genome.fa.s12.2.7.7.80.10.50.1000.12.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  12  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)
3548473--3548680	43	4.8	43	84	1	256	24	17	29	27	1.97
3548927--3548964	19	2.0	20	90	10	62	52	0	0	47	1.00
3555312--3555366	26	2.1	26	96	0	101	16	10	20	52	1.73
3559116--3559222	54	2.0	54	85	7	146	26	27	16	29	1.97
3575093--3575158	10	6.8	10	72	16	50	34	4	3	57	1.34
3575087--3575146	27	2.2	26	77	8	66	33	3	3	60	1.30
3581501--3581535	2	17.5	2	100	0	70	48	0	0	51	1.00
3582271--3582316	23	2.0	23	86	0	65	43	13	15	28	1.83
3582273--3582322	23	2.2	23	81	0	55	50	12	12	26	1.74
3588732--3588780	19	2.6	19	80	0	62	55	0	2	42	1.11
3588825--3588864	17	2.3	18	83	12	57	32	0	7	60	1.25
3588813--3588879	20	3.5	19	69	19	50	32	0	4	62	1.15
3589970--3590104	69	2.0	68	85	1	180	45	12	6	34	1.68
3595353--3595385	2	16.5	2	100	0	66	48	0	0	51	1.00
3601755--3601803	6	7.8	6	79	6	53	40	16	22	20	1.91
3601760--3601808	18	2.7	18	78	15	55	38	16	22	22	1.92
3601789--3601905	45	2.8	40	76	14	112	35	21	21	22	1.96
3601783--3601887	45	2.3	45	88	6	151	38	20	20	21	1.94
3603364--3603424	24	2.5	23	80	15	61	49	4	0	45	1.23
3603372--3603440	35	2.0	35	85	5	95	47	5	0	46	1.26
3608594--3608710	43	2.7	43	90	2	173	33	11	22	33	1.89
3614565--3614630	19	3.5	19	87	4	107	43	7	0	48	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3614557--3614635	37	2.1	37	95	0	149	41	8	0	49	1.34
3614906--3614982	19	4.1	19	79	3	93	51	0	10	37	1.36
3614900--3614970	37	1.9	37	97	0	133	49	0	9	40	1.36
3614900--3614974	18	4.1	18	76	6	71	52	0	9	38	1.34
3615050--3615121	27	2.7	27	81	10	78	16	27	25	30	1.97
3615051--3615135	27	3.3	25	79	11	68	18	25	23	31	1.97
3620737--3620777	18	2.4	18	84	8	59	56	0	0	43	0.99
3620737--3620790	18	3.3	16	78	12	56	53	1	0	44	1.11
3626136--3626174	20	1.9	21	89	5	62	33	10	17	38	1.84
3633264--3633306	17	2.6	16	81	3	50	60	2	0	37	1.10
3634016--3634066	25	2.0	27	84	7	70	43	0	3	52	1.19
3634029--3634092	30	2.1	30	85	5	85	42	0	7	50	1.31
3634604--3634657	22	2.5	22	75	0	54	25	5	5	62	1.39
3635276--3635315	16	2.5	16	91	0	62	47	2	7	42	1.45
3635412--3635458	24	2.0	22	88	8	67	57	2	0	40	1.11
3635859--3635895	18	2.1	18	94	0	65	54	0	2	43	1.14
3635921--3635946	11	2.4	11	100	0	52	53	0	7	38	1.30
3639256--3639360	54	2.0	53	83	5	131	39	4	3	52	1.41
3639409--3639457	9	5.7	9	90	9	84	55	10	0	34	1.34
3639409--3639457	16	2.8	18	87	12	84	55	10	0	34	1.34
3639404--3639460	25	2.3	25	93	0	96	54	10	0	35	1.35
3639539--3639571	16	2.1	16	94	0	57	45	6	3	45	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3639545--3639604	22	2.7	22	84	0	75	46	1	1	50	1.21
3640499--3640549	16	2.8	19	71	17	54	50	7	1	39	1.42
3640602--3640658	16	3.6	16	92	0	96	45	5	3	45	1.43
3640632--3640686	22	2.4	23	90	3	85	45	1	1	50	1.22
3643675--3643707	17	1.9	17	93	0	57	15	9	36	39	1.79
3645263--3645296	2	17.0	2	100	0	68	50	0	0	50	1.00
3647153--3647212	30	1.9	31	83	6	77	51	0	1	46	1.10
3647165--3647250	30	2.9	30	74	17	81	48	3	0	47	1.18
3647307--3647342	16	2.2	16	95	0	63	66	0	0	33	0.92
3651512--3651554	9	4.8	9	79	0	50	9	32	18	39	1.83
3662602--3662654	21	2.5	22	78	12	65	62	22	7	7	1.47
3662574--3662654	22	3.7	22	77	6	67	61	18	8	11	1.54
3665211--3665249	2	19.5	2	100	0	78	48	0	0	51	1.00
3670386--3670422	17	2.2	17	90	0	56	59	13	8	18	1.58
3672179--3672206	3	9.3	3	100	0	56	67	0	32	0	0.91
3683598--3683642	23	2.0	23	82	8	56	53	0	0	46	1.00
