genome.fa.s6.2.7.7.80.10.50.1000.37.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  37  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)
9979020--9979072	5	10.8	5	97	2	99	41	0	0	58	0.98
9979089--9979118	11	2.8	11	95	5	53	76	10	13	0	1.01
9980347--9980439	41	2.4	40	80	7	102	26	16	23	33	1.95
9993728--9993871	24	5.8	24	71	14	71	35	23	24	16	1.95
9993743--9993872	26	5.2	26	73	10	103	35	23	23	16	1.95
9993930--9993994	25	2.7	23	77	11	67	43	16	23	16	1.88
9997171--9997316	49	3.0	49	87	1	211	31	28	14	26	1.95
9998147--9998280	33	3.8	34	75	17	137	31	26	20	20	1.98
9998149--9998325	75	2.4	75	94	1	302	31	27	20	21	1.98
9998344--9998838	51	9.8	49	82	5	465	29	27	16	26	1.97
9998621--9998703	25	3.1	28	62	22	70	31	27	14	26	1.95
9998344--9998838	102	4.9	100	83	6	552	29	27	16	26	1.97
10001610--10001641	12	2.6	13	85	14	50	56	6	0	37	1.25
10007295--10007352	30	1.9	30	89	0	89	31	24	3	41	1.71
10008832--10008930	23	4.1	24	71	16	78	41	18	20	20	1.91
10009013--10009077	26	2.5	27	80	5	62	36	24	21	16	1.94
10013042--10013161	55	2.2	55	89	0	177	24	15	26	33	1.95
10013042--10013189	55	2.7	55	84	2	163	22	16	26	34	1.95
10017156--10017200	24	2.0	23	82	8	56	46	0	8	44	1.34
10020184--10020638	85	5.3	84	71	10	271	26	20	22	30	1.99
10020131--10020685	129	4.3	129	91	0	860	25	20	22	30	1.98
10020131--10020676	44	12.7	42	72	9	345	25	21	22	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10020953--10020998	24	1.9	24	86	0	65	32	26	6	34	1.82
10022423--10022522	1	100.0	1	69	0	65	5	4	6	85	0.84
10022423--10022520	8	11.8	8	75	16	83	5	4	6	84	0.86
10022423--10022517	33	2.8	33	90	7	140	5	4	6	84	0.88
10022423--10022521	43	2.4	40	82	16	121	5	4	6	84	0.85
10032413--10032458	24	2.0	23	82	4	56	26	6	2	65	1.28
10038723--10038786	21	3.0	22	82	13	64	53	1	0	45	1.10
10043910--10043959	18	2.9	17	82	11	57	70	8	6	16	1.32
10043910--10043956	22	2.1	22	84	0	58	74	6	4	14	1.17
10043995--10044071	39	2.0	39	97	0	145	45	38	3	11	1.59
10049608--10049697	12	7.5	12	76	8	58	73	6	7	12	1.25
10049675--10049699	6	4.2	6	100	0	50	68	0	16	16	1.22
10050617--10050645	7	4.3	7	95	4	51	72	0	13	13	1.13
10051854--10052338	43	11.3	43	89	1	645	29	22	25	22	1.99
10051855--10052338	85	5.7	85	88	1	655	29	22	25	22	1.99
10052410--10053008	44	13.7	43	70	9	288	28	18	24	28	1.98
10052369--10052902	216	2.5	217	85	3	707	27	19	24	27	1.99
10052670--10053022	173	2.0	173	90	0	553	29	18	22	29	1.97
10053379--10053455	39	2.0	39	97	0	145	46	38	3	10	1.56
10063979--10064017	20	1.9	21	89	5	62	43	0	0	56	0.99
10071017--10071195	94	1.9	94	83	2	234	33	18	25	22	1.97
10071039--10071230	94	2.0	94	80	4	208	33	18	26	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10076572--10076618	22	2.2	21	84	3	58	72	2	0	25	0.96
10080254--10080345	39	2.4	39	86	0	121	45	17	3	33	1.65
10082575--10082668	46	2.0	46	97	0	179	37	3	20	39	1.69
10083249--10083314	25	2.6	25	79	9	80	19	24	18	37	1.93
10083333--10083397	25	2.6	25	80	2	78	21	29	20	29	1.98
10086397--10086436	14	2.9	14	76	0	53	30	15	17	37	1.90
10086397--10086462	28	2.4	28	89	0	96	34	13	15	36	1.87
10086568--10086660	28	3.3	28	87	0	132	25	20	23	30	1.99
10088497--10088545	21	2.2	24	82	10	59	34	0	2	63	1.06
10104387--10104814	213	2.0	213	97	0	804	23	28	23	24	2.00
10105801--10105880	30	2.6	30	82	2	97	21	25	11	42	1.85
10105860--10106038	30	6.0	29	73	9	137	26	26	13	32	1.94
10105830--10106034	60	3.5	59	76	5	207	24	26	14	34	1.93
10107247--10107305	29	2.0	29	86	0	82	22	25	33	18	1.96
10111014--10111117	25	4.2	25	75	4	84	18	22	21	38	1.93
