genome.fa.s6.2.7.7.80.10.50.1000.24.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  24  of  168  ( 20060 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)
6214873--6215657	217	3.6	217	92	0	1232	27	22	20	29	1.98
6214873--6215568	44	16.0	44	70	16	244	27	22	19	29	1.98
6227825--6227857	2	16.5	2	93	0	57	48	3	0	48	1.17
6234616--6234663	16	3.0	16	75	0	51	39	12	10	37	1.77
6241008--6241079	29	2.4	30	79	6	83	47	11	13	27	1.77
6242736--6242804	36	1.9	35	88	8	104	36	13	27	23	1.92
6243252--6243294	22	2.0	22	100	0	86	37	13	25	23	1.92
6245767--6245791	13	1.9	13	100	0	50	52	24	0	24	1.48
6250789--6250864	40	1.9	40	83	5	100	21	27	28	22	1.99
6251192--6251235	21	2.1	21	87	8	63	27	11	0	61	1.30
6256585--6256642	28	2.1	28	93	0	98	1	31	6	60	1.33
6256613--6256725	38	3.0	38	93	0	190	3	27	10	58	1.48
6256571--6256705	66	2.0	66	87	2	191	2	29	10	57	1.47
6261547--6261671	44	2.8	45	69	21	107	44	2	4	48	1.37
6261752--6261974	66	3.6	64	68	21	181	43	1	5	49	1.37
6261714--6262011	120	2.5	120	92	1	481	43	1	5	50	1.34
6261839--6261890	15	3.6	15	80	12	56	44	0	1	53	1.11
6261787--6261974	61	3.1	61	70	14	199	42	1	6	48	1.39
6262137--6262241	44	2.5	40	76	18	115	32	29	3	34	1.76
6262135--6262243	45	2.6	44	81	11	131	32	29	4	33	1.78
6262223--6262271	16	3.1	16	96	0	89	22	36	4	36	1.73
6262491--6262524	6	5.7	6	89	0	50	17	0	52	29	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6263479--6263550	34	2.1	34	92	0	117	43	12	13	30	1.82
6265133--6265162	2	15.5	2	93	6	53	50	0	0	50	1.00
6265182--6265209	10	2.8	10	100	0	56	42	7	7	42	1.59
6270688--6270763	29	2.6	29	76	15	77	35	11	2	50	1.53
6273944--6273974	9	3.4	9	95	0	53	38	25	9	25	1.86
6297828--6297859	6	5.3	6	100	0	64	84	0	0	15	0.63
6305448--6305505	29	2.0	30	83	10	75	34	6	10	48	1.64
6306452--6306490	17	2.4	17	91	4	62	23	2	0	74	0.94
6307215--6307305	34	2.7	34	86	5	130	42	0	16	40	1.48
6307371--6307897	127	4.2	127	87	1	736	36	15	17	29	1.91
6307374--6307897	252	2.1	253	88	1	782	36	15	17	29	1.92
6311453--6311521	30	2.3	30	97	0	129	37	1	27	33	1.66
6312962--6313001	20	1.9	21	90	10	64	50	5	0	45	1.23
6314045--6314069	2	12.5	2	100	0	50	0	48	0	52	1.00
6323071--6323128	21	2.8	21	78	5	55	41	6	22	29	1.80
6323346--6323386	18	2.2	19	91	4	66	26	2	2	68	1.15
6323396--6323442	19	2.4	20	82	13	62	38	0	8	53	1.32
6323396--6323457	18	3.3	19	78	17	67	35	0	6	58	1.24
6323397--6323458	19	3.2	18	77	11	61	33	0	6	59	1.23
6323793--6323833	21	2.0	21	85	0	55	17	14	21	46	1.84
6324180--6324222	21	2.0	21	95	0	77	44	11	9	34	1.73
6325379--6325420	10	3.9	10	82	17	57	40	19	2	38	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6325366--6325420	23	2.4	23	96	0	101	40	16	3	40	1.66
6325366--6325417	13	4.2	13	80	14	65	42	13	3	40	1.62
6325402--6325541	43	3.3	43	91	4	212	43	16	10	29	1.81
6329548--6329682	73	2.0	70	84	12	183	51	3	13	31	1.58
6336104--6336162	29	2.0	29	86	3	82	52	13	8	25	1.68
6339148--6339200	27	2.0	27	88	0	79	28	33	15	22	1.94
6351990--6352616	67	9.4	67	83	3	685	31	16	26	24	1.96
6351990--6352609	201	3.1	198	83	4	755	31	16	26	25	1.97
6352751--6352820	26	2.6	26	77	8	70	37	17	21	24	1.94
6361219--6361275	29	2.0	29	82	6	71	28	12	7	52	1.64
6368290--6368370	22	3.7	22	86	0	117	30	13	25	29	1.94
6369009--6369033	13	1.9	13	100	0	50	48	16	4	32	1.64
6369048--6369109	16	4.2	15	76	17	67	58	17	0	24	1.39
6369120--6369190	33	2.2	33	84	5	90	53	21	2	22	1.59
6369129--6369198	33	2.1	33	89	0	104	52	17	4	25	1.62
