genome.fa.s4.2.7.7.80.10.50.1000.180.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  180  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)
56244277--56244308	13	2.5	13	94	0	55	56	12	0	31	1.37
56244520--56244577	30	1.9	30	85	0	80	31	25	1	41	1.66
56247131--56247219	18	4.8	18	79	14	101	43	11	1	43	1.47
56247122--56247217	17	4.8	20	65	24	60	42	11	1	44	1.47
56247149--56247226	39	2.0	41	94	5	142	43	10	0	46	1.37
56247298--56247334	12	3.1	12	96	0	65	62	0	0	37	0.96
56247362--56247390	12	2.4	12	100	0	58	48	10	0	41	1.37
56247386--56247748	9	41.8	9	67	19	150	48	18	1	31	1.57
56247412--56247547	34	3.7	35	73	16	123	47	21	1	29	1.59
56247435--56247759	25	13.3	26	72	14	121	48	18	1	31	1.56
56247395--56247574	37	4.9	37	73	14	120	49	19	1	30	1.56
56247567--56247661	7	12.4	7	70	25	52	53	16	0	29	1.43
56247512--56247631	44	2.7	44	96	2	213	51	17	0	30	1.46
56247392--56247744	16	21.9	16	65	25	115	49	18	1	30	1.55
56249563--56249612	21	2.4	21	93	0	82	32	14	50	4	1.61
56249979--56250189	43	4.9	43	84	1	280	29	20	25	25	1.99
56249984--56250214	43	5.4	43	80	3	196	30	19	25	24	1.98
56249962--56250230	86	3.1	86	83	1	315	28	18	26	26	1.98
56249987--56250230	129	1.9	129	81	1	292	29	19	25	26	1.98
56262054--56262097	16	2.8	16	85	0	70	20	27	15	36	1.93
56271649--56271714	12	5.5	12	83	0	51	12	40	0	46	1.41
56271648--56271712	18	3.6	18	89	0	85	12	40	0	47	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56272403--56272456	21	2.6	21	85	8	67	51	9	0	38	1.34
56272961--56273130	9	18.0	9	67	16	67	34	2	3	58	1.30
56273033--56273137	29	3.7	27	77	15	88	36	0	4	58	1.26
56283484--56283562	41	1.9	41	89	0	122	29	21	17	31	1.96
56284127--56284175	21	2.3	20	80	10	53	69	6	0	24	1.11
56284139--56284202	23	2.9	23	90	4	96	67	1	0	31	1.00
56289041--56289078	20	1.9	20	88	0	58	42	7	10	39	1.69
56291700--56291839	49	2.9	49	81	8	167	30	29	20	20	1.97
56295783--56295850	31	2.2	30	84	12	84	42	11	8	36	1.73
56296897--56297000	49	2.1	49	85	3	138	27	26	20	25	1.99
56296929--56297038	49	2.2	48	80	4	123	24	26	23	25	2.00
56300872--56300930	29	2.0	30	86	3	84	32	5	13	49	1.64
56300877--56300939	29	2.1	29	82	8	74	34	7	11	46	1.69
56313049--56313092	23	1.9	23	85	0	61	59	4	2	34	1.30
56316297--56316339	21	2.1	20	86	4	59	53	2	4	39	1.34
56320580--56320608	13	2.1	14	93	6	51	44	0	3	51	1.18
56327010--56327089	29	2.6	30	86	5	99	33	7	12	46	1.70
56327035--56327098	29	2.2	29	86	8	85	32	9	12	45	1.74
56327277--56327343	31	2.2	30	86	5	91	40	10	11	37	1.77
56328236--56328283	24	2.0	24	88	8	71	70	0	14	14	1.16
56335486--56335518	2	16.5	2	100	0	66	51	0	0	48	1.00
56336927--56336982	29	1.9	29	82	7	69	39	1	5	53	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56337040--56337085	12	3.8	12	76	23	51	50	0	0	50	1.00
56337028--56337085	26	2.3	25	85	8	73	48	0	1	50	1.11
56337026--56337084	21	2.9	21	82	5	59	49	0	1	49	1.11
56338554--56338715	39	4.2	39	95	0	288	9	19	54	15	1.68
56342076--56342117	21	2.0	21	86	4	59	76	2	9	11	1.12
56342966--56343024	29	2.0	30	83	3	75	49	15	5	30	1.66
56344938--56344981	23	1.9	23	85	0	61	34	2	4	59	1.30
56347098--56347156	29	2.0	30	83	3	75	49	15	6	28	1.70
56349179--56349282	51	2.0	51	100	0	208	44	17	17	21	1.87
56352785--56352914	11	12.4	11	77	14	98	40	2	0	57	1.11
56352768--56352890	42	3.0	42	87	10	177	35	1	0	62	1.05
56358215--56358245	15	2.1	15	100	0	62	35	12	6	45	1.68
56362147--56362171	2	12.5	2	100	0	50	52	0	0	48	1.00
56368926--56369042	49	2.4	49	97	0	216	26	34	11	28	1.90
56368926--56369071	49	3.0	49	89	3	177	29	33	11	25	1.91
