genome.fa.s6.2.7.7.80.10.50.1000.13.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  13  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)
3578985--3579038	18	2.9	18	86	8	65	51	7	1	38	1.41
3579653--3579690	19	2.0	19	100	0	76	15	21	10	52	1.72
3583012--3583059	21	2.2	22	89	10	73	58	14	0	27	1.37
3583686--3583726	16	2.5	17	80	15	50	70	0	4	24	1.06
3590960--3591004	22	2.0	22	83	8	56	48	2	2	46	1.26
3605896--3605937	22	1.9	22	90	0	66	54	16	19	9	1.69
3608785--3609055	36	7.0	36	77	16	267	28	21	13	36	1.91
3608855--3609091	46	5.6	46	75	18	271	28	21	13	37	1.90
3608819--3609091	82	3.3	82	96	0	492	29	20	12	37	1.90
3611123--3611164	21	2.0	21	85	0	57	45	11	4	38	1.62
3617441--3617602	29	5.7	29	64	11	73	35	17	20	26	1.95
3617425--3617626	58	3.5	57	79	4	219	37	18	19	24	1.94
3617541--3617626	29	3.0	29	81	6	111	39	19	18	22	1.92
3618926--3619218	27	11.0	26	82	4	293	17	18	21	42	1.89
3618927--3619222	54	5.5	54	81	4	357	17	18	21	42	1.89
3618927--3619219	81	3.6	81	85	3	396	17	18	21	42	1.89
3628786--3628898	9	13.9	8	70	22	58	20	5	1	72	1.13
3628960--3629035	3	25.0	3	75	15	59	25	3	5	65	1.31
3629255--3629366	40	2.8	39	87	6	161	36	3	0	59	1.15
3629303--3629356	28	1.9	28	81	7	65	35	3	0	61	1.14
3655066--3655526	44	10.6	44	73	11	303	29	20	21	28	1.98
3654997--3655526	217	2.4	217	86	1	715	29	20	23	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3657941--3658618	44	15.6	44	73	11	413	29	19	22	27	1.98
3657943--3658181	128	1.9	129	81	9	301	27	20	24	27	1.99
3657909--3658221	173	1.8	173	81	8	395	28	20	24	26	1.99
3657872--3658618	217	3.4	216	89	1	1102	29	19	23	26	1.98
3661094--3661554	44	10.6	44	74	10	310	29	20	22	28	1.98
3661025--3661554	217	2.4	217	87	0	731	29	20	23	26	1.98
3663972--3664689	44	16.6	44	74	11	411	28	20	22	27	1.99
3664062--3664172	40	2.8	40	95	1	195	21	23	26	28	1.99
3663903--3664567	257	2.6	257	85	5	824	29	20	24	26	1.99
3663940--3664689	217	3.5	217	83	4	860	29	20	23	27	1.99
3667622--3667754	44	3.0	43	78	8	142	33	18	19	29	1.95
3671615--3671676	31	2.0	31	87	6	90	50	14	6	29	1.68
3677803--3677867	32	2.1	32	94	2	114	46	12	9	32	1.73
3687832--3688519	44	15.8	44	69	15	319	29	20	23	27	1.99
3687917--3688511	89	6.8	87	70	16	349	28	20	23	27	1.99
3687831--3688157	173	1.9	173	79	9	373	28	21	22	27	1.99
3687824--3688519	217	3.2	216	91	0	1088	29	20	22	27	1.99
3688497--3688536	21	2.0	21	85	5	55	32	10	35	22	1.87
3692536--3693036	44	11.5	44	70	13	304	28	20	22	28	1.98
3692532--3693103	217	2.6	217	92	0	937	29	19	22	27	1.98
3693295--3693538	44	5.6	44	71	11	180	30	19	20	29	1.97
3694473--3694541	29	2.4	30	76	9	72	27	1	5	65	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3710371--3711572	44	27.9	43	72	13	546	29	20	22	27	1.99
3710700--3710779	39	2.1	39	97	0	151	30	22	22	25	1.99
3710546--3711527	128	7.6	127	69	16	441	28	20	23	27	1.99
3710593--3711174	216	2.7	216	88	4	813	28	20	23	26	1.99
3711107--3711261	40	3.8	41	74	9	154	25	22	22	29	1.99
3710850--3711475	300	2.1	301	91	0	1011	28	20	22	28	1.99
3711066--3711258	84	2.3	84	93	0	332	26	21	22	29	1.99
3711066--3711305	84	2.8	84	85	6	317	27	21	23	27	1.99
3716533--3716576	11	4.0	11	93	0	79	27	6	9	56	1.55
3728022--3728140	24	5.0	24	86	0	130	23	17	25	33	1.96
3728107--3728245	64	2.2	64	88	0	206	27	20	25	26	1.99
3728158--3728204	24	2.0	24	83	8	60	25	21	23	29	1.99
3729634--3729752	48	2.5	48	88	2	168	26	21	24	27	1.99
3729634--3729750	24	4.9	24	81	3	128	26	21	23	28	1.99
3729740--3730077	180	1.9	180	91	0	559	26	14	26	31	1.95
