genome.fa.s6.2.7.7.80.10.50.1000.16.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: 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  16  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)
4430233--4430614	35	10.7	35	78	7	250	25	24	13	37	1.92
4430278--4430360	41	2.0	41	92	0	139	22	31	10	34	1.89
4430241--4430614	105	3.5	105	80	6	349	25	24	13	37	1.91
4430319--4430614	70	4.2	68	77	3	277	25	24	12	37	1.91
4431150--4431201	24	2.2	24	86	6	70	36	3	7	51	1.49
4447617--4447641	13	1.9	13	100	0	50	68	8	8	16	1.38
4448434--4448494	21	2.9	20	73	14	52	37	3	1	57	1.25
4449929--4449979	18	2.6	19	81	9	50	35	0	3	60	1.15
4448391--4451978	750	4.8	750	96	2	6469	38	12	10	39	1.76
4450679--4450729	18	2.6	19	81	9	50	35	0	3	60	1.15
4451436--4451486	18	2.6	19	81	9	50	35	0	3	60	1.15
4453324--4453349	2	13.0	2	100	0	52	50	0	0	50	1.00
4464543--4464596	27	2.0	27	100	0	108	29	18	3	48	1.65
4465726--4465767	22	1.9	22	90	0	66	16	7	19	57	1.62
4468240--4468280	19	2.1	21	82	13	52	36	2	7	53	1.42
4471145--4471353	114	1.8	114	81	2	258	29	21	24	24	1.99
4471238--4471403	73	2.3	73	91	0	260	27	22	25	24	2.00
4471303--4471611	114	2.7	114	84	2	451	26	19	27	26	1.99
4471118--4471517	187	2.1	186	87	2	570	26	21	26	26	1.99
4471764--4471812	14	3.4	14	82	2	53	28	0	36	34	1.58
4471828--4471861	8	4.6	7	86	13	50	17	0	50	32	1.47
4471807--4471861	15	3.7	15	76	11	60	18	0	47	34	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4472060--4472094	15	2.4	14	86	9	52	22	0	37	40	1.55
4472081--4472124	21	2.2	20	83	4	52	18	0	43	38	1.50
4471683--4472283	297	2.1	279	82	11	693	29	1	27	41	1.66
4472623--4472980	150	2.4	147	93	4	612	34	15	17	32	1.91
4475653--4475782	23	5.7	23	85	5	174	47	34	2	15	1.58
4475653--4475783	45	2.9	46	88	2	192	47	35	2	15	1.58
4475910--4475938	13	2.2	13	100	0	58	37	17	0	44	1.49
4480597--4480770	23	7.7	23	77	7	169	50	33	2	13	1.54
4480597--4480772	46	3.9	46	83	8	202	50	34	2	13	1.53
4487153--4487222	35	2.0	35	97	0	131	41	2	27	28	1.70
4490982--4491009	5	5.6	5	100	0	56	82	0	0	17	0.68
4493379--4493502	62	2.0	62	98	0	239	21	27	20	30	1.98
4495933--4496062	23	5.7	23	83	5	165	49	32	2	16	1.58
4495936--4496062	68	1.9	68	86	3	184	48	32	2	16	1.59
4495933--4496063	45	2.9	46	87	2	174	48	32	2	16	1.58
4496190--4496218	13	2.2	13	100	0	58	37	17	0	44	1.49
4500874--4501048	23	7.7	23	77	6	171	50	33	2	13	1.55
4500874--4501049	46	3.9	45	83	8	198	50	34	2	13	1.55
4512460--4512699	27	8.9	26	81	11	250	45	19	17	17	1.86
4515414--4515502	29	3.1	29	85	0	124	23	22	15	38	1.93
4517318--4517358	21	1.9	22	90	5	66	73	7	0	19	1.07
4517969--4518041	30	2.4	30	88	0	101	30	32	16	20	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4519126--4519167	18	2.4	18	92	4	68	42	2	9	45	1.49
4520407--4520460	22	2.5	22	96	0	99	29	16	35	18	1.93
4521116--4521164	18	2.8	18	81	6	57	77	0	6	16	0.96
4521118--4521147	15	1.9	16	93	6	53	76	0	10	13	1.01
4522412--4522452	17	2.4	17	91	0	64	34	12	29	24	1.91
4523421--4523460	20	2.0	20	90	0	62	32	20	5	42	1.73
4523429--4523472	20	2.2	20	88	8	63	31	18	4	45	1.69
4528313--4528361	3	16.3	3	100	0	98	32	0	0	67	0.91
4528659--4528704	23	2.0	23	100	0	92	56	17	13	13	1.67
4529075--4529129	27	2.1	26	86	6	76	25	20	27	27	1.99
4529269--4529534	97	2.8	96	93	1	453	44	1	15	37	1.56
4540071--4540340	43	6.3	43	68	13	162	32	25	15	25	1.95
4540034--4540276	127	1.9	127	97	0	459	30	24	17	27	1.97
4540198--4540341	43	3.3	43	82	3	173	34	27	13	25	1.93
4551006--4551040	18	1.9	18	88	0	52	34	0	2	62	1.10
