genome.fa.s6.2.7.7.80.10.50.1000.57.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  57  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)
16200488--16200524	13	2.8	13	84	15	58	78	0	18	2	0.87
16203550--16203574	2	12.5	2	100	0	50	52	48	0	0	1.00
16205070--16205097	8	3.5	8	100	0	56	75	0	0	25	0.81
16207143--16207204	29	2.1	29	90	0	97	35	17	33	12	1.88
16208168--16208226	22	2.7	22	91	0	91	23	25	15	35	1.94
16215021--16215066	23	2.0	23	91	0	74	45	15	2	36	1.58
16217848--16217937	26	3.5	26	82	10	105	14	21	25	38	1.91
16222120--16222183	25	2.6	25	75	2	67	21	21	21	34	1.97
16223861--16223900	21	1.9	21	94	0	71	35	10	22	32	1.87
16224199--16224352	76	2.0	76	100	0	308	28	16	14	40	1.88
16226528--16226560	15	2.1	16	88	5	50	30	15	30	24	1.95
16237995--16238037	22	2.0	22	85	0	59	11	18	25	44	1.84
16238131--16238296	43	3.9	43	91	0	260	30	27	18	23	1.97
16238129--16238316	86	2.2	85	84	2	250	32	27	18	22	1.97
16238659--16238688	2	15.0	2	100	0	60	50	0	0	50	1.00
16243043--16243141	47	2.1	48	94	1	173	45	0	7	47	1.30
16243127--16243179	25	2.1	26	82	3	63	18	3	5	71	1.21
16243126--16243179	19	2.8	18	78	10	54	20	3	5	70	1.23
16243496--16243551	14	3.9	14	78	2	58	32	42	0	25	1.55
16243498--16243551	21	2.5	21	82	11	65	33	42	0	24	1.55
16243688--16243771	7	11.7	7	76	9	71	47	33	0	19	1.49
16243689--16243770	29	2.9	27	81	15	94	47	32	0	19	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16243696--16243771	22	3.5	22	77	10	52	48	31	0	19	1.49
16243997--16244075	41	1.9	41	92	0	131	31	26	20	21	1.98
16244007--16244686	114	6.0	114	86	2	929	27	24	22	25	2.00
16246490--16246539	21	2.4	21	86	0	64	36	34	6	24	1.80
16250600--16250659	30	2.0	30	86	3	84	43	0	36	20	1.52
16250873--16250909	9	4.1	9	89	0	56	32	10	10	45	1.74
16252967--16253159	50	3.8	50	87	3	271	21	30	22	26	1.99
16253497--16253563	30	2.3	29	78	2	80	28	19	13	38	1.89
16255108--16255770	235	2.8	235	93	0	1096	27	16	18	37	1.92
16264611--16264801	50	3.7	50	83	4	220	26	20	27	24	1.99
16265057--16265098	16	2.6	16	84	0	57	54	4	26	14	1.59
16266845--16266908	30	2.2	30	82	2	76	54	10	6	28	1.59
16266861--16266921	30	2.0	31	90	3	97	47	6	8	37	1.59
16266866--16266933	30	2.3	30	87	5	93	48	8	7	35	1.62
16267757--16267793	9	4.1	9	89	0	56	48	13	8	29	1.71
16268005--16268064	30	2.0	31	83	9	79	20	38	0	41	1.52
16274660--16274754	42	2.3	42	88	1	138	30	3	15	50	1.60
16276340--16276381	15	2.9	15	85	3	59	21	14	21	42	1.88
16279371--16279460	42	2.1	42	81	0	108	30	5	13	51	1.64
16280816--16280845	13	2.3	13	94	0	51	46	26	16	10	1.78
16295328--16295357	12	2.4	12	94	5	51	16	6	3	73	1.18
16309848--16309901	6	9.3	6	82	6	51	68	1	1	27	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16309848--16309901	9	6.2	9	75	14	51	68	1	1	27	1.10
16311455--16311548	44	2.1	44	84	2	116	27	25	15	30	1.96
16311501--16311898	221	1.8	220	88	1	609	28	22	18	30	1.97
16311894--16312102	50	4.2	50	74	0	184	23	24	21	30	1.99
16311892--16312122	100	2.3	100	87	3	331	24	23	20	31	1.98
16311976--16312130	50	3.1	50	68	3	132	25	20	20	32	1.97
16334868--16334898	16	2.0	16	93	6	55	70	0	0	29	0.87
16336385--16336434	22	2.2	23	89	3	75	70	2	2	26	1.09
16342159--16342307	38	3.9	37	80	11	133	33	10	11	44	1.75
16344970--16345041	32	2.2	32	97	2	135	41	19	29	9	1.83
16348419--16348510	38	2.4	39	87	5	125	34	7	10	46	1.67
16348419--16348577	39	4.1	40	74	13	102	32	8	10	48	1.69
16350542--16350577	2	18.0	2	100	0	72	50	0	0	50	1.00
16350876--16350900	13	1.9	13	100	0	50	56	0	0	44	0.99
16351372--16351446	19	3.9	19	70	20	59	65	6	0	28	1.18
16351398--16351454	19	3.2	17	71	20	53	61	8	0	29	1.26
