genome.fa.s17.2.7.7.80.10.50.1000.14.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: D04
Parameters: 2 7 7 80 10 50 1000
Length:  56598092

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   

This is table  14  of  185  ( 22116 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)
3767751--3767813	6	10.2	6	81	10	65	34	1	44	19	1.60
3767795--3767987	60	3.3	59	78	11	232	32	3	49	14	1.61
3767798--3767897	28	3.4	28	70	15	94	32	5	51	12	1.60
3767770--3767987	118	1.8	118	93	1	375	32	3	48	15	1.63
3768003--3768317	31	10.8	29	84	9	392	50	0	10	38	1.41
3768003--3768318	60	5.4	60	83	10	411	50	0	10	38	1.41
3768194--3768244	24	2.2	23	93	6	93	43	0	11	45	1.40
3768043--3768307	84	3.1	87	91	6	434	50	0	10	39	1.39
3772162--3772214	21	2.5	21	90	0	79	32	39	7	20	1.81
3776082--3776143	32	2.0	32	81	12	76	33	6	4	54	1.47
3777795--3777894	42	2.4	42	91	3	157	38	11	29	22	1.88
3781095--3781165	31	2.4	30	76	4	81	45	11	7	36	1.67
3784349--3784373	3	8.3	3	100	0	50	0	36	0	64	0.94
3796879--3796945	17	3.8	17	72	16	57	38	7	14	38	1.75
3799104--3799128	13	1.9	13	100	0	50	44	8	0	48	1.32
3802007--3802098	48	1.9	48	84	0	121	21	21	3	53	1.60
3802270--3802330	28	2.1	31	85	14	85	27	14	6	50	1.68
3811204--3811244	9	4.6	9	81	0	55	53	2	0	43	1.13
3823059--3823095	18	2.1	18	100	0	74	48	5	10	35	1.61
3823346--3823434	29	3.0	30	77	6	92	50	12	12	24	1.74
3823596--3823636	21	2.0	21	90	9	66	68	4	0	26	1.10
3824278--3824356	21	3.8	20	70	11	61	25	1	12	60	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3828447--3828644	41	4.8	41	86	3	238	28	18	29	23	1.98
3834631--3834739	25	4.4	25	76	0	101	26	23	13	35	1.93
3834631--3834739	50	2.2	50	81	3	121	26	23	13	35	1.93
3837518--3837561	23	1.9	22	82	17	54	38	22	0	38	1.55
3839944--3839982	18	2.2	18	85	0	51	12	23	2	61	1.43
3846566--3846611	20	2.3	20	100	0	92	43	13	21	21	1.86
3848314--3848354	19	2.0	21	86	9	59	24	31	0	43	1.54
3848315--3848475	72	2.2	72	78	12	163	27	27	0	45	1.54
3850925--3850984	21	2.9	21	78	11	70	33	25	23	18	1.97
3852170--3852201	16	2.1	16	94	5	57	40	0	0	59	0.97
3852789--3852830	20	2.0	21	86	4	59	59	0	0	40	0.97
3856670--3856713	17	2.7	15	83	13	52	50	0	2	47	1.13
3871859--3871884	13	2.0	13	100	0	52	38	15	15	30	1.88
3884178--3884373	97	2.0	97	96	0	365	32	11	15	40	1.83
3884753--3884796	23	1.9	23	85	0	61	50	0	0	50	1.00
3886932--3887250	73	4.4	73	91	1	487	27	23	26	22	2.00
3887145--3887458	114	2.8	114	89	3	474	24	21	27	26	1.99
3887778--3887809	14	2.3	14	100	0	64	28	0	34	37	1.57
3887827--3887875	7	6.4	7	78	17	53	18	2	46	32	1.60
3887827--3887875	15	3.2	15	85	8	55	18	2	46	32	1.60
3887824--3887874	23	2.2	24	92	3	86	15	1	49	33	1.56
3888102--3888142	21	1.9	22	85	5	57	21	0	36	41	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3888125--3888173	14	3.5	13	86	13	62	22	0	44	32	1.53
3887674--3888287	303	2.0	299	90	4	959	28	2	27	41	1.67
3888300--3888498	106	1.9	106	90	1	317	51	11	9	28	1.68
3888551--3888760	103	2.0	104	87	5	305	48	12	12	27	1.76
3888300--3888957	241	2.6	245	87	7	927	48	12	12	27	1.76
3890172--3890236	30	2.1	31	83	8	80	32	4	12	50	1.60
3890373--3890433	31	2.0	31	83	6	79	42	6	9	40	1.64
3909259--3909302	20	2.2	21	84	12	65	61	4	0	34	1.16
3909260--3909330	19	3.7	19	83	9	83	57	4	1	36	1.27
3909381--3909410	9	3.4	9	90	9	53	53	0	10	36	1.35
3912826--3912893	20	3.5	19	82	8	75	54	4	2	38	1.36
3912826--3912903	19	4.1	19	79	9	79	55	5	2	37	1.36
3916296--3916376	40	2.0	40	100	0	162	39	2	22	35	1.67
3916293--3916387	40	2.4	40	91	5	140	44	3	21	31	1.68
