genome.fa.s8.2.7.7.80.10.50.1000.179.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  179  of  190  ( 22705 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)
52344442--52344486	3	15.3	3	95	4	83	68	0	0	31	0.89
52345580--52345617	20	1.9	20	100	0	76	21	26	13	39	1.89
52345784--52346286	132	3.8	132	91	1	803	28	24	19	28	1.98
52354228--52354252	2	12.5	2	100	0	50	48	0	0	52	1.00
52355426--52355486	22	2.7	22	87	2	77	49	1	1	47	1.21
52355462--52355501	16	2.5	16	91	0	62	47	2	7	42	1.45
52355574--52355601	9	3.1	9	100	0	56	32	0	10	57	1.33
52355494--52355632	68	2.1	66	89	2	215	43	4	7	45	1.51
52355698--52355741	24	1.9	24	90	9	74	61	2	0	36	1.09
52357231--52357289	29	2.0	31	86	6	86	69	0	3	27	1.04
52357231--52357289	7	8.1	7	78	10	57	69	0	3	27	1.04
52365438--52365474	2	18.5	2	100	0	74	48	0	0	51	1.00
52376311--52376345	16	2.2	16	89	0	52	34	37	0	28	1.58
52381361--52381388	2	14.0	2	100	0	56	50	0	0	50	1.00
52384347--52384406	29	2.1	29	96	0	111	26	18	23	31	1.97
52387306--52387470	50	3.3	50	92	0	251	21	27	24	26	1.99
52394161--52394887	362	2.0	362	94	0	1283	33	15	11	39	1.84
52398417--52398670	109	2.4	108	88	2	375	32	16	16	34	1.92
52399063--52399215	22	7.0	22	90	0	225	26	26	14	32	1.94
52401062--52401100	18	2.2	17	86	13	53	33	0	20	46	1.51
52401205--52401233	8	3.6	8	100	0	58	24	13	27	34	1.93
52401320--52401395	23	3.3	23	96	0	143	21	21	26	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52407434--52407472	18	2.2	17	86	13	53	33	0	20	46	1.51
52407577--52407604	8	3.5	8	100	0	56	25	14	25	35	1.93
52407692--52407767	23	3.3	23	96	0	143	21	21	26	31	1.98
52414536--52414741	106	1.9	106	100	0	412	36	11	16	34	1.86
52415142--52415166	12	2.1	12	100	0	50	56	16	20	8	1.65
52419500--52419877	49	7.7	49	69	5	231	29	22	21	25	1.99
52419480--52419979	99	5.0	99	87	1	687	30	23	21	25	1.99
52419500--52419978	50	9.7	49	69	5	282	30	22	20	25	1.98
52421463--52421538	30	2.6	28	76	14	73	39	9	3	47	1.54
52421782--52421853	6	12.5	6	84	12	71	18	5	0	76	0.97
52421786--52421815	15	2.0	15	100	0	60	20	0	0	80	0.72
52422078--52422392	109	2.9	108	91	2	490	29	17	19	33	1.95
52424054--52424089	8	4.4	8	92	3	54	69	0	2	27	1.02
52426131--52426201	31	2.3	31	95	0	124	15	23	21	39	1.91
52426239--52426801	133	4.2	133	76	5	571	21	19	26	31	1.97
52426204--52426815	89	6.9	88	82	3	561	22	19	26	32	1.97
52426182--52426757	222	2.6	223	80	3	606	22	19	25	32	1.97
52426182--52426797	311	2.0	311	83	1	770	21	19	26	32	1.97
52436308--52436344	10	3.6	10	88	3	56	70	0	29	0	0.88
52436507--52436641	42	3.2	40	74	11	119	32	4	11	51	1.59
52436507--52436614	40	2.7	40	78	7	110	35	5	11	48	1.62
52441799--52442478	160	4.3	153	76	12	640	30	10	7	51	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52441799--52442477	317	2.1	318	92	1	1119	30	10	7	51	1.63
52442804--52442889	13	7.0	13	74	18	53	0	31	1	67	0.98
52442856--52442965	5	22.4	5	67	10	57	0	32	0	66	0.98
52442837--52442961	10	12.7	10	70	18	75	0	31	0	68	0.96
52442814--52442881	35	1.9	35	82	5	84	0	29	1	69	0.98
52442830--52442940	51	2.1	52	85	9	156	0	29	0	69	0.95
52442879--52442975	38	2.5	38	86	5	122	1	31	0	67	0.98
52442831--52442975	10	14.3	10	73	17	72	0	31	0	68	0.95
52445996--52446124	64	2.0	64	90	0	204	34	27	19	18	1.95
52448244--52448376	45	3.0	43	81	11	148	24	18	27	30	1.97
52448752--52448790	2	19.5	2	100	0	78	51	0	0	48	1.00
52452917--52452995	5	15.6	5	77	18	67	39	0	3	56	1.17
52452945--52452997	19	2.8	19	88	11	74	43	0	0	56	0.99
52452945--52452997	2	30.5	2	72	27	50	43	0	0	56	0.99
52454491--52454595	45	2.3	45	88	3	149	21	15	18	44	1.86