6369312--6369349	15	2.5	15	91	0	58	57	13	5	23	1.56
6374808--6374889	42	2.0	42	92	0	137	20	18	13	47	1.82
6379280--6379339	18	3.2	19	76	23	56	48	0	0	51	1.00
6388420--6388448	15	1.9	15	100	0	58	34	17	6	41	1.76
6389475--6389530	21	2.7	21	76	18	62	39	17	5	37	1.73
6395198--6395271	27	2.8	25	82	11	94	43	9	12	35	1.74
6397932--6397975	20	2.3	20	85	11	58	31	0	6	61	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6398803--6399029	91	2.5	90	83	0	274	31	20	18	29	1.97
6402225--6402307	4	20.8	4	97	0	157	26	0	22	50	1.49
6402525--6402596	31	2.3	31	82	0	99	25	11	18	45	1.81
6406560--6406636	40	1.9	39	87	7	111	63	2	0	33	1.08
6410024--6410070	18	2.8	16	78	15	58	38	27	14	19	1.91
6415406--6415474	27	2.6	27	95	0	120	30	18	14	36	1.91
6415466--6415620	27	5.8	27	84	0	213	18	16	23	42	1.88
6415439--6415607	54	3.1	53	80	5	164	19	15	21	43	1.88
6415439--6415618	81	2.2	81	83	6	215	19	16	22	41	1.90
6418102--6418198	17	5.6	18	78	11	78	37	31	16	14	1.89
6418397--6418440	22	2.0	23	86	4	63	34	0	0	65	0.93
6419130--6419195	29	2.2	30	83	2	89	43	12	7	36	1.70
6419765--6419797	15	2.3	15	89	5	50	51	0	6	42	1.26
6420095--6420125	13	2.4	13	100	0	62	38	6	0	54	1.26
6420178--6420230	27	2.0	27	84	0	70	52	1	0	45	1.11
6420205--6420289	38	2.2	39	78	14	88	49	1	2	47	1.22
6420918--6420946	2	14.5	2	100	0	58	48	0	0	51	1.00
6424432--6424518	43	2.0	43	93	0	147	28	13	12	44	1.81
6427576--6427609	2	17.0	2	93	0	59	47	0	0	52	1.00
6429020--6429191	50	3.4	50	83	1	193	25	26	29	18	1.98
6429828--6429863	19	1.9	18	88	5	54	50	5	5	38	1.49
6432953--6433045	45	2.1	45	89	0	141	30	20	19	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6433243--6433299	29	2.0	29	82	6	71	29	28	15	26	1.96
6434253--6434301	15	3.2	15	88	8	64	55	4	0	40	1.19
6434252--6434298	24	1.9	25	87	12	71	53	6	0	40	1.27
6435366--6435409	15	3.2	13	87	9	52	68	4	0	27	1.09
6436855--6436889	3	11.7	3	93	0	61	31	0	2	65	1.07
6440708--6440748	11	3.9	11	81	12	50	51	0	7	41	1.30
6444350--6444427	39	2.0	39	97	0	147	26	12	19	41	1.87
6447396--6447432	9	4.1	9	92	0	65	45	13	10	29	1.77
6452920--6452956	2	18.5	2	100	0	74	51	0	0	48	1.00
6453183--6453229	19	2.5	19	96	0	85	34	27	19	19	1.96
6453183--6453238	19	2.9	19	86	5	78	35	26	17	19	1.94
6453244--6453315	21	3.5	21	88	1	101	36	27	22	13	1.92
6453304--6453374	23	3.0	24	87	6	101	39	22	18	19	1.92
6453244--6453373	42	3.0	43	78	7	138	36	25	21	16	1.93
6453717--6453748	16	1.9	17	93	6	57	25	21	0	53	1.46
6454876--6454913	14	2.4	17	87	12	55	52	0	0	47	1.00
6454893--6454931	12	3.4	11	80	13	51	46	2	0	51	1.14
6454905--6454954	21	2.5	20	76	3	55	52	2	0	46	1.12
6460630--6460688	30	2.0	30	96	0	109	54	15	5	25	1.61
6460726--6460773	22	2.2	22	81	7	53	58	4	18	18	1.55
6467870--6468136	37	7.0	37	85	8	356	37	14	20	27	1.91
6467836--6468098	119	2.2	120	93	0	438	37	13	21	27	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6467868--6468180	156	2.0	156	92	1	520	36	15	21	27	1.93
6468098--6468192	45	2.1	45	90	3	147	30	17	23	28	1.97
6470606--6470638	15	2.1	16	88	5	50	60	0	18	21	1.36
6472542--6472659	43	2.7	43	78	10	125	46	21	20	11	1.82
6473262--6473289	6	4.7	6	100	0	56	0	0	82	17	0.68
6476069--6476181	32	3.5	32	80	6	129	36	13	8	41	1.75
6476583--6476631	25	2.0	25	88	8	73	57	2	14	26	1.48
6482953--6482996	23	1.9	22	82	17	54	38	22	0	38	1.55
6485848--6485897	2	25.0	2	95	0	91	50	0	2	48	1.12
6490604--6490665	16	4.1	16	76	14	60	33	0	0	66	0.92

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