genome.fa.s1.2.7.7.80.10.50.1000.68.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  68  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)
19918109--19918150	22	1.9	22	85	9	59	16	33	0	50	1.46
19920249--19920291	24	1.9	23	86	13	63	51	2	6	39	1.42
19929250--19929365	51	2.3	51	80	7	121	56	6	6	31	1.48
19929866--19929906	20	2.0	22	85	9	59	70	4	9	14	1.30
19931118--19931167	19	2.4	20	87	12	66	60	0	0	40	0.97
19931125--19931186	30	2.1	30	87	0	88	62	0	1	35	1.05
19932994--19933082	43	2.0	44	84	2	117	35	5	12	46	1.65
19933085--19933152	33	2.1	33	86	5	93	26	8	16	48	1.75
19937363--19937390	2	14.0	2	100	0	56	50	0	0	50	1.00
19938580--19938623	18	2.5	17	82	17	54	63	0	4	31	1.14
19942885--19942927	13	3.1	14	84	12	54	60	0	0	39	0.97
19943067--19943091	12	2.1	12	100	0	50	60	8	8	24	1.52
19945212--19945250	20	1.9	20	89	5	60	56	0	5	38	1.22
19945752--19945793	10	4.1	10	82	17	59	69	0	0	30	0.89
19945757--19945792	7	5.1	7	100	0	72	72	0	0	27	0.85
19947192--19947316	9	13.6	9	71	15	78	61	2	5	30	1.31
19947192--19947316	28	4.5	26	75	13	108	61	2	5	30	1.31
19947192--19947316	19	6.8	18	72	18	66	61	2	5	30	1.31
19947256--19947323	9	7.4	9	73	14	50	61	1	8	27	1.34
19948053--19948104	22	2.4	22	83	0	68	28	0	26	44	1.55
19948251--19948318	29	2.3	29	94	0	118	45	2	19	32	1.65
19950277--19950310	17	2.0	17	100	0	68	35	11	29	23	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
19950277--19950316	17	2.6	16	88	11	57	37	12	27	22	1.90
19951624--19951679	19	3.3	18	74	25	59	71	3	5	19	1.21
19951888--19951929	11	3.8	11	75	12	50	30	0	28	40	1.57
19951874--19951941	22	3.2	22	75	19	72	38	0	25	36	1.56
19952400--19952453	28	1.9	28	88	7	83	37	20	3	38	1.70
19953064--19953089	5	5.2	5	100	0	52	42	19	19	19	1.90
19953846--19953905	30	2.0	30	83	3	75	41	0	38	20	1.52
19954120--19954156	9	4.1	9	92	0	65	29	10	13	45	1.77
19958950--19958984	15	2.4	15	90	4	54	48	0	8	42	1.33
19975453--19975518	28	2.3	29	82	12	75	40	1	0	57	1.08
19980300--19980363	25	2.4	27	80	19	82	39	1	1	57	1.17
19980345--19980403	27	2.2	27	79	11	68	35	3	6	54	1.44
19992796--19993037	44	5.6	43	74	6	202	26	17	25	30	1.97
19992798--19993086	129	2.2	129	93	0	497	25	18	26	29	1.98
19996553--19996730	29	6.2	29	79	6	173	24	21	10	44	1.83
19996563--19996720	57	2.7	58	82	1	165	25	20	8	45	1.78
19996553--19996730	86	2.1	87	86	5	245	24	21	10	44	1.83
20000013--20000038	12	2.2	12	100	0	52	53	7	0	38	1.30
20000205--20000245	19	2.2	19	83	12	50	31	0	17	51	1.46
20000650--20000678	13	2.1	14	93	6	51	51	0	0	48	1.00
20003595--20003633	18	2.2	19	86	13	57	66	2	2	28	1.18
20003689--20003737	17	2.9	17	78	3	55	69	0	6	24	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20003833--20003898	23	2.9	22	82	10	71	62	3	1	33	1.20
20003833--20003878	24	2.0	23	87	12	67	58	4	2	34	1.30
20004143--20004184	21	2.0	21	95	0	75	52	9	11	26	1.68
20009464--20009518	27	2.1	26	86	6	76	41	21	12	23	1.88
20015158--20015194	17	2.2	17	90	9	58	67	2	0	29	1.04
20015157--20015195	16	2.4	16	84	16	53	64	2	0	33	1.08
20026832--20026877	22	2.1	22	83	0	56	32	10	34	21	1.88
20029160--20029221	31	2.0	31	90	0	97	37	27	6	29	1.82
20060380--20060423	22	2.0	21	83	12	54	40	0	0	59	0.98
20067441--20067482	20	2.0	21	86	4	59	40	7	0	52	1.29
20069602--20069635	18	1.9	17	94	5	59	32	29	8	29	1.87
20073869--20073903	17	2.1	17	94	0	61	34	2	28	34	1.72
20077097--20077126	5	5.8	5	96	4	51	83	0	0	16	0.65
20077090--20077151	11	5.6	10	73	19	52	79	3	3	14	0.99
20079774--20079863	44	2.0	44	86	0	126	52	3	10	34	1.51
20080056--20080146	44	2.0	45	87	6	132	52	2	6	38	1.40
