genome.fa.s4.2.7.7.80.10.50.1000.16.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: A04
Parameters: 2 7 7 80 10 50 1000
Length:  82679320

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   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255   

This is table  16  of  255  ( 30512 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)
4326569--4326662	46	2.1	46	86	7	131	52	10	11	25	1.70
4326695--4326755	23	2.6	24	89	5	99	40	11	4	42	1.62
4326695--4326755	24	2.7	23	87	5	88	40	11	4	42	1.62
4327407--4327437	14	2.2	14	94	0	53	6	22	45	25	1.76
4327458--4327488	7	4.4	7	100	0	62	12	0	0	87	0.55
4327480--4327524	23	2.1	21	84	12	56	2	22	0	75	0.91
4327488--4327535	21	2.2	23	85	7	64	0	29	0	70	0.87
4328072--4328173	30	3.4	30	82	2	107	43	3	22	30	1.71
4328443--4328661	54	4.1	55	86	9	308	36	16	16	29	1.91
4328443--4328653	107	2.0	104	89	4	325	36	17	16	29	1.92
4328640--4328674	14	2.5	14	90	0	52	60	2	17	20	1.49
4328762--4329009	85	2.8	87	81	10	308	36	18	18	26	1.94
4328922--4328955	16	2.1	16	88	0	50	64	5	11	17	1.45
4328762--4329016	91	2.9	88	83	9	324	36	18	18	26	1.94
4328974--4329968	192	5.2	192	97	0	1870	35	20	13	30	1.92
4329290--4329516	122	1.9	122	84	3	305	34	21	14	30	1.92
4328974--4329968	383	2.6	383	98	0	1884	35	20	13	30	1.92
4346490--4346540	26	1.9	27	84	11	70	45	0	0	54	0.99
4346575--4346612	19	2.0	20	89	5	60	21	0	13	65	1.26
4347296--4347376	40	2.0	40	85	0	108	62	9	2	24	1.38
4347362--4347419	20	2.9	19	71	14	55	62	0	3	34	1.12
4347398--4347444	23	2.0	23	87	0	67	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4356486--4356528	22	2.0	22	81	9	52	39	0	2	58	1.11
4363115--4363279	83	2.0	83	89	0	249	34	27	9	28	1.88
4367148--4367187	15	2.7	15	92	3	64	30	22	17	30	1.97
4367151--4367198	15	3.2	15	88	5	53	33	20	14	31	1.93
4367161--4367211	17	3.1	16	78	16	50	33	19	11	35	1.88
4370835--4371012	92	1.9	92	95	0	320	28	19	22	29	1.98
4371651--4371719	29	2.4	27	75	13	66	28	13	8	49	1.71
4379536--4379567	16	2.0	16	100	0	64	43	18	6	31	1.75
4382039--4382072	18	1.9	18	88	5	52	64	5	2	26	1.30
4383391--4383451	22	2.8	22	73	14	54	59	1	4	34	1.29
4383405--4383459	9	5.6	9	80	16	56	61	1	3	32	1.24
4383404--4383461	10	5.7	10	76	11	55	62	1	3	32	1.22
4389677--4389727	18	2.8	18	73	26	54	64	0	3	31	1.11
4390868--4390927	20	3.2	20	81	6	72	53	1	0	45	1.10
4390872--4390927	18	3.1	18	78	12	60	51	1	0	46	1.11
4391142--4391204	28	2.3	25	78	21	65	63	7	1	26	1.31
4391781--4391815	3	11.7	3	90	0	52	2	37	0	60	1.12
4395211--4395262	17	3.1	16	80	2	59	53	19	5	21	1.65
4403823--4403847	9	2.8	9	100	0	50	44	20	12	24	1.85
4409248--4409286	20	2.0	20	85	10	53	33	5	2	58	1.33
4409241--4409294	28	1.9	28	81	7	65	33	3	1	61	1.25
4411132--4411192	29	2.0	30	84	6	79	50	4	0	44	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4411194--4411231	20	1.9	20	88	0	58	65	2	0	31	1.06
4411972--4412100	9	13.8	9	70	19	61	38	0	4	55	1.26
4411969--4412100	19	7.0	18	71	15	63	39	0	4	55	1.26
4412004--4412103	9	10.4	9	73	13	76	35	1	6	58	1.30
4412021--4412093	30	2.5	28	82	8	83	34	1	6	57	1.34
4412043--4412103	30	2.1	29	84	9	79	34	0	6	59	1.24
4421284--4421335	18	2.7	19	88	5	70	67	0	3	28	1.08
4425259--4425301	22	2.0	22	85	0	59	16	6	13	62	1.51
4435156--4435249	37	2.5	38	78	15	97	48	1	13	36	1.50
4435300--4435326	3	9.0	3	100	0	54	66	0	0	33	0.92
4444350--4444549	92	2.2	91	80	9	230	42	12	17	28	1.85
4449406--4449502	48	2.0	48	97	0	185	51	10	7	30	1.63
4452615--4452667	23	2.3	23	83	6	63	39	1	1	56	1.21
4456384--4456438	28	1.9	27	82	17	67	50	7	0	41	1.30
4457786--4457834	23	2.1	23	82	14	57	12	6	2	79	0.99