56372236--56372279	23	1.9	23	85	0	61	38	11	20	29	1.87
56383092--56383148	27	2.1	27	96	0	105	61	5	7	26	1.43
56384904--56385061	79	2.0	78	91	1	253	29	13	19	37	1.90
56389696--56389733	17	2.2	17	90	4	58	18	0	26	55	1.43
56389696--56389734	16	2.3	18	86	8	55	20	0	25	53	1.45
56391088--56391156	9	7.7	9	85	6	86	42	23	10	24	1.85
56391088--56391156	27	2.6	27	88	4	104	42	23	10	24	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56392673--56392732	3	20.0	3	100	0	120	66	0	0	33	0.92
56393432--56393509	37	2.1	39	92	4	133	55	7	6	30	1.54
56394743--56394769	10	2.7	10	100	0	54	40	0	14	44	1.46
56395099--56395173	25	3.0	25	86	3	89	22	21	18	37	1.94
56397618--56397657	19	2.2	19	86	4	55	50	0	5	45	1.23
56399743--56399782	21	1.9	21	94	0	71	22	17	27	32	1.96
56399826--56399892	29	2.3	29	85	10	84	29	13	7	49	1.69
56400667--56400917	139	1.8	139	96	1	468	48	5	8	37	1.59
56407144--56407182	19	2.1	19	90	0	60	12	17	5	64	1.46
56407349--56407396	18	2.8	17	81	12	62	68	2	2	27	1.11
56407376--56407419	23	1.9	23	86	9	63	72	4	0	22	1.02
56407529--56407567	8	5.0	8	84	6	53	58	2	0	38	1.12
56407530--56407560	15	2.1	15	93	0	53	61	0	0	38	0.96
56407947--56408004	18	3.3	17	79	11	55	22	0	3	74	0.97
56408995--56409111	60	2.0	60	92	0	198	52	14	0	32	1.42
56413068--56413106	17	2.2	17	90	4	60	51	2	0	46	1.14
56415198--56415266	34	2.0	34	100	0	138	23	0	28	47	1.52
56415196--56415260	19	3.6	19	71	25	68	24	0	29	46	1.53
56417493--56417623	63	2.1	63	98	1	255	19	18	16	45	1.86
56419938--56420050	25	4.5	24	71	15	79	34	21	25	18	1.96
56419986--56420124	74	1.9	74	80	8	167	35	17	27	19	1.95
56419971--56420124	25	6.2	25	74	8	75	36	18	25	19	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56420084--56420141	25	2.3	25	81	0	62	34	18	25	20	1.96
56420930--56420964	4	9.0	4	93	6	63	25	0	0	74	0.82
56424473--56424503	14	2.2	14	100	0	62	41	9	25	22	1.84
56438951--56438986	15	2.5	14	86	8	54	44	8	0	47	1.33
56439535--56439589	4	13.0	4	85	11	58	25	0	3	70	1.03
56439534--56439598	16	4.1	15	72	16	51	26	0	3	70	1.01
56447049--56447084	15	2.5	14	86	8	54	44	8	0	47	1.33
56447181--56447241	30	2.0	30	100	0	122	19	27	9	42	1.83
56448322--56448446	49	2.6	48	76	8	137	25	19	20	35	1.95
56449139--56449227	40	2.1	44	83	10	114	39	8	6	44	1.62
56452852--56452898	22	2.2	22	84	3	60	59	2	8	29	1.39
56461314--56461343	16	1.9	16	93	6	53	33	0	3	63	1.11
56463616--56463648	17	1.9	17	93	0	57	27	0	21	51	1.48
56464874--56464948	23	3.2	24	61	21	59	32	6	32	29	1.83
56464872--56465011	46	3.0	45	94	4	244	33	8	28	29	1.87
56468657--56468707	25	2.0	25	81	7	59	11	31	1	54	1.47
56476423--56476498	27	2.7	27	75	15	75	61	9	3	25	1.43
56478956--56478998	22	2.0	22	95	0	77	23	20	23	32	1.98
56482370--56482416	19	2.4	20	85	3	60	27	10	4	57	1.51
56482624--56482699	33	2.4	32	75	18	77	36	6	0	56	1.25
56487513--56487554	7	6.0	7	81	18	52	69	0	16	14	1.20
56487513--56487554	21	2.0	21	86	9	59	69	0	16	14	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56488838--56489785	89	10.7	89	88	2	1221	31	16	23	28	1.96
56488840--56489806	133	7.3	132	80	6	941	31	16	23	28	1.96
56489800--56490234	44	9.9	44	65	12	194	30	19	23	27	1.98
56489802--56490233	132	3.3	132	95	0	765	30	19	23	27	1.98
56491919--56491970	3	16.7	3	80	7	59	30	5	1	61	1.30
56491907--56491954	19	2.5	19	90	6	71	27	8	4	60	1.44
56491909--56491963	28	1.9	28	88	3	83	29	7	3	60	1.41
56492162--56492213	27	2.0	26	81	11	61	32	5	0	61	1.20
56499737--56499798	24	2.6	24	89	0	88	22	46	4	25	1.71
56502493--56502574	3	27.3	3	97	0	155	1	0	31	67	0.99

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