52454921--52454949	14	2.0	15	93	6	51	75	0	10	13	1.04
52462316--52462356	21	1.9	22	95	5	75	43	0	31	24	1.54
52462340--52462382	17	2.4	17	88	7	59	53	0	23	23	1.46
52475930--52475985	9	6.2	9	78	0	58	21	69	3	5	1.24
52475926--52475985	15	4.0	15	78	8	59	21	70	3	5	1.22
52475945--52476013	21	3.3	21	85	0	93	15	66	7	10	1.42
52475930--52475994	12	5.4	12	83	0	76	20	69	3	7	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52475957--52476003	15	3.1	15	84	0	58	12	68	8	10	1.40
52475930--52476012	6	13.8	6	84	0	58	16	68	6	8	1.35
52476041--52476080	15	2.6	16	84	11	57	20	5	47	27	1.70
52480082--52480110	2	15.0	2	92	7	51	48	51	0	0	1.00
52491762--52491820	30	2.0	30	86	6	84	42	0	37	20	1.52
52498014--52498048	12	2.9	12	95	0	61	34	17	8	40	1.80
52498027--52498107	26	2.9	29	76	12	89	25	13	9	50	1.72
52498053--52498091	14	2.9	14	85	7	55	23	17	10	48	1.78
52498054--52498106	12	4.4	11	76	21	52	26	15	9	49	1.74
52502196--52502243	14	3.4	14	73	21	55	54	4	14	27	1.59
52511419--52511509	41	2.2	41	94	2	155	28	18	28	24	1.98
52537575--52537626	22	2.4	22	83	6	61	44	15	25	15	1.85
52537590--52537665	22	3.3	22	74	18	66	35	19	26	18	1.95
52544074--52544118	23	2.0	23	86	8	65	42	0	2	55	1.12
52544293--52544343	8	6.9	8	74	17	56	33	1	0	64	1.05
52544298--52544348	14	3.6	14	79	12	52	35	1	0	62	1.06
52544300--52544348	21	2.3	22	75	10	57	34	2	0	63	1.06
52548368--52548402	6	5.7	6	89	3	52	62	0	2	34	1.10
52556749--52556815	3	22.3	3	100	0	134	32	0	0	67	0.91
52556910--52556987	38	2.1	36	81	13	88	23	2	5	69	1.21
52562050--52562247	42	4.6	43	89	1	274	32	21	23	22	1.98
52562050--52562247	85	2.3	84	89	3	297	32	21	23	22	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52562435--52562460	4	6.5	4	100	0	52	23	0	0	76	0.78
52562431--52562486	16	3.5	16	85	7	78	23	5	3	67	1.27
52562989--52563031	22	1.9	23	86	13	63	53	34	0	11	1.37
52563569--52563925	114	3.1	112	70	11	285	27	19	24	28	1.99
52563571--52563989	228	1.8	228	82	5	542	26	19	24	29	1.99
52566758--52566798	18	2.4	18	80	8	50	41	7	7	43	1.60
52566792--52566823	16	2.1	16	88	11	50	46	0	0	53	1.00
52569719--52569776	29	2.0	30	83	10	75	46	1	1	50	1.22
52569875--52569954	31	2.6	30	74	5	79	48	5	7	38	1.53
52575210--52575270	20	3.1	19	71	15	52	67	4	3	24	1.26
52575354--52575425	31	2.3	31	83	4	92	38	13	9	37	1.78
52575508--52575542	18	1.9	18	88	0	52	45	11	5	37	1.64
52575789--52575830	19	2.1	21	86	8	61	23	7	7	61	1.47
52584136--52584182	15	3.3	14	79	8	51	12	6	0	80	0.88
52584922--52584997	3	25.3	3	100	0	152	32	0	0	67	0.91
52588575--52588637	21	3.0	21	80	15	69	23	1	4	69	1.16
52590042--52590069	14	2.0	14	100	0	56	7	42	7	42	1.59
52590760--52590791	17	1.9	16	93	6	55	12	12	0	75	1.06
52593637--52593770	18	8.0	17	70	17	93	39	0	2	57	1.16
52593690--52593719	15	2.0	15	93	0	51	43	0	0	56	0.99
52593927--52594017	44	2.0	45	85	6	123	32	29	4	32	1.77
52608036--52608078	11	3.7	11	79	11	50	39	2	0	58	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52608517--52608553	9	4.2	9	93	6	67	21	10	32	35	1.88
52608518--52608552	17	2.1	17	100	0	70	22	11	34	31	1.90
52612572--52612634	30	2.2	28	80	8	72	53	7	14	23	1.66
52612595--52612651	29	2.0	29	89	0	87	54	8	14	22	1.67
52626030--52626106	27	2.9	28	90	3	115	19	38	24	16	1.92
52640037--52640088	25	2.1	25	100	0	104	19	15	21	44	1.87
52640368--52640446	30	2.7	30	88	5	117	29	5	16	49	1.67
52640706--52640779	30	2.4	30	84	6	87	67	1	5	25	1.20
52644587--52644629	22	2.0	22	100	0	86	23	25	13	37	1.92
52644774--52644825	24	2.2	24	82	0	59	48	7	5	38	1.56

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