genome.fa.s9.2.7.7.80.10.50.1000.138.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  138  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)
46138399--46138429	16	1.9	16	93	0	53	67	12	0	19	1.22
46150532--46150563	15	2.1	15	100	0	64	31	18	6	43	1.75
46150533--46150567	15	2.5	14	90	9	54	34	22	5	37	1.78
46158744--46158794	18	2.8	18	74	14	50	50	0	5	43	1.26
46160904--46160946	15	2.9	15	89	3	70	65	13	20	0	1.27
46175906--46176086	43	4.2	42	85	7	249	19	20	29	30	1.97
46175906--46176086	86	2.1	85	97	1	344	19	20	29	30	1.97
46182269--46182405	9	16.1	9	68	14	76	37	1	18	43	1.59
46182271--46182408	16	8.2	16	73	12	84	36	1	18	42	1.60
46182549--46182846	31	9.6	31	73	19	232	38	2	12	47	1.52
46182619--46182670	9	6.2	9	78	17	67	32	0	21	46	1.52
46182619--46182670	16	3.1	16	88	5	77	32	0	21	46	1.52
46182696--46182793	22	4.6	22	70	19	82	36	2	11	50	1.50
46182733--46182845	53	2.1	53	88	3	165	38	1	10	49	1.48
46182950--46183086	27	5.0	27	73	21	122	39	2	8	48	1.49
46182950--46183125	31	6.1	31	79	16	166	38	2	9	49	1.50
46183035--46183223	9	20.8	9	71	20	65	33	1	13	50	1.51
46183037--46183094	22	2.6	23	86	10	77	37	1	10	50	1.47
46183006--46183126	53	2.3	53	97	0	224	37	3	9	49	1.53
46183097--46183138	12	3.7	12	76	23	54	33	4	9	52	1.55
46183088--46183144	22	2.8	21	89	10	91	33	3	10	52	1.53
46183138--46183232	27	3.6	27	78	7	88	30	1	18	49	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46183134--46183220	36	2.5	34	80	7	111	31	0	18	50	1.47
46183138--46183272	18	7.6	18	70	11	91	31	2	18	47	1.61
46183188--46183242	25	2.2	25	86	0	74	30	1	20	47	1.60
46183520--46183590	29	2.4	29	95	0	133	38	7	12	42	1.70
46186086--46186137	27	1.9	27	88	0	77	50	9	0	40	1.35
46186207--46186243	10	3.7	10	92	0	65	43	13	0	43	1.44
46187379--46187572	41	4.7	41	80	5	205	38	22	23	16	1.93
46187379--46187574	82	2.4	82	97	1	367	38	21	23	16	1.93
46196868--46196907	9	4.6	9	84	3	55	67	7	12	12	1.41
46197330--46197388	9	6.7	9	76	9	59	71	3	1	23	1.11
46198365--46198635	44	6.1	43	72	12	192	31	23	13	31	1.93
46198375--46198626	88	2.9	87	83	5	303	32	23	13	30	1.93
46198609--46198950	88	3.9	88	89	0	513	24	26	22	26	2.00
46198629--46198957	43	7.5	43	68	4	192	23	27	23	25	2.00
46198674--46199202	176	3.0	176	86	3	631	24	25	22	27	2.00
46199028--46199597	218	2.6	218	93	0	969	23	23	22	30	1.99
46200983--46201012	15	1.9	16	93	6	53	0	16	3	80	0.85
46205406--46205432	7	3.9	7	100	0	54	88	0	0	11	0.50
46205448--46205481	2	17.0	2	100	0	68	50	0	0	50	1.00
46205660--46205716	3	19.7	3	76	7	55	70	3	1	24	1.13
46205657--46205718	9	6.7	9	76	12	63	70	3	1	24	1.10
46211961--46211990	12	2.5	12	94	0	51	23	40	30	6	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46217872--46217921	18	2.7	19	79	14	61	52	0	10	38	1.35
46218045--46218096	14	3.6	14	82	5	68	26	7	3	61	1.41
46218365--46218402	20	1.9	20	100	0	76	50	5	18	26	1.68
46224602--46224632	13	2.4	13	94	0	53	3	19	45	32	1.66
46225115--46225378	68	3.9	68	89	0	357	25	21	17	36	1.94
46227441--46227493	23	2.3	24	77	9	65	24	18	13	43	1.86
46232598--46232654	22	2.6	22	88	0	78	22	14	15	47	1.82
46233957--46234059	13	7.9	13	78	4	109	33	4	24	37	1.77
46238019--46238054	11	3.4	10	92	3	54	0	2	27	69	1.02
46238013--46238070	21	2.7	22	81	10	66	5	5	20	68	1.28
46243082--46243185	31	3.4	31	74	10	106	46	8	1	43	1.45
46244337--46244387	16	3.1	16	77	5	57	45	1	1	50	1.24
46253752--46253817	13	5.1	13	80	7	80	28	9	25	36	1.87
46256129--46256180	25	2.1	25	82	7	61	28	34	15	21	1.94
46256146--46256229	25	3.4	25	84	0	105	30	26	17	25	1.97
46257156--46257222	25	2.7	25	78	0	89	26	26	20	25	1.99
