genome.fa.s1.2.7.7.80.10.50.1000.168.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  168  of  187  ( 22383 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)
49734574--49734625	6	8.7	6	78	0	50	11	7	11	69	1.37
49734565--49734629	24	2.7	23	83	9	76	12	9	9	69	1.37
49734585--49734649	24	2.9	24	80	8	66	7	13	6	72	1.27
49737930--49737991	31	2.0	31	100	0	124	41	16	9	32	1.80
49742987--49743015	3	9.7	3	100	0	58	68	0	0	31	0.89
49748805--49748848	23	1.9	23	85	0	61	34	6	0	59	1.24
49748919--49748995	30	2.6	28	77	6	73	31	6	0	62	1.21
49751222--49751276	3	18.3	3	100	0	110	32	0	0	67	0.91
49752728--49752762	18	2.0	18	88	5	54	25	11	2	60	1.45
49752720--49752774	17	3.2	16	78	16	58	25	7	3	63	1.37
49758402--49758642	50	4.9	49	82	1	257	21	28	21	28	1.99
49761451--49761531	42	1.9	42	85	5	110	17	33	24	24	1.96
49761461--49761548	42	2.1	42	80	4	97	22	31	21	23	1.98
49762201--49762401	40	5.0	40	86	0	267	31	15	31	20	1.94
49762320--49762385	20	3.3	20	66	8	62	30	18	37	13	1.89
49773129--49773186	19	3.0	20	85	7	66	43	20	25	10	1.84
49773129--49773186	20	3.0	20	84	2	73	43	20	25	10	1.84
49773725--49773761	18	2.1	18	100	0	74	10	5	32	51	1.60
49777029--49777068	17	2.4	17	91	0	62	30	25	17	27	1.97
49781139--49781173	2	17.5	2	100	0	70	51	0	0	48	1.00
49782101--49782235	41	3.3	41	86	0	144	30	26	23	19	1.98
49785262--49785456	50	3.9	50	77	4	153	23	26	22	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49792704--49792751	20	2.4	21	80	13	57	12	25	6	56	1.59
49806188--49806216	12	2.3	13	94	5	51	20	6	6	65	1.40
49811496--49811528	16	2.1	16	94	0	57	51	12	9	27	1.69
49824595--49824686	41	2.2	41	82	0	103	30	23	21	23	1.99
49826666--49826713	26	1.9	24	84	16	62	75	18	4	2	1.07
49840599--49840713	26	4.4	25	72	7	104	23	15	25	35	1.94
49840598--49840714	52	2.2	52	81	3	137	23	15	25	35	1.94
49854732--49854782	18	2.8	18	81	3	57	23	27	5	43	1.77
49854732--49854771	19	2.2	19	86	4	55	25	32	5	37	1.77
49861544--49861643	42	2.4	42	87	0	155	27	26	10	37	1.88
49862516--49862549	17	2.1	17	88	5	52	32	17	0	50	1.47
49868203--49868281	39	2.0	39	100	0	158	44	17	7	30	1.77
49869602--49869701	42	2.4	42	94	0	173	27	28	10	35	1.89
49870675--49870708	17	2.1	17	94	5	61	29	17	0	52	1.45
49875175--49875280	43	2.5	43	87	6	146	26	29	17	26	1.98
49882880--49882909	11	2.6	11	94	5	51	60	0	3	36	1.14
49888263--49888365	44	2.4	44	85	3	129	41	5	1	50	1.37
49894617--49894674	30	1.9	30	85	0	80	48	10	8	32	1.68
49897171--49897228	30	1.9	30	86	6	82	48	12	8	31	1.70
49902899--49902937	16	2.4	16	82	0	51	12	17	2	66	1.35
49903240--49903346	50	2.1	50	79	3	117	21	29	21	27	1.98
49914563--49914621	3	19.7	3	96	0	109	30	0	35	33	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49917078--49917143	27	2.4	27	87	0	87	31	33	15	19	1.93
49917099--49917152	27	2.0	27	92	0	90	31	35	12	20	1.90
49919036--49919271	50	4.7	50	93	0	382	25	22	31	21	1.98
49922597--49922645	24	2.1	22	82	17	55	67	2	10	20	1.30
49924747--49924816	34	2.2	33	90	10	110	20	27	12	40	1.88
49926745--49926807	25	2.5	25	81	0	81	23	22	25	28	1.99
49937239--49937300	29	2.1	29	82	11	74	19	6	17	56	1.62
49938212--49938291	16	4.9	16	80	7	81	45	8	22	23	1.80
49940096--49940145	22	2.4	21	80	9	59	38	0	24	38	1.56
49952119--49952143	13	1.9	13	100	0	50	40	24	4	32	1.73
49958735--49958858	44	2.9	43	77	14	121	33	27	14	24	1.94
49959585--49959626	18	2.3	18	95	0	75	64	11	2	21	1.38
49964333--49964397	32	2.0	32	93	0	112	23	16	12	47	1.80
49971467--49971506	15	2.7	15	80	11	55	17	20	27	35	1.95
50009289--50009356	25	2.7	25	84	4	75	29	19	25	26	1.98
