genome.fa.s1.2.7.7.80.10.50.1000.177.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  177  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)
52948330--52948394	24	2.7	22	75	13	58	52	3	1	43	1.26
52948668--52948715	20	2.4	21	82	6	55	47	0	6	45	1.27
52951264--52951490	104	2.2	105	80	4	244	22	29	24	23	1.99
52953388--52953421	15	2.1	17	89	10	54	64	2	0	32	1.08
52962563--52962707	41	3.5	41	91	0	227	26	20	28	24	1.99
52965592--52965667	20	3.8	20	80	13	77	75	1	19	3	1.04
52974099--52974296	42	4.7	43	80	2	220	31	29	15	23	1.95
52974099--52974296	85	2.3	84	82	6	247	31	29	15	23	1.95
52974099--52974310	43	5.0	43	81	2	230	32	29	16	22	1.95
52980334--52980360	13	2.1	13	100	0	54	37	11	0	51	1.37
52982660--52982703	22	2.0	22	82	8	54	59	11	2	27	1.44
52990686--52990712	2	13.5	2	100	0	54	48	0	0	51	1.00
52998148--52998219	26	2.7	27	85	10	103	43	9	15	31	1.79
53012306--53012443	43	3.3	43	83	3	174	29	31	17	21	1.96
53013892--53013957	33	1.9	35	87	6	100	31	9	12	46	1.72
53013907--53013945	20	2.0	20	90	5	62	28	10	10	51	1.68
53014044--53014082	20	2.0	20	94	0	69	48	2	0	48	1.15
53017299--53017324	11	2.4	11	100	0	52	61	15	0	23	1.33
53017567--53017616	25	2.0	25	88	0	73	58	4	32	6	1.41
53023734--53024137	77	5.2	76	84	1	450	41	15	18	24	1.89
53023743--53023938	40	5.1	39	69	12	127	41	13	18	26	1.88
53032294--53032331	2	19.0	2	88	0	58	50	5	0	44	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53032832--53032883	21	2.5	22	81	12	65	55	3	1	38	1.29
53032827--53032899	30	2.5	28	83	14	94	57	2	2	36	1.27
53032830--53032900	10	7.3	9	75	18	63	59	2	2	35	1.27
53032844--53032900	29	1.9	31	89	7	91	59	1	3	35	1.25
53032903--53032959	23	2.5	22	80	8	53	52	0	10	36	1.36
53032832--53033021	10	19.1	10	66	20	55	55	2	4	37	1.33
53033004--53033070	31	2.2	30	84	7	82	58	1	5	34	1.32
53033522--53033554	16	2.1	16	94	0	57	39	6	30	24	1.79
53033886--53033932	12	3.8	12	78	10	58	57	0	0	42	0.98
53033872--53033943	26	2.7	26	81	14	92	56	1	0	41	1.07
53036572--53036675	49	2.1	49	94	0	181	50	10	7	31	1.65
53039381--53039438	2	29.5	2	89	3	91	51	1	0	46	1.11
53040183--53040240	22	2.7	21	76	10	53	41	17	3	37	1.66
53040806--53040868	30	2.1	29	82	8	74	44	3	6	46	1.45
53040998--53041031	16	2.1	16	100	0	68	76	0	0	23	0.79
53042568--53042611	20	2.2	20	100	0	88	59	9	27	4	1.48
53042686--53042715	12	2.5	12	94	0	51	43	20	3	33	1.68
53044462--53044496	13	2.7	13	95	0	61	42	11	8	37	1.72
53045160--53045229	30	2.4	29	74	11	72	35	12	18	32	1.89
53045566--53045862	50	5.8	50	82	5	276	27	21	28	21	1.99
53053430--53053494	21	3.2	19	75	14	58	41	4	6	47	1.49
53054337--53054384	18	2.6	17	83	9	60	43	8	2	45	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53055611--53055663	2	26.0	2	96	3	97	49	1	0	49	1.12
53061962--53062029	35	1.9	35	85	5	93	61	2	0	35	1.11
53063174--53063216	17	2.5	17	81	11	52	41	4	0	53	1.21
53069339--53069378	20	2.0	21	85	5	55	20	7	10	62	1.50
53072632--53072678	25	2.0	24	84	12	62	4	38	6	51	1.47
53079319--53079344	9	2.9	9	100	0	52	34	0	23	42	1.54
53079359--53079402	6	6.8	6	80	14	52	0	18	0	81	0.68
53079358--53079404	19	2.3	21	92	7	80	0	19	0	80	0.70
53079365--53079402	14	2.8	14	88	4	51	0	18	0	81	0.69
53095757--53095791	17	2.0	18	88	5	54	60	0	5	34	1.21
53097657--53097743	21	4.0	21	80	8	86	33	8	3	55	1.46
53111262--53111469	89	2.4	87	80	9	201	31	20	20	26	1.98
53111177--53111629	217	2.1	217	94	0	789	29	21	21	27	1.99
53111262--53111834	305	1.9	306	90	2	920	29	20	22	27	1.99
53111176--53111814	44	14.8	44	72	10	417	29	21	22	27	1.99
53111957--53112085	45	2.9	45	75	16	124	31	16	26	26	1.96
