genome.fa.s6.2.7.7.80.10.50.1000.101.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  101  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)
29687802--29688500	76	9.2	74	84	6	710	29	17	20	33	1.95
29687802--29688500	227	3.1	226	83	5	874	29	17	20	33	1.95
29688835--29688995	30	5.4	29	77	7	119	33	21	4	40	1.75
29689269--29689302	15	2.3	15	94	0	59	26	58	11	2	1.47
29689373--29689402	11	2.8	11	95	5	53	66	0	33	0	0.92
29689475--29689518	16	2.8	15	83	10	52	72	0	27	0	0.85
29689479--29689564	27	3.1	28	76	14	81	73	0	25	1	0.91
29690453--29690693	17	13.8	17	73	14	188	28	16	11	43	1.82
29690458--29690645	18	10.7	17	73	16	152	28	16	10	44	1.81
29690453--29690693	35	6.9	35	83	4	281	28	16	11	43	1.82
29693052--29693097	24	2.0	24	87	12	69	30	4	0	65	1.12
29693056--29693108	25	2.3	22	78	12	61	28	1	0	69	0.99
29697005--29697032	3	9.3	3	100	0	56	64	0	0	35	0.94
29697179--29697229	16	3.2	16	85	0	66	25	27	5	41	1.78
29697552--29697611	30	2.0	30	96	0	111	56	15	3	25	1.54
29698643--29698672	14	2.2	13	94	5	51	30	3	0	66	1.07
29699192--29699248	11	5.4	10	79	10	53	71	1	0	26	0.95
29699208--29699254	20	2.3	20	86	10	69	76	2	0	21	0.89
29699495--29699525	13	2.4	13	94	0	53	45	0	9	45	1.36
29703496--29703524	2	14.5	2	100	0	58	51	0	0	48	1.00
29703632--29703659	2	14.0	2	100	0	56	50	0	0	50	1.00
29723630--29723655	6	4.3	6	100	0	52	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29729167--29729212	22	2.1	21	81	18	58	56	4	0	39	1.19
29729248--29729272	5	5.0	5	100	0	50	80	0	0	20	0.72
29739530--29739628	28	3.6	27	76	14	103	31	12	28	28	1.92
29740607--29740923	47	6.8	47	90	2	471	26	12	15	45	1.83
29752775--29752874	2	52.5	2	78	9	75	56	1	4	39	1.25
29756442--29756499	29	1.9	30	89	6	91	22	12	13	51	1.74
29772983--29773009	3	9.0	3	100	0	54	33	0	0	66	0.92
29773753--29773903	52	2.9	52	93	0	257	43	13	22	20	1.86
29774659--29774692	3	11.0	3	93	6	59	35	0	0	64	0.94
29779337--29779587	65	3.8	67	75	8	190	31	19	14	35	1.92
29779474--29779717	71	3.5	70	81	4	257	28	18	14	37	1.91
29791767--29791865	27	3.7	27	78	6	76	40	20	10	29	1.85
29794066--29794090	2	12.5	2	100	0	50	48	0	0	52	1.00
29794869--29794971	41	2.5	41	88	0	161	30	22	18	29	1.97
29801746--29801771	5	5.2	5	100	0	52	42	19	19	19	1.90
29803790--29803851	20	3.2	20	71	13	65	30	25	20	22	1.98
29803783--29803865	39	2.1	39	86	0	112	32	24	19	24	1.97
29818495--29818525	6	5.2	6	92	0	53	48	16	3	32	1.62
29818697--29818795	49	2.0	49	100	0	198	37	10	18	34	1.84
29822012--29822223	91	2.3	92	83	2	268	29	7	10	52	1.63
29822286--29822319	16	2.1	17	88	5	52	29	5	5	58	1.45
29832755--29832949	96	2.0	96	98	0	381	40	19	10	29	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29848639--29848679	20	2.0	20	85	0	55	46	2	9	41	1.50
29850065--29850107	23	1.9	23	81	13	54	37	0	18	44	1.50
29852198--29852309	56	2.0	56	87	0	161	22	27	27	22	1.99
29853415--29853608	105	1.9	101	87	4	280	32	17	24	26	1.96
29853415--29853646	105	2.3	101	82	5	277	33	17	24	24	1.97
29853553--29853629	33	2.3	32	80	6	82	33	16	23	25	1.96
29853553--29853683	66	2.0	65	80	7	149	35	17	24	22	1.95
29855566--29855658	46	2.0	46	100	0	186	24	34	8	32	1.86
29864183--29864216	14	2.4	14	90	9	52	44	0	0	55	0.99
29873691--29873731	6	6.8	6	100	0	82	51	0	0	48	1.00
29877277--29877335	22	2.7	22	82	10	68	42	23	5	28	1.75
29877322--29877372	22	2.3	22	79	0	57	37	19	9	33	1.85
29890622--29890664	19	2.1	21	83	8	54	55	2	0	41	1.12
29890628--29890674	14	3.3	15	82	8	62	61	0	0	38	0.96
29891469--29891532	29	2.2	28	83	8	74	37	1	9	51	1.44
29893839--29894249	135	3.0	135	92	1	687	21	24	14	39	1.91
