genome.fa.s1.2.7.7.80.10.50.1000.180.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: 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  180  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)
54052589--54052657	31	2.2	32	82	10	81	36	14	8	40	1.77
54057269--54057851	194	3.0	192	87	4	825	29	10	12	47	1.74
54068097--54068167	24	3.4	20	84	13	74	54	0	0	45	0.99
54068127--54068170	6	7.3	6	100	0	88	50	0	0	50	1.00
54074328--54074388	14	4.5	14	75	19	58	68	4	0	26	1.09
54080709--54080753	20	2.2	20	85	14	58	28	4	13	53	1.59
54084442--54084497	27	2.1	27	83	12	71	71	0	17	10	1.14
54085367--54085415	24	2.0	24	96	0	89	24	16	18	40	1.90
54098759--54099387	312	2.0	312	89	0	954	18	25	15	40	1.90
54109867--54109911	6	7.5	6	89	0	63	22	33	15	28	1.95
54109868--54109911	12	3.7	12	90	0	70	22	34	15	27	1.95
54109867--54109911	18	2.5	18	92	0	81	22	33	15	28	1.95
54125054--54125095	17	2.4	17	80	11	50	28	0	2	69	1.01
54129722--54129758	2	18.5	2	100	0	74	51	0	48	0	1.00
54134148--54134178	15	2.1	15	100	0	62	29	12	25	32	1.93
54134942--54134991	26	1.9	26	84	8	66	32	6	4	58	1.41
54135172--54135296	62	2.0	62	100	0	250	39	14	6	40	1.71
54139198--54139445	41	6.2	40	63	26	96	40	1	2	55	1.22
54139252--54139501	18	13.8	17	70	22	129	40	2	2	55	1.26
54139177--54139524	100	3.5	100	97	0	642	40	1	3	54	1.26
54139743--54139796	16	3.4	16	81	0	63	29	27	1	40	1.67
54140193--54140225	17	1.9	17	100	0	66	42	9	0	48	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54141480--54141525	23	2.0	23	87	12	67	47	6	0	45	1.28
54141667--54141706	21	1.9	21	89	0	62	60	2	0	37	1.11
54142508--54142685	92	1.9	91	87	3	259	28	8	10	52	1.65
54142508--54142726	91	2.4	89	83	9	234	31	7	8	53	1.58
54142997--54143044	21	2.2	23	77	11	55	52	0	2	45	1.12
54143094--54143143	25	2.0	25	81	14	59	66	6	0	28	1.15
54145936--54145994	31	1.9	31	82	6	75	49	5	13	32	1.64
54151597--54151674	39	2.0	39	100	0	156	38	20	7	33	1.81
54156994--54157039	19	2.4	19	88	0	65	26	21	8	43	1.81
54159206--54159273	26	2.6	26	73	0	73	32	22	5	39	1.78
54159394--54159424	9	3.4	9	90	0	53	25	12	22	38	1.90
54159478--54159514	9	4.1	9	92	0	65	45	13	10	29	1.77
54164516--54164567	27	1.9	27	84	0	68	26	32	32	7	1.85
54164649--54164675	3	9.0	3	100	0	54	66	0	33	0	0.92
54165995--54166063	3	23.0	3	100	0	138	66	0	0	33	0.92
54166244--54166287	23	2.0	22	90	4	70	54	2	9	34	1.44
54166780--54166820	20	2.2	19	86	8	57	63	17	14	4	1.47
54166969--54167026	22	2.7	21	76	10	53	41	17	3	37	1.66
54167211--54167656	149	2.9	155	84	10	587	53	7	10	28	1.63
54169942--54169984	8	5.4	8	97	0	77	51	23	0	25	1.49
54169941--54169992	24	2.2	23	86	3	77	53	23	0	23	1.46
54172881--54172932	3	17.3	3	100	0	104	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54172992--54173038	23	2.0	23	84	8	60	59	14	2	23	1.46
54172940--54173086	76	1.9	77	87	4	217	52	12	4	30	1.59
54173116--54173220	42	2.3	43	76	18	108	58	11	0	29	1.40
54173108--54173198	17	5.2	19	69	27	60	54	13	2	29	1.50
54173151--54173215	22	3.0	22	72	21	66	58	10	1	29	1.41
54173181--54173366	57	3.2	59	75	16	194	53	10	3	33	1.51
54173292--54173331	19	2.2	18	86	4	53	62	12	0	25	1.30
54173205--54173420	113	1.9	113	83	7	280	56	11	2	29	1.48
54173527--54173588	3	20.7	3	93	0	106	1	35	0	62	1.05
54176798--54176883	30	2.8	31	77	11	106	33	13	18	33	1.91
54182736--54182768	17	1.9	17	93	0	57	27	3	21	48	1.64
54187481--54187560	40	2.0	40	100	0	160	35	10	27	27	1.89
54191311--54191353	11	3.8	11	80	17	52	30	2	2	65	1.18
54191314--54191357	23	1.9	23	90	0	70	31	2	4	61	1.28
54192151--54192202	20	2.6	21	78	6	63	48	21	21	9	1.78
