genome.fa.s5.2.7.7.80.10.50.1000.12.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   199   200   201   202   203   204   205   206   207   208   

This is table  12  of  208  ( 24913 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)
3653415--3653561	17	8.3	18	70	11	81	44	9	12	34	1.74
3653415--3653622	36	6.1	34	65	17	103	46	9	12	32	1.73
3653501--3653558	20	3.0	20	87	5	75	41	8	10	39	1.70
3653557--3653622	17	3.8	17	71	15	62	53	9	12	25	1.67
3653566--3653622	18	3.2	18	73	14	55	52	8	10	28	1.65
3653574--3653665	44	2.1	43	82	8	105	54	10	13	21	1.69
3653524--3653671	62	2.4	61	81	10	158	49	10	11	29	1.71
3653649--3653691	21	2.0	22	86	4	61	41	6	9	41	1.64
3653671--3653723	16	3.2	17	81	7	74	49	11	9	30	1.70
3653709--3653749	20	2.0	21	86	13	59	41	9	4	43	1.59
3653867--3653904	20	1.9	20	88	0	58	42	7	13	36	1.73
3654126--3654168	19	2.2	19	83	4	50	72	2	4	20	1.14
3654350--3654390	14	2.9	14	85	0	55	0	31	0	68	0.90
3654981--3655106	30	4.2	29	75	15	107	36	2	26	34	1.70
3655448--3655638	57	3.6	56	70	20	165	29	14	18	37	1.91
3655448--3655569	55	2.2	55	82	5	138	30	13	17	38	1.89
3655417--3655569	57	2.7	54	76	9	146	31	12	15	40	1.85
3655524--3655612	45	2.0	45	82	10	112	25	15	13	44	1.83
3655885--3655979	49	1.9	49	86	2	136	43	9	8	38	1.68
3662259--3662388	66	2.0	66	93	3	226	19	30	13	36	1.90
3666822--3666869	19	2.6	19	93	3	80	14	8	12	64	1.49
3673342--3673522	91	2.0	91	86	4	258	42	18	13	24	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3676074--3676100	2	13.5	2	100	0	54	51	0	0	48	1.00
3678548--3678589	2	21.0	2	100	0	84	50	0	0	50	1.00
3678751--3678776	2	13.0	2	100	0	52	50	0	0	50	1.00
3679605--3679677	38	1.9	37	86	8	103	31	21	1	45	1.61
3679665--3679708	23	1.9	22	82	17	54	38	22	0	38	1.55
3679796--3679917	23	5.3	23	91	0	208	31	25	21	22	1.98
3695515--3695552	20	1.9	20	94	0	67	55	31	0	13	1.38
3708742--3708810	31	2.2	31	89	5	113	28	10	14	46	1.77
3714731--3714790	19	3.2	19	79	11	61	53	6	1	38	1.37
3718588--3718632	22	2.0	23	83	12	58	17	4	6	71	1.25
3724651--3725125	131	3.7	128	75	10	400	38	11	12	38	1.78
3730734--3730794	30	2.0	30	84	6	79	16	3	52	27	1.59
3730766--3730861	42	2.3	42	94	0	165	14	8	54	22	1.67
3730825--3730900	33	2.3	33	88	0	107	13	10	56	19	1.65
3730858--3731022	66	2.5	67	83	5	176	12	10	52	24	1.71
3730893--3731023	66	2.0	66	95	0	235	12	9	51	25	1.70
3735041--3735333	50	5.8	50	93	0	487	20	31	22	25	1.98
3750136--3750160	7	3.6	7	100	0	50	76	0	0	24	0.80
3755095--3755142	4	12.0	4	81	0	51	20	4	4	70	1.21
3755372--3755441	26	2.8	26	82	4	90	42	7	1	48	1.39
3756919--3756945	11	2.5	11	100	0	54	59	0	0	40	0.98
3760351--3760432	3	27.3	3	100	0	164	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)
3761553--3761649	51	1.9	51	84	0	131	38	3	16	42	1.64
3767107--3767144	3	12.7	3	100	0	76	31	0	0	68	0.90
3772783--3772822	20	2.0	20	90	0	62	27	10	12	50	1.72
3772768--3772834	34	1.9	35	90	3	109	31	8	13	46	1.74
3784279--3784316	18	2.1	19	90	5	60	21	21	5	52	1.66
3788873--3788912	18	2.2	19	86	4	55	37	0	0	62	0.95
3789796--3789843	21	2.3	21	85	7	62	29	4	0	66	1.10
3792289--3792390	51	2.0	51	84	0	132	38	0	16	44	1.55
3798725--3798769	18	2.5	19	82	10	58	40	0	0	60	0.97
3798721--3798812	29	3.2	28	76	11	89	34	0	2	63	1.07
3798724--3798778	10	5.7	10	75	14	53	38	0	0	61	0.96
3799291--3799320	15	1.9	15	93	6	51	23	6	0	70	1.11
3799901--3801022	560	2.0	560	99	0	2235	32	16	14	36	1.89
3801726--3801788	21	3.0	21	83	4	81	33	1	0	65	1.03
3805970--3806032	10	6.6	10	75	8	60	60	0	6	33	1.22
