genome.fa.s4.2.7.7.80.10.50.1000.139.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  139  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)
44806881--44806937	15	3.5	15	71	17	51	49	1	1	47	1.22
44809520--44809546	6	4.5	6	100	0	54	29	0	0	70	0.88
44813265--44813402	44	3.2	42	82	5	125	32	25	17	24	1.97
44813245--44813402	43	3.7	44	78	10	155	32	26	17	24	1.96
44813297--44813402	44	2.5	42	86	6	133	32	27	17	22	1.97
44817528--44817772	49	4.9	49	83	3	319	25	17	26	30	1.97
44817632--44817715	28	3.2	27	65	25	72	23	15	29	30	1.95
44821956--44821985	15	2.0	15	93	0	51	46	0	10	43	1.37
44822010--44822041	10	3.3	10	95	4	57	31	6	0	62	1.20
44826947--44827770	40	20.6	40	93	1	1366	27	19	27	25	1.98
44828649--44828760	40	2.8	40	90	0	161	26	21	28	23	1.99
44835290--44835319	15	2.0	15	93	0	51	50	0	10	40	1.36
44835286--44835348	27	2.3	26	76	10	63	38	0	11	50	1.38
44836188--44836216	13	2.2	13	100	0	58	55	13	0	31	1.39
44839094--44839124	11	2.7	11	95	5	53	80	0	3	16	0.83
44841929--44841980	25	2.1	25	96	0	95	11	23	19	46	1.82
44841936--44841989	25	2.2	25	82	0	63	16	22	18	42	1.89
44847645--44847706	31	2.0	31	93	0	106	14	6	19	59	1.56
44847654--44847720	31	2.2	30	81	10	73	16	5	16	61	1.53
44847731--44847762	17	2.0	17	88	11	50	50	12	6	31	1.65
44851040--44851147	26	4.2	26	93	0	189	32	7	24	36	1.83
44852769--44852909	27	5.2	26	84	6	174	17	23	24	34	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44852769--44852909	54	2.6	54	92	2	230	17	23	24	34	1.96
44859727--44859885	27	5.9	27	82	7	173	18	23	22	35	1.95
44859727--44859885	54	3.0	53	89	2	221	18	23	22	35	1.95
44869450--44869685	48	4.9	48	79	4	224	26	17	30	25	1.98
44869459--44869683	97	2.3	96	79	7	242	27	18	29	24	1.98
44870880--44870927	21	2.3	21	100	0	96	12	37	29	20	1.90
44870880--44870939	21	2.9	21	92	0	84	11	36	28	23	1.90
44876480--44876636	43	3.7	42	81	7	165	26	17	24	31	1.97
44878106--44878191	27	3.2	27	91	0	127	41	24	18	15	1.89
44880812--44880937	46	2.7	46	96	0	225	20	22	27	29	1.98
44882462--44882500	17	2.2	19	90	9	64	69	5	23	2	1.21
44884606--44884643	19	2.0	19	89	0	58	57	2	0	39	1.12
44884940--44884978	20	2.0	20	90	10	62	48	28	0	23	1.51
44884933--44884998	13	4.8	13	79	3	60	48	25	1	24	1.60
44888018--44888099	40	2.1	39	86	2	110	25	15	28	30	1.96
44890842--44890966	50	2.6	47	78	6	137	28	15	28	28	1.96
44890973--44891082	43	2.6	43	81	5	141	29	14	24	31	1.95
44894098--44894175	29	2.7	28	84	11	104	25	14	30	29	1.94
44894128--44894626	171	2.9	174	96	1	923	30	14	24	30	1.95
44902392--44902470	34	2.5	30	76	21	90	27	16	29	26	1.97
44902428--44902755	174	1.9	174	96	0	611	29	14	24	31	1.94
44902981--44903082	1	102.0	1	96	0	186	0	0	0	98	0.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44903111--44903273	1	163.0	1	100	0	326	100	0	0	0	0.00
44903456--44903523	29	2.3	29	85	5	93	27	30	13	27	1.94
44903624--44903702	29	2.7	30	82	13	110	30	30	13	25	1.94
44903371--44903696	173	1.9	174	91	1	539	31	24	14	29	1.94
44911699--44911777	29	2.7	30	82	13	110	29	30	15	25	1.96
44924872--44924949	29	2.7	28	84	11	104	25	15	30	28	1.96
44924902--44925229	174	1.9	174	97	0	620	29	14	25	30	1.95
44933001--44933078	29	2.7	28	84	11	104	25	14	30	29	1.94
44933031--44933359	176	1.9	173	95	1	595	30	14	24	31	1.95
44937340--44937423	28	3.0	28	76	10	82	32	17	27	22	1.97
44939104--44939142	20	2.0	20	100	0	78	17	35	35	10	1.84
44946036--44946078	21	2.0	21	100	0	86	30	4	27	37	1.77
44948955--44949132	27	6.6	27	83	3	196	29	28	15	26	1.96
44948976--44949131	82	1.9	81	86	3	224	29	28	15	26	1.96
44974231--44974264	17	2.0	17	100	0	68	41	35	5	17	1.74
