genome.fa.s4.2.7.7.80.10.50.1000.18.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  18  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)
4783728--4783838	33	3.4	34	81	10	106	42	17	9	31	1.80
4785175--4786280	120	9.2	120	96	1	1930	43	3	5	47	1.44
4785175--4786280	241	4.6	240	96	1	1939	43	3	5	47	1.44
4786229--4786263	18	2.0	17	88	5	52	45	0	0	54	0.99
4786428--4786518	45	2.0	45	85	2	121	37	28	6	27	1.82
4786499--4786567	16	4.2	16	92	3	120	36	37	1	24	1.65
4786499--4786567	33	2.1	32	94	2	120	36	37	1	24	1.65
4794209--4794239	16	1.9	16	93	0	53	58	0	0	41	0.98
4794576--4794649	35	2.1	35	85	9	98	16	14	16	52	1.75
4794631--4794845	73	2.9	73	88	2	315	14	19	19	46	1.84
4794688--4794806	36	3.3	36	71	23	113	16	18	21	42	1.89
4794655--4794852	37	5.4	37	68	13	113	14	20	19	45	1.85
4795234--4795273	20	2.0	20	85	0	53	65	2	7	25	1.32
4795313--4795367	26	2.1	26	89	0	83	61	5	1	30	1.29
4795346--4795391	17	2.6	17	89	3	65	67	4	2	26	1.21
4795346--4795391	9	5.2	9	76	12	51	67	4	2	26	1.21
4795362--4795410	18	2.7	18	84	12	57	65	0	6	28	1.16
4795533--4795899	148	2.5	145	93	2	601	26	18	23	31	1.97
4796472--4796524	21	2.4	22	78	9	54	64	0	7	28	1.21
4804556--4804747	98	1.9	99	82	1	242	31	14	21	32	1.94
4816059--4816115	24	2.5	25	81	16	70	36	0	1	61	1.07
4816061--4816111	21	2.5	21	76	20	54	37	0	1	60	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4818847--4818906	31	1.9	31	100	0	120	40	13	10	36	1.78
4820669--4820770	2	51.0	2	100	0	204	50	50	0	0	1.00
4821782--4821950	86	2.0	86	85	2	232	35	10	13	40	1.78
4824379--4824414	6	6.0	6	86	0	54	77	19	0	2	0.88
4827023--4827052	15	2.0	15	93	0	51	73	10	6	10	1.25
4832845--4833037	105	1.8	104	87	5	291	32	24	11	31	1.91
4832845--4833037	35	5.5	35	85	3	246	32	24	11	31	1.91
4847357--4847434	38	2.1	38	97	0	147	44	15	20	19	1.86
4856151--4856210	29	2.1	29	93	0	102	43	6	28	21	1.78
4868698--4868761	28	2.2	31	83	8	80	45	1	4	48	1.32
4873112--4873149	17	2.1	19	85	9	53	57	13	5	23	1.56
4881333--4881364	9	3.4	10	91	8	50	50	6	0	43	1.27
4882529--4882628	50	2.0	50	100	0	200	22	6	24	48	1.73
4887172--4887239	29	2.3	29	82	5	84	27	29	13	29	1.94
4887341--4887419	29	2.7	30	82	13	110	29	30	15	25	1.96
4890579--4890621	18	2.3	18	88	11	61	37	13	25	23	1.92
4891612--4891657	18	2.5	18	80	16	58	28	10	0	60	1.30
4899604--4899655	15	3.1	18	71	21	58	48	3	7	40	1.50
4901397--4901448	24	2.2	24	92	0	86	51	7	3	36	1.49
4909647--4909692	18	2.5	18	80	16	58	28	10	0	60	1.30
4914257--4914282	2	13.0	2	100	0	52	50	0	0	50	1.00
4914740--4914784	23	2.0	23	86	0	63	60	2	2	35	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4916758--4916783	13	2.0	13	100	0	52	53	7	0	38	1.30
4921305--4921336	16	2.0	16	100	0	64	37	6	18	37	1.76
4925520--4925582	30	2.1	30	84	0	81	36	12	15	34	1.86
4926909--4926948	20	2.0	20	85	4	55	50	0	0	50	1.00
4926917--4926955	10	3.9	10	82	0	51	51	0	0	48	1.00
4929952--4929985	17	2.0	17	88	0	50	47	0	0	52	1.00
4932866--4932903	15	2.4	16	86	4	51	10	10	0	78	0.95
4932869--4932908	21	2.0	20	85	9	55	10	10	0	80	0.92
4933887--4934010	64	1.9	64	86	0	176	29	16	16	37	1.91
4934074--4934383	44	7.1	44	69	10	208	36	21	22	19	1.95
4934086--4934383	88	3.4	88	92	2	483	36	21	22	19	1.95
4935087--4935130	21	2.1	21	87	8	63	15	9	0	75	1.05
4935485--4935526	22	1.9	22	90	0	66	23	7	2	66	1.28
4938175--4938829	327	2.0	327	97	0	1247	29	12	25	32	1.92
4944332--4944363	9	3.7	9	95	4	57	21	21	12	43	1.86
