genome.fa.s6.2.7.7.80.10.50.1000.21.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  21  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)
5468303--5468555	44	5.8	43	70	10	165	29	19	22	28	1.98
5468355--5468633	85	3.2	85	72	10	303	30	18	22	28	1.97
5468254--5468686	175	2.5	175	96	0	785	30	19	21	28	1.98
5468615--5468943	46	7.5	45	64	15	132	32	20	20	26	1.97
5468521--5469079	131	4.3	131	95	0	974	31	19	20	27	1.97
5469883--5469915	16	2.1	16	94	0	57	15	0	3	81	0.80
5473361--5473386	9	2.9	9	100	0	52	65	0	0	34	0.93
5474273--5474319	22	2.2	22	92	3	78	61	19	8	10	1.53
5474520--5474662	72	2.0	71	81	10	166	32	16	15	35	1.90
5475572--5475654	42	2.0	42	90	0	130	26	27	31	14	1.95
5475491--5475714	104	2.2	105	85	4	303	24	24	29	21	1.99
5480836--5480860	2	12.5	2	100	0	50	52	0	0	48	1.00
5481207--5481267	24	2.5	24	100	0	122	9	29	11	49	1.71
5486645--5486686	22	1.9	22	85	0	57	40	2	9	47	1.49
5489088--5489140	20	2.6	20	85	8	72	71	0	5	22	1.06
5489427--5489473	20	2.4	20	80	13	53	59	0	2	38	1.09
5489456--5489533	21	3.8	20	79	8	86	64	3	0	32	1.12
5489456--5489533	40	1.9	41	84	7	106	64	3	0	32	1.12
5489427--5489548	19	6.2	18	73	15	59	63	2	1	31	1.17
5489507--5489597	28	3.2	28	71	13	71	60	1	3	35	1.20
5490052--5490113	9	7.1	9	77	18	53	29	4	0	66	1.12
5490082--5490150	19	3.5	19	74	16	61	37	5	0	56	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5496021--5496047	2	13.5	2	100	0	54	51	0	0	48	1.00
5498172--5498198	4	6.8	4	100	0	54	0	25	0	74	0.83
5508934--5508977	14	3.1	14	77	9	54	43	34	9	13	1.76
5508995--5509061	7	9.7	7	83	3	91	31	31	10	26	1.90
5509825--5509857	2	16.5	2	100	0	66	48	0	0	51	1.00
5512138--5512162	2	12.5	2	100	0	50	48	0	0	52	1.00
5513387--5513441	29	1.9	28	82	10	67	41	9	5	43	1.59
5513638--5513706	21	3.5	20	69	26	65	56	15	14	13	1.67
5513625--5513721	39	2.5	39	96	0	185	52	17	16	13	1.75
5514777--5514820	18	2.4	18	85	7	54	52	4	2	40	1.34
5515007--5515083	14	5.0	15	70	20	52	33	9	15	41	1.79
5526160--5526259	41	2.4	41	81	0	110	22	31	28	19	1.97
5527648--5527673	3	8.7	3	100	0	52	30	0	0	69	0.89
5529603--5529645	19	2.3	18	84	15	52	20	23	13	41	1.88
5531673--5531737	8	7.3	9	86	13	91	80	9	0	10	0.92
5531670--5531764	44	2.2	42	81	9	111	77	7	5	9	1.10
5531752--5531784	7	4.6	7	96	3	57	87	0	12	0	0.53
5532591--5532625	14	2.6	14	90	4	54	65	0	20	14	1.26
5532591--5532628	20	1.9	20	84	10	51	63	0	21	15	1.31
5533835--5534759	46	20.1	46	88	0	1312	26	16	29	28	1.97
5534815--5535451	44	14.5	44	68	12	225	30	18	24	26	1.98
5534744--5535407	132	5.0	132	96	0	1204	31	17	24	26	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5536940--5537007	22	3.0	21	83	12	66	26	7	1	64	1.28
5538101--5538145	21	2.1	22	91	4	74	68	2	22	6	1.24
5539744--5539878	64	2.1	64	95	1	245	48	8	7	35	1.61
5543574--5543728	43	3.6	43	87	3	215	29	14	25	29	1.95
5543574--5543715	42	3.3	42	90	4	205	28	14	26	30	1.95
5543574--5543742	85	2.0	86	82	3	207	30	15	24	29	1.96
5544664--5544715	24	2.2	23	86	6	77	50	25	7	17	1.72
5545214--5545267	26	2.1	25	89	3	81	42	9	18	29	1.81
5545419--5545453	17	2.1	17	100	0	70	45	14	11	28	1.79
5545770--5545802	17	1.9	17	93	0	57	6	12	24	57	1.57
5552658--5552837	48	3.8	48	81	1	164	35	16	17	30	1.92
5558262--5558587	160	2.0	161	89	2	505	43	19	10	26	1.83
5564927--5565149	27	8.3	27	78	5	200	38	19	19	22	1.93
5564927--5565149	81	2.8	81	81	7	247	38	19	19	22	1.93
5569215--5569264	14	3.7	13	78	21	50	60	4	8	28	1.43
5577531--5577655	33	3.5	33	71	23	108	32	28	18	20	1.96
