genome.fa.s4.2.7.7.80.10.50.1000.179.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  179  of  198  ( 23681 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)
55967317--55967493	88	2.0	88	90	2	275	22	20	9	47	1.79
55984276--55984331	27	2.0	28	83	13	71	21	14	0	64	1.29
55988672--55988738	15	4.5	15	70	23	52	49	1	0	49	1.10
55989046--55989076	14	2.2	14	94	0	53	70	0	3	25	1.02
55994351--55994385	2	17.5	2	90	0	52	51	2	0	45	1.16
55998247--55998284	20	1.9	20	100	0	76	60	5	7	26	1.46
56000928--56000971	22	1.9	22	90	9	70	31	0	0	68	0.90
56000928--56000969	16	2.7	16	78	17	52	33	0	0	66	0.92
56003993--56004043	20	2.5	20	84	6	59	56	0	0	43	0.99
56005856--56005925	30	2.3	30	92	0	113	61	0	20	18	1.35
56007426--56007551	45	2.7	46	78	14	132	43	2	10	43	1.51
56007997--56008030	2	17.0	2	100	0	68	50	0	0	50	1.00
56015169--56015219	24	2.1	24	85	0	66	47	15	5	31	1.70
56021169--56021209	4	10.2	4	89	0	55	29	2	24	43	1.67
56037053--56037105	2	26.5	2	96	0	97	50	0	49	0	1.00
56049399--56049467	9	7.7	9	91	0	102	23	2	23	50	1.62
56049391--56049467	18	4.3	18	84	0	100	23	3	24	48	1.68
56049391--56049467	27	2.9	27	90	0	118	23	3	24	48	1.68
56049641--56049761	50	2.3	53	88	4	185	34	23	23	19	1.96
56049784--56049808	13	1.9	13	100	0	50	36	0	0	64	0.94
56058723--56059458	51	14.8	50	79	7	711	28	15	24	31	1.95
56058723--56059458	97	7.4	96	82	4	790	28	15	24	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56058723--56059443	148	4.9	148	80	7	750	28	15	24	31	1.95
56059414--56059899	143	3.4	143	86	1	677	29	19	22	28	1.98
56059762--56059967	44	4.8	44	73	8	181	27	21	25	25	1.99
56061398--56061442	23	2.0	23	86	8	65	6	4	20	68	1.29
56061545--56061591	3	16.0	3	86	4	69	31	2	2	63	1.18
56061553--56061604	9	6.0	8	86	4	50	26	3	1	67	1.18
56065253--56065294	21	2.0	22	86	9	61	54	9	14	21	1.68
56068662--56068725	24	2.8	22	80	4	74	48	1	1	48	1.20
56070714--56070739	12	2.2	12	100	0	52	30	30	0	38	1.58
56070712--56070833	51	2.4	51	90	4	183	27	30	0	41	1.56
56070834--56070898	30	2.2	31	94	5	116	36	0	0	63	0.95
56071977--56072001	7	3.6	7	100	0	50	28	0	12	60	1.32
56072653--56072687	18	1.9	18	88	0	52	25	34	8	31	1.86
56073089--56073273	71	2.6	71	94	0	325	37	2	14	45	1.58
56073279--56073434	29	5.3	29	96	2	285	45	26	0	28	1.54
56073431--56073552	55	2.2	55	97	0	226	36	11	5	45	1.64
56073536--56073560	10	2.5	10	100	0	50	44	8	0	48	1.32
56074164--56074188	13	1.9	13	100	0	50	8	0	24	68	1.16
56075280--56075312	12	2.8	12	90	4	50	36	3	9	51	1.49
56075168--56075377	112	1.9	112	93	0	366	40	4	14	40	1.66
56075718--56075867	41	3.7	41	90	0	237	28	18	28	24	1.98
56079151--56079358	43	4.9	43	79	9	257	33	25	18	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56079151--56079362	85	2.5	85	96	0	381	32	25	19	22	1.97
56079366--56079712	51	6.8	51	80	8	318	31	27	17	23	1.97
56079370--56079697	101	3.2	100	87	3	417	30	27	18	24	1.98
56079368--56079649	152	1.8	153	91	2	469	30	27	18	23	1.97
56079366--56079738	152	2.4	151	80	8	416	30	27	17	24	1.97
56082420--56082768	123	2.8	122	96	1	626	32	22	15	29	1.95
56082916--56082976	29	2.1	28	81	3	68	45	16	13	24	1.83
56086030--56086054	4	6.2	4	100	0	50	52	24	0	24	1.48
56087944--56087986	14	3.1	14	80	6	52	27	2	0	69	1.00
56088264--56088303	20	2.0	20	85	0	53	35	2	5	57	1.34
56090098--56090218	60	2.0	60	98	0	233	35	11	9	43	1.73
56093700--56093749	17	3.1	16	77	11	57	70	0	0	30	0.88
56093699--56093757	17	3.5	18	71	19	56	67	0	0	32	0.91
56106884--56106924	17	2.4	18	88	8	59	51	4	0	43	1.23
56108104--56108164	28	2.1	29	87	3	88	52	8	3	36	1.48
56108282--56108321	19	2.3	19	87	12	59	37	0	0	62	0.95
