genome.fa.s9.2.7.7.80.10.50.1000.142.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  142  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)
47283414--47283716	100	3.0	100	84	3	378	29	19	23	27	1.98
47283746--47283983	41	5.7	42	72	6	169	30	19	21	28	1.98
47283732--47284073	127	2.7	127	87	1	472	33	19	20	26	1.97
47285565--47285611	25	1.9	24	82	4	58	31	10	6	51	1.62
47296652--47296712	25	2.5	25	84	7	72	18	14	3	63	1.43
47300220--47300313	5	19.4	5	79	15	92	78	0	20	1	0.81
47300220--47300322	21	5.0	22	80	12	114	78	0	20	0	0.81
47301588--47302165	44	13.8	40	66	14	200	28	21	22	27	1.99
47301504--47301951	44	10.5	44	66	18	162	28	22	22	26	1.99
47301498--47302164	253	2.6	254	94	0	1174	28	22	22	26	1.99
47301498--47302166	127	5.3	127	94	1	1135	28	22	22	26	1.99
47303712--47303748	15	2.3	17	86	9	51	16	2	8	72	1.19
47303782--47303810	15	1.9	15	100	0	58	48	0	0	51	1.00
47303771--47303810	17	2.4	17	95	0	71	47	2	0	50	1.14
47303771--47303810	2	21.0	2	85	10	57	47	2	0	50	1.14
47305878--47306005	40	3.2	40	81	7	129	36	22	19	21	1.95
47306052--47306246	41	4.8	41	93	0	309	19	21	28	31	1.97
47306518--47306565	14	3.4	14	80	5	51	18	0	35	45	1.50
47306532--47306565	15	2.3	15	90	5	52	20	0	38	41	1.53
47306584--47306632	15	3.2	15	85	8	55	18	0	46	34	1.49
47306582--47306631	23	2.1	24	92	3	84	16	0	48	36	1.46
47306590--47306640	23	2.2	23	82	6	59	21	0	45	33	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47306580--47306652	38	1.9	38	88	5	112	20	0	45	34	1.52
47306815--47306861	14	3.3	15	82	8	53	27	4	29	38	1.76
47306856--47306945	36	2.5	37	78	7	103	24	0	38	36	1.56
47313068--47313340	43	6.4	42	87	2	314	21	17	32	27	1.96
47313068--47313340	86	3.2	86	86	4	376	21	17	32	27	1.96
47315892--47315934	21	2.0	21	90	0	68	44	9	9	37	1.69
47335074--47335115	21	2.0	21	86	4	59	64	2	2	30	1.19
47337946--47337990	18	2.5	18	88	0	72	33	13	11	42	1.79
47338414--47338585	72	2.4	72	83	4	233	27	6	13	52	1.64
47338423--47338609	72	2.6	72	83	4	191	26	5	13	54	1.61
47339974--47340027	3	18.0	3	88	0	54	31	9	35	24	1.87
47339996--47340033	12	3.2	12	88	0	58	28	5	39	26	1.78
47344170--47344735	124	4.5	124	87	2	740	31	16	21	30	1.96
47347892--47348052	21	7.6	21	81	3	198	25	1	28	44	1.65
47347895--47348050	64	2.4	63	84	6	206	26	1	28	43	1.65
47347893--47348052	85	1.9	85	85	2	223	25	1	28	43	1.65
47347892--47348052	43	3.8	43	86	1	218	25	1	28	44	1.65
47350513--47350784	46	6.0	46	89	4	401	35	9	26	29	1.87
47351139--47351532	43	9.2	44	82	5	443	25	0	28	45	1.58
47351500--47351555	27	2.0	28	83	10	71	25	0	35	39	1.56
47351139--47351532	22	18.4	22	82	5	452	25	0	28	45	1.58
47352941--47352979	20	2.0	20	85	10	53	53	7	2	35	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47353993--47354061	11	6.2	11	89	1	102	43	1	33	21	1.62
47353984--47354061	33	2.3	33	88	4	111	43	1	32	23	1.62
47354256--47354350	42	2.3	42	80	3	104	20	28	27	24	1.99
47364053--47364100	19	2.6	18	81	12	53	54	4	0	41	1.20
47364106--47364144	19	2.0	20	90	10	62	64	2	2	30	1.21
47364104--47364157	19	2.9	18	78	21	58	64	3	1	29	1.21
47372005--47372063	29	2.0	29	100	0	118	27	23	3	45	1.68
47372131--47372266	66	2.1	65	95	1	245	27	14	13	44	1.84
47372402--47373118	314	2.2	323	81	9	829	29	14	9	46	1.76
47372662--47373613	160	5.9	159	74	15	649	30	12	9	47	1.73
47379612--47379637	2	13.0	2	100	0	52	50	0	0	50	1.00
47380215--47380249	2	17.5	2	93	0	61	54	0	0	45	0.99
47380207--47380247	12	3.4	12	89	0	64	56	2	0	41	1.13
47380205--47380262	14	3.9	14	81	9	53	56	1	1	39	1.19
47380456--47380511	28	1.9	30	86	13	82	48	1	8	41	1.45
