genome.fa.s1.2.7.7.80.10.50.1000.163.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  163  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)
48024919--48024980	13	4.5	13	82	13	72	6	1	4	87	0.74
48024918--48024971	1	54.0	1	77	0	54	5	1	3	88	0.67
48024938--48025012	23	3.2	22	75	19	55	12	4	8	76	1.15
48029673--48029752	22	3.7	22	74	17	60	55	3	5	36	1.40
48029705--48029756	20	2.8	18	76	23	54	53	1	5	38	1.36
48032059--48032117	24	2.6	23	86	7	77	55	1	6	35	1.36
48036174--48036212	10	3.9	10	86	0	51	25	5	0	69	1.09
48036255--48036288	16	2.1	16	88	0	50	29	0	0	70	0.87
48036269--48036326	19	3.0	20	70	7	57	32	3	0	63	1.11
48036883--48036948	21	3.4	19	71	21	64	31	3	0	65	1.08
48036884--48036998	40	2.9	39	86	9	162	35	2	0	61	1.10
48036934--48037036	11	9.9	11	71	19	69	40	1	0	57	1.10
48036894--48037011	51	2.3	49	79	13	123	37	3	0	59	1.14
48036933--48037036	51	2.0	52	90	5	167	41	1	0	56	1.10
48040581--48040626	23	2.0	22	83	4	56	17	8	10	63	1.51
48044528--48044562	15	2.3	15	90	9	54	5	2	11	80	1.00
48048805--48048896	45	2.0	45	100	0	184	23	18	28	29	1.98
48051776--48051848	32	2.3	32	92	2	121	34	15	28	21	1.94
48052334--48052500	45	3.7	45	96	0	307	15	35	10	38	1.81
48052752--48052863	54	2.1	54	88	3	163	21	29	27	21	1.98
48054004--48054058	23	2.7	19	76	15	56	47	10	1	40	1.49
48056092--48056121	16	1.9	16	93	6	53	6	10	20	63	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48058642--48058746	30	3.5	30	68	17	90	40	10	23	25	1.87
48058613--48058746	61	2.2	61	91	0	223	41	10	23	24	1.85
48070692--48070718	13	2.1	13	100	0	54	55	0	7	37	1.28
48077024--48077063	11	3.5	11	89	3	62	25	25	0	50	1.50
48077026--48077073	21	2.2	22	82	10	55	27	27	2	43	1.66
48079983--48080066	33	2.6	32	78	3	87	23	11	41	22	1.87
48089521--48089566	16	2.9	16	80	0	56	47	4	19	28	1.68
48089555--48089645	46	2.0	44	83	8	112	30	3	24	41	1.71
48096069--48096098	10	2.8	11	90	10	53	83	0	16	0	0.65
48113771--48113809	20	1.9	21	85	15	55	46	0	10	43	1.37
48116308--48116366	26	2.3	26	84	0	82	38	11	16	32	1.86
48121038--48121086	25	2.0	24	84	11	64	51	8	4	36	1.51
48122633--48122669	9	4.1	9	89	0	56	45	10	10	32	1.74
48123059--48123096	16	2.4	16	90	0	58	31	0	34	34	1.58
48123075--48123184	45	2.6	43	80	9	129	33	5	29	31	1.80
48123330--48123364	18	2.0	17	88	5	52	54	0	0	45	0.99
48123217--48123532	157	2.0	156	95	0	569	44	2	5	47	1.39
48123467--48123533	16	4.2	16	75	19	61	55	0	0	44	0.99
48123486--48123533	18	2.8	18	74	22	50	56	0	0	43	0.99
48123470--48123516	15	3.3	15	82	11	55	55	0	0	44	0.99
48123283--48123516	75	3.0	74	62	18	170	47	2	3	46	1.34
48123289--48123534	78	3.1	78	64	15	200	47	2	3	46	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48123501--48123688	61	3.1	61	69	19	194	50	5	2	42	1.37
48123269--48123587	156	2.0	154	82	7	365	47	3	3	44	1.38
48123465--48123761	120	2.5	120	92	2	490	50	3	3	42	1.35
48123585--48123630	15	3.0	16	78	9	60	58	0	0	41	0.98
48123702--48123863	54	3.1	51	69	16	120	50	1	3	44	1.28
48123777--48123984	91	2.3	91	86	5	269	46	3	4	45	1.39
48125497--48125530	15	2.3	15	90	5	52	67	23	5	2	1.26
48126426--48126454	9	3.2	9	100	0	58	31	0	0	68	0.89
48126821--48126846	5	5.2	5	100	0	52	23	19	19	38	1.93
48126936--48126966	5	6.2	5	100	0	62	19	19	19	41	1.90
48128926--48128961	14	2.6	14	86	13	56	22	0	0	77	0.76
48129960--48130131	88	1.9	89	85	5	240	36	16	11	36	1.85
48130234--48130384	9	16.4	9	69	15	78	62	2	1	33	1.20
48130234--48130384	19	8.2	18	70	14	78	62	2	1	33	1.20
48130276--48130315	20	2.0	20	85	0	53	52	0	0	47	1.00
