genome.fa.s12.2.7.7.80.10.50.1000.15.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   

This is table  15  of  120  ( 14336 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)
4424129--4424262	70	1.9	69	89	1	205	41	13	11	33	1.80
4426459--4426510	24	2.2	24	89	0	77	51	9	5	32	1.58
4431577--4431628	12	4.4	12	81	11	63	42	7	21	28	1.80
4432811--4432853	18	2.4	18	88	0	59	41	44	2	11	1.53
4432957--4433041	18	4.7	18	83	0	107	28	7	20	44	1.77
4432963--4433041	27	2.9	27	88	0	113	27	7	20	44	1.78
4432957--4433041	9	9.4	9	80	0	89	28	7	20	44	1.77
4433600--4433650	5	10.2	5	83	8	59	74	0	5	19	1.02
4441367--4441411	20	2.2	20	92	0	72	35	0	4	60	1.17
4441375--4441426	20	2.6	19	80	14	52	44	0	1	53	1.11
4445082--4445508	222	1.9	222	96	0	782	31	17	20	31	1.95
4449873--4449906	3	11.3	3	100	0	68	0	32	0	67	0.91
4453367--4453409	21	2.0	21	81	4	50	48	2	2	46	1.27
4454917--4454971	17	3.2	18	79	7	69	60	0	0	40	0.97
4456192--4456221	2	15.0	2	100	0	60	50	0	0	50	1.00
4458005--4458061	24	2.4	24	82	5	71	52	5	1	40	1.34
4463015--4463056	22	1.9	22	90	0	66	52	40	4	2	1.35
4464178--4464220	3	14.3	3	100	0	86	0	0	32	67	0.91
4464798--4464948	75	2.0	75	94	0	266	31	15	15	37	1.89
4464873--4465248	110	3.4	111	91	1	583	30	15	19	34	1.93
4468695--4468732	20	1.9	20	88	0	58	65	10	5	18	1.41
4473333--4473399	27	2.5	26	92	4	116	41	4	0	53	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4473387--4473477	13	7.4	13	76	16	104	45	1	0	53	1.07
4473390--4473477	11	7.4	11	67	20	52	44	1	0	54	1.07
4473363--4473453	38	2.4	38	98	0	173	41	3	0	54	1.16
4475089--4475148	28	2.1	28	87	0	84	38	5	15	41	1.68
4476407--4476441	18	1.9	18	94	0	61	40	5	25	28	1.78
4491970--4492015	2	23.0	2	100	0	92	50	0	0	50	1.00
4502933--4503012	39	2.1	39	100	0	160	45	25	7	22	1.78
4523143--4523180	18	2.1	18	90	0	58	39	0	34	26	1.57
4523153--4523188	18	2.0	18	88	0	54	33	0	38	27	1.57
4526461--4526555	41	2.3	41	85	7	122	24	17	25	32	1.97
4529485--4529559	23	3.3	23	77	7	89	45	22	16	16	1.85
4561900--4562059	87	1.8	87	91	2	268	42	13	13	30	1.83
4562581--4562654	23	3.3	23	80	1	87	41	24	13	20	1.88
4565349--4565896	271	2.0	271	98	0	1069	31	8	22	37	1.84
4566032--4566194	46	3.6	46	94	1	285	32	14	23	29	1.94
4574702--4574756	26	2.1	27	86	3	76	45	5	18	30	1.72
4575497--4575535	6	6.5	6	81	0	51	20	2	43	33	1.65
4578702--4578772	30	2.3	31	83	9	83	61	8	7	22	1.48
4578790--4578862	31	2.4	31	80	0	83	47	10	15	26	1.77
4578972--4579015	22	2.0	23	86	13	65	70	2	4	22	1.17
4580281--4580320	6	6.5	6	83	16	55	50	0	17	32	1.47
4580348--4580414	23	3.0	22	82	4	71	61	0	2	35	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4580362--4580421	23	2.6	23	77	17	61	63	0	3	33	1.11
4584163--4584207	21	2.1	22	83	4	56	51	8	11	28	1.68
4587999--4588070	31	2.3	32	83	4	85	45	8	4	41	1.53
4588017--4588075	31	1.9	31	93	6	102	44	11	3	40	1.58
4600275--4600335	24	2.7	22	77	7	61	3	29	1	65	1.18
4600396--4600475	27	3.0	27	79	3	90	23	32	25	18	1.97
4604776--4604809	16	2.2	16	89	5	52	61	0	0	38	0.96
4604884--4604920	17	2.2	17	90	0	56	29	2	2	64	1.21
4608691--4608718	2	14.0	2	100	0	56	50	0	50	0	1.00
4610886--4610940	29	1.9	28	88	3	83	43	5	10	40	1.63
4614406--4614434	15	1.9	15	100	0	58	55	6	34	3	1.44
4614405--4614476	24	3.0	24	81	0	81	55	2	38	2	1.29
4614441--4614485	24	1.9	23	90	4	72	55	0	44	0	0.99
4617083--4617179	46	2.0	48	84	9	128	19	25	20	34	1.96
4621024--4621142	38	3.1	38	78	7	134	31	11	25	31	1.91
