genome.fa.s12.2.7.7.80.10.50.1000.17.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  17  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)
5266257--5266326	24	3.1	23	80	19	94	51	14	28	5	1.65
5266258--5266319	19	2.9	21	88	11	83	53	14	27	4	1.61
5267043--5267099	17	3.1	18	73	21	55	45	0	0	54	0.99
5267050--5267093	21	2.2	20	83	4	52	43	0	0	56	0.99
5267043--5267103	20	3.2	20	78	13	67	45	0	0	54	1.00
5267112--5267147	16	2.2	16	90	0	54	63	0	0	36	0.94
5268079--5268142	3	21.3	3	100	0	128	67	0	0	32	0.91
5269588--5269965	44	8.3	44	74	10	154	29	21	17	31	1.96
5269793--5269969	88	2.0	88	86	4	250	29	21	16	32	1.95
5269816--5269969	44	3.5	44	87	5	213	28	21	16	33	1.95
5278134--5278182	23	2.1	24	84	3	64	24	4	4	67	1.26
5278240--5278287	3	16.0	3	100	0	96	33	0	0	66	0.92
5278361--5278426	31	2.1	31	83	5	80	39	15	13	31	1.86
5278529--5278561	14	2.3	15	89	5	50	24	0	0	75	0.80
5278939--5278979	5	8.4	5	94	5	75	58	0	0	41	0.98
5279031--5279072	14	2.9	15	89	3	59	45	0	0	54	0.99
5279117--5279147	16	1.9	16	93	0	53	48	3	0	48	1.17
5286390--5286525	26	5.2	25	70	11	85	58	1	3	36	1.25
5286437--5286529	44	2.1	42	84	9	116	59	1	2	37	1.17
5286330--5286526	18	11.5	17	65	26	62	56	2	3	37	1.28
5286427--5286509	35	2.3	35	75	17	82	61	0	2	36	1.09
5286445--5286566	46	2.6	46	84	6	140	62	1	2	33	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5286427--5286508	8	10.4	8	74	19	57	60	0	2	36	1.10
5289433--5289458	2	13.0	2	100	0	52	50	0	0	50	1.00
5292521--5292555	17	2.0	18	94	5	63	11	22	40	25	1.88
5292776--5292842	27	2.5	27	87	0	98	31	19	17	31	1.95
5298922--5298948	2	13.5	2	100	0	54	48	0	0	51	1.00
5310237--5310279	22	2.0	22	81	9	52	39	27	6	25	1.81
5311223--5311250	12	2.3	12	100	0	56	50	10	7	32	1.64
5312079--5312158	31	2.6	31	93	0	133	45	20	15	20	1.86
5313060--5313322	83	3.2	83	93	0	436	29	17	14	39	1.89
5313785--5313834	7	7.1	7	83	0	55	44	36	0	20	1.52
5313778--5313834	21	2.7	21	83	0	78	45	33	0	21	1.52
5313849--5313889	21	2.0	21	85	0	55	51	24	2	21	1.60
5314128--5314334	41	5.1	41	82	7	208	33	28	19	18	1.95
5314137--5314375	82	2.9	81	83	6	252	33	28	17	19	1.95
5314239--5314381	41	3.5	41	91	0	205	32	33	15	18	1.92
5314433--5314508	40	1.9	39	91	2	125	23	21	18	36	1.95
5315748--5315868	52	2.2	57	81	13	148	61	1	4	32	1.24
5316900--5316947	25	1.9	25	83	8	62	35	2	16	45	1.59
5330952--5331070	16	7.8	16	70	19	67	44	2	3	49	1.32
5332406--5332465	31	1.9	31	90	6	95	35	6	23	35	1.81
5338403--5338468	34	1.9	34	87	6	98	34	9	10	45	1.70
5343306--5343495	42	4.5	42	84	3	215	32	21	19	26	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5343432--5343541	42	2.6	42	88	5	152	25	17	20	36	1.94
5343862--5343932	21	3.4	21	78	0	79	1	45	21	32	1.61
5349544--5349863	9	35.8	9	69	19	165	34	1	19	44	1.62
5349548--5349758	105	2.1	96	79	15	225	31	1	21	44	1.63
5349717--5349795	16	4.4	16	75	20	68	35	1	18	44	1.59
5349733--5349835	38	2.7	37	89	7	145	38	0	15	44	1.53
5349792--5349816	13	1.9	13	100	0	50	52	0	8	40	1.31
5350200--5350268	13	5.5	13	80	13	74	44	1	10	43	1.46
5350466--5350564	49	2.2	44	82	14	112	43	2	11	43	1.51
5350090--5350788	345	2.0	343	96	1	1292	47	2	8	41	1.49
5350545--5350603	13	4.5	13	85	8	75	47	1	10	40	1.47
5350545--5350614	26	2.8	27	79	12	78	47	1	10	41	1.46
5350997--5351031	16	2.2	16	89	0	52	54	2	11	31	1.51
5351072--5351110	10	3.9	10	86	0	60	58	2	0	38	1.12
5352325--5352410	43	2.0	43	90	4	138	37	19	17	25	1.94