3687295--3687333	20	2.0	20	89	0	60	35	2	0	61	1.10
3687623--3687677	26	2.2	25	83	3	65	43	1	1	52	1.22
3693466--3693505	20	2.0	20	90	0	62	27	10	12	50	1.72
3693451--3693517	34	1.9	35	87	3	100	32	8	11	46	1.72
3694305--3694352	11	4.8	11	78	19	52	31	0	0	68	0.90
3694309--3694364	28	2.0	28	83	10	71	23	0	3	73	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3694945--3694973	15	1.9	15	100	0	58	24	0	0	75	0.80
3695366--3695402	19	1.9	19	88	0	56	37	2	0	59	1.12
3695697--3695761	26	2.5	25	80	5	67	44	1	1	52	1.19
3704232--3704261	4	7.5	4	100	0	60	76	0	0	23	0.78
3707090--3707150	28	2.2	28	82	11	72	24	11	19	44	1.84
3707086--3707150	29	2.3	28	78	7	78	24	13	18	43	1.87
3707329--3707405	22	3.5	22	91	5	113	32	27	1	38	1.65
3707377--3707435	30	2.0	30	86	6	84	30	33	1	33	1.68
3707407--3707448	22	1.9	22	90	0	66	33	33	0	33	1.58
3709813--3710169	28	13.1	28	82	12	411	47	22	1	29	1.60
3709836--3709878	23	2.0	20	95	4	59	48	20	4	25	1.69
3709813--3710150	115	3.1	110	88	5	520	47	21	1	29	1.60
3710129--3710168	18	2.2	18	86	0	53	47	22	0	30	1.52
3710362--3710421	27	2.2	27	96	0	111	38	6	11	43	1.68
3713441--3713707	126	2.1	126	82	4	328	32	22	15	29	1.94
3713998--3714060	29	2.2	29	86	11	85	46	17	11	25	1.81
3717792--3717822	14	2.2	14	94	0	53	67	0	0	32	0.91
3719987--3720300	43	7.3	43	84	0	403	30	30	15	22	1.95
3720499--3720558	18	3.4	18	64	13	52	40	10	6	43	1.64
3722818--3722844	3	9.0	3	100	0	54	66	0	0	33	0.92
3723746--3724070	41	7.9	40	81	4	303	29	27	19	24	1.98
3723745--3724068	123	2.6	122	80	5	357	29	27	19	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3727232--3727258	7	3.9	7	100	0	54	29	0	0	70	0.88
3731308--3731367	18	3.2	19	76	23	56	50	0	0	50	1.00
3731314--3731370	25	2.3	25	82	11	64	49	0	0	50	1.00
3733151--3733196	19	2.3	20	85	3	58	63	4	4	28	1.33
3733661--3733704	21	2.2	19	84	8	52	34	0	4	61	1.16
3740743--3740775	11	3.0	11	100	0	66	0	9	27	63	1.24
3749226--3749399	38	4.7	36	68	14	113	44	0	5	49	1.29
3749296--3749444	28	5.5	26	67	16	97	44	0	3	51	1.18
3749223--3749565	110	3.0	110	88	8	542	44	0	4	50	1.28
3749330--3749556	120	1.9	120	96	0	418	44	0	4	50	1.28
3750337--3750380	20	2.2	20	95	0	79	34	2	13	50	1.55
3753863--3753928	30	2.3	30	84	5	82	30	9	9	51	1.64
3756983--3757106	63	2.0	63	98	0	239	53	1	11	33	1.46
3758920--3758970	23	2.2	24	85	3	68	58	5	3	31	1.40
3765613--3765677	29	2.2	29	81	5	78	49	7	13	29	1.70
3768539--3768802	114	2.3	114	88	1	386	23	23	26	26	2.00
3778476--3778524	22	2.2	22	100	0	98	34	12	12	40	1.80
3779787--3779834	22	2.0	23	84	11	62	54	2	2	41	1.24
3779862--3780109	43	5.8	43	89	0	345	25	18	30	25	1.98
3783220--3783296	14	5.0	15	71	20	52	42	15	9	32	1.78
3783236--3783275	20	2.0	20	90	0	62	50	12	10	27	1.72
3783224--3783290	34	1.9	35	90	3	109	46	13	8	31	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3783259--3783298	14	2.9	14	84	0	53	42	17	7	32	1.77
3784341--3784424	25	3.4	24	82	12	82	21	25	23	29	1.99
3784356--3784435	25	3.2	25	84	7	99	25	25	21	28	1.99
3797862--3797974	31	3.7	30	73	15	90	52	5	3	38	1.41
3800712--3800910	80	2.4	81	89	5	292	33	17	27	21	1.96
3800787--3800941	42	3.6	42	82	7	186	32	17	25	23	1.96
3802089--3802169	34	2.3	35	80	16	98	55	1	1	41	1.15
3802135--3802180	21	2.2	20	81	11	58	56	0	2	41	1.11
3805398--3805531	19	6.7	21	78	10	77	39	14	6	39	1.72
3805398--3805455	22	2.6	22	81	7	64	41	17	5	36	1.72

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