genome.fa.s4.2.7.7.80.10.50.1000.157.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  157  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)
49634744--49635085	50	6.7	50	84	4	400	28	23	28	19	1.98
49634744--49635085	100	3.3	100	88	4	463	28	23	28	19	1.98
49634745--49635085	150	2.2	154	84	3	447	27	23	29	19	1.98
49637826--49637869	23	1.9	23	86	9	63	47	0	2	50	1.13
49637826--49637876	22	2.4	22	83	9	61	47	0	1	50	1.12
49641871--49641943	38	2.0	37	91	5	121	45	13	12	28	1.80
49646792--49646877	44	2.0	44	80	0	100	25	22	20	31	1.98
49666134--49666163	7	4.3	7	91	0	51	26	3	0	70	1.03
49666619--49666935	107	3.0	107	91	0	519	30	19	18	31	1.96
49669546--49669604	20	3.0	20	80	9	75	44	10	8	37	1.69
49669925--49669971	14	3.3	14	82	5	58	4	23	0	72	1.02
49670599--49670623	6	4.2	6	100	0	50	16	0	48	36	1.46
49672912--49672940	14	2.0	15	93	6	51	48	6	6	37	1.57
49674935--49674988	5	11.0	5	76	11	58	18	3	1	75	1.03
49674936--49674992	16	3.4	17	85	7	73	17	5	1	75	1.07
49679474--49679960	44	11.1	44	68	12	194	30	19	24	26	1.98
49679441--49679988	132	4.2	132	87	1	715	30	19	24	26	1.98
49679972--49680456	181	2.7	179	89	2	713	30	18	21	29	1.97
49680158--49680423	51	5.7	50	68	21	166	31	18	20	28	1.96
49680446--49680475	14	2.1	14	100	0	60	23	13	43	20	1.86
49681113--49681160	21	2.2	21	85	10	62	16	4	2	77	1.03
49681109--49681166	16	3.5	17	81	11	75	15	6	1	75	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49684577--49684780	36	5.6	36	71	9	144	25	23	24	27	2.00
49690067--49690101	18	2.0	17	94	5	61	57	0	0	42	0.99
49690911--49690945	18	2.0	17	94	5	61	42	0	0	57	0.99
49697652--49697709	24	2.4	24	94	0	98	70	5	18	5	1.25
49708403--49708465	30	2.1	30	93	0	108	25	3	14	57	1.52
49708546--49708584	17	2.3	17	86	8	53	20	0	15	64	1.30
49710712--49710758	20	2.3	21	77	3	51	59	10	2	27	1.42
49711463--49711501	19	2.1	19	85	0	51	15	2	7	74	1.15
49716024--49716089	27	2.5	25	80	11	69	7	12	4	75	1.16
49716049--49716113	34	1.9	34	84	12	89	9	9	6	75	1.19
49716731--49716997	135	2.0	136	91	0	437	31	17	20	30	1.96
49718277--49718376	51	2.0	51	92	4	166	47	3	25	25	1.66
49718357--49718387	11	2.8	11	95	0	53	48	3	29	19	1.64
49718341--49718391	22	2.4	22	84	12	70	50	1	27	19	1.58
49725979--49726018	2	20.0	2	100	0	80	50	0	0	50	1.00
49726729--49726829	40	2.5	40	98	0	193	31	24	17	25	1.97
49734257--49734367	47	2.4	47	98	0	213	20	13	22	43	1.87
49747722--49747804	22	3.8	22	83	0	103	43	22	21	12	1.86
49748320--49748358	19	2.1	19	90	9	62	23	12	0	64	1.28
49751057--49751098	15	2.8	16	85	7	61	23	0	4	71	1.05
49751057--49751103	18	2.6	18	86	0	67	25	0	4	70	1.05
49756591--49756667	30	2.6	30	81	2	75	50	11	15	22	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49757090--49757116	8	3.4	8	100	0	54	37	0	0	62	0.95
49757101--49757182	19	4.2	18	74	18	58	41	2	1	54	1.21
49764133--49764170	19	2.1	19	90	5	60	34	0	7	57	1.28
49764136--49764180	19	2.3	19	82	14	56	35	0	8	55	1.31
49766091--49766133	2	21.5	2	90	9	70	46	2	0	51	1.13
49775020--49775049	15	2.0	15	100	0	60	33	26	6	33	1.83
49776450--49776475	5	5.2	5	100	0	52	38	19	19	23	1.93
49776424--49776475	26	2.0	26	81	7	61	34	15	26	23	1.94
49780696--49780761	30	2.2	29	81	5	87	21	10	9	59	1.58
49780834--49781018	10	18.0	10	67	26	54	22	2	18	56	1.54
49780834--49781030	8	21.9	9	70	21	96	22	3	18	55	1.58
49780860--49781014	33	4.5	35	70	17	112	23	1	18	56	1.52
49780887--49781018	5	26.4	5	71	19	75	21	1	19	56	1.50
49780926--49781019	12	7.3	13	75	17	72	21	2	20	56	1.53
49780934--49781030	4	22.2	4	73	21	63	20	4	20	54	1.61
