genome.fa.s4.2.7.7.80.10.50.1000.160.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  160  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)
50432862--50433734	132	6.6	132	93	0	1405	30	18	24	27	1.98
50432978--50433585	44	13.8	44	65	13	250	30	18	25	25	1.98
50460614--50461428	44	18.8	43	70	14	286	29	19	22	27	1.98
50460616--50461430	217	3.8	217	90	1	1231	29	20	22	27	1.98
50461685--50461726	17	2.5	17	88	0	57	42	38	16	2	1.61
50464683--50464771	3	29.7	3	95	0	115	58	0	7	33	1.27
50465502--50465534	16	2.0	17	88	5	50	48	0	3	48	1.17
50465654--50465692	5	7.4	5	88	5	51	58	0	0	41	0.98
50473515--50473566	8	6.1	8	78	12	50	73	1	0	25	0.94
50486701--50486746	23	2.0	23	100	0	92	39	8	0	52	1.33
50486744--50486787	23	1.9	23	85	0	61	84	6	2	6	0.86
50486813--50486895	27	3.1	27	78	0	94	22	21	42	13	1.88
50487208--50487238	3	10.3	3	100	0	62	32	0	0	67	0.91
50487237--50487331	3	31.7	3	97	0	181	0	1	32	66	0.99
50487679--50487717	14	2.7	15	84	8	53	61	5	5	28	1.39
50487691--50487719	14	2.1	14	100	0	58	55	0	6	37	1.27
50488685--50488721	17	2.2	17	95	0	65	48	8	13	29	1.71
50491293--50491409	10	11.7	10	68	20	75	1	31	0	66	1.02
50491301--50491337	14	2.6	14	100	0	74	5	21	0	72	1.04
50491316--50491426	18	6.1	18	74	15	95	0	32	0	66	0.98
50491315--50491417	38	2.7	38	89	3	145	0	33	0	66	0.99
50491353--50491426	14	5.1	14	72	22	55	0	31	0	68	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50491293--50491426	28	4.8	28	68	19	93	1	31	0	67	1.00
50491330--50491446	42	2.8	44	77	12	111	0	37	0	62	0.96
50491358--50491429	10	6.6	10	73	17	54	0	31	0	68	0.90
50491387--50491429	22	1.9	23	85	4	61	0	30	0	69	0.88
50491478--50491544	27	2.5	27	95	0	116	17	40	25	16	1.90
50491586--50491613	10	2.8	10	100	0	56	0	0	7	92	0.37
50491623--50491683	29	2.2	27	82	8	70	49	3	11	36	1.55
50491990--50492089	40	2.5	41	79	6	116	25	24	27	24	2.00
50492246--50492346	45	2.3	44	94	1	175	38	1	20	38	1.64
50492172--50492442	141	1.9	141	80	4	314	40	3	17	38	1.68
50511252--50511300	21	2.4	20	90	6	80	20	28	8	42	1.80
50511479--50511532	19	2.8	19	85	0	72	40	18	25	14	1.89
50512004--50512047	17	2.6	17	83	13	56	43	13	0	43	1.44
50520631--50520681	17	2.9	17	73	2	57	58	1	1	37	1.20
50524914--50524992	39	2.0	39	100	0	158	30	10	12	46	1.75
50525968--50526032	32	2.0	33	96	3	123	3	16	18	61	1.47
50531211--50531235	3	8.3	3	100	0	50	32	0	32	36	1.58
50536070--50536110	20	2.0	20	100	0	82	46	34	4	14	1.66
50541723--50541757	15	2.3	15	90	0	52	20	2	2	74	1.08
50547671--50547696	10	2.6	10	100	0	52	53	0	7	38	1.30
50547922--50548051	59	2.2	58	83	6	165	28	8	3	60	1.41
50547968--50548049	29	2.9	28	75	10	76	29	6	2	62	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50547960--50548080	59	2.1	58	83	10	149	29	6	1	61	1.30
50548030--50548086	19	2.8	20	77	17	57	26	8	0	64	1.22
50548180--50548359	89	2.0	89	87	5	258	35	7	17	38	1.79
50554685--50554872	42	4.5	42	84	2	227	28	19	20	31	1.97
50554685--50554872	84	2.3	83	86	0	259	28	19	20	31	1.97
50556715--50556800	9	9.1	10	81	7	92	27	2	1	68	1.09
50556719--50556824	9	11.4	9	75	11	90	26	2	1	68	1.13
50556715--50556798	20	4.5	19	79	13	75	28	2	1	67	1.10
50557669--50557714	21	2.0	23	84	12	60	30	23	15	30	1.95
50572237--50572430	100	1.9	99	88	1	289	26	18	12	41	1.87
50592660--50592708	25	2.0	25	88	8	73	46	0	2	51	1.12
50594429--50594553	41	3.0	41	85	1	151	27	18	21	32	1.97
50594750--50594774	13	1.9	13	100	0	50	24	8	20	48	1.76
50594786--50594833	2	24.0	2	95	0	87	47	2	0	50	1.12
50598368--50598392	2	12.5	2	100	0	50	0	48	0	52	1.00
50603198--50603222	5	5.0	5	100	0	50	40	0	0	60	0.97