3737793--3738547	114	6.6	114	89	0	1035	34	19	20	25	1.96
3737797--3738547	341	2.2	342	87	2	1089	34	19	20	25	1.96
3738981--3739023	22	2.0	21	86	4	59	16	2	30	51	1.57
3738995--3739034	21	1.9	21	85	10	55	20	2	30	47	1.63
3739117--3739148	14	2.3	14	94	0	55	9	0	43	46	1.35
3739145--3739169	7	3.6	7	100	0	50	24	0	16	60	1.36
3739138--3739177	14	2.9	14	80	0	53	20	0	27	52	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3739742--3739987	72	3.4	72	69	8	219	24	15	22	37	1.92
3739749--3740046	147	2.0	147	94	0	524	24	13	20	40	1.89
3741941--3742109	20	8.8	20	74	12	156	48	6	5	39	1.52
3741962--3742141	57	3.2	57	95	0	315	46	7	5	41	1.54
3742053--3742246	87	2.2	84	81	12	223	41	11	4	42	1.60
3747815--3747861	21	2.2	21	84	0	58	40	19	38	2	1.63
3748481--3748596	41	2.8	41	81	1	142	25	24	22	27	2.00
3751064--3751494	44	9.8	44	84	2	506	29	24	14	31	1.94
3751064--3751494	221	2.0	219	91	1	693	29	24	14	31	1.94
3751063--3751569	221	2.3	219	86	3	660	28	24	16	30	1.96
3751495--3752394	88	10.2	88	87	1	1126	24	26	23	25	2.00
3752200--3752329	44	3.0	43	65	7	100	20	25	26	26	1.99
3758935--3758989	21	2.7	21	91	5	87	36	18	10	34	1.86
3761441--3761618	97	1.8	98	90	3	288	34	17	18	29	1.94
3762038--3762083	19	2.3	20	85	7	58	28	2	4	65	1.23
3764285--3764504	5	44.0	5	90	3	354	40	1	19	39	1.62
3764707--3764746	21	2.0	21	85	5	55	17	7	12	62	1.52
3765210--3765244	17	2.1	16	89	5	52	62	0	0	37	0.95
3765199--3765247	20	2.3	20	82	6	62	65	0	2	32	1.04
3774947--3774979	16	2.1	16	88	11	50	36	3	15	45	1.61
3775721--3775749	15	1.9	15	100	0	58	55	0	0	44	0.99
3777788--3777985	69	2.8	70	82	1	245	32	24	21	22	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3777788--3777995	70	3.0	70	82	1	247	32	23	21	22	1.98
3778499--3778549	16	3.4	16	70	25	56	33	15	1	49	1.56
3778486--3778558	29	2.5	29	100	0	146	32	16	4	46	1.66
3778949--3779002	20	2.7	19	76	23	58	70	0	3	25	1.04
3779854--3779896	13	3.5	13	81	18	65	48	16	0	34	1.46
3779852--3779898	23	2.0	23	100	0	94	46	17	0	36	1.48
3779856--3779905	23	2.2	23	92	0	82	52	14	0	34	1.42
3781853--3781889	19	1.9	19	94	0	65	24	13	27	35	1.93
3782664--3782697	6	5.3	6	86	13	50	20	0	0	79	0.73
3789739--3789788	23	2.2	23	92	0	82	54	12	0	34	1.38
3814209--3814266	21	2.8	21	80	14	66	0	22	1	75	0.89
3814207--3814261	22	2.5	23	85	11	71	0	23	1	74	0.91
3825055--3825149	26	3.6	25	71	22	70	28	3	1	67	1.13
3825056--3825149	9	10.6	9	73	14	79	28	3	1	67	1.13
3825462--3825517	28	2.0	29	86	10	80	28	0	1	69	0.98
3827583--3827692	51	2.2	51	85	3	141	29	15	9	46	1.76
3829456--3829503	15	3.0	16	75	9	53	37	0	4	58	1.18
3832621--3832657	2	18.5	2	94	0	65	48	0	0	51	1.00
3835832--3835893	31	2.1	30	84	6	81	50	4	0	45	1.23
3842450--3842484	3	11.7	3	100	0	70	0	0	31	68	0.90
3842585--3842628	13	3.7	13	77	22	60	54	0	0	45	0.99
3842572--3842629	22	2.7	22	97	2	109	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3847012--3847038	11	2.5	11	100	0	54	33	22	11	33	1.89
3848106--3848149	16	2.6	17	89	3	63	18	0	25	56	1.41
3848109--3848149	17	2.5	16	88	4	55	17	0	26	56	1.41
3848602--3848643	20	2.0	21	81	9	50	54	2	7	35	1.41
3854875--3854920	20	2.2	20	80	7	56	69	2	21	6	1.22
3855776--3855822	3	15.7	3	90	0	76	31	2	2	63	1.18
3855874--3855926	21	2.5	21	84	12	72	30	0	5	64	1.17
3862686--3862803	30	3.8	29	76	15	101	27	23	16	32	1.96
3864297--3864383	2	43.5	2	100	0	174	50	0	49	0	1.00
3870988--3871027	11	3.6	11	89	0	62	65	2	0	32	1.06

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