4951885--4952008	64	1.9	64	83	3	160	28	17	16	37	1.92
4952072--4952325	44	5.8	44	71	10	216	36	22	21	20	1.95
4952082--4952337	88	2.9	88	93	1	426	37	21	21	19	1.95
4953114--4953161	12	3.8	12	76	10	51	29	4	4	62	1.32
4953313--4953354	22	1.9	22	90	0	66	23	7	2	66	1.28
4956003--4956657	327	2.0	327	98	0	1256	29	12	25	32	1.92
4958570--4958603	5	6.8	5	93	0	50	0	11	23	64	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4961761--4961795	15	2.3	15	90	0	52	20	2	31	45	1.65
4967909--4967940	9	3.7	9	95	4	57	21	21	12	43	1.86
4975849--4975972	64	1.9	64	86	0	176	29	16	16	37	1.91
4976035--4976343	44	7.1	44	68	12	183	36	21	22	19	1.95
4976047--4976343	88	3.4	87	93	2	506	36	21	22	19	1.95
4977646--4978298	326	2.0	326	97	0	1236	29	11	25	32	1.92
4980201--4980234	5	6.8	5	93	0	50	0	11	23	64	1.26
4983362--4983395	15	2.3	15	89	0	50	20	2	32	44	1.67
4988816--4988847	9	3.7	9	95	4	57	21	21	12	43	1.86
4996738--4996861	64	1.9	64	86	0	176	29	16	16	37	1.91
4996925--4997234	44	7.1	44	70	10	226	36	21	22	19	1.95
4996937--4997234	88	3.4	88	93	2	501	36	21	22	19	1.95
4998544--4999198	327	2.0	327	97	0	1229	29	12	25	32	1.92
5001109--5001142	5	6.8	5	93	0	50	0	11	23	64	1.26
5004301--5004335	15	2.3	15	90	0	52	20	2	31	45	1.65
5009786--5009817	9	3.7	9	95	4	57	21	21	12	43	1.86
5017899--5018208	44	7.1	44	69	10	208	36	20	22	20	1.95
5017911--5018208	88	3.4	88	92	2	483	36	21	22	19	1.95
5018985--5019032	12	3.8	12	76	10	51	29	4	4	62	1.32
5019185--5019226	22	1.9	22	90	0	66	23	7	2	66	1.28
5021867--5022521	327	2.0	327	98	0	1256	29	12	25	32	1.92
5024432--5024470	5	7.8	5	94	0	60	0	12	23	64	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5027627--5027661	15	2.3	15	90	0	52	20	2	31	45	1.65
5036104--5036154	10	5.1	10	79	9	50	37	0	11	50	1.39
5037556--5037597	20	2.1	20	95	0	75	42	21	11	23	1.86
5041344--5041416	36	2.0	36	100	0	146	39	8	27	24	1.84
5042280--5042347	25	2.7	26	82	8	79	27	17	23	30	1.97
5046079--5046128	21	2.7	18	77	19	57	56	8	4	32	1.47
5046085--5046126	21	2.0	22	95	4	77	52	9	4	33	1.55
5047284--5047350	33	2.0	33	100	0	134	20	23	2	52	1.61
5051547--5051586	20	1.9	21	85	10	55	57	0	7	35	1.27
5052921--5052964	24	2.0	23	86	13	65	22	36	11	29	1.89
5053953--5053994	22	2.0	21	85	4	57	7	0	9	83	0.81
5053947--5054000	23	2.4	23	76	14	60	5	0	14	79	0.90
5055822--5055869	25	2.0	23	84	8	60	41	2	10	45	1.50
5060168--5060203	18	2.0	18	94	0	63	69	0	30	0	0.89
5062565--5062629	18	3.6	18	68	15	53	35	13	4	46	1.64
5072705--5072921	64	3.4	64	94	1	357	41	5	6	46	1.52
5072894--5072923	14	2.1	14	93	0	51	56	6	0	36	1.26
5077005--5077057	21	2.6	20	85	11	72	5	13	7	73	1.23
5077062--5077114	3	17.7	3	100	0	106	67	0	0	32	0.91
5077130--5077159	12	2.5	12	100	0	60	6	16	0	76	0.99
5077872--5077905	4	8.5	4	86	0	50	23	5	0	70	1.09
5078001--5078041	17	2.3	18	80	12	50	26	4	0	68	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5078033--5078058	4	6.5	4	100	0	52	26	0	0	73	0.84
5078301--5078327	12	2.2	12	100	0	54	7	14	29	48	1.71
5078351--5078560	41	5.1	42	87	4	252	34	20	23	21	1.97
5078351--5078563	82	2.6	83	85	3	279	34	21	23	21	1.97
5078576--5078652	37	2.1	37	82	4	93	48	29	1	20	1.58
5078784--5078847	7	9.0	7	77	3	56	23	3	26	46	1.67
5078800--5078850	15	3.5	15	81	2	59	21	1	29	47	1.62
5079445--5079525	7	11.3	7	85	6	92	70	2	0	27	1.00
5079450--5079523	8	10.0	8	80	14	70	67	2	0	29	1.04
5079428--5079525	21	4.7	21	81	6	101	70	4	0	25	1.05

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