3930026--3930136	6	19.0	6	87	5	156	30	0	0	69	0.89
3930038--3930126	46	2.0	46	95	2	162	31	0	0	68	0.90
3930032--3930132	51	2.0	52	94	2	177	30	0	0	69	0.89
3939475--3939781	47	6.6	47	91	1	474	38	14	19	28	1.90
3939498--3939781	93	3.0	93	94	0	496	38	14	19	28	1.91
3939498--3939781	140	2.0	140	95	1	507	38	14	19	28	1.91
3940622--3940737	43	2.7	43	79	15	141	27	29	20	22	1.99
3945767--3945799	17	2.1	16	88	11	50	24	0	18	57	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3966213--3966265	17	3.2	17	86	5	72	50	3	1	43	1.30
3966224--3966264	16	2.5	16	84	4	55	51	4	2	41	1.36
3966311--3966336	3	8.7	3	100	0	52	69	0	30	0	0.89
3968725--3968762	18	2.2	17	90	4	58	34	0	0	65	0.93
3969015--3969052	9	4.3	9	80	6	51	26	0	2	71	1.00
3971345--3971432	30	2.8	32	75	14	87	52	12	11	23	1.71
3972633--3972696	23	2.8	22	80	4	74	17	15	26	40	1.89
3975112--3975289	89	2.0	89	100	0	356	39	26	4	29	1.76
3980821--3980958	74	1.9	74	84	6	190	31	10	21	35	1.88
3981076--3981116	8	5.1	8	91	8	66	36	0	0	63	0.95
3981082--3981116	17	2.1	17	100	0	70	34	0	0	65	0.93
3983652--3983784	68	1.9	71	84	4	182	33	7	16	42	1.76
3983971--3984084	41	2.8	40	90	5	174	27	19	21	31	1.97
3988685--3988800	41	2.8	42	92	2	182	31	22	17	28	1.96
3989864--3989901	16	2.4	16	100	0	76	26	13	0	60	1.33
3990365--3990408	19	2.2	20	88	4	63	34	6	2	56	1.38
3990627--3990655	14	2.0	15	93	6	51	51	20	0	27	1.47
3992796--3992841	2	23.0	2	100	0	92	50	0	50	0	1.00
4000362--4000394	13	2.5	13	95	0	57	57	6	9	27	1.53
4007842--4007898	27	2.2	26	84	9	71	28	8	0	63	1.24
4008015--4008057	22	1.9	23	85	4	61	58	4	0	37	1.19
4008090--4008311	86	2.6	84	78	4	192	25	18	27	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4008158--4008317	86	1.9	86	89	0	248	23	19	29	27	1.98
4008150--4008317	43	3.9	43	84	0	210	26	19	28	26	1.98
4008608--4008645	19	2.0	20	90	10	62	52	0	0	47	1.00
4011826--4011867	22	1.9	22	85	0	57	28	2	16	52	1.56
4015000--4015054	26	2.1	26	96	0	101	16	10	20	52	1.73
4018800--4018906	54	2.0	54	87	7	155	26	26	16	30	1.97
4041886--4041931	23	2.0	23	86	0	65	43	13	15	28	1.83
4041888--4041937	23	2.2	23	81	0	55	50	12	12	26	1.74
4048436--4048475	17	2.3	18	83	12	57	32	0	7	60	1.25
4048436--4048489	17	3.1	17	76	12	56	35	0	5	59	1.21
4063011--4063071	24	2.5	23	80	15	61	49	4	0	45	1.23
4063019--4063102	35	2.4	33	84	9	105	48	4	0	46	1.23
4067307--4067392	44	2.0	43	88	2	127	41	6	5	45	1.55
4068524--4068645	34	3.6	34	73	4	111	39	13	14	32	1.85
4071957--4072002	19	2.3	20	92	3	76	34	10	19	34	1.87
4074525--4074580	18	3.1	18	80	14	69	66	3	0	30	1.09
4075061--4075109	24	2.1	24	85	14	68	51	0	2	46	1.12
4076877--4076921	22	2.0	22	100	0	90	35	8	0	55	1.31
4077060--4077137	19	4.2	19	83	3	104	34	11	1	52	1.46
4077073--4077143	37	1.9	37	97	0	133	38	11	1	49	1.48
4077361--4077429	19	3.7	18	84	3	84	37	8	0	53	1.32
4077695--4077765	37	1.9	37	97	0	133	49	1	11	38	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4077701--4077765	19	3.5	19	82	4	96	49	1	10	38	1.47
4077843--4077920	27	2.9	27	85	7	106	17	29	23	29	1.97
4077844--4077929	27	3.2	26	85	4	102	18	26	23	31	1.97
4077967--4078014	24	2.0	24	95	0	87	52	0	8	39	1.32
4088702--4088741	16	2.5	17	92	8	66	50	0	0	50	1.00
4088944--4088984	18	2.4	18	84	8	59	56	0	0	43	0.99
4088944--4088997	18	3.3	16	78	12	56	53	0	0	46	1.00
4089540--4089564	2	12.5	2	100	0	50	0	52	0	48	1.00
4094425--4094463	20	1.9	21	89	5	62	33	10	17	38	1.84
4100499--4100642	72	2.0	70	90	2	225	61	5	27	5	1.41

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185