genome.fa.s3.2.7.7.80.10.50.1000.15.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  15  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)
4069303--4069347	23	1.9	23	82	13	56	64	2	8	24	1.34
4073175--4073363	95	2.0	95	84	3	243	34	21	7	36	1.82
4077486--4077581	44	2.2	44	76	0	102	43	12	20	22	1.86
4078501--4078544	11	3.8	12	80	19	58	25	31	0	43	1.55
4081059--4081132	29	2.6	29	84	2	87	54	31	0	14	1.41
4081088--4081292	44	4.6	44	84	4	261	52	27	0	20	1.47
4081117--4081231	15	7.8	15	68	16	53	53	29	0	17	1.44
4081093--4081301	22	9.6	20	76	13	168	52	27	0	20	1.47
4081270--4081329	29	2.1	29	84	3	77	46	30	0	23	1.52
4081271--4081322	14	3.6	14	77	12	61	50	28	0	21	1.49
4084506--4085069	250	2.3	250	90	0	878	29	22	17	29	1.97
4084506--4085072	125	4.5	125	83	3	728	29	22	17	29	1.97
4092001--4092060	28	2.2	28	90	3	95	48	25	11	15	1.78
4100541--4100615	34	2.4	31	82	13	82	38	9	2	49	1.49
4110704--4110743	2	20.0	2	94	0	71	50	0	2	47	1.14
4116405--4116444	5	7.8	5	97	2	71	0	17	0	82	0.67
4122971--4123032	31	2.0	31	83	0	79	30	3	11	54	1.51
4123204--4123269	31	2.1	32	85	2	89	56	15	4	24	1.58
4123675--4123768	29	3.2	29	67	8	73	58	11	9	20	1.60
4131951--4131975	6	4.2	6	100	0	50	84	0	16	0	0.63
4134929--4135038	37	3.0	37	76	19	115	40	2	3	53	1.33
4134949--4135145	62	3.0	67	71	21	189	40	4	4	51	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4136498--4136573	26	2.8	27	72	6	73	27	18	31	22	1.97
4144917--4144976	26	2.3	26	79	0	66	38	23	21	16	1.93
4153045--4153090	24	1.9	24	100	0	92	34	8	8	47	1.65
4156460--4156519	16	3.6	16	76	13	59	75	6	18	0	1.02
4156928--4156968	19	2.1	20	86	4	57	56	2	9	31	1.45
4161419--4161546	42	3.0	41	88	2	166	42	24	14	19	1.88
4162541--4162566	4	6.5	4	100	0	52	53	0	0	46	1.00
4166393--4166441	23	2.0	25	84	7	66	59	20	4	16	1.53
4181950--4182004	19	2.8	19	81	10	60	45	5	14	34	1.68
4188386--4188411	2	13.0	2	100	0	52	50	0	0	50	1.00
4195465--4195490	12	2.2	12	100	0	52	76	0	0	23	0.78
4196463--4196521	30	2.0	30	100	0	118	44	16	5	33	1.70
4199414--4199438	3	8.3	3	100	0	50	32	0	32	36	1.58
4215786--4215828	21	2.0	21	86	8	61	37	0	4	58	1.19
4215845--4215890	18	2.6	18	86	3	58	43	0	2	54	1.12
4215811--4215994	64	3.1	57	72	19	187	43	1	4	51	1.29
4215793--4216028	119	2.0	118	86	7	315	43	1	4	50	1.31
4218818--4218864	23	2.0	23	84	8	60	57	2	4	36	1.30
4218827--4218875	23	2.1	23	81	7	55	55	2	6	36	1.37
4229827--4229869	23	1.9	22	85	4	59	65	2	4	27	1.25
4230466--4230518	15	3.7	14	87	10	72	58	0	39	1	1.09
4230540--4230573	13	2.7	13	90	4	52	76	0	23	0	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4234868--4234937	27	2.6	27	86	0	113	20	25	31	22	1.98
4237813--4237863	26	2.0	26	100	0	102	47	9	19	23	1.79
4251655--4251683	10	2.9	10	100	0	58	72	0	10	17	1.11
4253694--4253744	7	7.3	7	85	14	70	72	0	1	25	0.95
4253692--4253734	20	2.2	20	95	0	77	74	0	2	23	0.93
4253692--4253755	14	4.6	14	75	16	62	75	0	3	21	0.95
4257423--4257447	10	2.5	10	100	0	50	72	0	0	28	0.86
4260887--4260922	17	2.0	19	89	10	58	27	0	0	72	0.85
4266530--4266555	2	13.0	2	100	0	52	50	0	0	50	1.00
4269120--4269162	3	14.7	3	95	4	79	69	0	0	30	0.88
4269819--4269844	13	2.0	13	100	0	52	30	15	15	38	1.88
4270672--4270807	44	3.1	44	74	5	123	28	25	15	30	1.96
4270793--4270878	44	2.0	44	95	0	154	33	25	11	29	1.91
4270874--4271087	89	2.4	89	92	0	347	29	24	15	29	1.96
4270874--4271087	44	4.8	45	79	4	245	29	24	15	29	1.96