20080113--20080147	18	2.0	18	88	5	54	60	2	2	34	1.26
20081061--20081152	20	4.6	21	68	14	59	33	2	4	59	1.29
20081288--20081328	18	2.3	18	86	0	55	29	2	14	53	1.54
20082782--20082820	17	2.3	17	86	8	53	43	0	0	56	0.99
20093580--20093638	25	2.2	27	82	8	68	71	8	3	16	1.25
20097203--20097232	16	1.9	15	93	6	51	46	16	10	26	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20112712--20112788	37	2.1	37	100	0	154	29	20	12	36	1.90
20112727--20112786	17	3.4	17	66	20	50	30	18	10	41	1.83
20125466--20125522	28	2.0	30	82	6	73	24	21	31	22	1.98
20132509--20132551	11	3.8	11	82	17	61	62	2	0	34	1.08
20136835--20136906	31	2.3	31	77	13	76	38	8	13	38	1.75
20145170--20145218	25	2.0	25	84	8	64	51	4	22	22	1.65
20146788--20146845	27	2.1	27	81	12	66	25	0	3	70	1.03
20148475--20148517	18	2.4	18	80	7	52	46	2	0	51	1.13
20167353--20167403	4	12.8	4	100	0	102	25	0	0	74	0.82
20169074--20169163	45	2.0	45	93	0	153	44	25	11	18	1.83
20175494--20175579	26	3.3	26	80	6	102	20	12	26	39	1.89
20180780--20180808	14	2.0	15	93	6	51	51	0	0	48	1.00
20186248--20186298	7	7.3	7	100	0	102	29	0	56	13	1.38
20187818--20187871	26	2.1	26	89	6	83	79	3	0	16	0.87
20188758--20188799	16	2.6	16	96	0	75	14	42	35	7	1.73
20189710--20189750	18	2.3	18	84	12	57	17	4	14	63	1.47
20201389--20201486	44	2.2	44	85	3	126	31	19	23	25	1.98
20201597--20201719	44	2.8	44	88	2	185	28	20	23	27	1.99
20201597--20201762	88	1.9	88	82	5	210	32	18	21	28	1.96
20201389--20202120	233	3.1	233	95	0	1293	33	18	20	27	1.96
20201830--20201952	44	2.8	43	76	7	122	30	17	21	30	1.96
20202524--20202569	23	2.0	24	87	12	69	78	4	0	17	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20202529--20202567	15	2.6	15	79	0	51	82	2	0	15	0.79
20202652--20202702	26	1.9	27	92	4	86	41	41	3	13	1.63
20203447--20203489	16	2.7	16	92	0	68	13	39	37	9	1.78
20204165--20204191	14	1.9	14	100	0	54	33	7	0	59	1.25
20208500--20208537	18	2.1	19	85	5	51	60	5	0	34	1.19
20214017--20214061	23	1.9	24	81	4	56	60	4	0	35	1.17
20224509--20224556	25	1.9	25	83	8	62	43	10	2	43	1.50
20232381--20232461	3	27.0	3	92	0	126	30	2	2	64	1.20
20241964--20242002	11	3.4	11	83	13	51	38	0	5	56	1.22
20243199--20243223	2	12.5	2	100	0	50	52	0	0	48	1.00
20245211--20245259	16	3.1	16	80	11	57	67	2	2	28	1.13
20245217--20245276	14	4.1	15	77	12	63	71	3	1	23	1.10
20247374--20247419	12	3.9	12	78	13	51	17	8	0	73	1.07
20255502--20255526	3	8.3	3	100	0	50	32	0	32	36	1.58
20258847--20258904	30	1.9	31	92	3	100	62	18	0	18	1.34
20260694--20260733	21	1.9	21	89	0	62	42	20	12	25	1.86
20261237--20261278	22	1.9	22	85	9	59	71	4	7	16	1.26
20261271--20261389	58	2.0	59	91	1	195	30	18	10	40	1.85
20268687--20268726	10	3.9	10	83	3	53	37	0	0	62	0.95
20268698--20268728	16	1.9	16	93	0	53	35	0	0	64	0.94
20268687--20268726	20	2.0	20	90	5	62	37	0	0	62	0.95
20270288--20270326	17	2.4	17	87	8	55	17	2	15	64	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20279287--20279330	4	11.0	4	85	0	52	22	6	2	68	1.25
20279389--20279432	12	3.7	12	81	0	61	6	2	27	63	1.31
20296741--20296779	19	1.9	19	85	10	51	71	17	0	10	1.12
20300637--20300690	4	13.5	4	88	0	72	24	5	1	68	1.21
20311613--20311644	2	16.0	2	100	0	64	50	0	0	50	1.00
20319008--20319056	24	2.0	26	84	8	66	30	2	2	65	1.15
20321481--20321509	12	2.3	13	94	5	51	68	6	10	13	1.37
20327246--20327312	33	2.0	33	100	0	134	35	26	5	31	1.81
20330741--20330805	33	2.0	30	83	16	78	63	0	1	35	1.04
20335720--20335744	12	2.1	12	100	0	50	8	40	20	32	1.81

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