genome.fa.s9.2.7.7.80.10.50.1000.199.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  199  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)
63116035--63116066	3	10.7	3	93	0	55	0	62	0	37	0.95
63116131--63116266	40	3.4	39	80	3	146	37	18	22	22	1.94
63117761--63117795	14	2.5	13	90	9	52	22	2	45	28	1.67
63117748--63117794	21	2.2	22	81	11	62	23	2	44	29	1.65
63118041--63118124	27	3.3	27	80	14	115	52	0	4	42	1.22
63118625--63118649	12	2.1	12	100	0	50	8	24	36	32	1.84
63118845--63119109	41	6.5	41	87	3	329	20	23	23	33	1.97
63119080--63119173	41	2.3	41	79	3	109	31	24	22	21	1.98
63118897--63119150	122	2.1	123	80	3	280	22	24	23	29	1.99
63122926--63123234	109	3.1	95	82	13	361	46	12	2	38	1.54
63123060--63123131	9	8.8	9	71	20	68	48	15	0	36	1.45
63122974--63123227	109	2.3	110	89	4	397	46	12	1	38	1.52
63122974--63123219	16	15.7	15	70	25	131	46	12	1	39	1.52
63128804--63128843	21	1.9	21	89	0	62	35	15	45	5	1.68
63128743--63128910	87	1.9	87	87	4	250	41	16	30	12	1.85
63128895--63128949	21	2.6	21	85	0	74	36	16	41	5	1.71
63128732--63128924	87	2.2	87	79	5	194	40	16	31	11	1.85
63129262--63129555	43	6.8	43	85	5	373	23	21	29	25	1.99
63129349--63129620	129	2.1	129	80	4	298	26	20	27	24	1.99
63133420--63133536	43	2.8	41	78	6	110	29	14	25	30	1.95
63133959--63134010	21	2.5	22	79	17	65	59	3	3	32	1.33
63134328--63134366	19	2.1	19	85	9	53	64	0	2	33	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63141507--63141551	24	2.0	23	86	8	65	42	2	11	44	1.52
63141580--63141628	24	2.0	24	100	0	98	30	12	20	36	1.89
63142524--63142575	21	2.5	22	81	9	56	34	1	5	57	1.33
63142511--63142584	31	2.4	30	80	6	87	36	1	4	58	1.26
63145815--63145858	13	3.5	13	84	9	56	45	2	0	52	1.13
63155359--63155397	19	2.1	19	85	0	51	43	0	5	51	1.24
63155245--63155564	159	2.0	159	100	0	640	30	7	18	43	1.77
63155518--63155556	19	2.1	19	85	0	51	43	0	5	51	1.24
63155549--63155575	11	2.5	11	100	0	54	25	0	0	74	0.83
63155542--63155575	16	2.1	17	88	5	52	29	0	0	70	0.87
63156508--63156583	40	1.9	40	88	0	116	35	23	21	19	1.96
63156508--63156603	40	2.4	40	82	0	111	38	23	20	16	1.93
63156678--63156830	41	3.7	41	85	5	202	22	19	26	31	1.98
63157275--63157326	20	2.6	20	82	11	70	15	0	48	36	1.45
63157270--63157329	13	4.4	14	78	18	63	16	0	45	38	1.48
63157270--63157329	7	8.7	7	78	15	63	16	0	45	38	1.48
63157368--63157440	7	10.4	7	80	0	83	16	1	47	34	1.55
63157368--63157448	28	2.9	28	83	3	101	18	1	46	33	1.57
63157445--63157474	15	2.0	15	93	0	51	30	0	26	43	1.55
63158038--63158094	27	2.1	27	100	0	114	57	3	17	21	1.54
63164383--63164409	5	5.4	5	100	0	54	62	0	0	37	0.95
63165076--63165125	24	2.0	24	84	3	64	66	4	2	28	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63180256--63180298	21	2.0	21	91	8	70	32	0	4	62	1.15
63180722--63180770	21	2.3	21	79	10	55	63	0	0	36	0.95
63181178--63181216	2	19.0	2	94	5	69	48	2	0	48	1.15
63188618--63188656	16	2.4	16	86	0	51	51	2	5	41	1.38
63188589--63188644	22	2.5	23	85	2	78	55	1	0	42	1.10
63188925--63188953	2	14.5	2	100	0	58	51	0	0	48	1.00
63201552--63201592	21	1.9	22	90	5	66	36	2	2	58	1.24
63201715--63201759	22	2.0	22	83	8	56	44	4	0	51	1.21
63208608--63208656	26	1.9	25	83	4	62	46	4	16	32	1.65
63209778--63209828	18	2.8	18	79	5	59	70	0	0	29	0.87
63211533--63211563	3	10.3	3	92	0	53	32	3	32	32	1.74
63229539--63229569	16	1.9	16	93	0	53	32	6	9	51	1.60
63233599--63233724	45	2.8	45	78	4	112	44	15	20	19	1.86
63233645--63233753	45	2.4	45	78	3	112	44	14	21	20	1.87
63239650--63239726	33	2.3	33	95	0	136	45	29	10	14	1.78
63240975--63241175	29	6.9	29	81	7	122	25	27	12	34	1.92
