genome.fa.s4.2.7.7.80.10.50.1000.11.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  11  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)
3746966--3747071	43	2.5	41	86	9	142	48	4	2	44	1.38
3750928--3750969	15	2.7	16	82	14	52	45	0	2	52	1.13
3750919--3750960	15	2.9	15	82	10	52	47	0	0	52	1.00
3751099--3751199	45	2.4	42	81	14	111	31	28	4	34	1.79
3751117--3751206	45	2.0	44	89	6	137	34	27	5	32	1.80
3751185--3751238	16	3.4	16	89	0	81	25	35	3	35	1.74
3756221--3756306	25	3.0	29	86	11	117	44	6	23	25	1.78
3760764--3760842	25	2.9	27	87	12	117	44	6	24	25	1.77
3774717--3774770	26	2.1	26	100	0	108	22	9	18	50	1.75
3783629--3783770	9	16.6	9	68	27	62	40	2	0	57	1.14
3783595--3783767	33	4.9	34	87	10	210	38	3	0	57	1.16
3784312--3784341	14	2.1	15	93	6	53	40	6	0	53	1.27
3784328--3784423	28	3.2	28	73	18	95	36	4	0	59	1.17
3784324--3784422	29	3.2	32	83	14	134	35	4	0	60	1.16
3784461--3784511	26	2.0	26	100	0	102	11	23	27	37	1.90
3784463--3784522	26	2.3	26	91	2	95	11	26	30	31	1.92
3787015--3787064	25	2.0	25	100	0	100	36	12	8	44	1.71
3787824--3787865	2	21.5	2	95	4	77	50	0	0	50	1.00
3790171--3790206	2	18.0	2	100	0	72	50	0	0	50	1.00
3791775--3791803	5	6.0	5	92	8	51	82	17	0	0	0.66
3799722--3799761	2	20.0	2	84	0	53	47	5	2	45	1.38
3800713--3801011	126	2.4	126	91	0	481	33	20	21	25	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3804626--3804663	18	2.1	18	90	0	58	42	10	26	21	1.85
3806269--3806331	18	3.5	18	70	18	51	60	3	0	36	1.13
3806498--3806539	11	3.7	11	81	15	50	45	2	28	23	1.66
3806684--3806764	40	2.1	39	80	2	90	18	24	30	25	1.98
3812688--3812723	5	7.2	5	90	0	54	22	55	19	2	1.56
3813178--3813222	22	2.0	22	86	8	63	20	2	2	75	1.01
3813187--3813216	16	1.9	16	93	6	53	20	3	0	76	0.92
3813188--3813244	21	2.7	20	81	10	60	24	3	0	71	1.01
3814728--3814887	41	3.9	41	91	0	266	21	21	27	28	1.99
3814954--3814978	2	12.5	2	100	0	50	48	0	0	52	1.00
3816241--3816359	49	2.4	49	95	0	220	33	0	12	52	1.45
3816240--3816359	27	4.9	25	81	15	144	33	0	12	53	1.44
3816540--3816606	27	2.5	27	95	0	116	16	32	19	31	1.94
3816962--3817126	44	3.8	42	84	7	195	21	18	30	29	1.97
3816964--3817126	87	1.9	87	83	5	213	22	19	30	28	1.97
3818721--3818745	10	2.5	10	100	0	50	76	8	0	16	1.02
3819923--3819967	23	2.0	23	90	0	72	2	31	6	60	1.35
3819909--3820038	66	2.0	62	91	7	208	3	28	9	59	1.44
3819946--3820096	38	4.0	38	78	6	180	3	26	9	60	1.42
3819991--3820048	5	11.0	5	80	7	62	1	22	3	72	1.09
3819984--3820038	28	2.0	28	92	0	92	1	29	5	63	1.27
3819957--3820104	76	1.9	76	86	2	208	3	25	9	61	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3820643--3820669	14	1.9	14	100	0	54	0	7	29	62	1.22
3826344--3826381	11	3.4	11	96	3	67	39	2	0	57	1.12
3826224--3826400	57	3.1	57	74	15	177	36	2	0	61	1.11
3828601--3828642	15	2.7	16	82	14	52	45	0	2	52	1.13
3828592--3828633	15	2.9	15	82	10	52	47	0	0	52	1.00
3828787--3828877	45	2.0	44	85	2	119	35	27	5	31	1.80
3828856--3828909	16	3.4	16	89	0	81	29	33	1	35	1.69
3843367--3843436	28	2.3	31	77	18	85	28	4	0	67	1.10
3843462--3843506	17	2.7	17	83	12	58	24	2	6	66	1.27
3843905--3843939	15	2.3	15	95	0	61	31	0	5	62	1.18
3843913--3843946	15	2.3	15	89	0	50	29	2	5	61	1.34
3846998--3847028	15	2.1	14	94	5	53	51	25	0	22	1.48
3849109--3849136	2	14.0	2	100	0	56	50	0	50	0	1.00
3853272--3853306	17	2.1	17	89	5	54	65	5	0	28	1.15
3853551--3853589	19	2.1	19	85	9	53	53	0	2	43	1.14
3854281--3854311	15	2.1	15	93	0	53	29	0	9	61	1.28