50617722--50617794	31	2.4	30	82	8	85	30	8	9	52	1.63
50617935--50618050	59	2.0	60	84	5	155	39	16	18	25	1.91
50625119--50625198	36	2.2	36	91	2	126	41	11	11	36	1.77
50631026--50631055	15	2.0	15	93	0	51	56	43	0	0	0.99
50633464--50633576	59	1.9	59	81	1	138	23	13	17	46	1.83
50636442--50636480	19	2.0	20	85	5	53	33	10	0	56	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50641018--50641052	14	2.5	14	90	0	52	25	17	8	48	1.75
50647339--50647399	17	3.4	17	70	12	59	34	3	11	50	1.55
50647334--50647445	37	3.0	37	96	0	197	33	4	14	47	1.64
50647355--50647419	20	3.4	19	69	14	62	35	4	15	44	1.67
50647339--50647435	17	5.4	17	63	13	50	32	3	13	50	1.57
50650397--50650426	15	2.0	15	100	0	60	46	0	6	46	1.29
50651904--50652072	42	4.0	42	88	3	243	34	23	18	24	1.96
50652049--50652252	42	4.9	42	86	5	288	25	20	22	31	1.98
50652007--50652251	83	2.9	84	84	4	316	27	21	20	30	1.98
50652568--50652635	21	3.2	21	85	0	91	2	42	20	33	1.67
50656818--50656843	6	4.3	6	100	0	52	19	15	50	15	1.79
50658425--50658499	16	4.5	17	91	6	127	57	9	0	33	1.31
50658425--50658499	33	2.3	33	93	4	125	57	9	0	33	1.31
50658519--50658872	114	3.1	113	78	5	390	28	24	18	29	1.98
50658847--50659098	114	2.2	112	83	4	292	28	23	17	31	1.96
50658957--50659306	188	1.9	188	87	1	515	26	23	18	31	1.98
50658538--50659326	301	2.6	299	87	3	1136	27	23	18	31	1.97
50659769--50659812	22	2.0	22	100	0	88	40	13	13	31	1.84
50667710--50667855	9	15.6	9	81	8	175	38	30	8	22	1.85
50667708--50667852	29	5.1	29	89	3	222	39	30	8	21	1.84
50667710--50667855	38	3.9	36	81	8	166	38	30	8	22	1.85
50667856--50667968	37	3.1	37	93	1	192	48	13	4	33	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50667862--50667959	17	5.4	17	64	13	52	51	12	3	33	1.55
50668009--50668091	24	3.5	24	93	0	139	31	27	1	39	1.64
50670783--50670853	37	1.9	37	100	0	142	54	11	2	30	1.50
50672905--50672937	16	2.1	16	94	0	57	36	3	36	24	1.71
50674127--50674422	91	3.3	91	94	0	511	45	3	3	47	1.36
50677741--50677770	6	5.0	6	100	0	60	50	0	0	50	1.00
50677657--50677832	96	1.8	96	87	6	266	36	6	11	44	1.67
50678364--50678425	31	2.0	31	100	0	124	41	16	9	32	1.80
50683964--50684005	11	4.0	11	75	12	52	0	11	16	71	1.14
50683967--50684018	20	2.6	19	90	3	77	0	13	17	69	1.19
50684543--50684603	31	2.0	31	100	0	122	42	14	9	32	1.79
50685524--50685548	13	1.9	13	100	0	50	20	16	8	56	1.65
50685513--50685618	52	2.1	52	87	1	151	35	12	4	47	1.62
50686199--50686261	23	2.7	24	79	16	87	52	22	7	17	1.70
50686228--50686273	22	2.1	22	84	8	58	58	19	4	17	1.55
50686291--50686369	23	3.2	23	65	16	59	43	18	12	25	1.86
50691290--50691316	14	1.9	14	100	0	54	0	0	7	92	0.38
50702454--50702543	6	14.7	6	89	4	81	42	30	8	18	1.81
50722300--50722333	16	2.1	16	88	5	50	50	2	17	29	1.61
50738629--50738715	30	2.9	30	85	0	84	20	22	29	26	1.99
50739853--50739892	21	2.0	20	85	5	53	50	20	12	17	1.78
50740580--50740650	21	3.4	21	90	0	106	23	25	26	23	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50741843--50741992	41	3.7	41	95	0	255	23	28	22	26	1.99
50742517--50742546	2	15.0	2	100	0	60	50	0	0	50	1.00
50747637--50747684	21	2.2	21	79	13	53	47	0	18	33	1.49
50760984--50761045	30	2.1	29	82	11	72	50	3	0	46	1.17
50761841--50761877	2	18.5	2	100	0	74	51	0	0	48	1.00
50763617--50763656	19	2.1	19	100	0	80	42	15	0	42	1.46
50764969--50765056	37	2.3	39	78	3	99	38	15	13	31	1.87
50768102--50768151	25	2.0	25	88	0	73	40	18	20	22	1.92
50772813--50772913	50	2.0	52	86	3	143	32	20	5	40	1.77
50779889--50779927	14	2.8	14	96	0	69	35	12	23	28	1.91

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