genome.fa.s4.2.7.7.80.10.50.1000.40.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  40  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)
10646650--10646857	46	4.5	46	76	7	181	23	27	19	28	1.98
10646686--10646860	94	1.9	92	85	2	242	23	28	20	28	1.99
10654095--10654137	19	2.2	20	87	4	61	34	11	18	34	1.87
10654183--10654291	25	4.4	24	87	5	139	27	22	23	26	1.99
10654183--10654305	25	5.0	24	84	8	92	26	22	23	26	2.00
10660201--10660463	40	6.6	40	88	3	325	26	27	20	24	1.99
10665080--10665128	25	2.0	25	87	0	71	36	22	14	26	1.92
10665159--10665212	11	5.4	10	78	12	58	35	11	18	35	1.86
10665259--10665378	25	4.9	24	84	7	143	27	25	23	24	2.00
10665572--10665658	32	2.8	31	89	5	140	32	14	26	26	1.95
10669808--10670062	126	2.0	126	89	0	393	39	17	18	24	1.92
10678049--10678102	25	2.2	25	96	3	101	29	3	31	35	1.75
10679485--10679702	40	5.5	40	88	3	289	25	27	22	24	2.00
10687809--10688027	40	5.5	39	86	4	271	26	28	22	23	1.99
10693549--10693683	60	2.2	60	84	8	168	28	25	18	27	1.98
10693676--10693731	19	2.9	19	81	2	58	32	23	17	26	1.97
10703705--10703797	43	2.1	43	82	2	105	34	18	15	32	1.92
10704829--10704935	27	4.0	27	81	0	115	32	15	21	29	1.95
10708542--10708714	46	3.7	46	78	11	140	21	29	20	28	1.98
10708443--10708717	94	2.9	94	75	11	269	22	30	19	27	1.98
10708396--10708709	140	2.2	143	80	7	336	22	31	19	27	1.97
10710200--10710235	16	2.3	16	95	4	65	36	5	13	44	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10717319--10717354	16	2.3	16	95	4	65	36	5	13	44	1.68
10726402--10726587	100	1.9	100	91	0	309	40	9	20	29	1.84
10727104--10727141	15	2.4	16	86	4	51	52	0	2	44	1.14
10727724--10727761	19	2.0	20	89	5	60	50	0	10	39	1.37
10727724--10727765	7	6.3	7	86	5	52	47	0	11	40	1.40
10743666--10743692	6	4.5	6	100	0	54	14	0	0	85	0.61
10746363--10746501	49	2.8	50	88	2	208	30	26	17	25	1.98
10747905--10748093	40	4.7	40	84	3	220	26	26	21	24	1.99
10749365--10749403	12	3.1	12	82	13	51	10	15	0	74	1.07
10755993--10756178	40	4.7	40	84	5	216	26	27	21	24	1.99
10757458--10757490	12	2.5	14	90	9	52	12	15	0	72	1.12
10757893--10758024	50	2.6	50	79	7	151	33	25	15	25	1.95
10761145--10761196	16	3.3	16	97	2	97	36	5	13	44	1.68
10763417--10763594	27	6.6	27	82	5	162	29	27	15	27	1.96
10763438--10763593	82	1.9	81	85	3	215	29	27	15	27	1.96
10771573--10771749	27	6.6	27	83	6	180	29	28	15	26	1.96
10771573--10771748	54	3.3	53	83	3	208	30	28	15	26	1.96
10771594--10771748	81	1.9	81	88	5	233	29	28	15	26	1.96
10775656--10775831	27	6.5	27	79	5	158	25	16	29	28	1.97
10775655--10775831	55	3.3	53	81	4	194	25	16	29	28	1.97
10783499--10783673	27	6.5	27	80	5	158	25	16	29	28	1.97
10783498--10783673	55	3.3	53	81	5	194	26	16	28	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10797946--10798154	40	5.3	40	91	1	296	25	28	21	24	1.99
