genome.fa.s13.2.7.7.80.10.50.1000.16.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: At_chr11
Parameters: 2 7 7 80 10 50 1000
Length:  102024878

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   256   
          257   258   259   260   261   262   263   264   265   266   267   268   269   270   271   272   
          273   274   275   276   277   278   279   280   281   282   283   284   285   286   287   288   
          289   290   291   292   293   294   295   296   297   298   299   300   301   302   303   304   
          305   306   307   308   309   310   

This is table  16  of  310  ( 37082 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)
4151942--4152113	93	1.8	93	94	0	308	20	21	30	27	1.98
4155009--4155087	15	5.4	15	73	10	65	11	17	12	58	1.63
4157475--4157634	46	3.5	46	96	0	284	21	23	27	26	1.99
4160851--4160890	21	1.9	21	89	0	62	7	22	42	27	1.80
4162817--4162949	47	2.8	46	86	5	160	51	6	10	31	1.60
4164935--4164985	24	2.1	24	85	7	68	29	0	1	68	1.00
4165619--4165662	19	2.3	20	81	18	58	47	0	6	45	1.29
4166222--4166343	63	2.0	59	81	9	138	38	4	9	47	1.56
4169368--4169761	125	3.1	124	85	3	513	29	16	15	38	1.90
4169861--4169968	33	3.2	34	81	6	130	45	14	0	39	1.45
4170321--4170360	17	2.3	18	95	4	73	45	0	10	45	1.37
4181245--4181591	122	2.9	122	94	1	592	29	19	10	39	1.86
4186135--4186182	24	2.0	24	100	0	96	41	8	20	29	1.81
4205159--4205197	21	2.0	20	85	10	53	48	10	7	33	1.66
4208514--4208582	30	2.3	30	100	0	138	20	8	8	62	1.50
4209248--4209372	63	2.0	63	98	0	241	26	15	20	37	1.92
4212451--4212489	19	2.1	19	85	9	53	33	20	5	41	1.74
4220366--4220786	211	2.0	211	99	0	833	32	19	19	28	1.96
4220736--4221205	119	4.0	119	94	1	791	34	17	17	30	1.93
4220736--4221205	237	2.0	238	92	1	791	34	17	17	30	1.93
4222748--4222863	42	2.6	44	78	13	123	33	1	2	62	1.19
4223020--4223053	18	1.9	17	88	5	50	14	0	5	79	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4223020--4223053	17	1.9	18	88	5	52	14	0	5	79	0.91
4225906--4225945	20	1.9	20	85	10	53	47	10	10	32	1.70
4230808--4230938	47	2.8	47	86	1	154	21	17	29	31	1.96
4233098--4233242	63	2.3	63	82	4	168	35	8	6	49	1.58
4233337--4233394	29	2.0	30	86	3	82	32	12	15	39	1.84
4233456--4233505	23	2.2	23	85	0	64	40	2	10	48	1.48
4233550--4233613	29	2.2	29	83	8	76	46	9	9	34	1.68
4245205--4245238	15	2.3	15	100	0	68	44	50	0	5	1.26
4245587--4245628	21	2.0	21	100	0	84	33	14	4	47	1.65
4246336--4246399	23	2.8	22	83	6	74	34	7	1	56	1.38
4246344--4246428	26	3.4	24	76	18	77	34	7	0	58	1.25
4246365--4246439	26	2.9	25	76	17	73	32	6	1	60	1.31
4246390--4246448	29	2.0	29	86	0	82	32	6	1	59	1.34
4247118--4247152	3	11.7	3	100	0	70	34	0	0	65	0.93
4249070--4249153	30	2.7	31	90	3	134	50	17	8	23	1.74
4250517--4250580	31	2.1	31	97	2	121	28	9	3	59	1.44
4254593--4254636	19	2.2	20	88	4	63	34	0	6	59	1.24
4254574--4254655	29	2.8	29	80	14	87	31	1	7	59	1.32
4254531--4254680	66	2.3	64	78	14	155	31	1	5	62	1.26
4254698--4254775	25	3.0	25	75	14	79	30	2	1	65	1.14
4254689--4254775	25	3.4	24	75	17	70	31	2	2	64	1.18
4257203--4257235	17	2.0	17	88	5	50	33	15	3	48	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4257521--4258391	46	18.9	46	97	0	1591	19	23	15	41	1.89
4263399--4263477	40	2.0	40	87	0	113	31	12	10	45	1.75
4266693--4266811	3	39.3	3	69	17	59	60	0	10	27	1.36
4268110--4269153	45	23.4	45	75	6	761	27	23	18	30	1.98
4268132--4269153	89	11.5	89	73	10	586	27	23	18	30	1.98
4268132--4269154	134	7.6	134	84	5	1006	27	23	18	30	1.98
4268706--4269330	44	14.0	43	73	10	305	27	23	19	30	1.98
4278731--4278776	19	2.3	20	88	3	67	45	4	19	30	1.70
4283145--4283199	22	2.4	23	85	11	69	74	1	1	21	1.01
4283145--4283208	6	11.0	6	72	11	53	75	1	1	21	0.98
4283152--4283219	28	2.4	27	76	9	73	72	1	2	23	1.07
4288615--4288954	170	2.0	170	95	1	610	38	16	14	30	1.89
4292348--4292605	3	85.3	3	69	15	131	60	1	9	28	1.37
4292341--4292377	17	2.2	17	95	0	65	62	2	5	29	1.31
