genome.fa.s6.2.7.7.80.10.50.1000.160.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  160  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)
47840003--47840051	18	3.0	16	88	8	64	40	0	0	59	0.98
47864427--47864453	2	13.5	2	100	0	54	48	0	0	51	1.00
47866508--47867211	48	14.7	47	79	7	612	19	2	51	26	1.60
47866767--47866796	15	2.0	15	93	0	51	10	0	56	33	1.32
47866761--47866896	21	5.9	21	70	23	87	15	1	51	31	1.52
47866472--47867213	240	3.1	237	84	3	846	19	2	51	26	1.59
47867104--47867187	21	3.7	21	73	17	87	16	3	55	23	1.56
47867173--47867331	66	2.4	66	81	2	176	21	5	44	28	1.73
47867196--47867316	36	3.6	33	69	15	95	20	6	44	28	1.76
47868479--47869333	48	17.8	48	79	4	484	22	3	49	24	1.66
47868476--47869160	144	4.8	144	84	1	719	23	2	51	22	1.61
47868836--47868921	21	3.8	21	77	16	91	24	1	55	18	1.49
47868479--47869178	96	7.3	96	85	0	675	23	2	50	23	1.62
47888175--47888207	16	2.1	16	88	5	50	21	24	0	54	1.45
47895719--47895830	29	3.9	29	82	5	138	34	20	4	40	1.73
47895718--47895831	58	2.0	58	87	3	167	35	21	4	39	1.73
47896173--47896259	13	7.0	13	76	18	64	63	0	36	0	0.95
47896175--47896259	3	26.3	3	79	13	73	64	0	35	0	0.94
47896945--47896978	17	2.0	17	88	0	50	26	11	5	55	1.58
47897101--47897394	17	16.2	18	67	16	135	34	13	9	43	1.76
47897100--47897196	34	2.8	35	90	6	162	32	13	10	43	1.78
47897174--47897218	22	2.1	22	87	4	65	40	11	8	40	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47897149--47897256	57	1.9	56	86	5	155	35	12	10	41	1.77
47897214--47897297	40	2.1	40	82	6	98	42	13	7	36	1.71
47897233--47897439	37	5.6	37	75	14	155	36	12	8	42	1.73
47897232--47897439	36	5.6	36	72	12	145	37	12	8	42	1.73
47897253--47897453	72	2.8	67	80	15	185	36	12	8	41	1.74
47903964--47904405	218	2.0	218	96	0	805	28	17	14	39	1.89
47924786--47924866	31	2.6	31	73	5	76	35	3	12	48	1.59
47926033--47926083	21	2.5	21	79	17	63	50	0	0	49	1.00
47941130--47941166	18	2.0	18	89	5	56	21	0	5	72	1.04
47943128--47943153	12	2.2	12	100	0	52	57	0	0	42	0.98
47948231--47948261	15	2.1	15	93	0	53	35	12	0	51	1.40
47948299--47948331	12	2.6	13	90	4	50	45	0	6	48	1.27
47951464--47951505	23	1.9	22	85	9	59	50	2	9	38	1.48
47957790--47957870	41	2.0	41	82	4	101	32	6	11	50	1.62
47969761--47969789	8	3.8	8	95	4	51	51	0	0	48	1.00
47978233--47978421	58	3.3	58	89	0	281	31	22	13	32	1.92
47978388--47978453	32	2.1	32	91	5	107	36	18	10	34	1.85
47978271--47978567	146	2.0	147	88	1	443	32	22	12	31	1.91
47978330--47978509	88	2.0	90	93	2	310	34	22	10	32	1.88
47978420--47978844	58	7.4	58	78	10	446	32	23	12	31	1.92
47985894--47986002	32	3.4	31	75	15	96	35	9	10	44	1.70
47999207--47999247	19	2.2	19	95	0	73	19	12	31	36	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48015925--48015971	24	2.0	24	91	0	76	14	23	8	53	1.69
48015940--48016121	41	4.5	39	78	8	168	21	23	7	47	1.76
48030047--48030089	11	3.9	11	81	0	50	65	13	2	18	1.38
48030047--48030089	22	2.0	22	85	0	59	65	13	2	18	1.38
48034620--48034676	29	2.0	29	85	0	78	35	12	17	35	1.87
48034690--48034768	31	2.5	30	85	4	95	48	7	3	40	1.50
48034708--48034776	31	2.2	31	84	0	84	46	11	4	37	1.60
48037498--48037551	27	2.0	27	96	0	99	38	22	12	25	1.90
48042360--48042453	44	2.1	45	86	2	136	34	6	10	48	1.63
48044531--48044587	28	2.0	28	86	0	78	40	3	17	38	1.67
48051387--48051434	19	2.6	18	81	15	53	64	2	0	33	1.05
48054747--48054802	30	1.9	30	82	13	73	28	8	16	46	1.77
48061418--48061563	77	1.9	77	92	0	247	30	27	13	29	1.94
48068327--48068491	50	3.2	51	83	5	172	26	23	28	21	1.99
48070184--48070221	16	2.4	16	95	0	67	36	2	34	26	1.71
