genome.fa.s9.2.7.7.80.10.50.1000.123.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: A09
Parameters: 2 7 7 80 10 50 1000
Length:  81831061

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   

This is table  123  of  259  ( 31025 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)
39803299--39803725	228	1.9	228	100	0	854	35	25	4	34	1.77
39807221--39807335	55	2.1	55	93	0	194	45	11	6	36	1.67
39809630--39809876	40	6.2	40	83	5	256	23	20	27	28	1.99
39809630--39809876	79	3.1	80	89	4	367	23	20	27	28	1.99
39815339--39815508	40	4.3	40	85	0	207	24	30	21	23	1.99
39823197--39823366	40	4.3	40	83	0	198	24	29	21	24	1.99
39823197--39823343	79	1.9	80	86	1	215	25	29	21	24	1.99
39827417--39827481	29	2.3	29	83	2	78	43	1	24	30	1.64
39829846--39829870	13	1.9	13	100	0	50	28	24	24	24	2.00
39831635--39831685	14	3.9	14	76	19	56	19	0	17	62	1.32
39836489--39836538	23	2.2	23	96	0	91	14	16	26	44	1.85
39842904--39842953	23	2.2	23	96	0	91	14	16	26	44	1.85
39850415--39850525	27	4.1	26	80	7	123	16	21	23	38	1.92
39850415--39850525	54	2.1	54	86	3	152	16	21	23	38	1.92
39853552--39853576	11	2.3	11	100	0	50	60	0	0	40	0.97
39855261--39855331	37	1.9	37	94	0	124	25	30	19	23	1.98
39855469--39855568	52	1.9	51	89	0	146	30	30	8	32	1.86
39855538--39855684	47	3.1	47	88	0	204	27	29	10	33	1.89
39861594--39861690	19	5.2	19	73	2	79	39	15	12	32	1.85
39861798--39861849	22	2.4	22	86	0	68	28	15	11	44	1.81
39872118--39872159	11	3.6	11	81	12	57	35	0	4	59	1.19
39878032--39878212	39	4.6	39	88	0	254	30	28	19	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39878028--39878212	78	2.4	78	88	1	282	31	28	20	20	1.97
39885666--39885703	19	2.0	20	85	15	53	39	21	0	39	1.53
39885933--39886103	93	1.8	93	88	0	261	30	28	18	21	1.97
39885928--39886100	46	3.7	46	77	10	181	31	27	18	21	1.97
39891093--39891136	23	1.9	23	85	0	61	36	6	11	45	1.67
39895657--39895734	39	2.0	39	100	0	156	30	25	17	25	1.97
39897905--39897929	13	1.9	13	100	0	50	24	24	24	28	2.00
39910463--39910488	12	2.2	12	100	0	52	69	15	7	7	1.35
39941263--39941426	42	3.9	42	85	7	215	30	14	24	30	1.95
39941272--39941426	85	1.8	84	86	4	222	30	14	24	30	1.95
39944172--39944285	29	4.0	29	83	6	135	26	16	28	28	1.97
39944179--39944291	57	2.0	57	84	3	147	26	17	29	26	1.98
39947083--39947139	25	2.3	24	82	8	62	75	1	19	3	1.04
39948386--39948570	40	4.6	41	78	7	195	25	22	27	25	2.00
39948439--39948593	79	2.0	79	79	7	172	27	20	26	25	1.99
39956423--39956607	40	4.6	41	82	7	213	24	23	27	24	2.00
39961491--39961652	42	3.9	42	84	6	229	31	14	25	28	1.95
39964583--39964727	43	3.4	43	90	2	220	30	13	22	34	1.92
39967881--39968025	43	3.4	43	90	2	220	30	13	22	34	1.92
39969133--39969186	3	18.3	3	86	3	56	37	1	5	55	1.34
39970348--39970394	15	3.3	14	75	16	51	34	0	4	61	1.15
39991938--39991970	13	2.6	13	90	4	50	15	0	0	84	0.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39992738--39992819	41	2.0	41	95	4	148	19	18	20	41	1.91
39992948--39993173	36	6.3	36	86	1	301	45	1	11	41	1.50
39993089--39993148	16	3.5	16	68	24	50	51	1	5	41	1.33
39993501--39993573	18	4.4	16	75	11	58	30	1	0	68	0.98
39993501--39993560	18	3.5	17	84	9	68	35	1	0	63	1.05
39993553--39993579	7	3.9	7	100	0	54	14	0	0	85	0.61
39995164--39995217	23	2.3	23	96	0	99	18	3	46	31	1.67
39999220--39999392	46	3.7	46	75	14	167	22	18	28	30	1.97
39999213--39999383	93	1.8	93	88	2	263	22	19	28	29	1.98
40001859--40001961	46	2.2	48	87	3	147	34	14	24	26	1.94
40003218--40003261	23	1.9	23	85	0	61	15	15	43	25	1.87
40004118--40004261	29	5.1	29	89	5	206	30	28	14	26	1.95
40004119--40004261	57	2.5	57	88	5	202	30	28	14	25	1.95
40005210--40005289	40	2.0	40	100	0	160	47	22	20	10	1.79
