genome.fa.s6.2.7.7.80.10.50.1000.25.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  25  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)
6504117--6504151	17	2.1	17	94	0	61	60	2	0	37	1.12
6505726--6505781	18	3.4	16	73	26	55	53	0	0	46	1.00
6505726--6505781	16	3.4	17	76	14	64	53	0	0	46	1.00
6506051--6506090	19	2.1	19	86	9	55	32	15	15	37	1.88
6507450--6507485	2	18.5	2	88	5	56	50	2	0	47	1.15
6507504--6507532	15	1.9	15	100	0	58	20	13	13	51	1.75
6508044--6508088	23	2.0	22	87	8	65	26	17	15	40	1.90
6510360--6510410	19	2.6	20	81	9	61	29	1	1	66	1.13
6510345--6510410	29	2.3	29	84	5	89	28	3	3	65	1.23
6510408--6510461	17	2.8	18	78	16	56	42	0	1	55	1.10
6510552--6510600	19	2.7	18	87	6	71	28	6	16	48	1.69
6517502--6517574	35	2.1	35	100	0	146	39	17	10	31	1.85
6525963--6526062	52	1.9	51	82	9	123	55	8	7	30	1.56
6526332--6526388	3	19.0	3	80	20	66	66	0	0	33	0.92
6526332--6526388	15	3.8	16	86	9	75	66	0	0	33	0.92
6526592--6526630	19	2.0	21	85	10	55	69	5	10	15	1.34
6526646--6526733	45	1.9	46	90	6	144	27	15	6	50	1.70
6526829--6526886	22	2.6	22	84	7	73	43	17	3	36	1.66
6526842--6526899	19	2.8	20	84	10	64	39	17	6	36	1.76
6527902--6528216	44	7.2	44	64	4	177	20	23	27	27	1.99
6527875--6528356	88	5.5	88	91	0	750	20	23	27	29	1.99
6528013--6528155	43	3.3	43	65	3	115	16	25	29	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6534105--6534229	56	2.2	56	91	2	198	43	7	13	36	1.72
6534223--6534285	23	2.7	23	85	4	83	31	1	23	42	1.64
6534252--6534435	29	6.1	29	88	7	269	29	1	26	42	1.62
6534249--6534457	63	3.6	58	84	11	261	30	0	25	43	1.61
6534340--6534457	29	4.5	24	88	8	105	28	0	27	43	1.61
6534249--6534425	92	1.9	92	91	2	293	30	1	24	43	1.62
6535623--6535647	7	3.6	7	100	0	50	60	12	0	28	1.32
6536735--6536776	20	2.1	20	86	8	59	66	0	0	33	0.92
6536727--6536789	31	2.1	29	88	5	90	63	1	0	34	1.04
6536785--6536818	17	1.9	18	88	5	52	64	0	11	23	1.26
6536833--6536929	22	4.7	22	80	14	116	35	0	32	31	1.58
6537271--6537307	12	2.9	13	84	8	58	45	0	0	54	1.00
6537266--6537306	13	3.2	13	82	6	57	48	0	0	51	1.00
6537425--6537485	17	3.4	17	76	17	61	37	0	3	59	1.14
6537393--6537434	21	2.0	21	90	0	66	40	2	7	50	1.43
6537425--6537486	16	3.5	17	72	20	54	37	0	3	59	1.13
6537474--6537515	21	2.0	21	85	0	57	19	2	2	76	1.01
6539138--6539169	2	16.0	2	100	0	64	50	0	0	50	1.00
6547798--6547864	33	2.0	33	100	0	134	29	22	20	26	1.99
6555585--6555619	16	2.2	16	94	0	61	51	0	0	48	1.00
6558017--6558079	31	2.0	31	100	0	126	46	15	12	25	1.82
6559389--6559447	26	2.2	25	78	21	59	64	6	1	27	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6560879--6560936	29	1.9	30	83	13	75	41	3	1	53	1.28
6560888--6560942	28	2.0	28	82	13	69	43	5	0	50	1.25
6562106--6562148	23	1.9	23	85	4	61	46	9	0	44	1.35
6563846--6563937	43	2.1	43	84	7	116	31	22	18	27	1.97
6564244--6564331	21	4.2	21	85	5	108	3	43	20	32	1.69
6566333--6566734	114	3.5	113	77	6	409	26	27	22	23	1.99
6576751--6576790	19	2.1	19	85	4	53	25	2	7	65	1.32
6582457--6582514	29	2.0	29	100	0	116	24	13	6	55	1.63
6585005--6585279	141	2.0	141	83	7	353	29	6	29	34	1.83
6589104--6589129	7	3.7	7	100	0	52	11	0	0	88	0.52
6591194--6591257	18	3.5	18	79	14	69	60	4	3	31	1.32
6591920--6591967	11	3.4	15	70	24	50	41	2	0	56	1.11
6591919--6591978	26	2.3	26	91	8	95	40	1	1	56	1.19
6594398--6594450	21	2.5	21	96	0	97	39	11	13	35	1.80
6594647--6594691	19	2.5	17	82	13	54	15	8	4	71	1.28
6594911--6594951	21	2.0	20	95	4	73	41	0	0	58	0.98