47380499--47380530	16	2.0	16	93	0	55	62	3	6	28	1.34
47382061--47382203	41	3.5	40	78	2	142	37	18	16	27	1.92
47382519--47382557	20	2.0	20	89	0	60	25	5	17	51	1.66
47388802--47388860	29	2.0	29	100	0	118	27	23	3	45	1.68
47388941--47389076	66	2.1	65	97	1	254	27	15	14	42	1.86
47389119--47390595	162	9.2	160	77	13	1099	29	12	9	47	1.73
47389471--47390586	165	6.9	164	76	12	902	30	12	9	47	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47389135--47390586	315	4.5	313	77	12	1002	30	12	9	47	1.73
47395294--47395367	15	5.2	15	71	12	66	27	25	20	27	1.99
47395296--47395386	28	3.2	28	85	0	119	28	28	17	25	1.98
47399133--47399194	32	1.9	32	86	0	88	62	1	1	33	1.14
47399151--47399292	40	3.5	40	90	5	205	61	0	3	35	1.13
47399259--47399283	11	2.3	11	100	0	50	52	0	8	40	1.31
47399151--47399309	41	3.8	40	84	8	160	61	0	3	35	1.12
47401291--47401345	28	1.9	28	85	3	74	56	5	1	36	1.33
47405439--47405478	11	3.6	11	93	6	64	22	35	0	42	1.54
47406692--47406716	7	3.6	7	100	0	50	28	0	12	60	1.32
47407827--47407940	25	4.8	25	72	18	109	39	0	14	45	1.46
47407945--47407990	9	5.2	9	97	2	85	30	0	10	58	1.32
47407805--47407964	68	2.3	67	88	4	257	39	0	13	47	1.42
47408021--47408415	23	17.8	23	80	8	419	48	24	0	27	1.51
47408019--47408415	155	2.6	156	91	3	624	48	24	0	26	1.51
47408017--47408415	67	6.0	66	83	9	456	48	24	0	26	1.51
47408017--47408415	199	2.0	198	87	5	583	48	24	0	26	1.51
47408479--47408548	17	3.9	17	72	15	61	44	5	1	48	1.35
47408420--47408662	115	2.1	116	91	2	391	41	9	6	43	1.61
47411793--47411826	18	1.9	18	88	5	52	55	0	5	38	1.24
47414546--47414923	126	3.0	124	92	1	614	32	22	14	30	1.94
47415330--47415493	60	2.8	59	81	6	170	23	18	12	45	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47415971--47416070	31	3.4	30	77	14	118	56	9	8	27	1.58
47417655--47417714	3	19.7	3	74	16	52	33	1	3	61	1.22
47417669--47417714	14	3.4	14	83	16	53	32	0	2	65	1.05
47418032--47418081	6	7.5	6	79	20	55	20	0	2	78	0.86
47425773--47425812	21	1.9	21	94	0	71	12	15	17	55	1.70
47426267--47426306	21	1.9	21	94	0	71	2	47	17	32	1.61
47426202--47426361	87	1.8	87	87	0	230	14	29	15	41	1.86
47428149--47428208	20	3.0	20	75	4	57	43	33	3	20	1.68
47428572--47428924	133	2.6	133	84	5	428	33	21	13	31	1.92
47435526--47435571	21	2.2	21	84	0	56	26	0	2	71	0.97
47436827--47436864	18	2.1	19	90	5	60	36	2	0	60	1.11
47441047--47441095	15	3.3	15	88	5	73	55	6	0	38	1.25
47451725--47451763	17	2.4	16	84	16	53	58	0	10	30	1.31
47452859--47452972	61	1.9	60	83	1	147	41	13	6	39	1.69
47453998--47454031	17	2.0	17	88	11	52	32	0	0	67	0.91
47454841--47454885	2	22.5	2	100	0	90	51	0	0	48	1.00
47460091--47460116	5	5.2	5	100	0	52	38	19	19	23	1.93
47460847--47460906	30	2.0	30	83	3	75	41	0	38	20	1.52
47461119--47461155	9	4.1	9	92	0	65	29	10	13	45	1.77
47472121--47472160	9	4.3	9	90	3	62	57	2	0	40	1.12
47472561--47472636	11	6.8	11	73	21	61	40	1	3	53	1.27
47472561--47472671	37	3.0	34	76	16	107	41	0	4	53	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47472825--47472879	25	2.2	26	87	9	78	43	5	9	41	1.59
47472832--47472888	25	2.3	25	85	8	73	40	3	14	42	1.62
47476216--47476252	2	18.5	2	100	0	74	48	0	0	51	1.00
47477509--47477567	26	2.3	26	90	0	91	11	47	30	10	1.73
47486673--47486732	18	3.6	18	67	17	56	58	18	5	18	1.57
47486670--47486733	32	2.0	32	96	0	119	57	17	6	18	1.60
47486675--47486729	15	3.5	15	75	18	58	56	20	5	18	1.61
47490772--47490815	22	2.0	23	86	4	63	50	2	0	47	1.13
47494656--47494776	37	3.2	37	96	2	224	22	13	18	46	1.83
47497091--47497148	16	3.4	16	73	17	55	60	1	0	37	1.07

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