5577703--5577784	27	2.7	30	85	10	98	34	29	20	15	1.94
5577558--5577889	102	3.3	102	90	2	515	34	27	18	20	1.96
5586274--5586308	9	3.9	9	88	0	52	45	0	2	51	1.16
5588634--5588683	3	16.7	3	100	0	100	66	0	0	34	0.92
5591837--5591862	3	8.7	3	100	0	52	0	30	0	69	0.89
5595272--5595315	22	2.0	23	86	13	65	2	15	4	77	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5598108--5598142	6	5.8	6	93	0	61	17	2	0	80	0.84
5603795--5603832	18	2.1	19	85	5	51	34	2	0	63	1.09
5604043--5604097	18	3.1	17	81	5	56	43	3	3	49	1.37
5604465--5604521	21	2.7	21	94	0	105	42	10	10	36	1.74
5604713--5604751	19	2.0	21	85	10	55	15	10	5	69	1.34
5607980--5608012	15	2.2	15	94	0	57	24	21	12	42	1.86
5612700--5612897	46	4.6	45	83	13	256	34	15	22	27	1.94
5612736--5612808	36	2.0	36	97	0	137	36	15	20	27	1.92
5612700--5612854	82	1.9	82	94	0	274	35	14	21	28	1.93
5617058--5617397	44	7.7	44	63	13	117	29	18	26	25	1.98
5617046--5617448	132	3.1	132	93	0	691	29	19	25	25	1.98
5618173--5618271	21	4.7	21	97	0	180	40	10	12	37	1.76
5618465--5618503	19	2.0	21	85	10	55	15	10	5	69	1.34
5618899--5618965	4	17.0	4	80	9	66	23	0	2	73	0.97
5620603--5620648	20	2.2	21	80	3	58	47	0	0	52	1.00
5620599--5620645	23	2.0	24	83	4	60	44	0	0	55	0.99
5624955--5625011	28	1.9	31	89	10	93	49	1	1	47	1.22
5625609--5625648	21	1.9	21	84	0	53	67	10	5	17	1.37
5628451--5628498	2	24.5	2	95	4	89	52	0	0	47	1.00
5640152--5640199	24	2.0	25	91	4	80	47	2	6	43	1.40
5640152--5640191	19	2.1	19	85	0	53	50	2	5	42	1.37
5640152--5640211	24	2.9	19	76	21	66	51	1	5	41	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5643942--5644275	168	2.0	168	96	0	614	31	24	17	26	1.97
5654416--5654455	21	1.9	21	84	0	53	57	2	5	35	1.34
5659516--5659643	29	4.3	29	78	5	121	44	25	11	17	1.83
5659517--5659629	61	1.9	58	85	5	154	43	24	11	20	1.85
5659760--5659913	54	2.9	54	83	0	200	27	26	15	30	1.96
5663872--5664001	29	4.3	30	69	13	104	46	23	10	19	1.80
5663849--5664016	91	1.9	90	86	3	239	47	20	11	20	1.81
5683767--5683802	2	18.0	2	100	0	72	50	0	0	50	1.00
5684844--5684888	23	1.9	24	90	4	74	42	13	4	40	1.64
5684844--5684902	21	2.7	22	84	10	68	40	13	6	38	1.71
5686387--5686442	29	1.9	29	96	0	103	44	21	17	16	1.86
5686416--5686584	42	4.0	42	94	0	284	34	22	21	21	1.97
5692048--5692338	9	32.2	9	76	10	245	33	2	15	49	1.57
5692048--5692345	27	11.0	27	79	8	284	33	2	14	49	1.56
5694923--5695192	84	3.3	83	79	8	246	31	21	16	30	1.95
5695457--5695612	84	1.9	84	87	2	233	34	21	14	29	1.93
5695453--5695629	84	2.1	84	82	6	216	33	22	15	28	1.94
5695472--5695666	84	2.3	84	78	5	189	32	20	16	30	1.95
5695809--5696062	90	3.0	81	79	13	278	43	26	1	27	1.66
5695933--5695986	7	7.9	7	78	15	51	40	44	0	14	1.46
5696054--5696093	14	2.9	14	80	0	53	32	45	0	22	1.53
5696818--5697252	229	1.9	229	87	2	631	29	27	20	22	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5696818--5697274	115	4.0	115	84	2	535	30	28	20	21	1.98
5696913--5697403	115	4.3	113	79	7	302	29	27	21	21	1.99
5699308--5699397	7	12.7	7	73	18	71	0	20	0	80	0.72
5699316--5699399	11	8.0	11	71	20	56	0	19	0	80	0.70
5699316--5699399	18	4.9	17	80	15	93	0	19	0	80	0.70
5699317--5699399	23	3.6	22	77	19	89	0	19	0	80	0.71
5699319--5699396	35	2.3	34	88	6	113	0	19	0	80	0.71
5699308--5699399	37	2.5	35	79	20	109	0	20	0	79	0.73
5699398--5699452	26	2.3	23	84	9	65	9	23	45	21	1.80
5699655--5699687	14	2.2	16	89	10	52	0	18	0	81	0.68

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