4465108--4465142	14	2.5	14	90	9	54	8	2	14	74	1.17
4470503--4470750	87	2.9	84	75	12	236	27	22	21	29	1.99
4470503--4470796	44	6.9	42	73	11	213	27	22	20	29	1.98
4470470--4470838	44	8.5	44	71	14	193	27	21	20	30	1.98
4470508--4470841	170	1.9	173	85	2	467	26	22	20	29	1.98
4485560--4485706	42	3.3	42	82	8	170	28	27	14	29	1.95
4485626--4485796	47	3.6	48	85	6	206	29	26	15	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4485587--4485796	47	4.6	46	82	6	194	29	26	15	28	1.96
4485805--4485833	7	4.1	7	100	0	58	13	27	13	44	1.82
4485832--4485980	31	4.8	31	88	0	208	25	27	19	27	1.99
4485956--4486084	50	2.5	51	88	5	190	26	23	16	34	1.95
4496155--4496204	22	2.3	22	82	10	66	34	2	2	62	1.18
4496155--4496211	22	2.6	22	75	10	62	35	1	3	59	1.25
4497075--4497129	22	2.5	22	88	8	78	61	3	0	34	1.13
4497109--4497160	24	2.1	26	89	7	81	55	3	0	40	1.18
4497198--4497236	13	2.9	13	80	3	51	79	0	10	10	0.94
4500434--4500547	51	2.2	51	95	0	201	33	14	23	28	1.94
4504890--4504981	29	3.2	28	76	14	75	63	2	3	31	1.23
4504916--4504966	20	2.5	20	78	6	59	56	1	0	41	1.10
4510684--4510729	21	2.2	21	85	11	60	54	26	0	19	1.44
4511290--4511328	14	2.9	14	88	3	53	74	7	0	17	1.05
4511286--4511334	12	4.2	12	80	16	50	77	6	0	16	0.96
4511286--4511340	22	2.4	25	85	11	73	72	9	0	18	1.10
4512145--4512186	22	2.0	21	85	4	57	40	4	7	47	1.52
4514614--4514657	20	2.3	19	84	4	52	63	2	0	34	1.07
4514615--4514658	19	2.3	18	81	11	52	61	2	0	36	1.09
4514620--4514670	19	2.5	21	81	15	70	54	5	0	39	1.24
4516297--4516344	20	2.5	20	86	3	62	64	2	6	27	1.28
4516980--4517024	9	4.9	9	97	2	81	0	11	0	88	0.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4517151--4517381	118	2.0	118	90	0	363	29	30	17	23	1.97
4518338--4518414	6	12.7	6	79	18	72	79	0	5	15	0.91
4520713--4520799	24	3.6	25	90	9	144	70	21	3	4	1.21
4520710--4520799	23	3.7	23	87	12	128	71	21	3	4	1.19
4523313--4523348	12	3.0	12	95	0	63	27	25	5	41	1.77
4531719--4531814	50	1.9	50	87	4	140	26	12	18	42	1.86
4531764--4531945	65	2.7	68	86	6	259	24	14	21	39	1.91
4531600--4532139	180	2.9	188	83	12	606	27	15	21	36	1.93
4532317--4532346	11	2.6	11	94	5	51	20	16	3	60	1.50
4532329--4532786	71	6.2	71	75	16	382	27	18	19	34	1.95
4532404--4532562	83	1.9	83	92	5	268	24	18	19	37	1.94
4532028--4532948	454	2.0	473	84	8	1237	28	17	19	34	1.95
4532482--4532785	74	4.2	72	73	16	195	28	18	18	34	1.95
4532714--4532882	91	1.8	92	82	3	216	28	17	19	33	1.95
4532641--4532948	166	1.9	167	79	10	362	28	17	20	33	1.95
4532807--4532962	75	2.1	74	82	7	181	32	14	18	34	1.91
4532807--4533351	236	2.3	233	81	9	644	28	15	18	37	1.91
4543823--4544887	146	7.1	145	82	9	1149	29	17	20	32	1.95
4543837--4544881	74	13.9	74	82	9	1143	29	17	21	31	1.96
4544499--4544962	83	5.7	82	72	16	335	26	17	21	33	1.96
4544124--4544961	159	5.4	155	81	8	697	29	17	21	32	1.96
4544746--4544882	73	1.9	73	87	0	202	24	18	25	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4550648--4550825	46	3.8	48	78	14	194	28	29	21	20	1.98
4550655--4550825	92	1.8	93	93	1	299	27	29	22	21	1.99
4557082--4557138	24	2.3	24	84	3	69	61	0	3	35	1.13
4560165--4560211	6	7.8	6	100	0	94	51	31	0	17	1.46
4562185--4562218	18	1.9	17	94	5	59	23	17	11	47	1.81
4563099--4563152	20	2.7	21	77	5	67	64	1	1	31	1.14
4563300--4563348	19	2.6	18	78	12	53	26	0	4	69	1.06
4563267--4563341	29	2.6	29	75	10	71	30	1	4	64	1.20
4563290--4563348	19	3.1	19	76	9	50	28	0	3	67	1.06
4570494--4570536	19	2.4	17	84	7	50	34	0	4	60	1.17

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   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255