genome.fa.s6.2.7.7.80.10.50.1000.26.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  26  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)
6757440--6757588	81	1.8	83	88	5	234	23	18	24	34	1.96
6757442--6757665	41	5.5	40	76	9	141	23	17	25	33	1.96
6763075--6763120	21	2.2	21	96	0	83	15	8	26	50	1.73
6765367--6765414	22	2.0	23	84	11	62	54	2	2	41	1.24
6766040--6766077	17	2.3	16	82	17	51	28	10	0	60	1.30
6766042--6766077	15	2.2	16	90	9	56	27	11	0	61	1.30
6766303--6766371	26	2.7	27	80	12	67	31	8	0	59	1.28
6771368--6771454	43	2.0	43	97	0	165	36	13	12	36	1.83
6772289--6772403	49	2.2	52	81	6	128	15	16	36	31	1.90
6776506--6776542	2	18.5	2	94	0	65	45	0	0	54	1.00
6779676--6779723	2	24.0	2	100	0	96	50	0	0	50	1.00
6781565--6781627	23	2.8	22	79	18	67	38	3	4	53	1.38
6781582--6781626	21	2.0	22	87	12	65	37	2	6	53	1.40
6792292--6792451	80	2.0	80	100	0	320	20	27	28	23	1.99
6794665--6794725	29	2.1	28	81	3	68	24	13	18	44	1.85
6802625--6802694	21	3.4	21	78	9	72	31	27	10	31	1.89
6805963--6806004	18	2.4	18	88	4	59	71	7	4	16	1.26
6806224--6806252	3	9.7	3	100	0	58	68	0	0	31	0.89
6820550--6820591	18	2.4	18	88	4	59	71	7	4	16	1.26
6820832--6820887	2	28.0	2	92	7	96	50	0	1	48	1.11
6820985--6821035	3	17.0	3	100	0	102	66	0	0	33	0.92
6825391--6825419	13	2.1	14	93	6	51	48	3	0	48	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6826771--6826815	21	2.1	22	87	4	65	64	0	26	8	1.23
6826771--6826808	11	3.5	11	82	7	51	65	0	23	10	1.23
6826923--6826961	3	13.0	3	100	0	78	66	0	33	0	0.92
6829111--6829583	155	3.0	154	84	8	652	52	7	10	29	1.63
6839448--6839488	20	2.0	20	85	9	55	36	0	7	56	1.27
6842372--6842430	30	2.0	30	89	0	91	45	10	32	11	1.74
6843206--6843231	6	4.3	6	100	0	52	69	0	15	15	1.20
6846200--6846234	17	2.1	17	100	0	70	25	11	17	45	1.81
6848384--6848569	47	4.0	46	90	4	286	40	15	11	31	1.84
6848384--6848569	92	2.0	92	97	0	354	40	15	11	31	1.84
6848543--6848598	29	1.9	29	96	0	103	39	16	10	33	1.83
6848598--6848682	21	3.9	21	71	17	66	45	14	10	29	1.78
6848576--6848673	45	2.2	45	92	0	160	43	14	11	30	1.80
6849023--6849057	15	2.3	15	90	9	54	51	22	0	25	1.48
6849700--6849823	43	2.9	43	79	13	130	30	27	18	23	1.98
6850968--6851001	16	2.2	16	89	5	52	55	20	0	23	1.43
6852139--6852262	56	2.3	52	82	8	135	22	29	20	27	1.99
6857199--6857256	30	1.9	31	85	3	82	44	0	36	18	1.50
6857544--6857574	9	3.4	9	90	0	53	38	22	12	25	1.90
6859075--6859119	3	15.0	3	100	0	90	66	0	0	33	0.92
6859543--6859581	19	2.1	19	85	0	51	66	20	10	2	1.33
6865185--6865249	25	2.6	25	95	0	112	33	26	18	21	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6869520--6869544	13	1.9	13	100	0	50	32	24	28	16	1.96
6870105--6870162	27	2.1	27	90	0	89	34	31	15	18	1.93
6870111--6870169	27	2.2	27	87	0	82	32	30	15	22	1.94
6878875--6878931	18	3.2	18	78	11	55	50	15	8	24	1.72
6879674--6879708	17	2.0	18	88	5	54	31	20	22	25	1.98
6879754--6879826	34	2.1	34	82	9	87	28	16	28	26	1.97
6879754--6879826	17	4.3	17	72	6	76	28	16	28	26	1.97
6894423--6894452	15	2.0	15	93	0	51	50	0	0	50	1.00
6904754--6904789	6	6.0	6	100	0	72	83	0	16	0	0.65
6908025--6908057	16	2.1	16	100	0	66	36	21	24	18	1.95
6912546--6912581	13	2.9	12	84	8	54	19	5	19	55	1.62
6928329--6928379	26	1.9	26	84	4	66	45	15	11	27	1.81
6937470--6937500	2	15.5	2	93	0	53	48	0	3	48	1.17
6938465--6938776	158	2.0	158	96	0	570	26	8	24	41	1.83
6938858--6938900	20	2.1	19	83	12	50	18	2	20	58	1.50
