genome.fa.s12.2.7.7.80.10.50.1000.19.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  19  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)
5883320--5883356	9	4.1	9	89	0	56	48	13	8	29	1.71
5883405--5883489	30	2.8	30	96	0	152	21	40	0	38	1.53
5883815--5883862	21	2.3	20	82	13	53	66	14	0	18	1.25
5884955--5884992	17	2.2	17	86	9	51	23	2	2	71	1.12
5884952--5884993	16	2.4	17	80	15	50	23	2	2	71	1.10
5885415--5885460	23	2.0	22	84	12	58	56	2	2	39	1.24
5886316--5886350	16	2.1	16	89	10	52	71	2	25	0	1.00
5889502--5889731	62	3.7	61	90	2	361	35	5	10	49	1.59
5890954--5890981	14	2.0	14	100	0	56	35	7	21	35	1.81
5892240--5892272	2	16.5	2	100	0	66	51	0	0	48	1.00
5902520--5902612	46	2.1	43	88	9	134	36	25	4	33	1.76
5902594--5902649	16	3.5	16	90	0	94	28	28	5	37	1.79
5903233--5903309	20	3.8	20	74	6	66	40	20	27	11	1.87
5905820--5905858	19	2.1	19	100	0	78	20	33	25	20	1.97
5907864--5908022	24	7.0	24	71	11	118	30	25	19	24	1.98
5907837--5907974	64	2.2	64	94	0	240	29	26	18	25	1.98
5917679--5917703	7	3.6	7	100	0	50	56	0	12	32	1.36
5917811--5917856	19	2.4	19	79	17	51	45	0	10	43	1.39
5917912--5917981	36	1.9	36	97	0	131	14	15	28	41	1.86
5919757--5919790	17	2.0	17	88	0	50	44	11	8	35	1.72
5928004--5928060	3	19.3	3	83	3	71	3	1	61	33	1.23
5935898--5936069	93	1.8	93	83	0	227	15	18	27	38	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5936052--5936103	3	17.3	3	77	0	50	1	3	36	57	1.28
5936816--5936871	24	2.2	26	78	15	64	55	1	39	3	1.28
5937797--5937845	22	2.2	23	96	3	91	55	0	6	38	1.25
5950062--5950130	24	2.9	24	86	0	102	27	13	17	42	1.86
5952440--5952486	3	16.0	3	91	4	78	34	63	2	0	1.06
5962218--5962257	14	3.0	14	82	10	57	0	25	0	75	0.81
5962218--5962270	27	2.0	26	85	3	70	0	26	1	71	0.96
5962335--5962364	11	2.7	11	94	0	51	63	3	0	33	1.11
5962470--5962509	20	1.9	22	90	10	66	52	0	0	47	1.00
5968323--5968564	50	4.8	50	84	0	313	26	21	29	22	1.99
5968328--5968615	50	5.8	48	74	10	145	27	21	27	23	1.99
5980965--5981011	22	2.1	22	100	0	94	19	25	38	17	1.92
5984436--5984470	18	2.0	17	88	5	52	45	0	0	54	0.99
5984254--5984610	119	3.0	120	96	2	655	43	2	5	48	1.40
5984556--5984590	18	2.0	17	88	5	52	45	0	0	54	0.99
5984831--5984892	16	3.9	16	78	0	70	29	27	1	41	1.65
5984821--5984885	32	2.0	32	84	0	85	24	27	3	44	1.68
5991522--5991548	2	13.5	2	100	0	54	51	48	0	0	1.00
5991548--5991583	2	18.5	2	94	5	65	50	0	0	50	1.00
5991643--5991687	2	22.5	2	100	0	90	48	0	0	51	1.00
5992374--5992438	19	3.1	21	80	12	80	40	16	6	36	1.74
5992364--5992438	19	3.5	22	79	12	68	42	16	5	36	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5992400--5992453	19	2.8	19	91	0	90	38	14	9	37	1.79
5995018--5995081	27	2.4	27	81	0	74	42	23	18	15	1.89
5996694--5996907	74	2.9	74	84	3	263	47	8	6	37	1.60
6002722--6002800	42	1.9	41	89	7	124	29	29	18	22	1.98
6007036--6007070	16	2.1	17	89	5	54	45	0	11	42	1.40
6007848--6007919	37	1.9	38	83	8	94	52	2	2	41	1.30
6013947--6014070	60	2.0	60	83	6	151	45	16	16	20	1.86
6016593--6016650	11	5.4	11	77	2	55	12	3	15	68	1.32
6020601--6020662	22	3.0	21	79	9	65	25	3	19	51	1.62
6030563--6030613	24	2.1	24	82	17	61	49	3	7	39	1.51
6030576--6030644	31	2.2	31	85	10	88	53	2	7	36	1.44
6031992--6032029	19	2.1	19	85	14	53	44	0	2	52	1.14
6043936--6044030	20	4.8	20	81	10	113	35	7	15	41	1.76
6045894--6045946	13	4.1	13	85	0	79	35	28	7	28	1.84
6061906--6061938	17	1.9	17	93	0	57	60	24	6	9	1.49
6061904--6061969	24	2.8	24	82	11	82	59	27	4	9	1.48
