genome.fa.s8.2.7.7.80.10.50.1000.36.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  36  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)
10204592--10204636	20	2.3	19	85	14	56	68	2	4	24	1.19
10204592--10204636	22	2.2	20	84	8	54	68	2	4	24	1.19
10211340--10211379	2	20.0	2	100	0	80	50	0	0	50	1.00
10222290--10222338	25	2.0	25	91	0	80	32	18	20	28	1.96
10236879--10236906	12	2.3	12	100	0	56	7	28	28	35	1.84
10237880--10237990	42	2.7	41	80	1	114	41	18	25	15	1.89
10241205--10241269	16	4.1	16	90	6	87	41	3	33	21	1.69
10241203--10241267	32	2.0	32	88	5	96	40	3	33	23	1.70
10241500--10241534	18	2.0	17	88	5	52	54	0	0	45	0.99
10241618--10241654	16	2.2	17	86	13	51	54	0	2	43	1.14
10241480--10241843	120	3.0	120	97	1	676	48	5	2	43	1.40
10241738--10241774	16	2.2	17	86	13	51	54	0	2	43	1.14
10242100--10242236	47	3.0	47	73	17	151	47	5	2	44	1.40
10245215--10245324	45	2.6	41	77	9	107	31	5	29	33	1.80
10245470--10245504	18	2.0	17	88	5	52	54	0	0	45	0.99
10245541--10245621	15	5.6	15	70	21	57	53	2	2	41	1.27
10245690--10245741	15	3.6	15	80	12	56	53	1	0	44	1.11
10245498--10245804	61	5.1	61	67	18	228	48	5	2	42	1.39
10245453--10245866	120	3.4	120	94	2	699	49	4	2	43	1.36
10249162--10249237	33	2.3	33	97	0	143	35	5	15	43	1.70
10249280--10249361	37	2.2	37	93	0	137	36	8	14	40	1.77
10252535--10252560	5	5.2	5	100	0	52	80	0	19	0	0.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10254481--10254537	30	1.9	30	89	7	89	36	1	1	59	1.18
10254551--10254597	20	2.3	20	85	10	60	31	0	0	68	0.90
10265236--10265292	21	2.8	21	86	5	73	17	26	15	40	1.90
10276462--10276530	31	2.3	31	97	2	131	31	15	5	46	1.70
10277455--10277498	23	1.9	23	90	0	70	61	4	2	31	1.28
10277459--10277501	11	3.8	11	80	17	52	65	2	2	30	1.18
10281152--10281261	30	3.7	30	77	9	107	30	3	19	46	1.67
10289471--10289570	2	47.5	2	96	4	139	48	6	0	46	1.27
10290086--10290137	2	26.0	2	100	0	104	50	0	0	50	1.00
10310419--10310478	30	2.0	31	83	6	79	16	43	1	38	1.58
10317379--10317513	69	2.0	68	94	1	234	41	14	13	30	1.84
10318005--10318084	8	9.5	8	89	8	115	42	22	11	23	1.86
10318005--10318084	17	4.8	16	88	8	115	42	22	11	23	1.86
10321763--10321825	32	2.0	32	83	0	81	31	30	19	19	1.96
10324189--10324248	30	2.0	29	84	9	77	43	5	21	30	1.74
10324370--10324689	50	6.4	50	83	2	399	26	22	30	20	1.98
10324373--10324689	101	3.1	101	89	0	465	26	22	30	20	1.98
10328183--10328211	9	3.2	9	100	0	58	10	0	68	20	1.18
10328183--10328217	18	1.9	18	88	0	52	11	2	65	20	1.37
10329595--10329662	24	3.1	24	65	30	69	42	19	5	32	1.75
10336038--10336138	51	2.0	51	98	0	193	39	22	9	27	1.86
10340119--10340166	23	2.1	23	84	7	62	18	31	18	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10340156--10340221	25	2.7	25	78	2	71	19	27	22	30	1.98
10340238--10340320	25	3.2	25	81	5	85	21	25	21	31	1.98
10342299--10342459	25	6.4	25	72	11	107	33	21	24	20	1.97
10342499--10342544	23	2.0	23	86	0	65	26	23	30	19	1.98
10342525--10342595	26	2.8	26	84	2	90	35	22	25	16	1.95
10356702--10356750	25	1.9	26	87	4	73	63	0	2	34	1.06
10356848--10356905	25	2.3	26	79	11	66	65	1	5	27	1.23
10358784--10358832	25	1.9	26	91	4	82	32	0	0	67	0.91
10358807--10358868	19	3.4	18	76	14	56	33	4	0	61	1.17
10358784--10358839	26	2.2	26	87	6	78	33	0	0	66	0.92
10358976--10359028	25	2.0	27	85	7	74	32	0	0	67	0.91
10366479--10366510	3	10.7	3	100	0	64	68	0	0	31	0.90
10373699--10373911	61	3.4	61	81	8	209	43	17	7	30	1.77
10373699--10374134	31	14.2	31	70	13	213	44	18	6	30	1.75
10373757--10374184	92	4.7	92	87	2	531	43	18	7	30	1.77
10374185--10374238	25	2.2	25	86	6	74	48	12	11	27	1.76