4551496--4551547	27	1.9	27	92	0	86	38	21	13	26	1.90
4555306--4555347	21	2.0	21	100	0	84	33	33	9	23	1.87
4556029--4556080	27	1.9	27	88	0	77	40	21	13	25	1.89
4559672--4559724	2	26.5	2	100	0	106	50	0	0	49	1.00
4563601--4563632	3	10.7	3	93	0	55	65	3	0	31	1.08
4565212--4565576	44	8.1	44	73	11	290	28	20	20	30	1.97
4565212--4565547	137	2.5	131	80	10	365	28	19	20	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4565607--4565718	51	2.2	51	83	0	134	28	21	18	31	1.97
4565795--4565910	44	2.6	44	82	2	126	28	23	19	28	1.98
4566162--4566247	43	2.0	43	95	0	154	32	27	11	27	1.92
4565847--4566607	403	1.9	403	93	0	1308	29	19	16	34	1.94
4578173--4578244	25	2.7	26	77	14	76	58	0	5	36	1.22
4578260--4578293	9	3.8	9	100	0	68	58	8	0	32	1.29
4581647--4581693	18	2.6	19	80	10	53	36	8	0	55	1.31
4585845--4585913	34	2.0	34	94	0	120	28	21	17	31	1.96
4587507--4587555	21	2.3	22	89	6	75	36	16	24	22	1.94
4589876--4589900	13	1.9	13	100	0	50	32	0	0	68	0.90
4598920--4598977	29	2.0	29	86	6	82	39	12	10	37	1.77
4599813--4599837	2	12.5	2	100	0	50	48	0	0	52	1.00
4602966--4603001	18	2.0	18	100	0	72	50	11	0	38	1.38
4603005--4603031	12	2.2	12	100	0	54	48	14	0	37	1.45
4603091--4603142	27	1.9	27	96	0	95	30	23	32	13	1.93
4603709--4603802	19	5.1	19	77	10	113	38	12	0	48	1.41
4603709--4603802	37	2.5	37	98	0	179	38	12	0	48	1.41
4608711--4608766	29	1.9	29	82	7	69	35	14	8	41	1.77
4611574--4611628	19	2.9	18	76	15	58	65	0	7	27	1.19
4611574--4611628	18	2.9	19	78	5	67	65	0	7	27	1.19
4611670--4611700	9	3.6	9	95	4	55	12	6	0	80	0.89
4611660--4611709	18	2.7	18	74	20	50	20	6	0	74	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4617052--4617091	21	1.9	21	94	0	71	42	20	20	17	1.89
4618540--4618591	3	17.7	3	90	4	79	30	1	1	65	1.14
4618646--4618720	20	3.5	20	73	19	69	26	4	6	62	1.38
4620418--4620468	27	1.9	26	84	11	68	70	7	3	17	1.27
4620767--4620879	34	3.3	32	75	16	95	54	5	3	36	1.40
4620918--4620967	24	2.1	24	85	7	66	64	0	8	28	1.22
4621046--4621089	17	2.6	17	85	3	63	47	0	11	40	1.39
4621213--4621251	3	13.0	3	88	0	60	66	2	2	28	1.18
4621593--4621649	21	2.7	21	94	0	96	36	14	8	40	1.76
4625056--4625122	29	2.5	26	80	11	64	43	1	0	55	1.09
4626253--4626301	5	10.6	5	87	10	52	85	10	4	0	0.71
4626263--4626308	18	2.5	18	85	3	65	82	13	2	2	0.85
4626253--4626306	23	2.3	23	84	9	74	85	9	3	1	0.80
4626399--4626437	19	2.1	19	90	0	60	35	38	23	2	1.68
4626445--4626480	10	3.8	9	86	13	54	86	2	11	0	0.68
4626996--4627364	35	10.2	36	70	15	155	31	13	10	44	1.78
4626983--4627352	18	20.6	18	73	10	262	28	14	11	45	1.78
4631712--4632121	205	2.0	205	95	0	739	37	16	21	24	1.93
4639386--4640062	78	8.6	78	83	8	816	29	16	18	36	1.92
4639386--4640107	158	4.6	158	91	1	1097	28	16	18	36	1.92
4649104--4649148	15	2.9	16	77	9	58	6	4	37	51	1.49
4658616--4658736	63	1.9	63	91	0	197	24	30	20	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4660503--4660533	9	3.4	9	90	0	53	25	12	22	38	1.90
4660586--4660631	9	5.1	9	94	0	83	45	13	10	30	1.77
4660989--4661019	16	1.9	16	93	0	53	25	29	0	45	1.54
4664255--4664803	114	4.8	114	87	1	710	24	21	26	27	1.99
4664240--4664803	229	2.5	228	85	2	758	23	21	26	28	1.99
4665350--4665401	7	7.3	7	75	12	52	15	1	50	32	1.55
4665464--4665506	21	2.0	21	86	0	59	23	0	25	51	1.49
4665466--4665516	21	2.4	21	80	0	57	27	0	23	49	1.51
4665903--4666124	74	3.0	72	68	14	182	24	15	21	37	1.93
4665889--4666171	148	1.9	148	86	0	404	24	16	21	37	1.93

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