genome.fa.s9.2.7.7.80.10.50.1000.10.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  10  of  226  ( 27023 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)
4488164--4488188	6	4.2	6	100	0	50	16	0	84	0	0.63
4488083--4488263	81	2.2	81	87	3	247	28	4	50	16	1.65
4493037--4493088	26	2.0	26	84	0	68	25	25	15	34	1.95
4494998--4495090	46	2.0	46	87	2	132	43	18	7	31	1.78
4502743--4502782	18	2.2	18	100	0	80	37	5	25	32	1.77
4509850--4509910	30	2.1	29	84	9	79	34	3	4	57	1.36
4510518--4510557	20	2.1	19	85	4	53	60	7	5	27	1.45
4513719--4513766	23	2.0	24	84	11	64	45	4	0	50	1.21
4525632--4525667	18	1.9	19	94	5	65	38	0	13	47	1.44
4528156--4528185	2	15.0	2	100	0	60	50	50	0	0	1.00
4542025--4542077	18	3.0	17	86	5	61	30	1	5	62	1.29
4543687--4543719	16	2.1	16	88	5	50	48	0	3	48	1.17
4584813--4584842	2	15.0	2	100	0	60	50	0	0	50	1.00
4604442--4604468	2	13.5	2	100	0	54	51	0	0	48	1.00
4615536--4615569	15	2.3	15	94	0	59	55	0	8	35	1.31
4625720--4625804	30	2.9	30	82	1	82	30	12	12	43	1.81
4630530--4630613	18	4.7	18	72	15	66	71	3	1	23	1.09
4630723--4630757	2	17.5	2	100	0	70	48	0	0	51	1.00
4635565--4635598	17	2.0	17	100	0	68	58	11	0	29	1.33
4639603--4639664	23	2.8	20	75	22	52	30	0	4	64	1.14
4660127--4660184	30	1.9	30	92	0	98	25	13	22	37	1.91
4668899--4668941	20	2.2	19	84	12	52	62	0	2	34	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4682607--4682656	23	2.1	25	85	7	68	52	10	2	36	1.47
4682671--4682896	23	9.7	23	70	11	115	56	4	5	33	1.43
4687751--4687776	13	2.0	13	100	0	52	53	7	0	38	1.30
4689651--4689678	13	2.2	13	100	0	56	64	21	14	0	1.29
4692532--4692693	83	2.0	82	87	1	234	41	17	8	31	1.80
4694021--4694087	22	3.0	22	93	0	107	25	25	14	34	1.94
4705774--4705831	11	5.0	12	70	14	50	63	1	0	34	1.04
4712264--4712311	18	2.8	17	78	9	53	47	2	0	50	1.12
4720653--4720728	40	1.9	40	100	0	152	53	6	10	28	1.60
4723285--4723333	24	2.1	24	85	7	66	44	2	2	51	1.24
4724342--4724375	16	2.1	16	100	0	68	64	0	5	29	1.17
4728475--4728500	10	2.6	10	100	0	52	34	0	0	65	0.93
4729704--4729747	21	2.1	21	95	0	79	29	0	11	59	1.32
4731241--4731278	14	2.7	15	88	8	53	39	2	15	42	1.61
4737177--4737227	25	2.0	25	82	14	61	41	7	1	49	1.43
4753693--4753722	12	2.4	13	94	5	53	23	16	23	36	1.94
4760620--4761449	411	2.0	411	93	1	1414	26	24	15	34	1.95
4766776--4766826	2	25.5	2	100	0	102	50	0	0	49	1.00
4779618--4779649	13	2.4	14	94	5	57	28	0	0	71	0.86
4779620--4779651	16	2.0	16	93	0	55	28	0	0	71	0.86
4782829--4782895	22	3.0	22	78	6	73	17	25	16	40	1.90
4785527--4785899	46	8.6	46	83	12	493	34	16	21	27	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4785527--4785854	82	3.9	82	89	7	494	34	15	21	28	1.94
4785527--4785898	128	2.9	126	87	8	458	34	16	21	27	1.95
4785527--4785899	174	2.2	174	93	0	633	34	16	21	27	1.95
4787863--4787917	28	1.9	30	88	7	87	49	3	0	47	1.19
4796584--4796610	4	6.8	4	100	0	54	0	22	0	77	0.76
4796453--4796662	105	2.0	101	93	3	357	25	16	15	42	1.87
4811549--4811595	2	23.5	2	100	0	94	51	0	48	0	1.00
4819511--4819590	6	13.3	6	69	10	56	2	30	13	53	1.53
4819499--4819634	24	5.7	24	83	0	164	1	31	17	49	1.56
4819487--4819558	18	4.0	18	73	7	65	0	31	16	51	1.45
4819625--4819670	18	2.6	18	78	0	56	2	36	13	47	1.54
4819620--4819672	24	2.2	24	82	0	61	1	37	15	45	1.57
4826182--4826268	42	2.1	42	97	0	165	31	8	21	39	1.83
4844445--4844477	2	17.0	2	93	6	59	51	0	0	48	1.00
4863476--4863511	12	3.0	12	87	0	54	44	27	0	27	1.55
