genome.fa.s9.2.7.7.80.10.50.1000.119.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  119  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)
40439283--40439321	9	4.2	9	80	6	51	0	17	0	82	0.68
40439273--40439321	19	2.7	18	84	6	55	2	18	0	79	0.83
40464569--40464623	6	8.5	6	81	15	65	78	1	1	18	0.94
40472253--40472301	22	2.3	22	79	6	57	22	14	12	51	1.75
40472201--40472300	20	4.8	21	71	11	62	21	13	14	52	1.74
40472201--40472301	42	2.4	42	79	8	125	20	12	13	52	1.74
40473928--40474015	42	2.0	43	89	4	133	51	10	9	29	1.67
40481767--40481861	46	2.1	46	97	0	181	41	23	1	34	1.62
40489762--40489795	17	2.0	17	100	0	68	23	11	23	41	1.87
40489765--40489803	17	2.3	17	90	0	60	28	12	23	35	1.91
40499699--40499739	20	2.0	20	90	0	64	24	24	14	36	1.93
40504786--40504982	98	2.0	98	96	0	367	37	24	10	27	1.88
40506503--40506615	19	5.8	19	87	4	172	36	15	10	37	1.83
40506503--40506614	40	2.8	40	90	2	165	36	15	10	37	1.82
40508799--40508863	31	2.1	31	91	0	103	24	35	21	18	1.96
40512683--40512739	30	1.9	30	85	0	78	31	8	28	31	1.87
40514987--40515038	17	3.1	17	94	0	86	26	11	21	40	1.87
40514995--40515045	17	3.0	17	94	0	84	27	11	21	39	1.88
40515015--40515053	17	2.3	17	86	0	51	28	12	23	35	1.91
40526096--40526146	25	2.0	25	100	0	102	33	3	27	35	1.75
40527162--40527204	20	2.2	20	95	0	77	23	2	46	27	1.64
40527949--40528175	27	8.5	27	79	1	251	31	18	24	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40527949--40528175	79	2.8	79	81	6	233	31	18	24	25	1.98
40528261--40528326	13	5.4	13	64	14	50	27	7	19	45	1.77
40528193--40528326	24	5.6	24	85	3	171	28	8	20	41	1.83
40528442--40528507	26	2.5	26	87	4	89	21	21	24	33	1.97
40528502--40528653	32	4.8	32	84	3	189	25	19	17	37	1.94
40528502--40528650	64	2.3	64	90	0	226	24	20	18	36	1.94
40534799--40534857	9	6.6	9	90	0	91	40	22	11	25	1.88
40534791--40534857	18	3.7	18	87	0	98	41	19	10	28	1.84
40548030--40548169	50	2.8	50	81	4	138	27	22	27	22	1.99
40551332--40551362	5	6.2	5	92	0	53	41	19	16	22	1.89
40556235--40556432	50	3.8	50	78	5	180	27	20	27	23	1.99
40558678--40558713	17	2.1	17	89	0	54	36	19	8	36	1.82
40560221--40560279	18	3.2	18	80	4	64	25	1	1	71	1.05
40561396--40561541	76	1.9	75	84	1	193	28	4	15	52	1.61
40570682--40570819	47	2.8	49	78	12	140	34	24	14	26	1.94
40581039--40581098	16	3.8	16	72	14	52	35	1	11	51	1.48
40585446--40585698	91	2.8	92	86	1	337	33	14	22	30	1.93
40585678--40585800	47	2.6	47	85	1	147	32	16	23	27	1.96
40596469--40596567	28	3.4	29	85	2	128	33	26	19	21	1.97
40596615--40596689	29	2.6	28	77	12	80	38	18	14	28	1.90
40602630--40602677	24	2.0	24	83	0	60	35	18	25	20	1.95
40607238--40607280	22	2.0	22	100	0	86	23	25	13	37	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40612178--40612234	15	3.6	15	72	11	51	43	3	1	50	1.29
40615675--40615726	25	2.0	26	85	3	70	40	7	11	40	1.70
40617998--40618139	50	2.9	50	81	1	169	27	21	28	21	1.99
40618390--40618418	12	2.4	12	100	0	58	55	6	17	20	1.65
40629034--40629087	28	1.9	28	92	0	90	29	25	27	16	1.97
40629029--40629094	28	2.4	27	82	7	87	30	24	25	19	1.98
40629304--40629445	64	2.2	64	84	2	187	35	23	21	19	1.96
40629304--40629462	64	2.5	64	83	2	167	35	21	22	20	1.96
40629280--40629495	32	6.8	32	74	2	148	35	19	21	22	1.96
40629434--40629513	32	2.5	32	81	4	90	38	21	18	21	1.93
40629306--40629513	96	2.2	96	79	5	231	37	21	20	20	1.95
40629505--40629569	26	2.5	26	84	0	76	38	23	18	20	1.93
40629691--40629766	24	3.2	22	80	12	80	50	22	5	22	1.69
40632071--40632336	48	5.5	48	89	0	343	28	20	27	24	1.99
40634729--40634763	13	2.7	13	90	0	52	45	0	11	42	1.40
40635735--40635776	14	2.9	14	85	7	57	16	2	2	78	0.96