4625349--4625388	20	2.0	20	85	4	55	37	15	0	47	1.45
4629755--4629792	18	2.1	18	90	0	58	15	13	18	52	1.74
4635563--4635616	23	2.4	22	76	11	56	24	18	22	35	1.96
4636379--4636418	19	2.2	18	95	4	71	42	15	2	40	1.60
4639580--4639604	13	1.9	13	100	0	50	8	0	24	68	1.16
4641401--4641585	41	4.5	41	86	2	237	28	22	29	20	1.98
4647381--4647405	13	1.9	13	100	0	50	8	0	24	68	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4648593--4648751	41	3.9	41	81	6	171	30	21	27	20	1.98
4648939--4649025	35	2.5	34	85	10	99	29	10	25	34	1.89
4658672--4658761	42	2.1	42	91	0	144	52	13	3	31	1.56
4667835--4667881	14	3.1	15	72	9	51	53	17	0	29	1.44
4672382--4672406	12	2.1	12	100	0	50	8	44	0	48	1.32
4678268--4678304	19	1.9	19	88	0	56	75	8	0	16	1.02
4690000--4690053	16	3.4	16	72	10	56	18	18	16	46	1.85
4689992--4690052	32	1.9	32	93	0	104	24	18	13	44	1.85
4699379--4699407	12	2.4	12	100	0	58	24	6	13	55	1.63
4704837--4704866	15	1.9	16	93	6	53	16	26	20	36	1.93
4705847--4705873	2	13.5	2	100	0	54	51	0	0	48	1.00
4706753--4706847	36	2.6	36	79	11	95	51	8	8	31	1.62
4706800--4706963	55	2.8	58	79	8	181	50	11	9	28	1.70
4707509--4707533	2	12.5	2	100	0	50	52	0	0	48	1.00
4708405--4708469	31	2.1	30	85	2	85	47	16	12	23	1.80
4708934--4708973	7	5.7	7	96	0	71	30	27	0	42	1.56
4708922--4708980	21	2.9	21	75	12	68	30	30	0	38	1.57
4710522--4710664	64	2.3	63	80	3	144	36	32	6	25	1.81
4719389--4719414	13	2.0	13	100	0	52	23	15	15	46	1.83
4726321--4726366	21	2.2	21	84	0	56	45	32	6	15	1.71
4726342--4726368	14	1.9	14	100	0	54	51	33	0	14	1.43
4727538--4727572	2	17.5	2	100	0	70	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4728107--4728293	41	4.6	41	93	4	297	20	29	21	28	1.98
4728148--4728321	82	2.1	82	85	4	235	22	29	21	25	1.99
4729110--4729155	2	23.0	2	95	0	83	50	2	0	47	1.13
4732296--4732330	18	1.9	18	88	0	52	25	20	22	31	1.98
4737604--4737710	11	10.4	11	71	21	63	59	0	2	37	1.12
4737590--4737661	30	2.4	29	86	11	92	56	0	2	40	1.13
4737614--4737647	17	2.0	17	88	0	50	64	0	0	35	0.94
4737596--4737728	40	3.3	40	89	4	214	61	0	2	36	1.08
4738640--4738673	7	4.9	7	92	0	50	29	8	26	35	1.87
4738641--4738689	21	2.3	21	89	10	73	28	4	28	38	1.75
4738835--4738867	14	2.4	14	94	0	57	3	6	18	72	1.18
4743340--4743388	21	2.3	21	89	10	73	30	4	26	38	1.75
4751002--4751068	31	2.2	31	89	5	100	22	20	11	44	1.84
4752612--4752678	31	2.2	31	83	0	80	34	13	16	35	1.88
4756923--4756965	21	2.0	22	86	4	61	41	2	13	41	1.57
4759835--4759868	2	17.0	2	100	0	68	50	0	0	50	1.00
4762010--4762043	2	17.0	2	100	0	68	50	0	0	50	1.00
4764163--4764188	12	2.2	12	100	0	52	30	30	7	30	1.85
4765179--4765213	2	18.0	2	94	5	63	51	0	0	48	1.00
4776441--4776468	3	9.3	3	100	0	56	67	0	0	32	0.91
4784251--4784311	29	2.1	30	87	3	88	47	9	19	22	1.79
4785447--4785490	3	15.3	3	86	9	65	63	0	36	0	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4785447--4785490	20	2.2	20	95	0	79	63	0	36	0	0.95
4785661--4785846	22	9.0	21	72	15	154	32	0	12	54	1.38
4785685--4785741	19	2.9	19	81	2	69	33	0	15	50	1.44
4785661--4785846	41	4.5	40	73	17	166	32	0	12	54	1.38
4785944--4786001	22	2.9	19	71	14	53	34	1	12	51	1.49
4785795--4786017	97	2.3	99	92	3	369	32	1	13	53	1.48
4785795--4786018	49	4.5	49	85	8	319	32	1	13	53	1.48
4786283--4786357	38	2.0	38	97	0	141	52	4	5	38	1.43
4786466--4786507	16	2.7	15	85	7	57	38	2	2	57	1.25
4788130--4788212	6	13.8	6	88	0	112	32	27	39	0	1.57

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