54197495--54197627	56	2.4	56	89	0	203	30	22	9	37	1.86
54200839--54201078	50	4.7	50	86	3	284	27	24	28	20	1.99
54200839--54201086	100	2.4	103	87	4	358	26	23	28	20	1.99
54207222--54207270	20	2.4	21	76	10	57	65	0	24	10	1.23
54207630--54207796	11	16.9	11	71	22	99	59	0	2	38	1.11
54207630--54207803	40	4.5	39	88	10	259	59	0	2	37	1.10
54217500--54217537	18	2.0	20	90	10	62	28	0	13	57	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54219042--54219100	21	2.8	21	97	0	109	11	27	28	32	1.92
54219289--54219318	6	5.0	6	95	0	51	53	0	16	30	1.44
54220466--54220517	23	2.3	23	93	0	86	42	11	5	40	1.65
54223432--54223456	13	1.9	13	100	0	50	60	0	0	40	0.97
54225457--54225613	43	3.7	42	84	3	199	27	28	18	26	1.98
54225457--54225634	43	4.2	42	80	8	146	28	28	17	25	1.98
54229161--54229191	7	4.4	7	95	0	53	32	48	0	19	1.49
54229230--54229270	7	6.0	7	78	16	50	39	46	0	14	1.45
54229233--54229270	13	2.8	13	81	18	51	39	47	0	13	1.42
54229179--54229322	74	1.9	76	85	2	202	43	26	1	28	1.63
54229366--54229391	7	3.7	7	100	0	52	30	53	0	15	1.42
54229862--54230006	41	3.6	39	80	8	164	31	24	18	25	1.98
54231059--54231258	107	1.9	107	92	0	337	32	15	25	26	1.95
54232079--54232129	19	2.9	18	82	8	52	41	3	15	39	1.66
54232079--54232127	18	2.8	17	82	11	55	40	4	16	38	1.67
54250064--54250120	25	2.3	25	79	8	64	15	24	22	36	1.94
54255544--54255952	44	9.1	44	72	13	207	28	21	16	33	1.95
54255669--54255932	139	1.9	139	82	3	334	27	23	17	32	1.96
54256280--54256322	3	14.3	3	100	0	86	0	32	0	67	0.91
54263758--54264237	239	2.0	239	92	1	793	25	23	19	31	1.98
54266284--54266317	13	2.5	14	95	4	61	67	0	0	32	0.91
54269674--54269720	23	2.0	23	87	0	67	34	2	0	63	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54272059--54272105	18	2.6	18	93	0	76	40	38	2	19	1.63
54272205--54272271	9	7.4	9	89	0	107	23	11	23	40	1.88
54274388--54274414	13	2.1	13	100	0	54	29	0	22	48	1.51
54275502--54275660	42	3.7	44	75	16	154	25	18	25	31	1.97
54275502--54275660	43	3.7	42	76	10	153	25	18	25	31	1.97
54280167--54280198	12	2.6	13	85	14	50	37	0	6	56	1.25
54287639--54287844	107	1.9	107	89	0	322	31	20	18	28	1.97
54288510--54288544	15	2.4	15	90	4	54	57	0	8	34	1.29
54293024--54293082	24	2.4	25	77	5	75	59	0	1	38	1.08
54307990--54308063	34	2.2	34	100	0	148	35	12	22	29	1.91
54308769--54308807	9	4.3	9	86	0	60	30	7	12	48	1.69
54321493--54322210	192	3.8	185	90	5	987	27	14	21	37	1.92
54325197--54325400	100	2.0	100	100	0	408	20	17	21	40	1.92
54333025--54333054	2	15.0	2	100	0	60	50	0	50	0	1.00
54337679--54337707	14	2.1	14	100	0	58	31	41	6	20	1.79
54338699--54338784	2	43.0	2	100	0	172	50	50	0	0	1.00
54339491--54339533	19	2.2	20	84	12	54	0	23	2	74	0.93
54353700--54353748	21	2.3	21	75	0	53	36	20	30	12	1.89
54353700--54353803	42	2.5	42	80	0	118	37	16	27	18	1.92
54353701--54353826	42	3.0	42	79	3	112	37	16	25	20	1.93
54358840--54358889	20	2.5	19	77	6	55	40	22	6	32	1.78
54359060--54359177	23	5.2	21	77	13	101	37	20	22	20	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54359090--54359178	24	3.8	24	82	8	78	39	21	20	19	1.93
54359380--54359475	49	2.0	49	91	2	158	39	20	3	36	1.69
54359423--54359719	67	4.4	67	92	0	504	41	16	3	38	1.64
54360823--54360852	5	6.0	5	100	0	60	0	80	0	20	0.72
54360825--54360858	15	2.3	15	89	0	50	5	79	0	14	0.91
54360914--54360959	24	1.9	24	86	8	67	39	34	0	26	1.57
54366786--54366819	4	8.5	4	86	0	50	26	5	0	67	1.13
54371600--54371673	21	3.5	21	73	0	76	16	21	18	43	1.88
54371607--54371730	42	3.0	42	84	2	151	16	23	16	42	1.88
54375639--54375922	85	3.4	85	86	2	394	33	22	21	22	1.97

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