46268844--46269096	29	8.8	29	81	2	258	37	11	28	22	1.89
46268844--46269096	86	2.9	87	83	2	276	37	11	28	22	1.89
46268844--46269099	115	2.2	116	85	2	345	37	11	27	23	1.89
46271137--46271217	40	2.0	40	87	2	117	30	25	22	20	1.98
46274133--46274231	50	2.0	49	86	2	135	27	12	17	43	1.84
46281764--46282000	64	3.7	64	80	3	237	36	20	21	21	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46281783--46281986	96	2.1	96	83	6	252	35	21	21	21	1.96
46281763--46281997	32	7.4	31	79	1	211	36	20	20	22	1.95
46281763--46281997	96	2.4	94	79	4	249	36	20	20	22	1.95
46282271--46282335	27	2.5	26	80	7	69	23	26	15	35	1.94
46283990--46284043	28	1.9	28	88	0	81	29	27	27	14	1.95
46284223--46284268	22	2.1	22	84	4	58	45	17	17	19	1.85
46284263--46284418	32	4.9	32	73	5	111	36	21	21	20	1.95
46284280--46284418	64	2.2	64	80	7	149	35	21	22	20	1.96
46284280--46284432	32	4.8	31	77	9	121	35	22	21	20	1.96
46284285--46284525	32	7.6	32	75	6	114	36	22	21	19	1.95
46284525--46284581	26	2.2	26	87	0	78	38	21	19	21	1.93
46284799--46284970	27	6.4	26	77	4	105	24	21	17	36	1.94
46284818--46284996	27	6.6	27	76	3	171	24	19	17	38	1.93
46284827--46284974	55	2.7	55	85	7	194	25	20	16	38	1.92
46284818--46284996	82	2.2	82	81	3	200	24	19	17	38	1.93
46285329--46285422	9	10.4	9	83	4	118	39	24	11	24	1.89
46290719--46290784	23	2.9	22	80	8	69	37	25	19	16	1.93
46291242--46291281	18	2.4	17	87	8	55	12	30	10	47	1.74
46295691--46295787	23	4.2	23	75	5	88	16	15	20	47	1.83
46295691--46295787	46	2.1	46	80	0	104	16	15	20	47	1.83
46302108--46302135	12	2.3	12	100	0	56	17	17	7	57	1.62
46302399--46302531	50	2.7	49	82	6	135	21	30	22	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46317300--46317361	31	2.0	31	100	0	124	6	29	0	64	1.18
46328721--46328756	5	7.0	5	96	3	63	22	0	0	77	0.76
46333229--46333325	38	2.6	38	88	0	140	29	25	15	28	1.96
46344560--46344631	27	2.7	27	82	0	99	30	23	26	19	1.98
46344636--46345214	19	28.3	19	69	23	198	29	0	14	55	1.41
46344639--46345130	101	4.6	101	81	13	528	29	0	13	56	1.40
46344855--46344902	8	5.6	8	81	13	60	27	0	14	58	1.37
46344841--46345135	27	11.0	27	72	17	183	29	0	14	55	1.40
46344775--46344982	115	1.8	115	97	0	398	29	0	12	57	1.36
46344640--46345214	65	8.9	64	69	19	264	29	0	14	55	1.41
46344890--46345062	80	2.2	80	96	0	328	29	0	13	56	1.38
46345038--46345213	23	7.8	23	86	11	242	30	0	17	52	1.44
46345038--46345213	42	3.9	46	86	11	242	30	0	17	52	1.44
46344966--46345214	88	2.8	92	83	10	267	30	0	16	53	1.43
46344740--46345195	195	2.4	195	84	11	597	29	0	14	55	1.40
46345207--46345328	60	2.0	60	87	3	174	31	1	13	53	1.49
46345446--46345482	16	2.4	16	90	4	58	32	2	5	59	1.34
46346748--46346788	14	2.6	17	75	25	54	60	0	39	0	0.96
46346955--46347041	22	4.2	21	81	11	90	29	1	10	58	1.39
46346955--46347043	20	4.4	20	81	7	90	30	1	10	58	1.38
46346986--46347046	19	3.2	19	77	11	61	36	0	8	55	1.30
46347492--46347533	16	2.7	15	85	7	57	38	2	2	57	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46352499--46352543	22	2.1	21	91	4	72	0	33	2	64	1.06
46352609--46352679	27	2.6	28	88	6	110	19	39	23	16	1.92
46353050--46353106	30	1.9	30	85	3	80	47	15	8	28	1.75
46360692--46360749	29	2.0	29	96	0	107	43	13	18	24	1.87
46364712--46364771	30	2.0	30	100	0	120	30	3	10	56	1.48
46369291--46369328	19	2.1	18	85	9	51	73	2	0	23	0.95
46369592--46369636	9	4.7	10	91	5	67	77	0	13	8	0.98
46369579--46369633	24	2.3	23	81	9	58	78	0	12	9	0.97
46369592--46369636	19	2.3	20	85	11	67	77	0	13	8	0.98
46369725--46369771	19	2.4	20	82	7	60	51	10	17	21	1.75

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