genome.fa.s4.2.7.7.80.10.50.1000.156.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  156  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)
49351126--49351192	17	4.1	17	73	21	54	73	2	0	23	0.97
49353422--49353454	16	1.9	18	88	11	52	48	6	0	45	1.27
49358938--49359015	38	2.1	38	87	4	113	38	2	10	48	1.51
49366075--49366118	21	2.1	21	87	4	63	56	2	11	29	1.46
49370365--49370496	31	4.2	31	80	4	140	49	15	6	28	1.70
49370356--49370473	62	1.9	62	87	0	173	47	16	5	30	1.70
49370363--49370494	62	2.1	62	82	4	156	48	15	6	28	1.71
49371750--49371785	17	2.0	19	89	10	58	58	19	0	22	1.40
49371801--49371839	20	2.0	20	85	10	53	53	30	5	10	1.56
49374223--49374305	31	2.7	31	76	9	89	24	16	31	27	1.97
49382312--49382336	4	6.2	4	100	0	50	24	48	0	28	1.52
49382470--49382721	126	2.0	122	94	3	443	43	7	22	27	1.79
49392262--49392317	13	4.5	13	71	10	55	66	0	0	33	0.92
49392264--49392322	24	2.4	25	83	5	68	69	0	0	30	0.89
49392902--49392967	13	4.9	14	68	18	50	57	1	0	40	1.08
49392905--49392967	27	2.3	28	76	13	69	57	1	0	41	1.08
49392902--49392958	15	4.1	15	76	19	52	56	1	0	42	1.10
49393442--49393542	34	3.0	32	80	9	112	45	0	10	43	1.39
49393434--49393560	34	3.7	33	78	11	105	42	0	13	43	1.49
49397194--49397230	18	2.1	18	89	0	56	40	5	29	24	1.77
49397199--49397236	18	2.1	18	90	0	58	39	7	26	26	1.83
49397781--49397806	7	3.7	7	100	0	52	57	15	0	26	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49401102--49401240	44	3.2	44	97	0	260	34	9	12	43	1.75
49409638--49409686	19	2.5	19	90	9	73	42	0	0	57	0.99
49411704--49411767	14	4.4	14	75	21	51	29	1	3	65	1.17
49411760--49411838	34	2.3	35	77	12	83	32	5	2	59	1.33
49413083--49413147	32	2.0	32	96	0	121	27	30	9	32	1.88
49422319--49422396	40	2.0	40	97	0	147	28	33	19	19	1.96
49422499--49422540	20	2.1	20	86	8	59	9	21	16	52	1.72
49424179--49424236	9	6.1	9	78	13	55	41	0	1	56	1.09
49424179--49424236	19	3.1	18	78	14	55	41	0	1	56	1.09
49424179--49424214	19	1.9	20	88	11	58	41	0	0	58	0.98
49438601--49438649	19	2.5	19	83	3	62	55	4	10	30	1.52
49439615--49439640	9	2.9	9	100	0	52	46	0	0	53	1.00
49452867--49452915	15	3.3	15	79	0	62	38	18	18	24	1.93
49452849--49452918	30	2.3	30	87	0	95	41	18	15	24	1.89
49463441--49463470	9	3.3	9	90	0	51	26	0	0	73	0.84
49466771--49466837	34	1.9	35	90	3	109	35	10	8	44	1.70
49467598--49467628	7	4.4	7	95	0	53	32	41	25	0	1.56
49468934--49469077	43	3.4	42	84	6	177	25	23	20	30	1.98
49474766--49474829	13	4.8	13	73	16	60	32	0	20	46	1.51
49474759--49474805	15	3.3	15	82	11	71	36	0	17	46	1.48
49474759--49474829	28	2.6	28	89	6	103	33	0	19	46	1.50
49474771--49474837	17	4.1	17	77	13	77	31	0	20	47	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49474775--49474845	9	8.4	9	74	14	71	30	0	22	46	1.52
49474842--49474903	5	12.6	5	98	1	117	40	0	17	41	1.50
49475014--49475150	9	15.0	9	74	13	111	33	0	19	45	1.56
49474813--49475141	47	6.7	47	73	18	260	33	1	19	45	1.61
49474813--49475182	205	1.8	202	86	6	541	34	1	18	45	1.60
49475233--49475345	9	12.4	9	68	9	59	35	0	15	48	1.46
49475500--49475618	38	3.2	38	64	13	102	51	5	6	36	1.50
49476262--49476321	23	2.5	24	86	5	95	25	13	15	46	1.81
49478242--49478491	7	34.9	7	66	10	76	43	34	2	20	1.64
49478320--49478378	22	2.7	23	84	7	70	42	32	1	23	1.64
49478360--49478394	15	2.4	15	90	4	54	45	34	0	20	1.51
49478360--49478480	49	2.4	48	78	6	125	45	28	1	23	1.63
49478774--49478878	40	2.6	39	86	5	147	25	24	21	27	2.00
49478815--49479085	114	2.4	113	85	4	341	29	22	18	30	1.97
49479011--49479156	75	1.9	75	91	0	238	23	22	21	32	1.98