4292470--4292541	32	2.3	31	77	15	76	59	1	9	29	1.38
4296574--4296629	28	2.0	28	92	0	94	26	19	21	32	1.97
4298170--4298327	71	2.4	65	76	13	160	33	15	29	21	1.94
4298701--4298732	16	1.9	17	93	6	57	37	3	9	50	1.51
4300265--4300340	5	15.0	5	74	15	59	21	2	0	76	0.91
4300271--4300337	7	8.7	7	72	18	53	20	2	0	76	0.92
4300265--4300327	12	5.4	12	74	25	64	22	1	0	76	0.88
4306218--4306255	16	2.4	16	82	4	51	21	7	0	71	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4309304--4309375	33	2.2	33	83	11	87	50	18	5	26	1.68
4310517--4310568	24	2.2	24	89	0	77	50	7	3	38	1.50
4314958--4315009	24	2.2	24	96	0	95	53	7	1	36	1.41
4315694--4316008	128	2.5	127	91	1	522	38	22	13	25	1.91
4316614--4316679	36	2.0	32	83	16	82	65	3	3	28	1.23
4316614--4316695	36	2.6	30	76	22	80	63	3	2	30	1.24
4317978--4318005	14	2.0	14	100	0	56	57	0	21	21	1.41
4318397--4318728	83	4.0	83	99	0	655	35	21	13	29	1.92
4325552--4325690	70	2.0	70	94	0	242	18	20	31	28	1.97
4329124--4329152	7	4.3	7	91	8	51	72	13	0	13	1.13
4329124--4329152	13	2.1	14	93	6	51	72	13	0	13	1.13
4338285--4338324	20	2.0	20	100	0	80	20	10	35	35	1.86
4338962--4339018	24	2.4	24	82	5	71	47	8	1	42	1.45
4350449--4350511	30	2.1	30	88	5	92	25	6	9	58	1.53
4351755--4351785	7	4.4	7	100	0	62	38	0	0	61	0.96
4357270--4357341	36	2.0	36	91	0	117	20	22	18	38	1.93
4363000--4363055	14	3.9	14	73	13	51	55	1	5	37	1.33
4363412--4363514	51	2.0	51	92	0	170	33	22	19	25	1.97
4364924--4365479	207	2.7	207	89	1	839	27	23	18	30	1.98
4368211--4368335	43	2.9	43	95	0	223	27	20	29	22	1.99
4368710--4368749	21	1.9	21	89	0	62	0	47	22	30	1.52
4369161--4369189	14	2.1	14	93	6	51	58	6	0	34	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4369356--4369394	17	2.4	17	86	4	53	48	0	10	41	1.37
4374225--4374414	9	20.6	9	72	11	107	37	1	13	47	1.52
4374225--4374387	71	2.3	69	84	4	202	38	1	12	47	1.50
4374261--4374445	96	2.0	90	86	9	259	38	2	11	47	1.53
4374201--4374414	114	1.9	114	84	5	290	38	1	13	47	1.51
4374261--4374445	87	2.1	87	84	7	234	38	2	11	47	1.53
4374519--4374574	15	3.8	15	76	21	64	51	0	1	46	1.11
4374784--4375663	356	2.5	358	96	0	1629	37	12	15	35	1.84
4375887--4375915	15	1.9	15	100	0	58	48	20	6	24	1.74
4376117--4376483	183	2.0	183	97	0	689	42	14	15	26	1.86
4376556--4376585	14	2.2	13	94	5	51	36	13	0	50	1.42
4379128--4379176	15	3.5	15	68	21	52	30	0	51	18	1.47
4379127--4379183	26	2.2	26	96	0	105	29	0	47	22	1.52
4379468--4379525	28	2.1	28	83	6	73	36	29	1	32	1.68
4379502--4379545	21	2.1	21	91	0	70	34	34	2	29	1.70
4379782--4379825	21	2.0	22	91	4	72	43	38	0	18	1.50
4379898--4380200	41	7.4	41	91	1	484	21	23	19	35	1.96
4388613--4388668	14	3.9	14	73	13	51	55	1	5	37	1.33
4390495--4390548	14	3.9	14	90	0	81	40	1	18	38	1.61
4390483--4390548	28	2.4	28	84	5	80	40	4	15	39	1.67
4390639--4390678	18	2.2	18	100	0	80	50	0	0	50	1.00
4390640--4390683	18	2.6	16	83	13	61	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4392266--4392291	3	8.7	3	100	0	52	69	0	0	30	0.89
4394446--4394546	39	2.7	36	77	17	98	50	7	0	40	1.38
4394790--4394823	12	2.9	12	86	4	52	32	0	0	67	0.91
4394947--4395009	30	2.1	30	91	5	101	58	9	3	28	1.45
4395049--4395091	22	2.0	22	85	0	59	58	11	11	18	1.63
4395056--4395096	11	3.7	11	80	0	55	56	9	14	19	1.66
4399959--4399998	19	2.1	19	85	0	53	70	5	0	25	1.08
4400159--4400221	19	3.3	19	95	2	108	50	12	0	36	1.41
4400159--4400264	19	5.5	19	81	11	99	52	9	0	36	1.40
4400152--4400280	39	3.3	38	78	8	116	55	8	0	34	1.36

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   256   
          257   258   259   260   261   262   263   264   265   266   267   268   269   270   271   272   
          273   274   275   276   277   278   279   280   281   282   283   284   285   286   287   288   
          289   290   291   292   293   294   295   296   297   298   299   300   301   302   303   304   
          305   306   307   308   309   310