genome.fa.s17.2.7.7.80.10.50.1000.16.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  16  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)
4356419--4356479	24	2.5	23	80	15	61	45	0	4	49	1.23
4357705--4357792	39	2.2	40	79	2	97	36	5	20	37	1.76
4357999--4358098	45	2.2	45	87	0	137	21	20	20	39	1.93
4360939--4360967	14	2.1	14	100	0	58	34	31	0	34	1.58
4368236--4368278	16	2.6	16	77	3	50	72	4	11	11	1.27
4372901--4372943	22	2.0	22	90	0	68	11	20	25	41	1.86
4373049--4373140	42	2.2	43	86	2	123	22	22	29	25	1.99
4373110--4373248	43	3.2	43	86	4	183	20	19	29	30	1.97
4373134--4373274	43	3.3	41	76	9	113	24	22	26	26	2.00
4373242--4373381	43	3.3	43	80	4	140	27	30	18	22	1.97
4373272--4373405	43	3.1	44	83	3	139	32	29	17	20	1.96
4373754--4373846	21	4.4	21	78	5	98	7	44	13	34	1.73
4373822--4373865	21	2.1	21	86	0	61	2	40	18	38	1.63
4373857--4373983	66	1.9	66	85	6	177	16	25	18	39	1.91
4373876--4374006	66	2.0	66	84	3	174	16	24	18	41	1.90
4378925--4379006	41	2.0	42	83	9	107	34	23	12	30	1.91
4379687--4379772	39	2.2	39	85	6	113	39	39	2	18	1.64
4380832--4380894	7	8.7	7	86	6	81	47	38	1	12	1.51
4380832--4380894	29	2.2	29	88	5	92	47	38	1	12	1.51
4380832--4380894	22	2.9	22	92	0	99	47	38	1	12	1.51
4381182--4381516	113	2.9	112	82	8	372	29	25	22	22	1.99
4381412--4381555	74	1.9	74	81	6	175	26	23	25	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4396442--4396506	26	2.6	25	83	9	80	41	4	3	50	1.38
4396442--4396500	24	2.4	24	85	5	82	40	3	3	52	1.35
4399088--4399156	31	2.2	32	82	7	88	44	10	17	27	1.80
4403347--4403376	12	2.5	12	94	0	51	76	13	0	10	1.01
4403573--4403597	13	1.9	13	100	0	50	88	0	12	0	0.53
4404127--4404179	27	2.0	27	85	7	72	11	5	5	77	1.11
4408136--4408187	27	2.0	24	82	10	59	34	7	7	50	1.60
4417064--4417140	29	2.5	31	83	4	95	49	12	11	25	1.75
4420922--4420949	10	2.8	10	100	0	56	32	10	7	50	1.64
4423383--4423452	18	3.6	18	68	20	59	42	8	25	22	1.82
4427960--4428008	18	2.7	18	75	9	55	36	0	0	63	0.95
4428962--4428998	16	2.4	16	95	4	67	56	5	2	35	1.36
4429122--4429239	60	2.0	60	88	3	175	53	12	0	33	1.45
4429232--4429376	19	7.3	19	73	18	102	55	12	0	31	1.37
4429307--4429372	21	3.2	21	85	10	91	59	10	0	30	1.31
4429381--4429442	27	2.3	27	82	0	70	17	29	25	27	1.98
4429516--4429578	27	2.3	27	83	5	83	58	0	0	41	0.98
4435195--4435260	31	2.2	31	86	2	89	45	4	6	43	1.49
4436421--4436445	13	1.9	13	100	0	50	72	0	0	28	0.86
4442246--4442279	17	2.1	16	88	5	50	55	0	8	35	1.31
4442712--4442736	11	2.3	11	100	0	50	44	28	8	20	1.79
4446840--4446864	10	2.5	10	100	0	50	60	20	8	12	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4448604--4448668	32	2.0	32	96	0	121	26	6	20	47	1.73
4448760--4448878	40	3.0	38	82	4	130	38	19	21	20	1.93
4448915--4449071	41	3.8	42	83	4	169	21	19	26	33	1.97
4448915--4449071	83	1.9	83	83	7	203	21	19	26	33	1.97
4449695--4449729	15	2.4	15	90	4	54	17	0	42	40	1.49
4450920--4451220	82	3.7	81	73	7	221	28	15	20	34	1.94
4450365--4451699	448	3.0	449	92	2	2120	30	15	19	34	1.93
4451468--4451627	82	2.0	82	82	5	198	27	16	18	37	1.92
4451873--4451911	14	2.8	14	80	0	51	76	7	10	5	1.13
4452233--4452293	16	3.8	16	82	4	86	22	4	13	59	1.53
4452230--4452294	33	2.0	33	100	0	130	23	6	12	58	1.56
4452863--4452893	12	2.6	12	94	0	53	6	9	16	67	1.39
4453852--4453911	33	1.9	30	80	12	68	33	8	15	43	1.76
4453937--4453969	10	3.1	11	86	8	50	33	9	21	36	1.85
4454028--4454060	13	2.5	13	95	0	57	42	12	0	45	1.41