49479116--49479242	40	3.2	40	89	0	182	22	25	22	29	1.99
49481588--49481634	24	2.0	24	84	16	62	48	17	0	34	1.47
49487523--49487579	25	2.4	25	80	14	66	56	3	1	38	1.27
49502304--49502361	16	3.7	15	72	9	53	68	5	6	18	1.31
49502335--49502369	16	2.2	16	89	0	52	82	5	2	8	0.91
49502689--49503009	157	2.1	157	88	4	472	27	9	9	53	1.63
49503109--49503172	27	2.4	27	86	5	85	10	35	31	21	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49507526--49507632	53	2.0	53	100	0	214	35	14	13	36	1.85
49508300--49508360	19	3.2	18	76	19	61	52	0	0	47	1.00
49509122--49509212	42	2.2	42	81	0	101	30	24	24	20	1.99
49509736--49509815	3	26.7	3	100	0	160	67	0	0	32	0.91
49512177--49512256	40	2.0	40	83	9	101	30	25	21	23	1.99
49523963--49524068	22	4.8	22	86	0	140	32	14	26	27	1.94
49525727--49525798	18	4.4	16	76	10	58	38	0	1	59	1.06
49525759--49525804	6	7.7	6	100	0	92	32	0	0	67	0.91
49526480--49526553	20	3.5	20	71	16	67	48	5	1	44	1.34
49526477--49526567	45	2.0	46	86	2	130	46	4	1	48	1.29
49530988--49531024	19	2.1	19	85	10	51	45	10	8	35	1.69
49541308--49541392	41	2.0	42	91	6	138	34	15	0	50	1.44
49545678--49545719	19	2.1	19	86	8	57	35	2	4	57	1.33
49545715--49545744	16	1.9	16	93	6	53	53	10	0	36	1.35
49550233--49550279	2	23.5	2	91	0	76	0	48	4	46	1.21
49555018--49555049	2	16.0	2	100	0	64	50	0	50	0	1.00
49555097--49555121	3	8.3	3	100	0	50	36	0	64	0	0.94
49555850--49555878	3	9.7	3	100	0	58	65	0	0	34	0.93
49557350--49557391	22	1.9	22	85	0	57	35	0	2	61	1.09
49557990--49558114	10	13.0	9	70	14	81	58	2	2	36	1.24
49557963--49558123	29	5.5	30	68	20	81	58	3	1	36	1.25
49557985--49558114	19	6.8	18	72	15	75	58	3	2	36	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49578076--49578113	2	19.0	2	100	0	76	50	0	0	50	1.00
49584119--49584143	5	5.0	5	100	0	50	80	0	0	20	0.72
49590135--49590206	28	2.6	28	91	4	110	40	12	1	45	1.50
49590234--49590336	51	2.0	51	100	0	206	38	21	19	20	1.93
49590328--49590430	27	3.8	27	90	0	161	25	29	29	16	1.97
49590473--49590570	4	24.5	4	74	17	71	67	0	32	0	0.91
49590467--49590593	21	6.0	21	73	20	97	66	0	33	0	0.92
49590480--49590570	17	5.7	15	74	20	71	67	0	32	0	0.91
49590497--49590599	51	2.0	52	81	16	124	67	0	32	0	0.90
49590476--49590604	63	2.1	62	88	10	192	66	0	33	0	0.92
49590494--49590586	33	3.0	30	71	15	91	65	0	34	0	0.93
49590939--49590963	13	1.9	13	100	0	50	64	8	20	8	1.46
49593628--49593733	26	3.3	36	67	26	101	50	11	0	36	1.45
49593881--49593975	3	31.7	3	100	0	190	67	32	0	0	0.91
49593974--49594032	3	19.3	3	92	3	100	64	1	0	33	1.04
49594251--49594317	27	2.5	27	92	0	107	14	28	29	26	1.96
49594251--49594326	27	2.8	27	84	4	100	15	27	28	27	1.96
49594387--49594462	28	2.7	28	87	2	107	46	1	10	42	1.46
49600222--49600299	38	2.0	38	85	5	102	43	11	8	35	1.72
49603455--49603502	22	2.2	21	82	10	60	31	31	0	37	1.58
49603467--49603512	22	2.1	22	100	0	92	30	30	0	39	1.57
49603484--49603542	30	2.0	30	93	0	100	30	35	0	33	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49603514--49603555	22	1.9	22	95	0	75	30	35	0	33	1.58
49603570--49603603	17	1.9	18	88	5	52	23	11	0	64	1.26
49603598--49603663	31	2.2	30	91	2	105	36	0	1	62	1.05
49603598--49603663	20	3.2	20	75	14	64	36	0	1	62	1.05
49607279--49607593	123	2.5	124	94	1	569	35	20	13	30	1.91
49612697--49612721	7	3.6	7	100	0	50	12	0	0	88	0.53
49614815--49614846	13	2.5	13	94	0	55	31	0	12	56	1.37
49614940--49615144	50	4.0	50	87	5	284	26	22	31	19	1.98
49614940--49615144	100	2.0	103	90	5	326	26	22	31	19	1.98
49634619--49634650	13	2.5	13	94	0	55	31	0	12	56	1.37

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