4282700--4282751	2	26.5	2	96	3	97	50	0	0	50	1.00
4285996--4286039	22	2.0	21	87	12	63	13	47	0	38	1.43
4291004--4291087	31	2.7	32	84	1	98	39	15	15	29	1.88
4291505--4291592	43	2.1	41	87	8	124	43	2	1	53	1.20
4293103--4293147	19	2.4	19	82	13	58	15	4	13	66	1.39
4293241--4293291	18	2.7	20	79	14	63	37	0	1	60	1.08
4298005--4298043	21	1.9	20	84	5	51	23	17	10	48	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4298372--4298469	27	3.6	27	87	0	142	20	34	27	17	1.95
4298744--4298860	40	2.8	40	78	10	119	34	4	11	50	1.57
4298764--4298879	40	2.8	40	71	19	94	31	5	12	50	1.61
4298744--4298879	43	3.2	41	74	22	106	32	4	12	50	1.60
4299872--4299942	35	2.0	35	97	0	133	32	8	35	23	1.85
4308198--4308617	158	2.7	153	72	13	413	30	10	7	50	1.65
4308325--4308902	286	2.0	285	94	0	1021	30	11	7	51	1.64
4309272--4309382	47	2.4	48	79	8	113	0	36	0	63	0.94
4309311--4309404	10	9.6	10	73	14	72	0	31	0	68	0.90
4309316--4309404	20	4.3	20	76	10	90	0	31	0	68	0.90
4309311--4309401	42	2.1	43	87	2	130	0	31	0	68	0.90
4309297--4309402	47	2.2	48	85	6	144	0	32	0	67	0.91
4309354--4309422	30	2.3	30	80	7	77	0	37	0	62	0.96
4309461--4309528	27	2.5	27	85	0	91	19	29	35	16	1.93
4309658--4309700	22	2.0	22	95	0	77	32	34	0	32	1.58
4310997--4311064	31	2.3	29	80	11	77	42	11	8	36	1.73
4313552--4313584	11	2.9	12	86	13	52	33	0	0	66	0.92
4313585--4313624	18	2.2	18	86	8	55	67	12	0	20	1.22
4313707--4313769	30	2.1	30	87	0	90	57	11	4	26	1.53
4320548--4320582	6	5.8	6	93	0	61	54	0	28	17	1.43
4325088--4325126	20	2.0	20	89	0	60	48	15	17	17	1.81
4325134--4325318	69	2.7	69	83	5	223	23	11	18	47	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4329647--4329679	10	3.3	10	91	0	57	0	12	0	87	0.53
4329848--4329908	27	2.2	28	91	2	97	6	14	32	45	1.71
4329963--4330055	11	8.1	11	73	13	71	0	26	0	73	0.84
4329963--4330012	18	2.8	18	88	8	68	0	22	0	78	0.76
4329964--4330040	28	2.8	28	76	9	77	0	27	0	72	0.85
4329964--4330038	7	10.7	7	74	16	57	0	25	0	74	0.82
4329963--4330053	35	2.6	34	81	8	85	0	27	0	72	0.85
4330505--4330672	30	5.6	30	87	4	223	36	2	25	36	1.69
4330507--4330672	59	2.8	60	87	3	228	36	2	24	36	1.69
4330808--4331270	78	6.0	76	86	5	565	33	20	17	27	1.95
4332147--4332207	9	6.6	9	78	14	54	0	13	3	83	0.76
4332147--4332208	10	6.3	10	77	9	56	0	12	3	83	0.75
4332147--4332199	19	2.8	18	83	8	70	0	15	1	83	0.74
4332147--4332197	26	1.9	27	88	11	79	0	15	1	82	0.76
4332147--4332198	18	2.8	18	88	8	70	0	15	1	82	0.75
4332147--4332206	18	3.3	17	83	6	66	0	13	3	83	0.77
4332147--4332207	19	3.3	19	78	21	67	0	13	3	83	0.76
4339608--4339649	17	2.4	18	72	4	50	38	14	4	42	1.66
4340116--4340153	8	4.5	8	87	12	58	0	13	0	86	0.56
4340115--4340155	15	2.7	15	85	7	57	0	14	0	85	0.60
4340334--4340394	27	2.2	28	94	2	106	4	14	34	45	1.67
4340450--4340519	4	19.8	4	73	19	50	0	24	0	75	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4340450--4340542	11	8.1	11	70	9	60	1	25	0	73	0.90
4340450--4340514	10	7.0	10	72	13	59	0	23	0	76	0.78
4340450--4340510	17	3.6	17	82	12	72	0	22	0	77	0.78
4340616--4340655	20	2.0	21	90	5	64	0	25	0	75	0.81
4340957--4341086	30	4.4	30	80	9	140	35	3	25	36	1.72
4340982--4341093	59	1.9	59	81	3	136	35	2	23	38	1.69
4346800--4346861	10	5.9	10	74	10	52	33	32	3	30	1.74
4346800--4346862	21	3.0	21	88	2	90	33	33	3	30	1.74
4348793--4348854	33	1.9	33	86	3	90	25	19	24	30	1.98
4352428--4352476	25	1.9	26	87	4	73	2	18	6	73	1.14

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