10116526--10116558	17	1.9	17	93	0	57	30	0	18	51	1.46
10117084--10117128	22	2.1	21	91	4	72	42	11	0	46	1.39
10124783--10124830	14	3.1	14	78	18	51	66	8	0	25	1.19
10124776--10124836	16	3.8	16	74	23	56	68	6	0	24	1.13
10129469--10129554	34	2.5	34	90	0	127	34	36	10	18	1.85
10138806--10138834	9	3.3	9	95	4	51	34	0	0	65	0.93
10139546--10139633	43	2.0	43	88	0	131	38	10	3	47	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10140016--10140056	17	2.4	17	87	0	55	58	0	2	39	1.11
10140520--10140562	20	2.2	20	91	0	68	69	13	9	6	1.35
10140568--10140618	25	2.0	25	85	7	68	45	15	31	7	1.75
10141655--10141679	13	1.9	13	100	0	50	16	32	24	28	1.96
10147573--10147607	17	2.1	17	100	0	70	20	11	17	51	1.75
10148893--10148936	22	2.0	23	86	4	63	34	6	13	45	1.70
10156250--10156392	64	2.2	65	93	2	243	34	14	24	25	1.94
10156789--10156839	24	2.1	25	82	10	61	49	5	3	41	1.45
10161865--10161897	3	11.0	3	93	0	57	30	0	36	33	1.58
10162735--10162761	4	6.8	4	100	0	54	22	0	0	77	0.76
10167190--10167249	6	9.8	6	78	21	63	81	13	0	5	0.84
10167196--10167249	14	4.2	14	84	15	73	81	12	0	5	0.85
10167192--10167257	32	2.1	30	83	10	80	80	12	1	6	0.96
10167196--10167249	26	2.1	26	90	10	85	81	12	0	5	0.85
10168077--10168123	7	7.0	7	85	9	71	68	0	17	14	1.22
10168077--10168123	13	3.5	14	85	8	71	68	0	17	14	1.22
10168077--10168123	20	2.3	20	96	0	85	68	0	17	14	1.22
10169339--10169527	46	4.1	46	88	0	270	28	16	24	30	1.96
10169640--10170046	132	3.1	132	92	0	679	31	17	22	28	1.97
10171071--10171095	11	2.3	11	100	0	50	16	0	0	84	0.63
10181178--10181221	22	2.0	22	100	0	88	45	13	9	31	1.75
10184836--10184892	19	3.3	19	68	27	63	40	24	3	31	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10184832--10184894	32	2.0	32	100	0	126	39	22	3	34	1.70
10184971--10185051	42	1.9	42	92	0	135	14	37	27	20	1.92
10192098--10192136	21	1.9	21	89	5	62	79	0	15	5	0.90
10192534--10192580	16	2.9	16	87	0	67	25	12	2	59	1.45
10192642--10192685	23	2.0	21	83	16	54	6	22	0	70	1.11
10197633--10197660	14	2.0	14	100	0	56	35	7	7	50	1.57
10198809--10198940	66	2.0	66	95	0	237	37	12	6	43	1.68
10199360--10199387	2	14.0	2	100	0	56	50	0	0	50	1.00
10199418--10199466	25	1.9	25	83	4	62	51	8	0	40	1.32
10201588--10201636	18	2.8	17	72	6	53	75	0	8	16	1.03
10202395--10202479	40	2.1	39	85	8	109	29	7	21	42	1.79
10202415--10202474	23	2.9	21	73	16	63	26	5	21	46	1.72
10202415--10202502	40	2.2	41	87	6	126	29	7	19	43	1.79
10202721--10202805	45	1.9	44	90	2	134	23	15	20	41	1.90
10206455--10206495	11	3.7	11	80	0	55	19	14	9	56	1.66
10208733--10208808	37	2.1	37	100	0	152	43	15	13	27	1.84
10209762--10209816	27	2.0	27	82	6	67	50	1	3	43	1.30
10217679--10217710	5	6.4	5	100	0	64	78	0	0	21	0.76
10221011--10221055	20	2.3	20	92	3	74	26	4	2	66	1.22
10221022--10221068	20	2.3	20	85	0	58	29	2	2	65	1.15
10229254--10229292	15	2.5	16	83	4	53	7	7	2	82	0.94
10230373--10230419	9	5.2	9	80	17	53	57	0	8	34	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10230373--10230424	25	2.0	27	88	7	81	59	0	7	32	1.26
10232406--10232604	27	7.3	27	82	5	231	39	19	17	24	1.92
10232406--10232604	81	2.4	82	90	0	310	39	19	17	24	1.92
10232417--10232628	27	7.8	28	78	3	132	39	19	17	23	1.92
10238466--10238513	6	7.8	6	76	4	51	20	4	2	72	1.11
10238441--10238516	12	5.9	12	75	14	71	19	5	2	72	1.16
10238464--10238575	20	5.8	20	71	18	76	20	5	2	71	1.18
10243057--10243097	21	2.0	21	90	0	64	60	7	2	29	1.36
10245900--10246028	40	3.2	40	81	3	163	35	21	20	22	1.96
10246087--10246271	41	4.5	41	88	4	275	23	23	24	29	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