29897229--29897304	24	3.2	24	100	0	152	47	15	7	28	1.74
29898377--29898618	83	2.9	82	91	3	405	51	12	6	29	1.64
29902011--29902072	31	2.0	31	96	0	115	50	6	20	22	1.71
29911610--29911640	9	3.4	9	95	0	53	25	9	22	41	1.84
29916855--29916890	18	1.9	19	88	5	56	55	0	2	41	1.14
29921100--29921141	15	2.7	16	82	14	52	45	0	2	52	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29921091--29921132	15	2.9	15	82	10	52	47	0	0	52	1.00
29921356--29921409	16	3.4	16	97	0	99	29	35	0	35	1.58
29928370--29928416	18	2.4	19	82	10	51	55	2	4	38	1.31
29928505--29928642	19	6.8	19	70	19	68	55	2	4	37	1.35
29928505--29928603	22	4.8	21	72	21	68	55	2	4	38	1.30
29928902--29928956	21	2.5	22	80	14	60	61	0	3	34	1.13
29928902--29928958	22	2.6	22	78	13	64	61	0	3	35	1.13
29929390--29929418	2	14.5	2	100	0	58	51	0	0	48	1.00
29931007--29931083	29	2.5	31	77	12	88	42	7	16	32	1.77
29935496--29935538	17	2.3	19	84	11	54	65	0	27	6	1.18
29936518--29936569	19	2.7	19	84	0	68	63	11	13	11	1.52
29942067--29942225	21	7.6	21	81	2	176	18	19	17	44	1.87
29942066--29942222	42	3.7	42	91	1	235	18	19	17	45	1.86
29942067--29942236	63	2.7	62	83	3	200	17	20	17	44	1.87
29948007--29948066	24	2.5	24	91	0	93	11	36	0	51	1.38
29949915--29949943	5	5.8	5	100	0	58	79	0	0	20	0.74
29950488--29950521	12	2.9	12	86	4	52	32	0	0	67	0.91
29950645--29950707	30	2.1	30	90	0	99	58	12	3	25	1.49
29955233--29955280	16	3.1	14	77	16	51	70	2	2	25	1.09
29957693--29957758	27	2.5	27	81	13	75	42	12	12	33	1.79
29957693--29957769	26	2.9	26	76	14	77	42	10	15	31	1.81
29967794--29967841	23	2.1	23	100	0	96	43	12	18	25	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29973571--29973611	12	3.4	12	86	10	57	56	0	9	34	1.32
29977804--29977832	15	1.9	15	100	0	58	62	17	0	20	1.33
29985945--29986026	24	3.3	24	77	13	78	18	23	17	41	1.90
29990321--29990348	13	2.2	13	100	0	56	64	14	0	21	1.29
29990718--29990757	16	2.4	16	84	15	55	42	0	0	57	0.98
29991534--29991579	22	2.2	21	88	7	67	21	2	2	73	1.04
29997485--29997513	9	3.2	9	100	0	58	10	0	31	58	1.31
29997626--29998147	125	4.2	124	84	3	697	29	17	22	29	1.97
29997626--29998147	126	4.2	125	83	3	683	29	17	22	29	1.97
29997626--29998147	250	2.1	250	88	2	771	29	17	22	29	1.97
29999556--29999605	22	2.2	22	85	7	64	34	8	6	52	1.55
30000122--30000350	109	2.1	106	92	2	377	31	17	16	33	1.93
30003887--30004760	21	40.7	21	80	7	859	23	0	31	44	1.58
30004213--30004439	7	32.3	7	63	23	50	25	0	30	44	1.55
30004666--30004718	14	3.8	13	75	20	54	16	0	37	45	1.48
30004666--30004722	28	2.1	27	93	3	96	17	0	40	42	1.49
30003887--30004760	43	20.3	43	82	7	956	23	0	31	44	1.58
30005313--30005378	18	3.4	18	73	18	60	43	9	28	18	1.80
30005327--30005374	23	2.1	23	100	0	96	37	8	33	20	1.83
30005967--30006006	7	5.7	7	100	0	80	57	15	0	27	1.38
30006174--30006211	20	1.9	20	84	10	51	55	7	2	34	1.43
30007150--30007247	51	1.9	51	85	4	135	45	2	25	26	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30007209--30007283	11	6.7	11	74	21	68	45	1	26	26	1.62
30007209--30007283	33	2.2	34	83	9	100	45	1	26	26	1.62
30008452--30008499	12	4.1	12	76	15	55	47	2	0	50	1.12
30008544--30008598	25	2.2	25	81	12	60	49	5	1	43	1.36
30010231--30010261	16	1.9	16	93	0	53	70	9	9	9	1.33
30016846--30016910	30	2.2	30	100	0	130	24	3	13	58	1.50
30025397--30025480	34	2.5	34	71	11	82	54	4	7	33	1.49
30027306--30027809	174	2.9	174	96	0	893	26	25	19	28	1.99
30027719--30028905	132	9.0	132	88	1	1605	28	24	18	28	1.98
30028107--30028432	44	7.4	44	66	7	126	26	24	18	29	1.98

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