10379522--10379617	34	2.8	34	85	0	111	44	15	7	32	1.74
10382434--10382522	21	4.5	20	67	23	55	47	0	2	50	1.13
10386977--10387020	18	2.4	18	100	0	88	25	25	18	31	1.97
10387143--10387608	43	10.9	43	93	0	781	29	26	21	22	1.99
10387677--10387706	14	2.1	14	100	0	60	53	33	0	13	1.40
10387915--10387968	21	2.6	21	87	0	81	5	46	18	29	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10388020--10388070	21	2.4	21	90	0	75	3	43	17	35	1.68
10387939--10388136	87	2.3	87	83	5	231	10	32	18	38	1.85
10394492--10394550	27	2.1	28	90	6	102	52	3	3	40	1.35
10395691--10395721	16	1.9	16	93	0	53	32	6	25	35	1.82
10396470--10396514	23	2.0	23	82	8	56	40	31	6	22	1.80
10397378--10397510	41	3.2	41	78	3	115	26	28	25	19	1.99
10397603--10397949	113	3.1	113	93	0	577	26	22	24	27	2.00
10400573--10400639	23	2.9	23	97	0	125	26	23	25	23	2.00
10403392--10403435	16	2.7	17	89	6	65	31	2	0	65	1.05
10403392--10403441	16	3.1	17	86	11	61	36	2	0	62	1.07
10407082--10407145	28	2.3	28	94	0	110	20	21	15	42	1.89
10407132--10407312	24	7.5	24	76	5	143	19	27	21	30	1.98
10407228--10407320	25	3.8	25	78	8	84	21	26	20	31	1.98
10407223--10407337	25	4.6	25	74	10	76	20	27	20	32	1.97
10409387--10409414	9	3.1	9	100	0	56	64	10	10	14	1.50
10410333--10410377	22	2.0	22	100	0	90	22	8	17	51	1.73
10414602--10414673	25	2.9	25	79	8	76	19	27	19	33	1.96
10417557--10417613	15	3.5	15	71	17	51	47	3	1	47	1.29
10417646--10417682	16	2.3	16	86	13	58	40	0	0	59	0.97
10417817--10417845	9	3.2	9	100	0	58	48	0	0	51	1.00
10420732--10420857	61	2.1	61	84	0	162	38	6	15	40	1.72
10421244--10421277	12	2.9	12	95	4	61	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10421398--10421460	30	2.1	30	87	0	90	58	15	3	22	1.51
10438772--10438856	44	1.9	44	87	0	125	30	21	17	30	1.96
10439148--10439328	50	3.6	50	71	5	168	25	25	21	27	1.99
10438882--10439469	267	2.2	267	90	0	933	27	25	20	26	1.99
10445784--10445826	19	2.3	19	100	0	86	16	13	13	55	1.69
10451376--10451405	15	2.0	15	93	0	51	66	16	0	16	1.25
10451829--10451880	21	2.5	21	87	0	77	65	5	0	28	1.16
10452397--10452422	12	2.2	12	100	0	52	61	26	0	11	1.30
10459919--10460044	30	4.2	30	82	1	137	33	14	18	34	1.91
10469929--10469973	18	2.6	17	83	13	56	71	2	4	22	1.15
10474709--10474901	50	3.8	50	87	6	273	20	30	22	26	1.99
10474709--10474890	101	1.8	101	90	3	296	20	30	23	25	1.99
10487418--10487443	2	13.0	2	100	0	52	50	0	50	0	1.00
10492291--10492330	21	2.0	20	90	5	62	50	0	2	47	1.14
10495018--10495065	24	1.9	26	83	8	64	22	12	16	47	1.80
10498027--10498087	21	2.9	21	92	0	95	45	14	24	14	1.83
10499869--10499927	26	2.3	26	81	0	73	33	22	23	20	1.97
10500009--10500072	25	2.6	25	89	0	92	39	20	26	14	1.90
10505009--10505070	23	2.7	23	92	0	97	45	16	8	30	1.76
10508143--10508629	50	9.8	50	86	2	613	27	19	29	22	1.98
10510121--10510171	23	2.2	23	89	0	75	43	21	7	27	1.80
10516310--10516350	18	2.3	18	80	12	50	24	0	2	73	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10517070--10517142	30	2.4	30	80	11	87	35	2	0	61	1.10
10517067--10517138	31	2.3	30	81	11	83	37	2	0	59	1.12
10517093--10517208	18	6.1	18	71	15	90	38	1	0	59	1.08
10517078--10517235	40	3.8	41	92	4	239	34	2	0	62	1.14
10517089--10517189	11	9.9	11	69	28	64	35	1	0	62	1.07
10532881--10533006	57	2.2	57	87	4	173	49	4	15	30	1.65
10539706--10539731	11	2.4	11	100	0	52	61	0	0	38	0.96
10539728--10539756	8	3.6	8	100	0	58	75	0	0	24	0.80
10554990--10555088	16	6.2	16	84	4	119	27	26	5	41	1.76
10554990--10555088	32	3.1	32	88	0	144	27	26	5	41	1.76

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