53114664--53114721	31	1.9	30	82	6	73	27	10	0	62	1.28
53116707--53116758	25	2.0	26	85	3	70	26	19	34	19	1.95
53117016--53117049	17	2.0	17	94	0	59	11	38	35	14	1.83
53118034--53118062	2	15.0	2	92	7	51	51	0	0	48	1.00
53118097--53118133	18	1.9	18	89	10	56	67	0	8	24	1.17
53126025--53126057	15	2.1	16	88	5	50	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53128252--53128289	19	2.0	19	94	0	67	34	15	13	36	1.87
53132368--53132401	18	1.9	18	94	5	61	29	2	0	67	1.05
53133031--53133063	5	6.6	5	100	0	66	57	21	0	21	1.41
53137923--53137962	17	2.4	17	95	0	71	35	10	15	40	1.80
53142026--53142055	15	1.9	16	93	6	53	36	0	20	43	1.52
53142371--53142453	25	3.3	24	83	3	94	19	26	22	31	1.98
53142897--53142938	20	2.1	20	100	0	84	40	4	19	35	1.72
53145006--53145049	20	2.2	20	83	0	52	65	2	0	31	1.05
53147834--53147899	24	2.7	26	76	21	72	30	4	4	60	1.37
53148107--53148143	18	2.0	19	85	15	51	59	5	2	32	1.34
53152269--53152319	13	3.9	13	77	10	59	37	0	1	60	1.08
53152965--53153007	17	2.6	17	92	7	72	37	0	25	37	1.56
53155681--53155841	85	1.9	86	89	3	254	32	22	18	26	1.97
53157748--53157819	29	2.4	30	88	6	103	30	15	16	37	1.90
53164686--53164734	20	2.5	20	83	3	55	34	4	0	61	1.15
53167102--53167143	20	2.1	20	86	8	59	21	19	14	45	1.85
53167130--53167236	42	2.5	42	85	7	146	18	20	16	43	1.88
53171703--53171981	101	2.8	101	94	1	479	24	17	27	30	1.97
53171749--53171981	51	4.6	50	80	5	272	23	18	27	30	1.97
53171903--53171983	26	3.2	26	66	22	71	22	16	28	33	1.95
53171994--53172202	43	4.9	43	78	9	241	22	19	24	33	1.97
53171989--53172202	85	2.5	84	93	2	356	22	19	24	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53175170--53175202	15	2.1	16	88	5	50	36	3	3	57	1.29
53175210--53175250	21	2.0	20	85	4	55	48	7	0	43	1.30
53175435--53175485	26	2.0	26	81	14	61	35	15	9	39	1.81
53177646--53177695	25	2.0	25	100	0	100	60	8	20	12	1.57
53178065--53178107	20	2.2	20	83	8	52	62	9	0	27	1.25
53183963--53184207	90	2.7	89	85	4	348	26	22	12	39	1.89
53183963--53184207	45	5.5	45	89	2	316	26	22	12	39	1.89
53187697--53187824	67	1.9	67	93	0	220	27	10	11	50	1.71
53190439--53190482	12	3.8	12	82	11	56	70	6	0	22	1.11
53190519--53190576	14	4.1	14	95	0	107	65	0	12	22	1.25
53201105--53201142	16	2.5	16	87	8	53	50	0	0	50	1.00
53201973--53202004	7	4.6	7	96	0	55	21	0	46	31	1.52
53203911--53203940	3	10.0	3	100	0	60	33	0	33	33	1.58
53208448--53208603	77	2.0	77	88	2	233	23	18	19	38	1.93
53223335--53223390	28	2.0	28	100	0	112	21	32	7	39	1.80
53223466--53223515	26	2.0	25	84	11	66	32	10	28	30	1.89
53230417--53230456	6	6.7	6	88	0	53	42	0	40	17	1.49
53234222--53234259	2	19.0	2	94	0	67	47	0	2	50	1.15
53241790--53241860	28	2.5	28	86	0	88	30	12	29	26	1.93
53242933--53243248	22	13.4	23	70	19	185	24	12	18	44	1.85
53242933--53243227	47	6.3	47	92	1	351	24	12	18	44	1.84
53242933--53243227	94	3.1	94	88	1	405	24	12	18	44	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53242933--53243268	94	3.6	93	83	7	326	24	12	19	43	1.85
53242933--53243268	141	2.4	141	80	4	338	24	12	19	43	1.85
53243304--53243359	27	2.1	27	100	0	112	48	3	7	41	1.48
53249706--53249776	28	2.5	28	86	0	88	30	12	29	26	1.93
53250763--53251078	22	13.4	23	70	18	183	24	12	18	44	1.84
53250763--53251057	47	6.3	47	92	0	349	24	11	19	44	1.84
53250763--53251057	94	3.1	94	88	0	403	24	11	19	44	1.84
53250763--53251098	94	3.6	93	83	6	324	24	12	19	44	1.85
53250763--53251098	141	2.4	141	80	3	336	24	12	19	44	1.85
53252410--53252607	52	3.7	52	78	11	195	40	2	29	26	1.69

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