40636373--40636543	64	2.7	64	83	0	198	27	8	29	35	1.86
40642230--40642263	17	2.1	17	88	5	52	38	0	2	58	1.13
40644706--40644798	45	2.1	45	91	0	150	27	19	20	32	1.97
40647019--40647045	8	3.4	8	100	0	54	74	0	0	25	0.83
40654395--40655190	395	2.0	396	92	1	1330	18	14	19	46	1.84
40671384--40671521	50	2.8	50	93	0	231	26	22	28	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40673907--40673952	16	2.9	16	100	0	92	39	0	30	30	1.57
40673942--40674034	44	2.1	46	93	4	163	27	5	31	35	1.80
40673942--40674047	46	2.5	44	83	11	132	30	4	31	33	1.78
40674192--40674228	16	2.2	17	86	13	51	59	0	0	40	0.97
40674185--40674224	14	2.9	15	82	14	50	52	0	0	47	1.00
40674220--40674249	15	1.9	16	93	6	53	50	6	0	43	1.28
40674197--40674377	51	3.2	51	66	24	137	49	3	2	43	1.35
40674209--40674516	61	5.1	61	68	13	260	50	4	2	42	1.38
40674180--40674531	120	2.9	120	97	0	668	50	4	2	42	1.37
40674180--40674455	61	4.6	59	68	14	181	50	3	2	43	1.34
40674312--40674348	16	2.2	17	86	13	51	59	0	0	40	0.97
40674340--40674369	15	1.9	16	93	6	53	50	6	0	43	1.28
40674434--40674468	18	2.0	17	88	5	52	54	0	0	45	0.99
40674180--40674467	59	4.8	59	67	16	175	51	3	2	42	1.33
40674460--40674489	15	1.9	16	93	6	53	50	6	0	43	1.28
40675641--40675665	13	1.9	13	100	0	50	8	28	16	48	1.74
40685692--40685745	23	2.3	24	75	9	58	66	0	7	25	1.17
40704025--40704308	36	7.9	36	78	6	245	37	16	20	24	1.93
40704035--40704298	73	3.6	71	77	7	271	36	17	21	25	1.94
40704039--40704298	109	2.4	109	83	2	335	36	17	21	24	1.94
40705897--40706460	140	4.0	140	82	5	683	31	21	19	27	1.97
40705897--40706460	280	2.0	280	85	4	771	31	21	19	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40713624--40713650	12	2.2	12	100	0	54	18	14	40	25	1.89
40723244--40723297	28	2.0	26	82	17	65	24	11	12	51	1.72
40728011--40728041	6	5.2	6	100	0	62	0	48	0	51	1.00
40731777--40732159	50	7.5	50	86	2	469	21	29	21	27	1.99
40741395--40741450	24	2.3	24	90	3	85	23	23	21	32	1.98
40741383--40741450	25	2.8	25	86	2	102	23	25	20	30	1.98
40742324--40742433	53	2.1	53	100	0	220	28	7	26	38	1.83
40747756--40747795	20	2.0	20	100	0	80	30	40	5	25	1.77
40749354--40749378	2	12.5	2	100	0	50	52	0	0	48	1.00
40759547--40759629	40	2.1	40	90	4	132	26	12	14	46	1.79
40761608--40761640	11	3.2	11	83	16	52	63	18	0	18	1.31
40761558--40761641	9	9.4	9	71	23	63	58	20	0	21	1.40
40768267--40768389	40	3.1	40	91	0	201	46	15	10	27	1.79
40771566--40771607	22	1.9	22	90	0	66	23	35	14	26	1.93
40772366--40772398	16	2.1	16	100	0	66	18	18	39	24	1.92
40779857--40779894	18	2.1	18	95	0	67	36	10	5	47	1.61
40787239--40787312	19	3.8	19	91	7	121	36	9	16	37	1.81
40787240--40787302	21	3.1	21	95	4	112	38	9	14	38	1.78
40787239--40787339	19	4.9	21	80	14	95	35	8	16	38	1.80
40787302--40787346	23	2.0	23	86	4	65	31	6	15	46	1.72
40787508--40787546	19	2.0	21	85	10	55	15	10	5	69	1.34
40794412--40794643	44	5.3	44	65	6	137	25	27	25	21	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40794363--40794662	88	3.4	88	91	0	474	27	27	24	20	1.99
40794363--40794699	176	1.9	176	86	1	478	26	28	24	20	1.99
40794676--40795080	44	9.5	44	81	7	460	28	19	24	26	1.99
40794676--40795080	82	4.8	85	82	8	425	28	19	24	26	1.99
40794676--40795080	126	3.2	126	91	2	596	28	19	24	26	1.99
40795396--40795502	44	2.4	44	82	3	126	28	20	19	30	1.97
40795932--40795975	21	2.1	21	100	0	88	38	9	13	38	1.77
40795931--40795986	21	2.8	19	87	10	85	37	8	16	37	1.80
40795944--40796009	23	3.0	23	82	12	77	37	6	16	39	1.74
40795975--40796019	23	2.0	23	86	4	65	33	4	15	46	1.66

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