48070203--48070295	44	2.1	46	91	4	154	29	3	30	37	1.73
48070203--48070308	39	2.5	43	86	10	139	30	2	31	35	1.72
48070435--48070781	120	2.9	119	93	3	610	50	4	1	43	1.30
48070595--48070778	56	3.2	55	71	22	180	50	4	1	42	1.33
48070756--48070796	21	2.0	21	95	0	73	53	9	2	34	1.47
48080574--48080608	18	1.9	19	88	11	56	77	0	0	22	0.78
48081108--48081159	13	4.0	13	75	9	52	65	5	1	26	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48081109--48081159	26	2.0	25	84	3	66	66	3	1	27	1.20
48080855--48081670	155	5.3	150	86	5	1066	52	8	9	29	1.63
48080858--48081670	309	2.7	304	89	4	1197	52	8	9	29	1.63
48083141--48083173	16	2.0	17	88	5	50	36	3	9	51	1.49
48093596--48093704	46	2.4	45	90	4	175	34	15	22	27	1.94
48097024--48097098	24	3.5	24	69	25	76	28	6	4	61	1.39
48097466--48097535	28	2.7	26	85	10	97	51	4	7	37	1.49
48097471--48097532	28	2.2	28	94	0	106	48	4	8	38	1.54
48097527--48097560	16	2.0	18	88	11	54	55	0	5	38	1.24
48107957--48108015	27	2.2	26	79	8	66	25	1	3	69	1.13
48115749--48115773	13	1.9	13	100	0	50	72	4	0	24	1.02
48121102--48121136	15	2.3	15	90	0	52	5	34	25	34	1.80
48121133--48121181	18	2.9	17	80	14	57	16	42	18	22	1.88
48121204--48121263	15	4.0	15	93	0	93	15	33	21	30	1.94
48137163--48137188	4	6.5	4	100	0	52	23	0	0	76	0.78
48141011--48141071	26	2.6	22	74	18	59	50	0	9	39	1.35
48154927--48154951	13	1.9	13	100	0	50	44	0	16	40	1.47
48155130--48155226	33	2.8	34	74	20	87	51	1	3	44	1.24
48155215--48155266	21	2.5	21	100	0	104	50	7	0	42	1.31
48155448--48155472	13	1.9	13	100	0	50	52	8	8	32	1.60
48156246--48156289	6	7.3	6	100	0	88	84	0	0	15	0.63
48166559--48166860	149	2.0	149	98	0	586	23	15	18	42	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48172558--48172701	20	7.1	19	68	17	69	33	4	0	61	1.22
48172588--48172685	41	2.4	40	81	8	117	35	6	1	57	1.31
48173038--48173087	25	1.9	27	84	8	68	40	0	0	60	0.97
48176023--48176100	32	2.4	31	89	10	120	48	2	11	37	1.53
48176428--48176504	37	2.1	37	95	0	136	57	1	14	27	1.46
48180841--48180892	16	3.2	16	91	0	77	28	0	34	36	1.58
48181106--48181146	15	2.8	16	82	10	52	51	0	0	48	1.00
48181110--48181159	16	3.0	18	78	21	56	54	0	0	46	1.00
48181022--48181338	157	2.0	157	95	1	566	44	2	4	48	1.36
48181373--48181424	15	3.6	15	80	12	56	53	1	0	44	1.11
48181058--48181393	157	2.1	155	84	7	403	47	3	3	45	1.35
48181260--48181549	120	2.5	113	88	7	406	50	4	3	42	1.37
48181590--48181650	28	2.2	28	85	5	81	50	3	0	45	1.17
48187994--48188042	18	2.7	19	75	12	50	26	6	0	67	1.14
48192442--48192500	29	2.0	30	90	3	93	33	3	8	54	1.48
48192444--48192511	30	2.3	29	82	7	75	35	4	5	54	1.45
48192761--48192932	86	2.0	86	100	0	344	59	3	9	27	1.45
48200379--48200435	12	4.8	11	78	18	53	1	24	3	70	1.13
48205210--48205250	20	2.0	20	90	9	66	70	0	0	29	0.87
48210335--48210360	12	2.2	12	100	0	52	23	0	30	46	1.53
48219364--48219610	123	2.0	123	94	1	433	29	18	27	25	1.98
48220888--48220929	21	2.0	21	81	9	50	38	2	0	59	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48223108--48223169	31	2.0	31	84	3	81	37	12	9	40	1.77
48225289--48225326	14	2.7	14	88	8	51	23	0	7	68	1.16
48225494--48225575	31	2.7	31	87	9	107	58	1	2	37	1.19
48225510--48225657	41	3.6	41	88	10	223	62	0	3	33	1.17
48225600--48225666	30	2.2	31	91	2	109	61	0	4	34	1.16
48225494--48225627	11	12.9	11	66	23	67	59	0	2	37	1.15
48255235--48255273	16	2.4	16	86	0	51	28	33	2	35	1.71
48255248--48255304	16	3.6	16	95	0	87	33	36	0	29	1.58
48256156--48256229	8	8.5	8	72	20	51	32	0	2	64	1.07
48256440--48256584	58	2.5	59	84	4	177	22	14	10	52	1.72

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