56112225--56112279	29	1.9	28	85	10	76	25	16	7	50	1.70
56114506--56114530	12	2.1	12	100	0	50	48	0	0	52	1.00
56115897--56115943	24	2.0	24	84	16	62	51	17	0	31	1.46
56116599--56116649	9	5.3	9	79	11	57	0	21	3	74	0.98
56116597--56116674	12	6.2	12	72	10	50	0	23	2	74	0.94
56116597--56116674	14	5.1	14	70	17	50	0	23	2	74	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56116599--56116679	5	15.6	5	72	18	51	1	23	2	72	1.03
56116611--56116673	25	2.6	23	80	11	81	0	25	3	71	1.01
56116687--56116781	36	2.7	35	80	9	111	45	6	0	48	1.28
56116683--56116772	44	2.0	43	83	8	110	45	4	0	50	1.22
56117197--56117233	18	2.0	19	89	5	58	45	0	0	54	1.00
56117199--56117241	19	2.3	19	84	8	52	46	0	0	53	1.00
56121520--56121559	14	2.8	14	80	3	53	65	2	0	32	1.06
56122602--56122663	29	2.1	30	85	8	83	43	11	4	40	1.62
56124193--56124258	24	2.8	24	79	4	71	36	18	28	16	1.93
56124250--56124317	28	2.4	28	87	0	91	45	17	14	22	1.85
56126611--56126643	2	16.5	2	93	0	57	54	45	0	0	0.99
56131576--56131658	29	2.7	31	71	14	82	21	8	13	56	1.63
56132609--56132655	22	2.1	23	88	4	69	63	4	0	31	1.13
56135154--56135406	84	3.0	84	85	0	335	37	16	20	25	1.93
56141387--56141464	39	2.0	39	100	0	156	20	10	15	53	1.70
56143650--56143732	38	2.4	32	78	21	112	34	18	13	33	1.89
56148407--56148490	38	2.2	38	91	0	141	34	21	10	33	1.88
56152117--56152210	31	3.0	31	95	3	170	44	13	9	31	1.76
56165219--56165286	36	1.9	35	85	8	93	48	5	1	44	1.36
56168687--56168731	20	2.2	20	80	11	56	66	6	22	4	1.33
56168688--56168731	19	2.4	19	85	11	56	65	6	22	4	1.35
56169052--56169086	15	2.4	15	90	4	54	48	0	8	42	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56188310--56188377	31	2.2	31	84	7	86	22	11	19	47	1.81
56188391--56188476	31	2.9	30	81	10	104	36	9	12	41	1.75
56188715--56188935	73	3.0	73	97	1	408	47	8	8	35	1.63
56189430--56189481	24	2.2	24	89	0	77	55	9	1	32	1.43
56194290--56194337	3	16.0	3	82	0	60	58	4	0	37	1.18
56194291--56194337	18	2.6	18	93	0	76	57	4	0	38	1.18
56194290--56194337	12	4.0	12	91	0	69	58	4	0	37	1.18
56196476--56196527	24	2.2	24	89	0	77	55	9	1	32	1.43
56197290--56197343	18	2.9	19	76	12	60	61	1	1	35	1.18
56212871--56212913	17	2.6	16	79	13	52	55	2	2	39	1.25
56212877--56212922	16	2.9	16	75	18	51	52	4	2	41	1.33
56218663--56218707	2	22.5	2	100	0	90	51	0	0	48	1.00
56219405--56219448	16	2.7	16	89	3	61	47	6	0	45	1.29
56219796--56219835	2	20.0	2	100	0	80	50	0	0	50	1.00
56222338--56222373	16	2.2	16	100	0	72	25	0	36	38	1.56
56222354--56222444	45	2.0	45	85	2	121	27	6	28	37	1.82
56222589--56222643	16	3.4	16	80	16	53	49	1	0	49	1.11
56222609--56222643	18	2.0	17	88	5	52	54	0	0	45	0.99
56222698--56222778	26	3.0	27	74	13	78	51	2	1	44	1.22
56225251--56225281	13	2.4	13	94	0	53	54	6	32	6	1.51
56232447--56232471	5	5.0	5	100	0	50	20	0	0	80	0.72
56235000--56235026	13	2.1	13	100	0	54	22	7	0	70	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56238336--56238435	8	12.1	8	67	21	55	66	6	1	27	1.22
56238329--56238382	16	3.3	16	78	2	54	66	5	0	27	1.13
56238337--56238409	16	4.5	16	75	16	62	68	6	1	23	1.21
56238359--56238438	26	3.0	26	82	14	76	62	6	1	30	1.27
56240538--56240710	73	2.4	73	81	9	226	26	24	23	24	2.00
56240636--56240954	113	2.8	114	80	4	385	27	22	24	26	2.00
56241470--56241537	14	4.6	14	75	10	55	27	1	30	39	1.66
56241693--56241865	83	2.1	82	92	1	283	31	1	24	43	1.62
56241618--56241946	179	1.8	181	84	6	450	31	1	24	42	1.64
56243991--56244177	50	3.6	51	86	5	214	21	28	24	26	1.99

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   188   189   190   191   192   
          193   194   195   196   197   198