63240975--63241059	30	2.9	30	86	8	104	20	28	15	36	1.92
63240976--63241088	59	1.9	59	83	3	147	23	27	14	35	1.93
63241048--63241175	58	2.2	58	90	0	193	28	27	10	34	1.89
63241662--63241699	19	2.1	18	85	14	51	52	10	0	36	1.36
63249035--63249078	23	1.9	23	90	0	70	61	4	2	31	1.28
63249039--63249081	11	3.8	11	80	17	52	65	2	2	30	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63249583--63249608	13	2.0	13	100	0	52	23	23	7	46	1.78
63261287--63261386	2	50.0	2	95	0	173	47	0	53	0	1.00
63262704--63262755	26	2.0	26	100	0	104	42	19	11	26	1.85
63265044--63265085	14	3.0	14	83	10	50	38	0	2	59	1.10
63276687--63276938	129	1.9	130	89	0	389	36	15	20	27	1.93
63279226--63279254	14	2.1	14	100	0	58	20	6	13	58	1.58
63283915--63283940	5	5.2	5	100	0	52	76	0	0	23	0.78
63283922--63284011	46	2.0	46	86	4	128	47	1	8	42	1.42
63288910--63288953	21	2.0	22	91	4	72	38	2	0	59	1.10
63290524--63290617	6	15.2	6	78	11	84	15	1	6	76	1.04
63290585--63290638	21	2.6	21	85	2	65	14	1	11	72	1.21
63297299--63297345	21	2.2	21	85	7	60	61	6	23	8	1.48
63297338--63297377	6	6.5	6	82	5	53	75	0	22	2	0.93
63297309--63297386	25	3.1	25	81	7	95	67	2	21	7	1.28
63305298--63305332	17	1.9	19	88	11	56	65	11	2	20	1.37
63305343--63305387	22	2.0	22	87	8	65	64	11	13	11	1.50
63305343--63305401	22	2.6	22	81	10	57	66	8	13	11	1.45
63306665--63306707	18	2.5	17	82	10	52	55	9	6	27	1.57
63307685--63307763	29	2.6	29	84	11	88	62	1	0	36	1.04
63308044--63308117	19	3.9	19	89	0	112	33	4	4	58	1.36
63308051--63308143	38	2.4	39	83	3	125	34	4	2	59	1.29
63308035--63308123	19	4.7	19	83	6	101	30	3	3	62	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63308035--63308122	9	9.4	9	71	7	68	30	3	3	62	1.28
63310642--63310748	37	2.7	40	72	10	103	33	19	14	31	1.93
63310885--63310909	11	2.3	11	100	0	50	56	8	0	36	1.29
63310860--63310936	15	5.0	16	72	23	58	49	15	0	35	1.45
63310914--63310960	24	2.0	24	84	16	62	51	17	0	31	1.46
63312636--63312675	21	1.9	21	85	10	55	37	0	2	60	1.11
63312723--63312781	29	2.0	29	83	6	75	35	1	0	62	1.05
63312720--63312781	30	2.0	31	84	9	83	35	1	0	62	1.05
63313390--63313442	27	2.0	27	81	7	63	35	0	0	64	0.94
63313401--63313453	25	2.1	25	85	3	70	30	0	0	69	0.88
63313404--63313463	23	2.5	25	80	17	74	30	0	0	70	0.88
63318098--63318175	22	3.5	22	70	19	70	34	14	19	32	1.91
63318201--63318283	39	2.1	39	86	0	112	42	16	21	19	1.89
63318226--63318830	93	6.2	93	74	11	424	39	16	20	23	1.92
63318451--63318748	54	5.5	54	83	2	348	39	17	19	23	1.92
63318747--63318908	78	2.1	78	83	2	200	38	14	21	25	1.91
63318941--63319066	54	2.3	54	81	0	153	38	18	18	24	1.92
63319088--63319234	42	3.5	42	74	7	138	38	12	22	25	1.90
63319352--63319481	54	2.4	54	88	0	179	40	17	20	22	1.92
63319235--63319501	147	1.8	147	81	4	333	41	16	19	22	1.90
63319584--63319697	42	2.8	40	82	11	124	42	16	21	19	1.89
63319602--63319821	42	5.2	42	80	2	181	42	15	21	20	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63319808--63319988	54	3.4	54	86	0	254	33	19	23	23	1.97
63320275--63320519	42	5.8	42	82	0	220	39	13	25	21	1.90
63320239--63320522	84	3.4	84	88	1	358	39	14	25	20	1.91
63320252--63320521	126	2.1	126	83	0	333	38	14	25	21	1.91
63320662--63320782	54	2.2	55	76	8	131	42	14	19	24	1.88
63323378--63323419	20	2.1	20	90	0	66	50	0	4	45	1.23
63327255--63327306	24	2.2	24	89	0	77	57	7	1	32	1.38
63344887--63345018	69	1.9	67	87	3	192	30	13	12	43	1.82
63355834--63355891	26	2.2	26	78	6	64	6	12	27	53	1.63
63359882--63360118	44	5.4	44	92	2	368	49	11	2	35	1.54

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