4865017--4865059	21	2.0	23	81	9	54	34	0	6	58	1.25
4867838--4868021	46	4.0	46	92	2	282	36	8	26	28	1.85
4869681--4869729	20	2.4	20	83	10	55	63	4	4	28	1.31
4873374--4873506	63	2.1	63	88	0	203	27	9	35	27	1.88
4880906--4880940	18	1.9	18	88	0	52	51	2	0	45	1.16
4880914--4881005	48	2.0	47	85	6	125	40	6	3	50	1.45
4881081--4881123	19	2.3	20	80	15	56	58	2	0	39	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4886590--4886625	15	2.4	15	100	0	72	36	19	5	38	1.75
4892491--4892543	26	2.0	26	85	7	72	26	33	18	20	1.96
4892633--4892670	19	2.0	20	84	5	51	39	18	0	42	1.50
4915425--4915491	34	1.9	35	84	3	91	44	13	8	32	1.75
4917507--4917568	3	20.3	3	96	3	115	33	0	0	66	0.92
4918128--4918164	3	12.3	3	100	0	74	32	32	0	35	1.58
4926066--4926189	64	1.9	64	90	0	194	29	8	28	33	1.87
4932238--4932298	30	2.0	30	96	0	113	40	11	21	26	1.87
4936778--4936819	20	2.1	20	90	0	66	50	14	9	26	1.73
4937843--4937869	11	2.5	11	100	0	54	0	7	0	92	0.38
4942614--4942742	64	2.0	64	100	0	258	30	23	18	27	1.98
4955792--4955838	24	2.0	24	95	0	85	65	0	2	31	1.04
4966927--4967030	35	3.0	35	95	0	181	39	20	2	37	1.67
4987111--4987137	2	13.5	2	100	0	54	0	48	0	51	1.00
4995936--4996475	126	4.3	126	90	2	816	35	19	19	25	1.95
4998462--4998493	14	2.2	15	94	5	57	90	3	6	0	0.53
5002351--5002397	21	2.2	21	85	7	60	8	21	38	31	1.83
5003305--5003337	7	4.7	7	100	0	66	57	15	0	27	1.38
5014270--5014355	29	3.0	28	77	13	84	17	12	18	51	1.76
5014471--5014517	24	2.0	24	95	0	85	36	6	27	29	1.82
5019930--5019983	17	3.2	17	73	21	51	40	0	5	53	1.24
5020511--5020539	13	2.2	13	100	0	58	34	13	0	51	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5025436--5025477	21	2.0	21	85	0	57	54	21	9	14	1.68
5025830--5025957	4	32.0	4	98	0	247	49	25	0	25	1.56
5027225--5027301	35	2.3	35	82	8	88	37	14	20	27	1.91
5041903--5041967	30	2.3	29	80	15	73	49	6	10	33	1.63
5043494--5043557	29	2.2	29	83	5	76	50	3	1	45	1.27
5046288--5046331	2	22.0	2	100	0	88	50	0	0	50	1.00
5050776--5050928	45	3.4	45	90	0	234	41	21	17	18	1.90
5050782--5050955	45	4.2	39	83	9	154	39	21	18	19	1.92
5052785--5052877	46	2.0	46	91	4	152	37	9	22	30	1.86
5055126--5055187	28	2.1	28	88	5	88	40	1	6	51	1.37
5056315--5056376	21	3.0	21	73	0	61	20	12	25	40	1.89
5060851--5060893	6	7.3	6	84	5	61	48	0	2	48	1.14
5060849--5060892	23	1.9	23	95	0	79	50	0	2	47	1.13
5061122--5061170	24	2.0	24	84	7	64	53	2	14	30	1.52
5064062--5064101	13	3.1	13	88	0	62	42	22	7	27	1.80
5082436--5082560	57	2.3	57	83	8	161	32	1	1	64	1.13
5082497--5082554	22	2.6	23	78	13	59	32	0	1	65	1.03
5087371--5087395	12	2.1	12	100	0	50	24	36	24	16	1.94
5087556--5087604	9	5.4	9	87	0	62	44	24	6	24	1.76
5087556--5087604	18	2.7	18	87	0	71	44	24	6	24	1.76
5091606--5091752	59	2.5	59	85	3	188	31	8	14	44	1.75
5091644--5091758	59	1.9	59	94	0	203	31	10	13	45	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5091698--5091906	82	2.6	82	90	3	336	31	9	10	49	1.68
5094306--5094385	42	1.9	42	82	2	99	42	1	5	51	1.31
5094912--5095022	52	2.1	51	90	3	168	35	20	8	36	1.83
5097265--5097294	3	10.0	3	100	0	60	66	0	33	0	0.92
5129254--5129305	28	1.9	26	84	7	68	67	5	5	21	1.33
5132375--5132426	24	2.2	24	82	0	59	40	3	5	50	1.45
5158208--5158255	20	2.4	20	89	0	69	47	6	12	33	1.66
5158365--5158403	20	2.0	19	90	5	60	38	2	20	38	1.66
5158444--5158505	20	3.1	20	69	0	52	40	4	16	38	1.69
5158444--5158601	40	3.8	40	71	11	118	39	5	17	37	1.71

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226