5352368--5352691	147	2.2	146	79	6	332	36	24	14	24	1.93
5352999--5353023	7	3.6	7	100	0	50	48	52	0	0	1.00
5354105--5354650	114	4.8	110	77	9	447	26	24	18	31	1.97
5354240--5354650	228	1.8	228	85	4	578	25	24	18	31	1.97
5354105--5354650	113	4.8	111	77	5	477	26	24	18	31	1.97
5357300--5357494	76	2.6	75	82	2	230	28	20	17	33	1.96
5357425--5357689	115	2.3	114	81	3	307	29	23	16	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5357640--5357743	54	1.9	55	84	2	138	30	25	16	26	1.97
5357526--5357860	170	2.0	170	85	2	458	28	24	17	29	1.97
5357695--5358121	114	3.7	115	78	5	393	25	21	17	35	1.95
5360169--5360231	32	2.0	32	87	6	92	47	7	6	38	1.58
5371608--5371687	26	3.1	26	98	1	153	45	11	13	30	1.79
5371957--5371982	12	2.2	12	100	0	52	42	7	7	42	1.62
5374537--5374585	6	8.2	6	100	0	98	51	0	16	32	1.45
5381072--5381105	6	5.7	6	92	0	50	17	20	38	23	1.93
5383008--5383038	16	1.9	16	93	0	53	61	0	38	0	0.96
5388575--5388604	15	2.0	15	100	0	60	26	6	20	46	1.75
5389073--5389213	73	1.9	73	85	2	194	31	22	26	19	1.98
5389133--5389213	25	3.3	24	69	22	62	29	22	29	18	1.97
5389716--5389744	10	2.7	11	94	5	51	37	20	0	41	1.53
5389911--5389952	21	2.0	21	100	0	84	38	19	0	42	1.51
5395472--5395539	26	2.7	26	76	2	66	39	20	19	20	1.92
5395612--5395683	24	3.0	23	71	16	65	33	19	29	18	1.95
5401510--5401585	25	3.1	25	77	19	79	13	18	1	67	1.30
5401541--5401585	23	2.0	23	82	8	56	17	15	0	66	1.25
5408992--5409030	7	5.6	7	100	0	78	28	0	30	41	1.57
5420540--5420577	18	2.1	19	90	5	60	73	2	5	18	1.14
5424113--5424177	32	2.0	32	96	0	121	35	16	21	26	1.95
5426059--5426091	15	2.1	16	88	5	50	72	0	0	27	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5426059--5426107	16	2.9	17	77	20	57	69	2	0	28	1.00
5426059--5426112	18	3.1	18	78	7	58	68	1	0	29	1.00
5426066--5426187	64	1.9	62	80	12	142	61	2	4	31	1.30
5426194--5426240	20	2.3	20	75	7	51	63	2	6	27	1.30
5426261--5426354	49	2.0	47	89	8	147	32	13	12	40	1.83
5426733--5426757	13	1.9	13	100	0	50	8	8	0	84	0.79
5426982--5427012	11	2.8	11	90	0	53	67	0	0	32	0.91
5426982--5427016	11	3.1	11	91	4	52	65	0	0	34	0.93
5432767--5432826	31	1.9	31	86	6	86	58	0	1	40	1.08
5432767--5432947	40	4.5	40	91	4	276	61	0	2	35	1.13
5437144--5437174	9	3.4	9	90	0	53	25	12	22	38	1.90
5437228--5437264	9	4.1	9	92	0	65	45	13	10	29	1.77
5437529--5437563	14	2.5	14	95	0	61	31	8	0	60	1.27
5441682--5441724	23	1.9	23	90	4	70	44	13	6	34	1.72
5441708--5441760	19	3.0	17	73	10	52	33	20	9	35	1.85
5441679--5441736	22	2.6	22	81	7	73	41	17	5	36	1.72
5462001--5462091	30	3.0	30	100	0	182	40	19	3	36	1.68
5473021--5473051	9	3.4	9	90	0	53	25	12	22	38	1.90
5473104--5473140	9	4.1	9	92	0	65	45	13	10	29	1.77
5479072--5479348	46	6.0	46	91	1	414	29	24	9	36	1.86
5481209--5481256	24	2.0	24	92	8	80	31	25	0	43	1.55
5484297--5484334	19	2.0	19	94	0	67	15	18	26	39	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5484652--5484711	11	5.6	10	75	13	57	73	5	21	0	1.02
5486414--5486447	17	2.0	17	100	0	68	52	23	17	5	1.66
5487115--5487172	30	1.9	30	89	0	89	10	27	37	24	1.88
5490271--5490305	2	17.5	2	93	0	61	48	2	0	48	1.16
5510917--5510982	32	2.1	32	85	5	89	40	6	15	37	1.72
5513053--5513108	29	1.9	29	82	7	69	32	3	10	53	1.53
5515818--5515864	22	2.1	23	84	7	62	63	4	4	27	1.31
5518616--5518697	24	3.4	24	79	3	85	12	43	6	37	1.67
5519646--5519671	7	3.7	7	100	0	52	61	0	0	38	0.96
5520630--5520666	17	2.2	17	90	4	58	51	0	2	45	1.15

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