genome.fa.s4.2.7.7.80.10.50.1000.117.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  117  of  198  ( 23681 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)
37381928--37381965	2	19.0	2	100	0	76	50	0	0	50	1.00
37383016--37383063	19	2.5	19	83	12	62	68	2	16	12	1.29
37383016--37383063	20	2.5	20	86	10	64	68	2	16	12	1.29
37395162--37395201	10	4.3	10	81	15	50	67	0	0	32	0.91
37395162--37395201	18	2.2	19	90	4	64	67	0	0	32	0.91
37411874--37411956	25	3.3	25	68	18	64	34	21	15	27	1.94
37411944--37412001	25	2.3	25	82	5	73	43	24	10	22	1.84
37413966--37414085	59	2.0	59	95	0	213	37	20	11	30	1.88
37432577--37432706	36	3.6	36	84	0	161	30	25	19	25	1.98
37436867--37436930	24	2.6	24	85	7	76	57	3	3	35	1.30
37440782--37440977	85	2.3	86	89	0	277	27	30	17	25	1.97
37440779--37441013	43	5.5	43	82	1	265	27	29	17	25	1.97
37440779--37441013	128	1.8	128	85	1	328	27	29	17	25	1.97
37442667--37442746	39	2.1	39	100	0	160	31	18	12	37	1.88
37444977--37445012	3	12.0	3	100	0	72	66	0	33	0	0.92
37446049--37446176	57	2.2	57	80	5	134	41	33	0	25	1.56
37446594--37446718	41	3.0	40	88	2	169	29	28	23	19	1.98
37449441--37449498	30	1.9	30	86	6	82	44	1	20	32	1.62
37449962--37450144	57	3.2	57	87	0	258	40	4	18	36	1.71
37463704--37463860	29	5.4	29	80	4	147	39	22	12	24	1.89
37463704--37463851	58	2.6	58	84	4	174	41	22	12	22	1.88
37463815--37463909	29	3.4	28	80	11	88	36	26	14	22	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37465763--37465947	51	3.6	51	76	11	200	30	24	17	27	1.97
37465758--37465943	101	1.8	99	86	5	257	30	24	17	26	1.97
37468609--37468901	51	5.8	51	75	8	249	29	14	25	30	1.95
37468613--37468897	102	2.8	101	82	7	346	28	14	25	31	1.94
37474273--37474446	51	3.4	50	82	7	217	31	25	18	24	1.98
37496278--37496317	14	2.7	15	88	11	57	27	2	5	65	1.27
37501289--37501329	11	3.8	11	78	15	50	26	26	2	43	1.67
37514684--37514790	49	2.2	48	88	5	153	34	23	13	28	1.92
37515210--37515255	13	3.5	13	76	5	56	52	15	6	26	1.67
37530217--37530976	217	3.5	217	89	1	1119	28	23	20	28	1.99
37530546--37530666	45	2.7	45	80	13	126	26	27	19	26	1.99
37544041--37544110	34	2.1	34	97	0	131	25	15	31	27	1.96
37545273--37545329	20	2.8	20	76	10	71	31	21	31	15	1.94
37545589--37545618	6	5.0	6	100	0	60	50	0	0	50	1.00
37546445--37546478	18	2.0	16	88	11	50	64	0	0	35	0.94
37560178--37560229	18	2.6	21	76	20	65	44	5	13	36	1.68
37565566--37565591	13	2.0	13	100	0	52	46	23	7	23	1.78
37592673--37592770	28	3.3	28	84	9	115	31	22	23	22	1.98
37592871--37592951	26	3.1	25	71	7	72	34	19	20	24	1.96
37593152--37593234	27	3.1	27	75	13	80	26	16	19	37	1.93
37593201--37593647	27	16.6	27	87	1	468	18	16	23	41	1.90
37600855--37600941	45	2.0	44	83	2	111	49	2	8	40	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37601127--37601164	3	12.3	3	88	5	58	63	2	2	31	1.22
37601282--37601377	39	2.4	38	77	13	95	43	18	19	17	1.88
37601416--37601815	163	2.4	161	82	7	439	18	19	30	31	1.96
37601416--37601815	41	9.8	40	82	5	385	18	19	30	31	1.96
37602220--37602866	280	2.3	285	87	5	914	29	2	25	43	1.66
37602876--37602910	18	1.9	18	88	0	52	31	0	25	42	1.55
37604680--37604787	21	5.2	21	65	24	52	48	15	1	34	1.56
37604680--37604924	34	8.4	28	67	25	86	46	16	2	34	1.59
37604695--37604938	9	26.7	9	68	22	102	46	17	2	34	1.59
37604763--37604789	12	2.2	12	100	0	54	51	14	0	33	1.43
37605315--37605368	19	2.9	18	83	10	65	38	1	0	59	1.08
37607089--37607122	16	2.1	16	88	0	50	35	0	2	61	1.11
37607209--37607417	43	4.9	43	84	0	265	26	17	30	25	1.97
37613940--37614010	30	2.4	30	83	4	90	16	19	32	30	1.95
37621076--37621133	30	1.9	30	92	0	98	18	27	29	24	1.98