3805971--3806044	38	2.0	37	89	7	114	63	0	6	29	1.20
3812985--3813341	179	2.0	179	94	0	624	41	17	14	26	1.87
3814407--3814451	18	2.5	18	85	7	56	35	13	22	28	1.92
3814427--3814456	15	2.0	15	93	0	51	26	16	23	33	1.96
3814420--3814454	18	1.9	18	100	0	70	28	14	22	34	1.93
3818382--3818452	31	2.2	32	82	5	90	52	14	4	29	1.60
3825085--3825127	22	2.0	22	86	4	61	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3826570--3826600	9	3.4	9	95	0	53	25	0	0	74	0.82
3834418--3834453	2	18.0	2	100	0	72	50	0	0	50	1.00
3837932--3838014	39	2.2	38	86	6	114	20	19	20	39	1.92
3837959--3838156	45	4.4	45	87	3	290	19	18	21	40	1.92
3837932--3838152	45	5.2	39	77	14	183	19	19	21	39	1.92
3839618--3839665	23	2.1	23	92	0	78	25	20	14	39	1.91
3840696--3840766	33	2.2	33	92	0	115	35	40	8	15	1.78
3841076--3841117	15	2.9	15	86	10	52	57	0	42	0	0.99
3846119--3846152	17	2.0	17	100	0	68	29	11	5	52	1.61
3847919--3847951	15	2.3	15	89	5	50	27	0	3	69	1.03
3850762--3850812	3	17.0	3	100	0	102	33	0	0	66	0.92
3850864--3850896	2	16.5	2	93	0	57	48	3	0	48	1.17
3863331--3863471	69	2.1	67	78	12	150	29	7	9	53	1.60
3863930--3863994	31	2.1	31	88	0	94	46	9	9	35	1.68
3864252--3864323	19	3.7	19	83	12	94	61	5	0	33	1.19
3864242--3864326	38	2.2	39	76	21	90	60	5	0	34	1.21
3874818--3874876	26	2.2	28	84	6	77	52	0	1	45	1.10
3874847--3874897	21	2.7	18	77	16	57	52	0	3	43	1.19
3877444--3877487	2	22.0	2	100	0	88	0	50	0	50	1.00
3877487--3877538	2	26.0	2	96	0	77	44	50	0	5	1.26
3877479--3877527	16	3.1	16	87	0	62	34	51	0	14	1.43
3877477--3877531	18	3.1	18	86	0	65	34	50	0	14	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3884602--3884662	31	2.0	31	90	0	95	34	14	8	42	1.76
3889952--3890000	9	5.4	9	85	0	62	26	8	22	42	1.81
3891939--3891988	26	1.9	26	87	0	73	66	2	2	30	1.14
3891939--3892001	27	2.3	26	83	5	72	61	1	1	34	1.15
3900641--3900671	15	2.1	15	100	0	62	32	25	19	22	1.97
3907193--3907244	24	2.2	24	82	6	61	50	9	3	36	1.54
3909030--3909063	14	2.5	14	95	4	61	14	0	35	50	1.44
3921047--3921093	2	23.5	2	100	0	94	48	0	0	51	1.00
3921769--3921794	13	2.0	13	100	0	52	61	0	0	38	0.96
3923944--3923988	17	2.6	18	80	16	51	35	2	4	57	1.31
3923945--3923990	19	2.5	20	75	13	53	36	2	2	58	1.22
3925087--3925120	17	2.0	17	94	0	59	44	0	5	50	1.26
3926014--3926055	21	2.0	21	95	0	75	28	11	26	33	1.92
3926776--3926823	21	2.4	20	79	6	53	37	20	10	31	1.87
3929233--3929276	2	22.0	2	100	0	88	0	50	0	50	1.00
3929976--3930004	3	9.7	3	100	0	58	0	34	0	65	0.93
3933058--3933089	15	2.1	16	94	5	57	15	6	0	78	0.95
3934167--3934196	5	6.0	5	100	0	60	80	0	0	20	0.72
3935675--3935838	83	2.0	83	91	2	267	28	11	18	41	1.86
3941259--3941427	89	1.9	89	91	0	275	37	14	15	31	1.89
3943406--3943694	148	2.0	147	97	0	551	48	18	5	26	1.70
3943422--3943725	148	2.1	146	89	5	461	50	17	5	25	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3943462--3943758	148	2.0	145	79	10	311	51	16	6	24	1.69
3945864--3945890	3	9.0	3	100	0	54	33	33	0	33	1.58
3955198--3955237	20	2.0	20	90	0	62	10	35	25	30	1.88
3961887--3961928	16	2.6	16	82	17	52	28	4	0	66	1.12
3961909--3961942	11	2.8	12	86	13	52	35	0	0	64	0.94
3961953--3961987	17	2.0	18	88	5	54	37	31	8	22	1.85
3966297--3966326	11	2.7	11	94	0	51	70	6	0	23	1.11
3968575--3968602	3	9.3	3	100	0	56	32	0	0	67	0.91
3972383--3972452	31	2.3	31	82	0	86	35	10	18	35	1.84
3975191--3975260	31	2.3	31	82	2	79	40	1	12	45	1.51

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   199   200   201   202   203   204   205   206   207   208