genome.fa.s9.2.7.7.80.10.50.1000.113.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  113  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)
38770098--38770199	54	1.9	54	83	2	134	27	21	14	36	1.93
38770104--38770224	54	2.3	54	81	4	129	26	22	16	34	1.95
38774292--38774360	28	2.5	28	85	0	84	30	15	24	28	1.96
38787007--38787073	31	2.2	31	86	0	89	26	38	10	23	1.87
38787041--38787176	62	2.2	62	81	0	155	22	38	13	25	1.91
38788354--38788461	53	2.0	53	98	0	207	19	22	35	23	1.96
38794361--38794408	20	2.3	20	86	10	62	31	20	25	22	1.98
38807130--38807169	16	2.5	17	92	8	66	45	30	15	10	1.78
38807093--38807210	54	2.2	54	89	3	175	41	31	15	11	1.83
38807146--38807306	38	4.2	39	81	4	186	36	29	19	14	1.91
38810277--38810309	17	2.0	16	94	5	57	45	0	0	54	0.99
38820643--38820750	53	2.0	54	85	5	148	37	19	19	24	1.94
38824386--38824423	19	2.1	19	90	5	60	57	7	0	34	1.28
38824992--38825107	60	1.9	61	85	5	164	25	18	18	37	1.93
38824991--38825143	60	2.6	59	80	10	161	24	18	17	39	1.91
38841940--38841983	18	2.4	18	80	3	52	47	15	13	22	1.81
38856029--38856216	51	3.7	51	86	2	245	25	15	28	30	1.96
38871383--38871426	22	2.0	22	86	0	61	9	15	27	47	1.76
38871520--38871721	43	4.7	43	90	2	316	32	28	17	21	1.96
38874353--38874380	12	2.3	12	100	0	56	75	10	0	14	1.06
38874510--38874581	20	3.8	18	74	15	58	76	6	4	12	1.13
38875640--38875672	14	2.3	15	89	5	50	39	39	0	21	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38875612--38875681	21	3.3	21	80	7	79	35	37	0	27	1.57
38875937--38876050	7	16.0	7	70	13	54	45	35	0	18	1.50
38875938--38876051	21	5.3	21	73	9	79	45	35	0	19	1.50
38876299--38876371	37	1.9	38	88	2	112	32	24	20	21	1.97
38876306--38877126	114	7.2	114	86	2	1057	27	25	20	25	1.99
38890506--38890570	32	2.0	32	90	0	103	52	7	33	6	1.55
38891710--38892212	44	11.1	45	71	12	253	32	20	20	27	1.97
38891759--38892195	226	1.9	225	91	2	707	32	20	20	27	1.97
38893669--38893772	52	1.9	53	84	5	138	34	6	3	54	1.45
38893905--38893929	4	6.2	4	100	0	50	28	0	0	72	0.86
38893981--38894015	12	2.9	12	88	12	54	8	8	8	74	1.23
38894047--38894104	3	19.3	3	89	7	91	29	1	1	67	1.11
38894905--38894989	43	2.0	43	100	0	170	25	11	12	49	1.75
38894909--38895008	43	2.4	42	88	5	132	26	11	13	50	1.74
38896066--38896137	10	7.5	10	73	16	55	62	1	1	34	1.13
38896065--38896182	9	12.2	9	69	19	53	60	0	4	34	1.22
38896089--38896146	18	3.2	19	79	13	59	63	1	0	34	1.04
38896356--38896439	39	2.2	39	78	4	89	33	2	1	63	1.15
38896377--38896445	29	2.5	28	82	13	81	33	1	1	63	1.12
38896429--38896469	16	2.6	16	77	14	57	24	0	0	75	0.80
38896575--38896804	93	2.5	90	83	6	268	32	10	16	39	1.84
38899722--38899774	26	2.0	26	82	7	63	50	13	13	22	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38900164--38900197	17	2.1	16	88	5	50	8	11	2	76	1.12
38903597--38903635	7	5.4	7	85	14	53	74	0	10	15	1.07
38903593--38903635	21	2.1	20	91	4	68	76	0	9	13	1.01
38904883--38904968	44	2.0	44	86	4	120	25	20	25	27	1.99
38904909--38905435	128	4.1	128	88	1	772	30	20	23	25	1.98
38905507--38905622	44	2.6	44	74	5	119	27	22	27	22	1.99
38906358--38906391	17	2.1	16	88	5	50	8	11	2	76	1.12
38911177--38911372	96	2.1	96	90	2	306	33	17	13	35	1.89
38913172--38913200	8	3.6	8	100	0	58	75	0	0	24	0.80
38915951--38915980	2	15.5	2	93	6	53	50	0	0	50	1.00
38920395--38920461	17	3.4	19	76	19	66	40	2	0	56	1.14
38925571--38925623	19	2.8	19	75	8	54	62	3	5	28	1.35
38925836--38925867	9	3.6	9	100	0	64	43	0	0	56	0.99
38925826--38925870	18	2.5	17	86	10	63	42	0	2	55	1.12
38925839--38925893	29	1.9	28	82	10	67	40	0	1	58	1.09
38925836--38925886	18	2.6	20	84	9	61	39	0	1	58	1.09