49780932--49781028	29	3.5	27	78	13	108	19	4	20	55	1.59
49780887--49781013	64	2.0	66	92	3	213	22	1	19	56	1.50
49784695--49784766	30	2.4	32	84	9	89	25	15	4	55	1.58
49785631--49785689	20	3.0	21	83	14	72	38	1	8	50	1.43
49785631--49785689	19	3.1	19	90	4	91	38	1	8	50	1.43
49793619--49793651	14	2.3	15	94	5	59	75	0	24	0	0.80
49793956--49793992	2	18.5	2	100	0	74	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49796103--49796140	2	19.0	2	100	0	76	50	0	0	50	1.00
49801593--49801745	43	3.7	41	85	3	200	32	18	21	27	1.97
49801598--49801756	85	1.9	83	84	2	210	35	18	20	26	1.95
49802122--49802186	21	3.1	21	90	0	103	4	44	16	33	1.69
49803802--49804163	9	40.3	9	70	15	225	38	0	16	44	1.52
49803867--49804163	16	18.4	16	71	18	158	37	0	16	45	1.51
49803802--49804163	25	13.4	27	75	14	225	38	0	16	44	1.52
49804186--49804236	19	2.8	19	85	5	70	54	1	0	43	1.11
49806057--49806089	16	2.1	16	88	5	50	33	0	6	60	1.21
49806131--49806173	15	2.8	15	78	3	50	46	32	0	20	1.51
49806236--49806316	28	2.9	28	77	12	69	45	32	2	19	1.64
49806264--49806316	21	2.5	20	79	8	52	45	32	3	18	1.68
49806449--49806505	20	2.8	20	81	7	71	47	36	0	15	1.46
49806640--49806724	7	11.7	7	71	10	55	37	44	2	15	1.59
49806640--49806727	38	2.4	37	87	9	126	37	44	2	15	1.60
49806962--49807424	114	4.0	114	83	0	566	27	28	19	25	1.98
49807321--49807567	73	3.4	73	84	2	302	24	26	23	25	2.00
49815055--49815101	17	2.8	17	77	3	51	63	0	0	36	0.94
49815643--49815670	9	3.1	9	100	0	56	32	10	10	46	1.73
49817981--49818014	15	2.3	15	89	0	50	61	17	2	17	1.46
49818021--49818058	13	2.8	14	80	19	53	65	7	5	21	1.38
49818021--49818073	27	2.0	26	85	3	70	67	9	3	18	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49818281--49818335	27	2.1	27	83	6	69	65	0	3	30	1.10
49818456--49818587	28	5.0	28	69	22	90	59	4	1	34	1.27
49818439--49818505	30	2.2	32	83	5	84	62	4	0	32	1.15
49820236--49820393	44	3.7	43	76	5	133	28	20	20	29	1.98
49820837--49820981	45	3.3	44	70	4	130	28	28	15	26	1.96
49820829--49821002	88	2.0	88	89	0	267	27	26	18	27	1.98
49833164--49833211	14	3.3	14	77	11	51	60	0	2	37	1.09
49833306--49833379	28	2.8	26	79	8	78	60	5	0	33	1.19
49847580--49847620	20	2.1	20	86	4	57	60	0	4	34	1.18
49848757--49848811	20	3.2	17	82	14	60	38	0	12	49	1.41
49848875--49848921	20	2.3	20	75	7	51	42	10	2	44	1.51
49859986--49860086	46	2.2	46	85	5	143	46	2	7	42	1.48
49859965--49860086	45	2.7	46	82	6	151	45	3	7	43	1.48
49869713--49869780	25	2.5	28	86	11	97	36	10	1	51	1.45
49870095--49870131	3	12.3	3	94	0	65	29	0	2	67	1.04
49870130--49870179	3	16.7	3	100	0	100	0	0	32	68	0.90
49870258--49870365	44	2.4	45	92	7	184	40	8	6	44	1.60
49873357--49873383	11	2.5	11	100	0	54	40	14	7	37	1.74
49877015--49877069	12	4.4	12	80	8	65	60	3	1	34	1.25
49877021--49877065	20	2.2	20	88	0	63	57	4	2	35	1.31
49878694--49878726	13	2.6	13	90	4	50	15	0	36	48	1.45
49878702--49878742	13	3.2	13	85	0	55	14	0	39	46	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49878871--49879005	27	5.0	26	76	18	109	0	28	0	71	0.92
49878889--49878932	16	2.7	16	77	16	54	0	22	0	77	0.77
49878892--49878999	18	6.1	17	69	19	69	0	27	0	72	0.85
49878891--49879005	5	23.2	5	72	13	53	0	26	0	73	0.84
49878919--49879006	4	22.0	4	77	21	55	0	28	0	71	0.86
49878913--49879005	11	8.7	10	68	17	53	0	27	0	72	0.85
49878861--49879006	33	4.5	32	74	22	110	0	28	0	70	0.92
49878875--49879017	32	4.4	32	75	15	118	0	31	0	67	0.95
49879142--49879207	27	2.4	27	87	2	87	48	0	13	37	1.43
49881137--49881185	21	2.3	21	78	3	53	63	4	0	32	1.13

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