genome.fa.s6.2.7.7.80.10.50.1000.27.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  27  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)
7086475--7086542	16	4.2	16	96	0	127	23	0	38	38	1.55
7088933--7088974	18	2.3	18	88	8	59	59	2	7	30	1.37
7095488--7095552	29	2.2	29	100	0	130	32	12	18	36	1.88
7097329--7097354	13	2.0	13	100	0	52	23	23	23	30	1.99
7099143--7099168	11	2.4	11	100	0	52	57	7	26	7	1.54
7105915--7105956	12	3.8	12	81	18	63	61	0	0	38	0.96
7105915--7105956	21	2.0	21	100	0	84	61	0	0	38	0.96
7109337--7109444	26	4.2	26	82	0	126	29	21	21	27	1.98
7118853--7118931	33	2.5	31	81	4	86	20	15	15	49	1.80
7118920--7118999	33	2.4	33	78	0	97	17	21	12	48	1.80
7130237--7130286	20	2.5	20	100	0	100	50	10	4	36	1.55
7130962--7131017	28	2.0	28	96	0	103	53	5	25	16	1.63
7136134--7136194	26	2.3	28	81	10	67	4	31	0	63	1.15
7148260--7148299	2	20.0	2	100	0	80	50	0	0	50	1.00
7150249--7150304	3	18.7	3	81	0	67	60	3	3	32	1.31
7168823--7168876	22	2.4	22	84	9	65	44	11	3	40	1.58
7170009--7170037	5	5.8	5	100	0	58	41	17	0	41	1.49
7174683--7174725	19	2.2	20	84	12	63	32	18	0	48	1.48
7174915--7175035	23	5.3	23	84	2	102	37	19	22	20	1.95
7174917--7175043	46	2.8	45	84	4	139	37	18	22	21	1.95
7174953--7175047	23	4.1	23	87	0	127	40	18	20	21	1.92
7177448--7177516	27	2.6	27	76	0	75	27	26	20	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7184364--7184924	285	2.0	285	98	0	1077	25	25	14	35	1.93
7191716--7191761	20	2.3	21	85	7	60	28	4	4	63	1.33
7196222--7196251	15	2.0	15	100	0	60	33	26	20	20	1.97
7196237--7196527	42	7.0	42	80	10	337	35	26	17	20	1.95
7196237--7196527	84	3.5	84	96	0	537	35	26	17	20	1.95
7198525--7198699	44	4.1	41	80	7	181	34	25	18	20	1.96
7205409--7205558	41	3.7	41	87	0	219	24	28	18	28	1.98
7205964--7205996	12	2.8	12	90	4	50	51	9	3	36	1.49
7206078--7206110	12	2.8	12	90	4	50	51	9	3	36	1.49
7205898--7206222	114	2.9	113	95	0	580	40	14	4	41	1.66
7207195--7207219	13	1.9	13	100	0	50	68	24	0	8	1.16
7212729--7213428	44	15.7	44	68	9	272	31	19	19	29	1.96
7212691--7213071	183	2.1	183	86	2	548	30	17	20	31	1.95
7212906--7213436	222	2.4	222	88	1	776	31	19	20	28	1.97
7212729--7213436	89	7.9	89	77	7	463	31	18	19	29	1.96
7212728--7213436	133	5.3	133	77	6	579	31	18	19	29	1.96
7214036--7214098	26	2.4	26	81	7	65	74	4	7	12	1.19
7214900--7214977	8	9.2	8	72	13	50	29	3	1	65	1.18
7215108--7215206	3	33.0	3	97	0	189	33	1	0	65	0.99
7216850--7216880	15	2.1	15	93	0	53	22	12	9	54	1.67
7217827--7217869	19	2.3	19	100	0	86	48	4	11	34	1.60
7224007--7224091	2	42.0	2	88	11	104	45	0	5	48	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7224763--7224877	41	2.8	41	85	0	149	25	19	23	32	1.97
7226538--7226621	18	4.2	18	69	25	62	21	23	1	53	1.53
7226970--7227018	22	2.2	23	82	10	57	44	8	6	40	1.59
7227026--7227062	17	2.2	17	90	4	58	51	8	0	40	1.32
7236959--7237024	6	11.0	6	100	0	132	33	0	16	50	1.46
7241453--7241522	33	2.1	33	89	5	106	22	14	35	27	1.93
7242530--7242579	18	2.6	19	84	12	59	36	0	6	58	1.23
7242530--7242580	19	2.7	20	82	14	63	35	0	5	58	1.22
7242863--7242910	23	2.1	23	100	0	96	22	8	20	47	1.77
7245385--7245421	18	2.1	18	100	0	74	32	16	27	24	1.96
7247359--7247393	17	2.0	18	94	5	63	42	0	11	45	1.40
7261693--7261798	27	3.9	27	88	0	149	32	12	18	36	1.88
7261692--7261841	54	2.8	54	79	4	151	32	12	18	37	1.87
7261690--7261839	27	5.6	27	77	7	126	32	12	18	37	1.87
7270037--7270089	24	2.2	24	83	12	65	50	0	3	45	1.19
