78	20	12	10	56	1.65
4440095--4440157	12	5.4	12	71	22	55	47	0	3	49	1.17
4440095--4440157	22	2.7	23	77	20	69	47	0	3	49	1.17
4440120--4440256	61	2.3	57	82	6	157	44	1	3	50	1.28
4440222--4440273	25	2.0	26	88	3	79	53	7	0	38	1.30
4443835--4443864	15	2.0	15	93	0	51	23	6	6	63	1.43
4447142--4447176	18	1.9	18	94	0	61	8	5	2	82	0.91
4447744--4447776	14	2.3	15	89	5	50	81	3	0	15	0.80
4449612--4449654	8	5.1	8	78	10	50	55	0	9	34	1.32
4453478--4453524	21	2.2	22	77	11	53	63	12	14	8	1.50
4456398--4456464	31	2.1	32	94	5	118	41	0	0	58	0.98
4456398--4456464	33	2.1	31	91	5	107	41	0	0	58	0.98
4456436--4456499	20	3.1	20	75	6	65	40	3	0	56	1.15
4456434--4456499	21	3.1	22	68	22	59	40	3	0	56	1.15
4462543--4462578	15	2.4	15	90	0	54	30	16	0	52	1.44
4465399--4465433	15	2.4	15	90	4	54	48	0	8	42	1.33
4469418--4469487	4	16.5	4	77	21	56	22	1	0	75	0.88
4469410--4469495	17	5.1	17	71	16	72	22	2	0	75	0.91
4469411--4469480	5	13.4	5	78	13	70	21	1	0	77	0.85
4469411--4469487	31	2.4	32	84	6	111	22	1	0	76	0.86
4469419--4469495	36	2.2	35	86	6	102	23	2	0	74	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4469642--4469701	22	2.8	21	79	5	57	25	46	10	18	1.79
4470640--4470830	101	1.9	101	84	4	260	26	16	25	31	1.96
4472793--4472853	30	2.0	31	90	9	99	45	6	21	26	1.76
4475440--4475481	21	2.0	21	95	0	75	30	4	26	38	1.77
4477422--4477485	30	2.1	31	94	2	112	42	6	25	26	1.78
4477420--4477469	15	3.2	16	72	11	59	44	6	24	26	1.76
4478911--4478963	13	4.1	13	75	7	54	35	20	3	39	1.71
4479077--4479110	18	1.9	17	88	5	50	50	0	2	47	1.16
4483171--4483243	29	2.5	29	93	0	119	52	9	12	26	1.69
4484794--4484869	9	8.4	9	92	0	116	23	9	25	42	1.83
4484794--4484869	27	2.8	27	93	0	134	23	9	25	42	1.83
4491791--4491841	19	2.6	20	79	14	61	27	1	7	62	1.33
4492539--4492568	16	1.9	15	93	6	51	83	0	16	0	0.65
4495215--4495263	2	25.0	2	95	4	91	51	0	0	48	1.00
4499337--4499369	16	1.9	18	88	11	52	33	0	9	57	1.30
4499689--4500533	308	2.7	306	79	8	849	35	14	10	39	1.81
4501570--4501610	21	2.0	21	90	0	64	48	21	12	17	1.79
4508725--4508758	16	2.1	17	94	5	61	52	0	38	8	1.33
4510477--4510513	19	1.9	19	88	0	56	59	10	0	29	1.31
4513727--4513760	16	2.1	17	88	5	52	41	2	0	55	1.15
4519332--4519356	12	2.1	12	100	0	50	36	8	16	40	1.77
4527751--4527837	9	10.0	9	69	9	56	34	3	18	43	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4527782--4527837	26	2.2	25	90	3	85	32	3	21	42	1.70
4528248--4528313	33	2.0	33	90	0	105	33	6	16	43	1.73
4528979--4529005	12	2.2	12	100	0	54	51	25	7	14	1.68
4530129--4530408	125	2.2	124	82	6	327	29	18	17	34	1.94
4530712--4530779	16	4.3	15	74	18	57	51	32	2	13	1.56
4530714--4530948	7	32.4	7	68	13	93	44	33	1	20	1.60
4531088--4531161	7	10.6	7	79	5	87	45	27	1	25	1.61
4540590--4540637	22	2.2	22	88	3	71	43	2	10	43	1.50
4549282--4549336	25	2.2	26	81	15	71	23	9	16	50	1.73
4550405--4550723	46	7.1	46	76	7	233	34	3	23	37	1.73
4550362--4550712	23	15.6	23	71	11	199	33	3	23	39	1.71
4551258--4551284	5	5.4	5	100	0	54	0	18	0	81	0.69
4565996--4566044	22	2.1	23	88	7	73	30	22	4	42	1.72
4568601--4568639	12	3.3	12	78	7	53	53	7	0	38	1.30
4568590--4568646	23	2.4	23	97	2	105	56	8	0	35	1.31
4571037--4571165	3	42.0	3	84	4	168	31	1	3	64	1.18
4571718--4571754	13	2.7	14	84	16	51	21	5	5	67	1.31
4575935--4575976	21	2.0	21	85	0	57	42	7	9	40	1.65
4579787--4579816	2	15.5	2	93	6	53	46	0	0	53	1.00
4583052--4583148	26	3.7	26	92	0	158	35	20	26	17	1.95
4583326--4583576	27	9.3	27	81	2	272	17	17	20	44	1.87
4583326--4583554	107	2.1	107	84	4	291	17	18	20	44	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4583329--4583576	81	3.1	81	85	1	327	18	17	20	44	1.87
4584215--4584283	34	2.0	34	86	5	95	47	14	27	10	1.76
4587898--4587940	21	2.0	21	86	8	61	34	0	6	58	1.25
4587919--4587999	38	2.1	38	86	8	112	44	1	2	51	1.22
4588232--4588271	16	2.5	16	91	0	62	32	22	7	37	1.82
4592608--4592680	29	2.5	29	93	0	119	52	9	12	26	1.69
4597086--4597728	319	2.0	319	98	0	1259	33	11	19	35	1.88
4599571--4599613	23	1.9	23	81	13	54	48	4	2	44	1.36
4611483--4611532	19	2.5	20	74	6	57	24	4	8	64	1.38
4612537--4612595	28	2.2	27	79	11	68	40	1	1	55	1.20

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