37623528--37623608	40	2.0	40	100	0	162	27	24	19	28	1.99
37646078--37646125	24	2.0	23	84	8	60	50	8	0	41	1.33
37646944--37646983	13	2.9	14	85	7	55	32	0	2	65	1.06
37649036--37649064	2	15.0	2	92	7	51	51	0	0	48	1.00
37649482--37649536	28	2.0	28	85	0	74	32	9	1	56	1.41
37654734--37654770	19	1.9	19	94	0	65	51	0	21	27	1.48
37657328--37657499	50	3.3	50	78	6	148	28	20	27	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37664787--37664958	50	3.3	50	78	6	148	28	20	27	23	1.99
37665228--37665266	12	3.2	12	88	0	51	53	5	20	20	1.64
37670540--37670566	2	13.5	2	100	0	54	48	0	0	51	1.00
37679015--37679093	26	3.0	26	100	0	158	58	11	11	18	1.62
37679522--37679558	18	2.1	18	89	0	56	29	0	2	67	1.04
37689911--37689953	22	2.0	21	86	4	59	67	4	0	27	1.10
37694098--37694136	11	3.4	12	82	10	55	64	0	0	35	0.94
37701495--37701522	14	2.0	14	100	0	56	7	35	14	42	1.73
37702958--37702988	15	2.1	15	100	0	62	41	12	6	38	1.69
37713628--37713857	29	7.9	29	81	1	221	20	27	14	37	1.92
37720339--37720372	16	2.1	16	88	0	50	47	8	17	26	1.77
37734269--37734510	50	4.7	50	81	6	247	27	23	26	22	2.00
37740375--37740399	2	12.5	2	100	0	50	0	0	48	52	1.00
37759214--37759294	35	2.3	35	95	0	144	38	13	6	41	1.70
37762141--37762277	70	1.9	71	84	10	183	31	19	27	21	1.97
37762214--37762377	88	1.9	87	86	6	233	27	23	27	21	1.99
37762539--37762698	44	3.6	45	77	3	148	26	21	26	25	2.00
37766610--37766651	20	2.1	20	90	0	66	38	2	0	59	1.10
37766783--37766831	24	2.0	26	84	8	66	57	6	10	26	1.55
37767769--37767840	22	3.3	22	69	21	69	41	6	4	47	1.50
37767941--37767966	13	2.0	13	100	0	52	61	0	0	38	0.96
37767924--37768010	44	2.0	45	86	2	122	56	2	5	35	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37768345--37768394	22	2.5	19	81	15	57	38	8	4	50	1.51
37768381--37768406	12	2.2	12	100	0	52	42	0	0	57	0.98
37769931--37769969	6	6.5	6	96	0	51	41	35	7	15	1.76
37769931--37769969	12	3.2	12	92	0	60	41	35	7	15	1.76
37775441--37775490	25	1.9	27	84	15	70	48	8	0	44	1.32
37775577--37775617	13	2.9	14	77	22	50	53	0	0	46	1.00
37775650--37775701	15	3.2	15	73	19	50	55	0	1	42	1.10
37775712--37775929	109	2.0	109	91	0	355	33	13	10	43	1.77
37776171--37776203	13	2.4	14	85	5	50	57	0	0	42	0.98
37780258--37780442	23	8.1	23	80	5	151	43	37	2	15	1.61
37780263--37780442	45	4.0	45	80	9	186	43	37	2	16	1.62
37782231--37782276	16	2.9	16	81	12	67	19	8	13	58	1.60
37782787--37782839	21	2.5	21	75	0	52	16	30	30	22	1.96
37783881--37787061	447	7.1	447	94	0	5364	32	9	17	40	1.81
37783881--37787061	895	3.6	893	93	0	5391	32	9	17	40	1.81
37787471--37788600	447	2.5	443	91	1	1839	32	8	17	41	1.79
37791229--37791776	293	1.9	295	94	0	983	34	10	17	37	1.84
37791967--37794064	447	4.7	448	94	0	3452	32	9	17	40	1.82
37798431--37799399	447	2.2	448	94	1	1692	32	8	18	40	1.81
37803890--37804843	447	2.1	448	91	0	1581	32	8	17	41	1.80
37807566--37812066	447	10.1	447	88	0	6499	31	8	17	39	1.80
37817150--37817193	23	1.9	23	90	0	70	40	20	9	29	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37823408--37823465	21	2.8	21	91	0	98	20	18	41	18	1.91
37831539--37831571	17	1.9	17	100	0	66	42	6	27	24	1.78
37835105--37835137	17	1.9	17	100	0	66	42	6	27	24	1.78
37846252--37846382	43	3.0	43	85	0	136	28	26	19	25	1.98
37846450--37846508	22	2.6	22	94	2	100	42	3	3	50	1.35
37847455--37847545	45	2.0	45	84	4	119	40	10	19	28	1.86
37852744--37852783	7	5.7	7	84	0	53	45	35	0	20	1.51
37852907--37853017	7	15.6	7	71	10	64	49	28	1	19	1.59
37853434--37853656	41	5.4	41	80	2	250	30	26	20	21	1.98
37853401--37853657	41	6.2	41	78	3	165	29	28	21	21	1.98

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