50022079--50022304	27	8.4	27	86	6	307	42	20	18	19	1.89
50032747--50032812	25	2.6	25	77	15	64	51	4	4	39	1.43
50041119--50041162	24	2.0	21	86	13	61	52	4	2	40	1.34
50055405--50055775	104	3.6	103	94	1	618	19	20	29	30	1.97
50064966--50065045	41	2.0	41	87	0	115	28	20	22	28	1.98
50064978--50065071	41	2.3	41	81	0	107	26	19	24	29	1.98
50065414--50065438	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50065488--50065528	11	3.7	11	80	0	55	31	4	14	48	1.65
50065585--50065635	18	2.7	19	73	14	61	35	9	17	37	1.83
50069238--50069288	3	17.0	3	100	0	102	66	0	0	33	0.92
50079569--50079678	54	2.0	54	98	0	211	24	24	12	38	1.90
50091664--50091712	10	4.8	10	80	5	53	6	12	2	79	0.99
50099264--50099360	51	1.9	51	82	4	124	39	8	24	27	1.84
50100493--50100636	29	5.0	28	76	5	101	38	20	15	25	1.92
50100489--50100650	58	2.8	58	81	2	164	37	19	15	27	1.92
50100489--50100690	88	2.3	89	81	4	223	36	19	16	27	1.93
50100511--50100651	58	2.4	58	83	2	165	36	19	16	27	1.93
50100657--50100759	29	3.6	29	76	5	91	37	20	14	27	1.91
50101187--50101221	17	2.1	17	94	5	63	25	0	14	60	1.35
50104114--50104216	39	2.7	39	98	1	199	40	17	24	17	1.90
50104404--50104479	26	2.9	26	88	0	107	27	22	18	31	1.97
50104464--50104588	29	4.3	29	93	0	205	24	16	23	35	1.95
50104578--50104661	29	2.9	29	83	0	105	25	17	22	34	1.96
50104464--50104615	58	2.6	58	85	2	180	25	15	22	36	1.93
50104491--50104661	58	2.9	57	78	3	155	25	16	23	34	1.95
50105375--50105424	26	1.9	26	83	0	64	24	30	34	12	1.91
50105366--50105430	26	2.5	26	72	2	60	23	29	33	13	1.93
50106212--50106275	21	3.0	21	93	0	110	46	18	21	12	1.82
50112288--50112316	12	2.4	12	100	0	58	34	0	6	58	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50114695--50114728	17	1.9	18	88	5	52	38	41	0	20	1.53
50120600--50120636	18	2.1	18	94	0	65	10	40	35	13	1.80
50121430--50121463	17	1.9	18	88	5	52	35	44	0	20	1.52
50128130--50128277	74	2.0	74	98	0	287	32	17	6	43	1.73
50131007--50131195	51	3.7	51	85	2	238	22	16	28	32	1.96
50131115--50131195	26	3.2	26	64	28	64	22	13	29	34	1.92
50131009--50131193	101	1.8	101	88	3	282	23	16	27	32	1.96
50131202--50131290	45	2.0	45	90	0	142	23	16	25	33	1.96
50134932--50135000	35	2.0	35	100	0	138	43	8	14	33	1.76
50137066--50137128	33	1.9	33	96	0	117	19	34	15	30	1.93
50144067--50144112	22	2.1	22	91	0	74	28	4	63	4	1.33
50147653--50147682	9	3.3	9	90	0	51	53	3	0	43	1.17
50153172--50153208	18	2.1	18	100	0	74	21	32	0	45	1.52
50153723--50153800	40	2.0	40	90	5	124	29	17	3	48	1.65
50156150--50156260	55	2.0	55	98	0	213	48	10	1	38	1.49
50156608--50156646	21	1.9	20	84	5	51	28	30	7	33	1.85
50157639--50157736	48	2.0	48	86	0	133	34	7	20	37	1.80
50157705--50157817	59	1.9	60	88	1	174	23	7	33	35	1.82
50159014--50159059	19	2.4	19	85	0	56	30	4	2	63	1.26
50170678--50170702	8	3.1	8	100	0	50	76	0	0	24	0.80
50171821--50171858	13	2.8	14	85	14	53	50	0	15	34	1.45
50172548--50172589	20	2.0	22	90	9	70	7	2	33	57	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50174652--50174847	43	4.6	41	76	10	171	34	23	17	23	1.96
50174614--50174851	85	2.8	85	86	1	300	33	24	17	24	1.96
50174680--50174848	42	4.0	42	75	16	159	33	24	16	24	1.96
50179999--50180198	43	4.7	41	75	9	161	36	24	15	24	1.94
50179971--50180160	85	2.2	85	87	4	269	36	24	14	24	1.93
50180007--50180198	85	2.3	85	84	1	242	36	24	14	25	1.93
50184445--50184519	37	2.0	37	97	0	141	26	9	21	42	1.83
50193771--50193809	20	2.0	20	90	5	62	15	0	12	71	1.14
50203918--50203957	12	3.3	12	83	13	55	75	0	0	25	0.81
50205234--50205275	21	2.0	21	85	0	57	35	7	19	38	1.79

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