44975294--44975327	14	2.4	14	90	0	50	58	11	0	29	1.33
44987597--44987637	22	1.9	21	85	5	55	19	43	19	17	1.88
44991707--44991740	17	2.0	17	88	0	50	41	0	14	44	1.45
44995545--44995764	40	5.6	40	83	4	259	26	26	22	25	2.00
45007240--45007421	76	2.4	78	82	12	211	26	27	21	24	1.99
45007247--45007421	39	4.6	40	78	14	192	25	27	21	25	1.99
45015232--45015414	40	4.6	40	82	4	217	24	26	23	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45015204--45015414	80	2.7	80	83	2	239	25	27	23	24	2.00
45022882--45022906	2	12.5	2	100	0	50	52	0	0	48	1.00
45023049--45023187	68	2.0	70	92	4	237	35	11	5	48	1.61
45023169--45023224	26	2.2	26	96	0	103	25	19	7	48	1.74
45023169--45023217	13	3.8	13	75	0	53	28	16	8	46	1.75
45023181--45023223	13	3.3	13	76	0	50	23	18	6	51	1.70
45028713--45028739	14	1.9	14	100	0	54	44	11	7	37	1.68
45035061--45035139	37	2.1	37	90	0	122	25	31	18	24	1.98
45035258--45035882	47	13.1	47	93	2	989	29	29	9	31	1.88
45035258--45035879	239	2.6	239	95	0	1100	29	30	9	31	1.88
45035258--45035882	96	6.5	96	92	2	1001	29	29	9	31	1.88
45040316--45040367	25	2.1	25	100	0	104	44	11	11	32	1.77
45069946--45070022	40	1.9	40	86	0	109	14	14	33	37	1.86
45076048--45076126	40	2.0	40	89	0	122	13	16	32	36	1.88
45080413--45080469	17	3.4	17	73	9	53	28	10	10	50	1.69
45082392--45082565	46	3.8	46	77	17	180	28	28	20	21	1.98
45082399--45082570	93	1.8	93	90	2	274	27	29	20	21	1.98
45082396--45082585	46	4.1	44	70	20	111	29	28	20	21	1.98
45084762--45084799	19	2.0	20	89	5	60	47	18	0	34	1.49
45089321--45089594	46	6.0	46	92	0	377	40	14	23	20	1.90
45089880--45089912	17	2.0	17	94	5	59	48	0	15	36	1.45
45092710--45092741	10	3.2	10	90	0	55	0	15	0	84	0.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45093587--45093616	14	2.1	14	100	0	60	20	10	13	56	1.65
45098833--45099161	172	1.9	174	84	2	439	29	11	16	42	1.83
45106015--45106106	37	2.4	37	81	12	98	41	3	4	51	1.38
45106161--45106193	17	1.9	17	100	0	66	48	3	0	48	1.17
45107373--45107435	19	3.5	19	69	30	57	52	30	0	17	1.45
45110179--45110420	132	1.8	132	90	1	387	30	18	17	33	1.94
45110181--45110469	132	2.2	133	85	2	377	31	19	16	31	1.94
45110209--45110538	132	2.5	131	82	3	358	27	20	18	33	1.95
45118330--45118409	38	2.1	38	90	0	124	20	22	28	28	1.98
45118381--45118612	43	5.4	43	88	1	315	14	23	31	30	1.94
45122816--45122895	38	2.1	38	83	0	97	22	21	26	30	1.99
45122888--45123098	43	4.9	43	92	2	361	12	24	33	29	1.92
45127048--45127197	40	3.8	40	90	1	230	24	28	23	23	1.99
45129138--45129224	40	2.2	39	77	2	93	21	19	6	51	1.70
45135608--45135663	20	2.8	20	70	10	51	35	1	3	58	1.26
45135773--45135807	16	2.2	16	94	0	61	22	0	2	74	0.95
45144106--45144147	13	3.2	13	74	12	50	45	0	0	54	0.99
45144106--45144166	26	2.1	27	85	14	79	49	0	1	49	1.10
45145105--45145154	7	7.0	7	79	2	55	46	0	2	52	1.12
45145137--45145174	19	2.1	18	85	14	51	36	2	5	55	1.37
45148687--45148741	21	2.6	21	82	0	56	23	30	23	21	1.99
45154346--45154378	12	2.9	12	91	8	52	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45154336--45154388	10	5.1	10	84	8	61	62	1	0	35	1.06
45154346--45154389	22	2.0	22	95	0	79	56	2	0	40	1.11
45157843--45157884	22	2.0	21	85	4	57	50	0	4	45	1.23
45159257--45159338	28	2.9	29	80	8	80	28	14	6	51	1.66
45159284--45159362	28	2.7	29	84	5	97	24	12	8	54	1.66
45159273--45159390	29	4.2	28	76	5	94	24	14	7	53	1.67
45159760--45159819	21	2.8	22	75	10	61	25	15	20	40	1.90
45159810--45159900	45	2.0	45	82	4	112	30	25	9	34	1.88
45164217--45164266	23	2.2	23	100	0	100	8	28	26	38	1.84
45169115--45169190	25	3.1	25	83	5	84	27	23	18	30	1.98

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