4454000--4454060	24	2.4	27	74	23	69	44	11	1	42	1.50
4465600--4465719	43	2.8	42	78	15	131	25	20	25	29	1.99
4466638--4466801	23	7.0	23	77	6	123	26	14	18	40	1.88
4466647--4466805	70	2.2	72	84	7	218	27	14	18	39	1.89
4467192--4467253	5	12.2	5	85	11	74	43	0	0	56	0.99
4467193--4467254	2	35.0	2	73	23	59	45	0	0	54	0.99
4468258--4468332	19	4.0	19	69	20	68	36	1	25	37	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4474989--4475023	16	2.2	16	90	5	54	80	0	0	20	0.72
4476466--4476533	30	2.2	31	86	2	93	26	22	19	32	1.97
4476386--4476600	89	2.4	86	82	5	252	23	19	17	39	1.92
4481342--4481428	14	6.1	15	65	20	53	47	0	2	50	1.13
4481413--4481471	17	3.7	16	73	15	52	54	1	1	42	1.20
4481444--4481477	16	2.1	16	94	0	59	55	0	0	44	0.99
4485608--4485645	18	2.1	19	90	5	60	21	21	5	52	1.66
4493019--4493054	18	1.9	18	88	5	54	58	2	0	38	1.13
4493494--4493582	9	8.5	11	89	10	70	65	1	3	30	1.16
4493513--4493577	3	22.0	3	87	9	98	66	0	1	32	1.01
4495418--4495531	43	2.7	43	80	13	144	25	18	25	30	1.98
4496434--4496482	2	24.5	2	87	0	71	53	2	0	44	1.12
4496434--4496473	14	2.9	14	100	0	80	55	0	0	45	0.99
4496495--4496601	23	4.6	23	72	2	88	25	14	16	42	1.87
4496492--4496670	71	2.5	72	80	9	206	29	12	17	40	1.87
4499356--4499466	40	2.8	40	95	0	195	41	2	0	54	1.20
4499366--4499445	11	7.5	11	73	18	71	40	3	1	55	1.26
4499356--4499482	40	3.2	40	90	1	182	39	2	0	57	1.17
4499455--4499495	22	1.9	22	95	5	75	39	0	0	60	0.96
4501907--4501954	21	2.2	22	81	7	53	22	2	4	70	1.15
4507928--4507967	20	2.0	20	85	9	55	35	10	10	45	1.71
4509016--4509073	30	1.9	30	100	0	116	24	6	8	60	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4509369--4509404	15	2.3	16	90	4	56	69	2	2	25	1.15
4509537--4509582	10	4.5	11	78	13	53	15	0	8	76	1.02
4512309--4512355	21	2.2	22	92	3	78	21	38	19	21	1.94
4517251--4517298	19	2.5	20	89	3	71	56	6	0	37	1.25
4517251--4517304	19	2.9	18	86	8	56	51	5	0	42	1.25
4517999--4518150	37	3.9	37	80	13	164	26	21	15	36	1.93
4518067--4518439	52	7.6	46	83	11	388	28	22	14	34	1.93
4518110--4518433	52	6.3	52	87	5	453	28	22	14	35	1.93
4518110--4518425	151	2.1	153	92	3	528	28	22	13	35	1.93
4518067--4518433	203	1.8	203	92	0	617	28	22	14	35	1.93
4528239--4528286	21	2.3	21	100	0	96	31	8	16	43	1.78
4529616--4529663	19	2.5	20	89	3	71	56	6	0	37	1.25
4529616--4529669	19	2.9	18	86	8	56	51	5	0	42	1.25
4531371--4531417	22	2.1	22	84	7	60	36	2	4	57	1.30
4531574--4531715	70	2.0	70	100	0	284	46	2	9	40	1.52
4531698--4531754	16	3.6	16	90	0	87	45	3	3	47	1.37
4531728--4531789	22	2.7	23	90	5	90	48	1	1	48	1.21
4533866--4535053	500	2.4	492	77	5	1203	38	13	11	36	1.81
4535628--4535662	15	2.3	15	90	0	52	40	8	2	48	1.49
4539926--4539987	31	2.0	31	93	0	106	50	16	8	25	1.72
4550437--4550569	45	3.0	43	79	13	148	25	17	26	30	1.97
4551989--4552032	24	1.9	23	86	9	63	34	4	22	38	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4560577--4560625	21	2.2	23	82	7	57	59	2	0	38	1.09
4561862--4561912	21	2.4	21	96	0	93	9	27	17	45	1.80
4561862--4561931	21	3.3	21	87	0	68	14	24	14	47	1.81
4563440--4563484	22	2.1	22	87	4	65	13	17	26	42	1.86
4563554--4563730	42	4.2	42	84	3	153	27	32	17	23	1.97
4563575--4563757	42	4.3	43	83	4	194	31	31	16	20	1.95
4563596--4563762	86	2.0	84	85	5	228	29	31	16	22	1.96
4564032--4564122	43	2.1	43	87	2	130	43	9	10	35	1.73
4568098--4568124	13	2.1	13	100	0	54	29	7	7	55	1.55
4568580--4568631	7	7.4	7	84	0	59	32	44	0	23	1.54

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