6600089--6600117	6	4.8	6	100	0	58	86	0	13	0	0.58
6601364--6601586	44	5.1	44	69	10	150	29	19	26	24	1.99
6601352--6601678	132	2.5	132	94	1	557	29	22	24	23	1.99
6601352--6601717	132	2.8	132	89	2	434	30	21	24	24	1.99
6601665--6601748	43	1.9	43	87	2	123	32	20	20	27	1.97
6601666--6602078	44	9.6	43	72	11	199	28	20	23	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6601663--6602124	44	10.7	44	70	15	198	29	20	22	27	1.98
6601654--6602134	217	2.2	217	88	2	711	29	19	23	27	1.98
6601792--6602124	44	7.7	43	73	15	202	28	19	24	27	1.99
6602434--6602530	21	4.7	21	92	2	153	40	9	12	38	1.75
6602728--6602771	20	2.3	18	84	7	52	15	9	4	70	1.30
6602994--6603057	3	22.3	3	84	15	91	35	0	0	64	0.94
6602998--6603069	36	1.9	38	83	10	96	37	4	0	58	1.18
6609375--6609423	18	2.8	17	82	17	57	32	0	22	44	1.53
6617228--6617252	6	4.2	6	100	0	50	68	0	32	0	0.90
6628995--6629023	4	7.2	4	100	0	58	0	0	24	75	0.80
6635147--6635209	33	1.9	32	90	3	99	34	20	4	39	1.74
6640441--6640489	20	2.5	20	80	6	55	40	10	14	34	1.79
6644415--6644440	6	4.3	6	100	0	52	50	0	0	50	1.00
6650647--6650680	14	2.4	14	90	0	50	38	2	2	55	1.30
6662903--6663726	268	3.1	267	89	1	1247	28	20	25	26	1.99
6663733--6664071	44	7.8	44	74	11	225	29	20	22	27	1.98
6666271--6666300	15	2.0	15	93	0	51	23	6	10	60	1.52
6667094--6667200	54	2.0	54	98	0	205	34	25	14	25	1.94
6677814--6677852	19	2.0	20	90	5	62	46	25	0	28	1.53
6681839--6682085	46	5.4	46	94	0	399	29	22	16	31	1.96
6684974--6685005	16	1.9	16	93	6	55	0	9	0	90	0.45
6684977--6685004	12	2.3	12	100	0	56	0	7	0	92	0.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6688312--6688350	10	3.9	10	80	12	53	25	0	2	71	0.98
6688314--6688350	20	1.9	20	94	5	67	24	0	2	72	0.97
6691107--6691297	102	1.8	102	82	7	242	28	15	25	30	1.96
6691284--6691331	17	2.8	18	81	9	55	79	0	2	18	0.84
6692858--6692903	17	2.7	17	89	0	65	36	13	13	36	1.83
6693723--6693842	51	2.3	51	86	1	177	40	19	19	20	1.91
6693787--6693877	39	2.3	39	90	3	139	42	20	15	20	1.88
6693733--6693902	90	1.9	90	87	2	252	40	20	20	20	1.92
6696357--6696411	28	2.0	28	85	7	76	56	1	3	38	1.28
6697448--6697504	21	2.7	21	83	5	80	14	15	26	43	1.85
6697454--6697504	21	2.4	21	90	0	84	15	15	25	43	1.86
6702001--6702042	21	2.0	20	86	4	57	28	28	11	30	1.92
6704237--6704784	284	1.9	284	91	1	893	35	12	21	30	1.91
6709476--6709572	49	2.0	49	81	0	113	35	16	24	23	1.95
6711257--6711288	16	1.9	17	93	6	57	28	0	0	71	0.86
6711419--6711453	2	17.5	2	100	0	70	48	0	0	51	1.00
6717516--6717548	13	2.6	13	90	4	50	39	0	0	60	0.97
6717516--6717547	15	2.3	15	89	10	50	37	0	0	62	0.95
6720954--6720985	9	3.6	9	91	0	55	40	0	3	56	1.15
6721292--6721325	15	2.3	15	94	0	59	17	2	14	64	1.40
6721342--6721375	17	2.0	17	88	11	52	32	8	0	58	1.29
6729100--6729190	37	2.5	36	82	8	112	40	32	13	13	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6731239--6731278	19	2.1	19	100	0	80	40	20	10	30	1.85
6734683--6734740	25	2.3	24	80	11	64	31	0	5	63	1.16
6737870--6737940	36	2.0	36	88	0	106	23	11	15	49	1.77
6743199--6743223	2	12.5	2	100	0	50	52	0	0	48	1.00
6744897--6744928	17	1.9	16	93	6	55	21	12	25	40	1.88
6747963--6748057	46	2.1	46	97	0	181	34	2	22	41	1.66
6752545--6752621	22	3.4	22	67	19	68	35	2	25	36	1.70
6752540--6752634	46	2.1	46	100	0	190	33	2	23	41	1.66
6757442--6757621	41	4.4	41	79	5	184	22	18	25	34	1.96
6757439--6757556	40	2.9	40	81	6	139	25	16	22	35	1.95

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