3854338--3854370	2	17.0	2	93	6	59	48	0	0	51	1.00
3859025--3859051	2	13.5	2	100	0	54	51	0	0	48	1.00
3862891--3862993	51	2.0	51	96	0	188	34	28	8	28	1.87
3862896--3862977	27	3.1	27	63	16	64	34	29	8	28	1.87
3863824--3863859	11	3.2	11	88	4	54	16	33	0	50	1.46
3863823--3863870	22	2.1	23	81	11	55	20	31	0	47	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3863839--3863962	51	2.4	51	87	2	178	29	25	0	44	1.60
3864865--3864917	22	2.3	23	84	12	65	50	3	3	41	1.38
3864957--3865007	6	8.3	6	81	12	50	54	0	5	39	1.24
3866283--3866311	2	14.5	2	100	0	58	51	0	0	48	1.00
3867012--3867272	40	6.5	40	95	1	461	28	20	22	27	1.99
3869325--3869372	2	24.0	2	100	0	96	50	0	0	50	1.00
3870379--3870418	19	2.0	20	90	4	64	15	12	55	17	1.70
3870784--3870808	10	2.5	10	100	0	50	60	8	0	32	1.26
3870763--3870822	26	2.4	24	81	10	66	65	5	0	30	1.14
3872598--3872693	39	2.4	39	86	8	124	30	27	20	21	1.98
3873933--3874068	8	16.2	8	80	11	130	53	0	0	45	1.05
3873929--3874068	28	5.1	28	82	11	157	53	0	0	45	1.05
3873938--3874068	20	6.8	20	80	17	154	53	0	0	45	1.05
3873932--3874095	73	2.3	71	83	10	224	53	0	1	45	1.08
3874299--3874325	13	2.1	13	100	0	54	44	7	0	48	1.31
3878328--3878404	14	5.0	15	71	20	52	42	14	9	33	1.77
3878344--3878383	20	2.0	20	90	0	62	50	12	10	27	1.72
3878332--3878398	34	1.9	35	90	3	109	46	13	8	31	1.74
3881275--3881313	20	2.0	20	89	0	60	48	12	10	28	1.74
3881444--3881672	89	2.6	88	78	5	280	39	17	9	33	1.82
3881752--3881799	18	2.6	18	87	9	62	70	0	6	22	1.09
3881743--3881809	28	2.5	25	79	13	64	68	1	5	23	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3882008--3882101	30	3.2	28	72	13	82	35	3	3	58	1.30
3882009--3882104	29	3.3	28	70	23	81	36	3	3	57	1.30
3882076--3882124	19	2.6	19	90	6	73	44	0	0	55	0.99
3882160--3882319	86	1.9	85	86	1	230	31	9	21	37	1.85
3885381--3885409	14	2.1	14	100	0	58	37	0	6	55	1.27
3892604--3892633	12	2.5	12	94	0	51	53	0	0	46	1.00
3893354--3893401	18	2.6	17	79	20	53	25	4	2	68	1.18
3893353--3893409	27	2.1	27	81	12	64	28	3	1	66	1.18
3893416--3893451	19	1.9	19	88	5	56	36	0	8	55	1.30
3895109--3895195	29	2.9	30	77	13	90	63	5	5	25	1.39
3896925--3896965	2	20.5	2	94	0	73	51	2	0	46	1.14
3899284--3899368	42	2.0	42	100	0	170	41	21	16	21	1.90
3904176--3904217	19	2.2	19	83	8	50	30	16	4	47	1.67
3907126--3907170	18	2.6	18	96	3	83	35	0	20	44	1.51
3907289--3907317	8	3.6	8	100	0	58	24	13	27	34	1.93
3907404--3907501	23	4.3	23	86	2	135	21	18	25	34	1.96
3939523--3939579	23	2.5	23	72	16	55	29	0	7	63	1.21
3939684--3939743	31	2.0	31	83	3	77	35	8	11	45	1.71
3949576--3949612	15	2.3	17	86	9	51	40	24	0	35	1.55
3951812--3951890	40	2.0	40	87	0	113	40	24	16	18	1.91
3951979--3952367	41	9.5	41	92	0	544	19	20	31	29	1.97
3952779--3952808	15	2.1	15	93	6	53	30	0	36	33	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3953028--3953073	21	2.2	21	88	0	65	15	2	47	34	1.57
3953070--3953096	7	3.9	7	100	0	54	29	11	29	29	1.91
3953063--3953100	14	2.7	14	87	0	58	26	7	34	31	1.85
3955837--3955893	27	2.2	26	87	3	78	28	5	1	64	1.25
3955998--3956047	20	2.5	19	80	6	55	56	2	2	40	1.22
3960191--3961451	634	2.0	634	100	0	2522	35	18	17	29	1.94
3961502--3961534	11	3.1	11	91	4	50	54	0	3	42	1.15
3971449--3971741	41	7.2	40	87	3	338	22	18	29	29	1.98
3971449--3971767	123	2.6	123	84	5	389	22	18	28	29	1.97
3971449--3971807	41	8.8	41	83	5	329	22	18	27	31	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   188   189   190   191   192   
          193   194   195   196   197   198