genome.fa.s4.2.7.7.80.10.50.1000.126.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  126  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)
40314183--40314287	40	2.6	40	80	3	113	46	9	19	24	1.79
40314902--40315004	40	2.6	40	92	0	161	41	9	23	25	1.84
40313467--40316352	715	4.0	717	83	5	3273	38	14	23	23	1.92
40315619--40315759	40	3.5	40	96	0	255	42	11	21	24	1.85
40318356--40318403	6	7.7	6	86	6	60	70	0	10	18	1.15
40318920--40318957	20	1.9	20	88	0	58	63	7	0	28	1.23
40318967--40319035	28	2.4	29	78	9	70	65	2	4	27	1.26
40319011--40319048	20	1.9	20	88	0	58	68	2	0	28	1.03
40319937--40320017	42	1.9	42	87	5	119	33	18	9	38	1.84
40323490--40323524	2	17.5	2	100	0	70	48	0	0	51	1.00
40325045--40325083	19	2.1	19	85	9	53	43	10	2	43	1.52
40325584--40325626	16	2.7	16	85	0	59	32	9	13	44	1.76
40336045--40336132	28	3.2	27	79	6	97	48	6	20	23	1.73
40344393--40344423	13	2.3	14	94	5	55	51	0	6	41	1.27
40344615--40344799	41	4.5	41	81	2	203	19	26	16	37	1.93
40354308--40354346	16	2.4	17	86	4	53	76	0	5	17	0.96
40359340--40359383	22	2.0	22	82	8	54	43	6	11	38	1.67
40360801--40360842	21	2.0	21	85	0	57	42	2	0	54	1.13
40362189--40362222	2	17.0	2	100	0	68	50	0	0	50	1.00
40367067--40367160	27	3.5	26	72	4	71	39	17	24	19	1.92
40367066--40367184	54	2.2	54	81	3	132	36	19	26	17	1.94
40381728--40381896	60	2.8	59	74	16	193	35	11	3	49	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40387987--40388080	39	2.4	39	83	0	107	30	5	21	42	1.75
40393078--40394614	510	3.0	509	95	0	2772	23	13	21	40	1.89
40396970--40396996	2	13.5	2	100	0	54	48	0	0	51	1.00
40400582--40400623	21	2.0	21	100	0	84	23	14	23	38	1.92
40400607--40400771	43	3.8	43	76	10	167	23	18	27	30	1.97
40403002--40403045	13	3.5	13	75	12	56	56	4	2	36	1.32
40403442--40403525	22	3.8	22	90	0	114	29	28	14	27	1.95
40405772--40405808	9	4.1	9	92	0	65	45	13	10	29	1.77
40406079--40406112	7	4.9	7	88	0	50	8	73	0	17	1.08
40407507--40407539	17	1.9	17	100	0	66	27	24	0	48	1.51
40408352--40408410	18	3.1	18	75	15	64	50	0	3	45	1.18
40408330--40408410	40	2.0	43	90	7	132	50	0	3	45	1.19
40410141--40410186	20	2.3	20	82	17	69	39	0	0	60	0.97
40415878--40415923	18	2.5	18	85	3	56	52	41	0	6	1.27
40415889--40415937	25	1.9	26	91	4	82	53	40	2	4	1.32
40421764--40421793	14	2.1	14	100	0	60	30	6	26	36	1.82
40423406--40423434	7	4.3	7	91	8	51	72	0	0	27	0.85
40423406--40423434	13	2.1	14	93	6	51	72	0	0	27	0.85
40423449--40423511	27	2.4	27	81	2	74	53	1	0	44	1.10
40423426--40423515	32	2.8	32	74	16	94	52	2	0	45	1.13
40423793--40425045	114	11.0	114	91	0	1877	24	22	25	28	1.99
40425595--40425627	14	2.3	15	94	5	59	30	0	33	36	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40425714--40425932	89	2.6	83	83	5	242	28	2	25	43	1.66
40425764--40425932	89	1.9	90	88	1	259	27	2	26	42	1.70
40425959--40426012	22	2.6	21	71	23	51	51	0	5	42	1.25
40426002--40426045	8	5.2	8	82	17	54	56	0	9	34	1.31
40426007--40426055	9	5.4	9	88	9	73	61	0	8	30	1.25
40426085--40426175	47	1.9	48	88	2	139	45	7	1	46	1.39
40427430--40427476	21	2.2	21	84	0	58	40	12	0	46	1.42
40428731--40428877	41	3.4	41	68	22	111	46	17	0	34	1.53
40428824--40428907	8	10.5	8	74	14	59	50	15	0	34	1.45
40428824--40428907	17	4.7	17	72	21	64	50	15	0	34	1.45
40428732--40428873	32	4.7	29	70	22	112	47	16	0	34	1.52
40428853--40428901	9	5.7	9	85	4	66	46	18	0	34	1.49
40429003--40429074	17	4.2	17	72	13	58	44	13	1	40	1.53
40429011--40429074	25	2.5	26	87	2	94	43	14	1	40	1.54
40429553--40429701	43	3.5	43	88	0	217	29	18	28	22	1.98
40441262--40441306	22	2.0	22	83	12	56	60	8	2	28	1.39