7275125--7275158	18	1.9	17	88	5	50	52	8	0	38	1.33
7276128--7276194	22	3.1	22	78	22	79	56	2	0	40	1.14
7276943--7276988	20	2.3	20	96	0	83	30	2	30	36	1.70
7277302--7277352	22	2.3	22	86	6	68	47	3	7	41	1.51
7284165--7284213	20	2.7	18	77	22	57	51	4	2	42	1.32
7290315--7290354	19	2.1	19	90	0	62	52	0	0	47	1.00
7300563--7300659	20	4.6	20	70	20	65	30	2	3	63	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7300607--7300659	20	2.6	21	84	6	72	30	1	0	67	1.01
7303480--7303542	28	2.2	29	86	11	85	47	0	3	49	1.17
7305786--7305816	16	1.9	16	93	0	53	41	0	3	54	1.16
7306347--7306387	21	2.0	21	85	9	57	36	2	0	60	1.10
7311007--7311032	2	13.0	2	100	0	52	50	0	0	50	1.00
7311574--7311732	79	2.0	79	84	10	209	22	10	13	53	1.70
7313489--7313556	34	2.0	34	91	0	109	26	22	16	35	1.94
7315057--7315129	38	1.9	38	91	0	119	32	36	0	30	1.58
7318541--7318590	23	2.2	23	92	0	82	36	20	16	28	1.93
7327920--7328007	27	3.3	27	78	0	86	19	27	20	32	1.97
7328869--7328920	26	2.0	26	100	0	104	34	15	11	38	1.83
7329147--7329183	17	2.2	17	90	0	56	43	2	13	40	1.58
7333076--7333115	21	1.9	21	90	10	64	27	5	20	47	1.70
7337770--7337882	27	4.2	27	80	2	120	20	15	23	41	1.89
7337770--7337882	54	2.1	54	85	6	149	20	15	23	41	1.89
7340016--7340310	50	5.9	50	82	3	319	28	20	28	22	1.99
7340512--7340562	12	4.3	12	78	9	52	52	3	25	17	1.61
7341785--7341822	6	6.0	6	88	11	58	18	2	15	63	1.43
7341882--7341918	15	2.4	16	90	4	58	16	0	32	51	1.45
7342315--7342363	23	2.1	24	84	3	64	38	46	2	12	1.53
7343514--7343565	22	2.4	22	96	3	97	13	19	28	38	1.89
7343514--7343573	22	2.8	21	89	2	84	15	18	25	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7343661--7343828	42	4.0	42	87	2	237	32	21	20	25	1.98
7343656--7343828	85	2.0	86	89	1	267	32	21	20	25	1.97
7344230--7344278	21	2.3	21	89	0	71	2	46	18	32	1.60
7347961--7348091	9	14.7	9	70	14	58	36	1	17	44	1.58
7348026--7348090	25	2.8	25	77	15	77	36	0	18	44	1.50
7349716--7349747	6	5.3	6	96	0	55	18	12	50	18	1.78
7350645--7350675	8	4.0	8	95	4	55	22	0	0	77	0.77
7350902--7350996	7	13.3	7	72	11	50	47	28	4	20	1.68
7350944--7351214	151	1.8	150	90	0	434	46	32	2	17	1.63
7351656--7352155	72	6.9	72	83	3	542	25	21	20	32	1.97
7351656--7352135	145	3.3	144	82	2	568	26	22	19	32	1.97
7352700--7352737	20	1.9	20	89	10	60	34	7	0	57	1.28
7353908--7353964	16	3.6	16	95	0	87	29	0	36	33	1.58
7354211--7354245	18	2.0	17	88	5	52	54	0	0	45	0.99
7354170--7354241	28	2.6	28	73	6	65	52	2	0	44	1.15
7354323--7354364	15	2.7	16	82	14	52	52	2	0	45	1.13
7354332--7354373	15	2.9	15	82	10	52	52	0	0	47	1.00
7354138--7354389	132	1.9	135	95	3	456	49	3	1	44	1.30
7354329--7354617	120	2.4	120	91	5	453	50	4	2	41	1.38
7354446--7354483	16	2.4	17	82	13	53	55	0	0	44	0.99
7354442--7354493	15	3.6	15	80	12	56	53	0	0	46	1.00
7354419--7354509	44	2.1	43	83	6	112	53	2	2	41	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7354361--7354544	60	3.1	59	64	16	144	49	6	2	41	1.41
7354578--7354616	17	2.5	15	80	15	51	51	0	5	43	1.24
7354583--7354616	17	2.0	17	94	0	59	50	0	5	44	1.26
7354649--7354843	93	2.1	92	86	6	270	46	5	4	44	1.44
7368899--7368936	20	1.9	20	94	0	67	47	7	18	26	1.76
7373332--7373374	14	3.1	14	80	12	54	51	4	2	41	1.35
7374343--7374376	2	17.0	2	100	0	68	50	0	0	50	1.00
7380788--7380904	22	5.6	22	72	20	81	38	27	21	12	1.90
7380764--7380924	38	4.1	38	72	18	132	38	26	20	14	1.91
7388842--7388937	50	1.9	51	82	2	122	37	12	14	35	1.84

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