6949978--6950002	5	5.0	5	100	0	50	20	20	20	40	1.92
6952488--6952611	54	2.3	54	83	2	142	27	26	26	19	1.99
6954683--6954741	26	2.3	26	87	0	82	38	11	18	30	1.87
6959799--6959887	40	2.2	38	75	11	88	41	3	0	55	1.17
6961515--6961561	22	2.2	21	85	7	60	55	14	8	21	1.66
6961995--6962031	19	1.9	19	88	0	56	10	13	2	72	1.21
6972045--6972071	13	2.1	13	100	0	54	85	0	7	7	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6975592--6975644	27	2.0	27	92	0	88	37	11	15	35	1.83
6977973--6978016	21	2.1	21	83	8	54	59	11	6	22	1.55
6978153--6978294	30	4.8	30	76	12	123	40	14	14	31	1.85
6979348--6979424	29	2.6	30	85	4	93	37	9	10	42	1.71
6979373--6979435	29	2.2	29	85	0	81	36	12	7	42	1.72
6990149--6990198	18	2.8	18	78	0	55	42	4	16	38	1.66
6996835--6996878	18	2.4	18	78	10	54	40	2	15	40	1.60
7004802--7004832	16	1.9	16	93	0	53	3	29	6	61	1.37
7011293--7011341	6	7.8	6	86	8	71	0	28	0	71	0.86
7011293--7011342	26	1.9	26	100	0	100	0	28	0	72	0.86
7012384--7012436	18	2.9	18	80	2	61	43	45	0	11	1.40
7012528--7012594	9	7.4	9	81	0	80	28	11	19	40	1.87
7012528--7012594	18	3.7	18	85	0	89	28	11	19	40	1.87
7012534--7012594	27	2.3	27	94	0	104	27	11	19	40	1.86
7012754--7012790	12	3.1	12	92	0	65	18	24	32	24	1.97
7015954--7016171	91	2.4	91	79	3	242	33	14	11	40	1.82
7018569--7018600	15	2.1	15	94	0	55	15	6	9	68	1.36
7019439--7019509	35	2.0	35	100	0	142	26	14	19	39	1.90
7031399--7031456	5	9.7	6	76	23	52	43	0	3	53	1.17
7031357--7031458	17	5.6	17	68	28	59	41	0	2	54	1.22
7038145--7038175	12	2.6	12	94	0	53	29	45	19	6	1.75
7039548--7039584	5	7.6	5	87	6	58	24	0	0	75	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7039543--7039584	15	2.9	14	86	6	66	26	0	0	73	0.83
7041248--7041344	19	5.2	19	76	10	76	45	2	2	50	1.25
7041254--7041310	20	2.9	19	84	7	62	47	1	0	50	1.11
7041284--7041325	22	1.9	22	85	0	57	47	4	0	47	1.23
7044127--7044311	46	4.0	46	95	0	325	35	8	27	28	1.86
7054735--7054811	37	2.1	37	97	0	145	18	20	11	49	1.78
7061180--7061216	3	12.3	3	100	0	74	67	0	0	32	0.91
7064609--7064649	19	2.2	19	95	0	73	34	7	7	51	1.58
7065651--7066169	261	2.0	263	83	2	668	44	22	11	21	1.84
7066596--7066638	17	2.6	17	82	7	54	25	0	0	74	0.82
7066596--7066638	16	2.7	16	80	19	54	25	0	0	74	0.82
7067154--7067211	29	2.1	28	80	6	64	56	3	15	24	1.54
7067219--7067284	18	3.6	18	72	13	53	42	1	1	54	1.18
7075795--7075822	5	5.6	5	100	0	56	39	0	0	60	0.97
7076703--7076741	21	1.9	20	84	5	51	61	0	2	35	1.10
7078447--7078515	3	24.3	3	73	24	53	30	4	1	63	1.22
7078448--7078515	11	5.8	11	74	19	50	30	4	1	63	1.23
7078468--7078516	17	2.9	16	77	16	55	32	2	2	63	1.17
7078522--7078564	21	2.0	21	86	0	59	32	11	2	53	1.50
7080228--7080268	16	2.6	16	84	0	55	65	0	7	26	1.18
7080265--7080313	21	2.4	21	80	6	57	40	4	6	48	1.47
7080774--7080816	18	2.4	18	84	7	61	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7081782--7081852	37	2.0	37	84	13	96	52	2	12	32	1.54
7083068--7083121	23	2.3	23	96	0	99	25	0	24	50	1.50
7083049--7083259	29	7.3	29	83	11	263	29	0	24	45	1.57
7083032--7083239	92	2.3	87	89	6	312	28	0	25	45	1.54
7085387--7085420	15	2.3	15	90	5	52	67	5	0	26	1.13
7085518--7085575	29	2.0	29	90	9	93	58	1	0	39	1.08
7085609--7085657	22	2.2	21	80	16	55	30	0	32	36	1.58
7085612--7085710	52	1.9	52	87	4	146	36	1	30	32	1.65
7085664--7085710	22	2.1	22	88	7	69	40	2	29	27	1.68
7085899--7085957	29	2.2	26	81	9	64	45	15	13	25	1.82

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