6062137--6062174	20	1.9	20	84	10	51	50	15	2	31	1.58
6064333--6064579	50	4.8	50	82	6	257	27	21	28	22	1.99
6070557--6070904	178	2.0	176	91	2	563	22	14	18	43	1.86
6073507--6073553	6	7.8	6	100	0	94	31	17	34	17	1.92
6083304--6083367	23	2.6	25	78	9	78	18	17	28	35	1.93
6094079--6094133	15	3.8	15	78	19	55	34	16	1	47	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6094314--6094430	24	4.8	25	70	7	80	34	21	23	21	1.97
6096806--6097144	170	2.0	170	91	1	545	29	16	15	39	1.89
6097204--6097456	129	2.0	130	91	0	418	30	11	19	39	1.86
6108042--6108085	11	3.9	11	79	5	52	70	4	25	0	1.06
6110188--6110504	125	2.5	125	95	0	553	29	17	22	29	1.97
6113121--6113245	59	2.1	59	95	0	223	39	8	10	42	1.69
6113309--6113449	21	6.6	21	84	5	167	24	0	29	46	1.53
6113313--6113437	43	2.9	43	85	4	173	25	0	26	48	1.52
6113312--6113436	64	2.0	64	91	3	207	24	0	27	48	1.52
6113313--6113449	22	6.4	22	84	9	167	24	0	27	47	1.52
6113495--6113519	7	3.6	7	100	0	50	56	0	0	44	0.99
6113444--6113648	105	1.9	106	94	2	360	35	1	17	45	1.58
6113583--6113625	12	3.3	12	78	15	50	53	0	0	46	1.00
6113586--6113625	7	5.9	7	83	16	57	52	0	0	47	1.00
6115801--6115839	17	2.3	17	86	8	53	17	5	2	74	1.12
6115987--6116024	2	20.0	2	86	10	53	47	0	2	50	1.15
6115997--6116056	16	3.8	16	77	18	63	43	0	6	50	1.28
6116532--6116560	14	2.1	14	93	6	51	31	6	0	62	1.22
6117753--6118811	531	2.0	531	98	0	2037	31	24	16	27	1.96
6118905--6118947	17	2.4	19	80	11	54	65	0	0	34	0.93
6119025--6119066	11	3.8	11	83	0	57	50	4	23	21	1.68
6122207--6122252	15	3.0	15	83	3	56	47	17	8	26	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6125192--6125243	11	4.7	11	79	9	61	63	0	34	1	1.06
6125192--6125243	25	2.1	25	89	7	79	63	0	34	1	1.06
6125192--6125252	22	2.8	22	82	7	70	65	0	31	3	1.09
6125179--6125251	11	6.6	11	76	6	58	68	1	27	2	1.11
6126543--6126580	20	1.9	20	88	0	58	57	31	0	10	1.32
6126618--6126686	29	2.4	28	75	17	70	52	27	1	18	1.54
6126684--6126736	28	1.9	28	84	3	72	56	20	1	20	1.51
6126806--6126879	20	3.5	20	80	8	67	56	20	0	22	1.42
6126784--6126879	42	2.3	42	78	7	97	53	23	0	22	1.47
6126985--6127036	21	2.5	20	79	11	52	57	25	1	15	1.48
6127217--6127298	7	11.9	7	71	2	58	48	28	0	23	1.51
6127217--6127310	14	6.8	14	77	2	73	51	27	0	21	1.48
6127217--6127284	21	3.3	21	72	12	68	48	26	0	25	1.51
6127548--6127572	7	3.6	7	100	0	50	60	28	0	12	1.32
6127896--6127935	21	1.9	21	84	0	53	52	22	0	25	1.47
6127841--6127949	55	2.0	55	80	3	121	50	23	0	24	1.55
6128333--6128423	43	2.1	43	81	4	103	37	28	12	21	1.90
6132210--6132365	7	22.0	7	71	12	77	44	32	1	22	1.61
6132190--6132267	22	3.6	22	77	8	79	41	37	1	20	1.61
6132227--6132370	14	10.1	14	78	9	103	45	29	1	22	1.61
6132233--6132267	15	2.4	15	90	4	54	45	34	0	20	1.51
6132188--6132370	21	8.5	22	73	12	78	44	31	1	22	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6132190--6132370	28	6.4	28	71	12	120	44	31	1	22	1.63
6132594--6132772	40	4.5	40	87	0	232	27	22	22	26	1.99
6132594--6132959	80	4.6	80	70	8	273	26	22	21	29	1.99
6132831--6132959	40	3.2	40	84	3	152	24	21	20	32	1.98
6133262--6133300	14	2.8	14	88	0	60	66	23	0	10	1.22
6133253--6133300	21	2.3	21	81	0	51	64	18	0	16	1.29
6133268--6133300	7	4.7	7	96	0	57	69	18	0	12	1.18
6133581--6133750	21	8.1	20	72	18	89	55	22	1	20	1.50
6133605--6134086	20	23.7	20	68	17	125	52	25	0	21	1.50
6133628--6133701	36	2.1	36	82	5	87	56	27	0	16	1.40

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