40441814--40441851	20	2.0	20	89	5	60	42	0	2	55	1.14
40451146--40451199	28	1.9	28	84	0	72	25	11	3	59	1.48
40451181--40451225	7	6.3	7	86	2	54	46	13	0	40	1.43
40451183--40451227	21	2.1	21	87	0	63	44	15	0	40	1.47
40451328--40451427	51	1.9	52	90	6	159	42	1	7	50	1.36
40461335--40461456	28	4.4	28	90	0	172	32	23	21	22	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40461576--40461652	26	3.0	26	82	3	93	37	23	18	20	1.94
40461775--40461879	27	3.9	28	81	6	99	25	15	18	40	1.89
40461802--40462343	54	10.2	53	76	12	336	19	17	19	43	1.88
40461804--40462343	27	20.3	26	75	11	246	19	17	19	43	1.88
40461874--40461908	18	1.9	18	100	0	70	22	14	17	45	1.84
40461821--40461961	71	2.0	72	80	4	160	22	16	18	42	1.89
40461893--40462368	81	5.9	81	81	4	444	17	17	20	44	1.87
40461893--40462343	27	16.7	27	79	5	385	17	17	20	44	1.87
40461893--40462368	54	8.8	54	80	7	441	17	17	20	44	1.87
40463200--40463334	68	2.0	68	94	0	234	29	34	9	25	1.88
40464685--40464848	28	5.9	28	86	0	222	32	24	20	23	1.98
40464969--40465071	26	4.0	26	88	5	154	35	21	23	19	1.96
40464969--40465071	52	2.0	52	92	0	170	35	21	23	19	1.96
40465216--40465734	27	19.3	26	78	8	359	17	17	21	43	1.88
40475465--40475508	5	8.6	5	85	5	61	75	2	20	2	1.03
40475461--40475498	15	2.6	15	91	4	60	78	0	21	0	0.74
40475548--40475583	11	3.4	11	92	3	56	72	0	8	19	1.10
40476206--40476281	27	2.8	29	79	15	76	63	2	0	34	1.09
40476171--40476314	10	15.6	9	70	17	73	62	4	1	31	1.23
40476222--40476348	28	4.4	29	76	18	104	58	3	0	37	1.20
40476223--40476283	19	3.2	19	80	19	65	63	1	0	34	1.04
40476240--40476282	9	4.9	8	81	18	50	62	2	0	34	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40477164--40477257	10	9.9	9	70	18	66	29	2	3	64	1.20
40477173--40477197	11	2.3	11	100	0	50	24	0	0	76	0.80
40478864--40478925	18	3.5	17	91	4	70	46	16	8	29	1.75
40478883--40478925	9	4.8	9	88	0	68	46	13	9	30	1.75
40478865--40478924	27	2.2	27	85	5	77	46	16	8	28	1.76
40479053--40479124	18	3.9	18	87	1	99	11	2	47	38	1.54
40482130--40482186	20	2.8	20	76	5	62	29	3	1	64	1.20
40482130--40482186	26	2.2	26	77	0	60	29	3	1	64	1.20
40485686--40485882	40	4.9	40	81	1	214	32	16	21	28	1.95
40485687--40485882	81	2.4	80	81	0	221	33	16	21	29	1.95
40490431--40490551	59	2.1	59	88	0	179	34	18	14	33	1.90
40493390--40493422	11	3.0	11	87	12	50	18	0	27	54	1.44
40493480--40493528	8	5.9	8	78	7	53	18	0	4	77	0.92
40493477--40493533	17	3.4	16	78	9	60	19	0	5	75	0.99
40493534--40493713	40	4.5	40	84	2	236	30	15	24	30	1.96
40494468--40494502	14	2.5	14	90	9	54	17	2	0	80	0.84
40495249--40495340	5	18.4	5	81	10	109	18	3	1	77	0.97
40499317--40499389	6	12.3	6	83	12	89	15	1	4	79	0.95
40502331--40502375	3	15.0	3	95	0	81	64	0	2	33	1.06
40502377--40502421	3	15.0	3	100	0	90	33	0	0	66	0.92
40507357--40507406	24	2.1	24	85	3	66	48	6	6	40	1.52
40507410--40507455	24	1.9	24	81	0	56	34	0	13	52	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40508387--40508420	14	2.5	14	95	4	61	14	0	35	50	1.44
40508871--40508933	28	2.2	29	82	2	83	19	3	20	57	1.54
40509073--40509121	21	2.2	23	85	7	66	18	4	22	55	1.60
40512477--40512527	24	2.2	25	86	10	72	19	0	5	74	1.02
40516497--40516561	30	2.1	31	91	2	105	55	12	6	26	1.60
40517895--40518268	124	3.0	123	92	1	606	29	15	22	32	1.95
40523552--40523589	20	1.9	20	84	10	51	55	7	2	34	1.43
40524531--40524561	11	2.8	11	90	0	53	51	6	19	22	1.69
40525477--40525888	164	2.5	161	85	5	526	29	14	12	43	1.82
40525842--40525990	74	2.0	74	93	1	253	27	17	14	40	1.89

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