40011903--40011969	28	2.6	26	80	13	75	64	0	1	34	1.03
40011903--40011969	25	2.6	27	84	13	81	64	0	1	34	1.03
40011923--40011979	25	2.3	25	77	14	64	68	0	3	28	1.06
40014815--40014992	27	6.6	27	84	3	205	29	28	15	26	1.96
40014836--40014991	82	1.9	81	88	3	233	29	28	15	26	1.96
40030036--40030060	12	2.1	12	100	0	50	8	8	32	52	1.60
40030117--40030438	41	7.9	41	87	1	403	33	21	20	24	1.97
40030117--40030448	123	2.7	122	85	2	450	34	21	20	24	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40030724--40030789	7	9.1	7	78	5	60	45	37	0	16	1.48
40030967--40031007	21	2.0	21	90	0	64	9	0	31	58	1.31
40031018--40031064	22	2.2	21	84	3	58	14	2	31	51	1.55
40033272--40033333	27	2.3	27	94	0	106	48	6	3	41	1.45
40033922--40034038	9	13.0	9	79	12	107	46	18	0	35	1.50
40033905--40034040	47	2.8	44	79	18	139	44	17	0	36	1.54
40033907--40033986	38	2.0	40	90	4	128	42	18	1	37	1.59
40033922--40034038	56	2.2	52	85	11	148	46	18	0	35	1.50
40035758--40035783	12	2.2	12	100	0	52	34	7	26	30	1.85
40039891--40040082	43	4.5	43	76	7	158	27	16	22	33	1.96
40039891--40040083	86	2.2	84	81	8	212	26	16	23	33	1.96
40039963--40040119	43	3.7	42	81	10	167	27	16	21	34	1.95
40053901--40054073	89	1.9	89	96	2	321	43	20	3	32	1.68
40054720--40054857	43	3.2	42	80	8	170	33	17	14	34	1.90
40061220--40061356	43	3.2	43	86	0	193	32	16	15	35	1.90
40072796--40072856	24	2.5	24	86	5	79	34	29	16	19	1.94
40077823--40077897	31	2.3	33	86	4	91	68	8	2	21	1.28
40084225--40084275	25	2.0	25	85	7	68	29	21	19	29	1.98
40084319--40084363	10	4.4	10	91	5	72	35	17	15	31	1.92
40084319--40084363	21	2.2	20	92	4	72	35	17	15	31	1.92
40084408--40084476	25	2.8	25	84	0	75	28	24	20	26	1.99
40084423--40084489	25	2.7	25	78	15	68	32	20	19	26	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40084697--40084775	31	2.5	32	89	4	117	32	18	25	22	1.97
40086093--40086153	30	2.0	30	90	0	95	37	8	24	29	1.84
40094483--40094522	20	2.0	20	100	0	80	25	20	30	25	1.99
40102655--40102821	39	4.3	39	91	1	255	22	27	19	30	1.98
40105419--40105587	46	3.7	44	75	16	123	24	27	18	29	1.98
40109705--40109850	37	3.9	37	95	0	247	27	30	18	23	1.97
40110059--40110349	47	6.1	47	88	4	411	26	30	12	31	1.92
40110059--40110349	147	2.0	141	90	4	447	26	30	12	31	1.92
40112291--40112470	85	2.1	86	97	1	344	26	27	8	37	1.85
40118460--40118500	21	2.0	21	85	0	55	46	0	2	51	1.14
40118539--40118573	18	1.9	18	88	0	52	31	5	2	60	1.35
40121787--40121849	28	2.2	28	94	0	108	31	9	14	44	1.77
40122062--40122254	98	2.0	98	92	0	323	30	15	19	34	1.93
40125583--40125612	14	2.1	14	100	0	60	43	0	20	36	1.52
40127283--40127339	27	2.1	27	100	0	114	19	7	21	52	1.69
40129218--40129248	15	2.0	16	93	6	55	38	0	0	61	0.96
40133238--40133266	14	2.1	14	100	0	58	27	27	6	37	1.82
40134006--40134184	85	2.1	85	98	0	349	37	8	27	26	1.85
40135446--40135885	47	9.1	47	86	5	547	31	12	29	26	1.92
40135523--40135597	22	3.3	22	64	29	57	30	14	30	24	1.95
40135446--40135885	98	4.5	98	85	6	572	31	12	29	26	1.92
40135694--40135769	23	3.3	23	63	23	59	28	10	31	28	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40135696--40135773	25	3.2	25	63	23	67	28	10	32	29	1.90
40135859--40135949	46	2.0	46	84	0	119	32	9	31	25	1.89
40136094--40136239	37	3.9	37	95	0	247	23	19	30	26	1.98
40137167--40137200	17	2.1	16	89	10	52	11	8	0	79	0.94
40139180--40139226	18	2.6	18	93	0	85	40	6	19	34	1.77
40147774--40147808	17	2.1	17	100	0	70	40	14	11	34	1.82
40156149--40156407	27	9.6	27	82	4	270	28	27	15	27	1.96
40156170--40156406	81	2.9	81	93	1	386	28	27	15	27	1.96
40171961--40172080	48	2.5	48	98	0	231	37	20	0	42	1.52
40177697--40177735	20	1.9	21	89	5	62	28	25	12	33	1.93

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