16351383--16351454	38	1.9	37	91	5	119	63	8	0	27	1.23
16353802--16353975	87	2.0	87	96	2	323	36	25	10	26	1.89
16376718--16376773	21	2.7	21	85	0	76	28	8	33	28	1.87
16380850--16380909	27	2.3	27	79	2	68	35	21	26	16	1.95
16385148--16385181	5	6.8	5	100	0	68	0	17	0	82	0.67
16385357--16385403	20	2.3	21	77	3	51	8	23	0	68	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16387162--16387210	3	16.7	3	95	4	91	32	32	0	34	1.58
16393400--16393435	2	18.0	2	100	0	72	50	0	0	50	1.00
16394011--16394064	23	2.3	23	100	0	108	27	18	16	37	1.93
16395777--16395809	17	1.9	17	93	0	57	84	0	6	9	0.76
16399832--16399920	42	2.1	42	100	0	178	39	19	4	37	1.72
16401183--16401236	25	2.1	26	82	3	65	70	5	3	20	1.23
16411468--16411508	21	2.0	21	85	0	55	36	12	9	41	1.76
16413762--16413822	21	2.9	22	85	9	83	70	3	0	26	1.02
16429519--16429809	120	2.4	121	93	2	505	42	0	3	53	1.24
16429683--16429735	22	2.5	20	77	19	54	37	0	5	56	1.23
16430016--16430072	16	3.6	16	87	0	87	22	33	5	38	1.77
16432002--16432207	42	4.8	42	91	3	299	33	21	22	21	1.97
16432569--16432626	21	2.8	21	94	0	98	3	36	20	39	1.70
16432568--16432638	21	3.4	21	88	3	90	2	38	19	39	1.67
16436920--16437127	9	23.8	9	68	13	121	30	2	21	45	1.64
16437023--16437076	16	3.2	16	80	10	54	25	0	22	51	1.48
16437357--16437475	57	2.1	57	96	1	222	47	5	9	38	1.58
16437416--16437728	76	4.2	76	95	2	587	46	5	7	40	1.55
16437413--16437728	149	2.1	151	96	2	591	46	5	7	40	1.55
16437853--16437991	67	2.1	67	95	2	253	45	13	4	36	1.64
16438051--16438086	16	2.2	16	95	0	63	52	8	11	27	1.65
16440071--16440156	44	2.0	44	81	4	102	36	19	19	24	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16440703--16440768	7	9.4	7	88	0	87	45	45	0	9	1.35
16440703--16440764	14	4.4	14	91	0	97	43	48	0	8	1.32
16441692--16441727	18	2.0	18	89	10	56	69	5	0	25	1.10
16441696--16441735	18	2.2	19	86	4	55	70	5	0	25	1.08
16441844--16442265	114	3.7	114	96	0	772	28	22	18	30	1.97
16442327--16442596	114	2.4	113	80	7	278	29	23	18	28	1.98
16441836--16442548	114	6.3	114	83	5	718	28	23	17	30	1.97
16445916--16445972	29	2.0	29	100	0	114	42	10	12	35	1.77
16452551--16452606	23	2.4	23	90	0	94	41	19	25	14	1.89
16461884--16461958	25	3.0	25	76	18	75	25	21	22	30	1.99
16461841--16461954	50	2.3	51	81	3	133	24	19	23	32	1.97
16463149--16463182	13	2.6	13	90	0	50	17	26	38	17	1.92
16465860--16465912	6	8.8	6	97	0	88	28	0	3	67	1.07
16473699--16473741	21	2.0	21	90	0	68	32	18	9	39	1.83
16474927--16475181	127	2.0	127	95	0	456	28	19	12	39	1.89
16503320--16503380	26	2.3	26	91	0	95	60	3	4	31	1.34
16503399--16503438	21	1.9	21	84	0	53	57	2	7	32	1.40
16504592--16504631	20	2.0	20	85	14	55	12	10	42	35	1.76
16504699--16504733	14	2.4	15	85	9	54	25	5	14	54	1.62
16508087--16508595	251	2.0	251	96	0	946	20	15	18	45	1.86
16514437--16514474	17	2.2	17	86	9	51	36	28	5	28	1.79
16516232--16516279	15	3.1	15	77	11	51	54	0	10	35	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16516998--16517037	16	2.5	17	88	8	57	17	2	17	62	1.44
16517714--16517745	16	2.0	16	93	0	55	40	18	12	28	1.87
16521330--16521374	22	2.0	22	87	8	65	28	0	20	51	1.48
16522509--16522537	15	1.9	15	100	0	58	68	6	10	13	1.37
16538544--16538731	51	3.7	50	80	6	209	30	27	14	26	1.95
16540250--16540296	25	1.9	24	82	4	58	53	10	17	19	1.72
16553856--16553926	12	5.9	12	71	12	56	9	15	4	70	1.30
16554938--16554969	12	2.7	12	100	0	64	12	6	6	75	1.19
16556165--16556209	20	2.2	20	85	14	58	53	13	4	28	1.59
16557880--16557918	19	2.1	19	85	4	53	38	15	15	30	1.88

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