38932516--38932601	46	1.9	45	92	4	147	23	20	20	34	1.96
38937464--38937495	7	4.6	7	92	0	55	25	0	3	71	1.00
38938237--38938349	49	2.3	50	86	6	149	28	15	22	34	1.94
38939396--38939436	20	2.0	21	86	9	59	48	0	14	36	1.44
38944731--38945171	221	2.0	221	88	0	648	33	13	20	32	1.92
38948668--38948697	2	15.0	2	100	0	60	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38953823--38953941	25	4.8	25	77	8	118	26	23	21	27	1.99
38953823--38953941	50	2.4	50	84	0	157	26	23	21	27	1.99
38953926--38954015	41	2.2	41	89	0	135	24	23	26	25	2.00
38956001--38956053	22	2.4	22	87	3	70	37	13	13	35	1.83
38960394--38960445	24	2.2	24	85	0	68	34	1	5	57	1.33
38960471--38960512	9	4.7	9	94	5	68	26	7	0	66	1.17
38960852--38960885	2	17.0	2	93	0	59	47	0	2	50	1.16
38963025--38963067	19	2.3	18	84	15	52	20	23	13	41	1.88
38964335--38964371	17	2.1	18	90	5	58	29	24	0	45	1.53
38965121--38965150	8	3.6	8	91	8	51	86	0	13	0	0.57
38965113--38965150	17	2.2	17	90	0	58	84	0	13	2	0.73
38965936--38965995	5	12.8	5	78	15	58	83	15	1	0	0.73
38965933--38965986	15	3.5	15	80	12	65	81	16	1	0	0.78
38965981--38966032	22	2.2	24	83	10	63	76	1	11	9	1.09
38967276--38967420	50	2.9	50	79	6	159	34	21	17	26	1.95
38967543--38969077	50	31.6	48	73	13	894	31	21	20	26	1.98
38968279--38969020	95	7.8	95	90	0	1108	29	20	22	26	1.99
38967537--38969127	190	8.2	192	80	8	1394	31	21	21	26	1.98
38967543--38969149	95	16.5	100	84	5	694	31	21	20	26	1.98
38969201--38969239	18	2.2	18	100	0	78	23	30	12	33	1.92
38970783--38970888	3	35.7	3	74	16	69	32	5	2	59	1.35
38970761--38970813	24	2.2	24	86	0	70	33	1	5	58	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38970765--38970822	21	2.6	23	82	15	68	36	1	5	56	1.32
38973128--38973177	25	2.0	25	84	7	66	36	4	4	56	1.37
38973806--38973943	64	2.2	64	97	0	258	47	4	5	43	1.45
38976078--38976163	18	4.9	17	73	21	79	63	0	6	29	1.20
38976708--38976752	22	2.0	23	86	4	65	46	31	2	20	1.62
38982840--38983368	27	19.8	27	82	3	541	36	19	19	24	1.95
38982867--38983368	241	2.1	240	86	3	688	37	19	19	23	1.94
38983525--38983595	27	2.7	26	81	12	74	21	23	21	33	1.97
38983591--38983640	26	1.9	26	83	0	64	20	16	26	38	1.92
38983631--38983789	32	5.0	32	79	4	160	23	18	18	39	1.92
38983633--38983800	64	2.7	63	83	8	191	23	17	19	39	1.92
38983795--38983859	22	3.0	22	77	4	69	20	21	15	43	1.88
38986652--38986676	12	2.1	12	100	0	50	32	16	8	44	1.76
39011523--39011564	18	2.4	18	84	4	50	42	2	11	42	1.54
39011916--39011990	39	1.9	39	86	0	105	21	17	29	32	1.96
39013194--39013235	19	2.2	20	86	4	59	33	7	9	50	1.62
39016540--39016587	18	2.7	18	71	9	53	43	2	14	39	1.57
39026764--39026877	43	2.7	43	80	13	135	28	26	19	25	1.98
39026806--39026887	43	1.9	43	80	14	98	31	29	19	19	1.96
39068181--39068280	50	2.0	49	98	1	191	34	12	14	40	1.82
39075265--39076120	453	1.9	452	91	0	1390	28	10	21	39	1.86
39077167--39077221	17	3.1	17	77	15	58	41	18	3	36	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39078593--39078627	10	3.4	10	84	7	52	34	8	25	31	1.86
39078846--39078879	16	2.0	17	88	11	52	23	0	29	47	1.52
39080015--39080086	28	2.6	28	69	8	83	41	0	0	58	0.98
39080157--39080202	20	2.4	19	78	7	56	58	2	0	39	1.10
39087029--39087167	50	2.6	52	86	6	183	25	30	20	24	1.99
39087029--39087177	56	2.9	50	85	6	190	24	29	20	25	1.99
39098567--39098668	27	3.8	27	88	0	141	37	19	18	24	1.94
39098711--39098830	21	5.7	21	86	8	156	38	10	13	38	1.78
39098798--39098840	22	1.9	23	85	4	61	34	9	13	41	1.77
39099424--39099481	27	2.1	27	84	9	73	27	0	5	67	1.12

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