48130319--48130375	8	6.6	8	80	13	60	68	5	0	26	1.11
48130296--48130394	46	2.2	46	84	14	125	63	4	2	30	1.24
48130332--48130385	27	1.9	29	92	7	94	64	3	0	31	1.11
48130319--48130394	19	4.2	19	81	6	79	67	5	1	26	1.20
48130592--48130669	20	3.9	21	68	21	58	30	6	0	62	1.20
48135232--48135281	26	1.9	25	84	8	64	26	12	2	60	1.43
48135356--48135399	11	3.9	11	84	3	61	45	2	31	20	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48137601--48137625	3	8.3	3	100	0	50	68	0	0	32	0.90
48142473--48142522	2	25.0	2	100	0	100	50	0	0	50	1.00
48143469--48143520	20	2.5	20	79	14	61	28	0	7	63	1.22
48143467--48143521	22	2.5	22	85	2	67	30	0	7	61	1.23
48143468--48143521	21	2.6	21	82	8	67	29	0	7	62	1.22
48143558--48143591	10	3.6	10	84	15	54	35	0	0	64	0.94
48143560--48143593	9	3.8	9	92	0	59	38	0	0	61	0.96
48144690--48144716	5	5.4	5	100	0	54	40	40	0	18	1.51
48149481--48149539	19	3.1	18	75	20	50	40	1	3	54	1.27
48153175--48153200	3	8.7	3	100	0	52	65	0	34	0	0.93
48158273--48158301	5	6.0	5	92	8	51	79	0	0	20	0.74
48164495--48164521	2	13.5	2	100	0	54	51	0	0	48	1.00
48182646--48182722	39	2.0	39	100	0	154	24	7	23	44	1.80
48188635--48188704	25	2.8	25	91	0	104	67	7	11	14	1.42
48195553--48195598	17	2.7	17	82	0	56	39	0	0	60	0.97
48195582--48195623	11	3.9	11	76	17	52	42	2	0	54	1.13
48195591--48195630	21	1.9	21	89	0	62	40	2	0	57	1.12
48195589--48195648	22	2.8	22	80	7	61	43	1	3	51	1.28
48213520--48213628	37	3.0	35	75	15	89	39	2	5	52	1.39
48213566--48213621	25	2.2	27	78	12	64	39	1	5	53	1.34
48218563--48218611	13	3.6	13	78	10	53	24	28	26	20	1.99
48218644--48218701	25	2.3	25	90	0	89	22	31	32	13	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48224517--48224556	17	2.4	17	83	4	55	27	2	2	67	1.16
48226107--48226229	49	2.5	49	82	5	151	31	29	14	24	1.95
48229028--48229274	50	4.8	50	80	4	219	28	19	27	23	1.98
48231719--48231763	19	2.4	18	81	3	54	17	8	2	71	1.23
48232545--48232597	17	3.1	18	83	5	65	50	0	0	49	1.00
48232530--48232597	23	2.8	24	82	8	84	50	4	0	45	1.22
48232548--48232606	23	2.6	22	86	7	66	52	1	0	45	1.10
48232568--48232719	62	2.5	62	95	0	268	51	5	2	40	1.38
48232698--48232746	20	2.7	18	77	22	57	51	4	2	42	1.32
48233121--48233157	19	1.9	20	88	5	58	24	32	16	27	1.96
48233219--48233258	9	4.3	9	90	3	62	40	0	2	57	1.12
48239754--48239814	32	1.9	32	83	12	81	47	1	3	47	1.28
48243631--48243661	8	3.9	8	95	0	53	16	0	0	83	0.64
48244549--48244573	2	12.5	2	100	0	50	48	0	0	52	1.00
48257506--48257613	48	2.2	48	95	0	189	41	6	0	50	1.34
48262647--48262736	4	22.5	4	100	0	180	50	24	0	25	1.50
48265112--48265359	4	62.0	4	93	0	397	24	3	25	47	1.67
48270336--48270398	10	6.4	10	73	21	53	26	1	0	71	0.95
48270305--48270430	40	3.2	39	82	7	155	34	3	0	62	1.11
48270334--48270389	30	1.9	28	89	7	85	28	1	0	69	0.98
48270386--48270448	33	2.0	32	84	6	83	36	1	0	61	1.05
48274153--48274192	14	2.9	14	84	0	53	32	7	17	42	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48274176--48274216	20	2.0	20	90	0	64	26	9	12	51	1.70
48274161--48274227	34	1.9	35	87	3	100	31	8	11	47	1.71
48277742--48277799	2	29.0	2	82	0	53	0	62	0	37	0.96
48277743--48277799	18	3.3	18	85	7	73	0	63	0	36	0.95
48280757--48280855	50	2.0	50	97	0	189	34	7	13	45	1.70
48285608--48285642	2	17.5	2	100	0	70	48	0	0	51	1.00
48285889--48285936	20	2.5	19	79	3	51	29	22	6	41	1.78
48285828--48285983	78	2.0	78	89	0	240	31	26	8	33	1.86
48297109--48297155	25	1.9	24	82	4	58	40	8	2	48	1.45
48299651--48299813	44	3.6	44	85	11	229	30	14	24	30	1.95

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