10805876--10806084	40	5.3	40	90	1	287	25	28	21	24	1.99
10805879--10806137	80	3.3	80	84	3	238	25	28	21	24	1.99
10805874--10806137	120	2.2	117	79	5	287	25	28	21	24	1.99
10811099--10811124	13	2.0	13	100	0	52	53	7	15	23	1.67
10811768--10811833	32	2.1	32	88	0	96	30	15	13	40	1.85
10812751--10812785	18	1.9	18	100	0	70	45	17	20	17	1.85
10814378--10814555	27	6.6	27	84	3	205	29	28	15	26	1.96
10814399--10814554	82	1.9	81	88	3	233	29	28	15	26	1.96
10816532--10816623	27	3.4	27	84	0	121	33	17	16	32	1.92
10825209--10825351	27	5.3	27	79	3	137	32	17	21	27	1.96
10825209--10825351	54	2.6	54	84	2	171	32	17	21	27	1.96
10825571--10825634	30	2.1	30	100	0	128	32	15	23	28	1.95
10826238--10826318	40	2.0	40	100	0	162	33	17	4	44	1.70
10826493--10826540	18	2.7	18	90	6	71	35	8	0	56	1.30
10826492--10826525	3	11.3	3	93	0	50	32	5	0	61	1.20
10827379--10827435	25	2.2	26	81	9	64	59	3	3	33	1.31
10828090--10828127	16	2.2	18	86	9	53	34	5	2	57	1.35
10828745--10828799	6	8.5	6	88	8	65	49	0	12	38	1.41
10845307--10845361	27	2.0	27	86	6	76	49	10	0	40	1.38
10853837--10853871	18	2.0	18	94	5	63	54	5	11	28	1.59
10854587--10854646	10	6.0	10	84	11	79	68	1	8	21	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10855303--10855484	96	1.9	97	87	1	267	31	25	13	29	1.94
10857990--10858047	3	20.7	3	80	19	72	72	0	0	27	0.85
10857989--10858057	13	5.2	13	81	10	86	75	0	0	24	0.81
10857993--10858057	5	13.4	5	80	18	59	75	0	0	24	0.81
10857989--10858058	8	8.1	8	77	12	50	75	0	0	24	0.80
10863666--10863699	17	1.9	18	94	5	61	58	5	8	26	1.51
10864416--10864475	10	6.0	10	84	11	79	68	1	8	21	1.25
10866306--10866338	7	4.7	7	100	0	66	72	0	0	27	0.85
10866907--10866942	18	2.0	18	94	0	63	47	0	5	47	1.25
10868340--10868364	12	2.1	12	100	0	50	40	36	8	16	1.77
10868890--10868977	3	29.3	3	71	21	53	28	3	1	67	1.14
10868889--10868970	12	7.0	12	73	14	64	26	3	1	68	1.14
10869180--10869237	12	5.3	11	80	13	50	34	0	5	60	1.19
10881261--10881431	46	3.7	46	76	13	179	30	27	18	22	1.97
10881266--10881436	93	1.8	93	92	0	288	30	28	19	22	1.98
10881846--10881880	16	2.1	17	89	5	54	34	20	8	37	1.83
10883820--10883903	15	5.7	15	72	14	59	55	13	17	13	1.68
10883829--10883908	30	2.7	30	79	14	85	55	12	18	13	1.70
10886852--10887023	46	3.7	46	74	13	181	29	27	20	22	1.98
10886857--10887027	93	1.8	93	92	0	288	29	28	20	22	1.98
10889429--10889523	43	2.2	43	83	5	111	28	22	24	25	1.99
10889799--10889911	43	2.6	44	75	6	113	38	19	16	25	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10889884--10890003	44	2.8	44	76	7	138	35	22	22	20	1.96
10890434--10890458	12	2.1	12	100	0	50	40	36	8	16	1.77
10890524--10890583	13	4.7	13	68	4	50	15	50	15	20	1.79
10890503--10890591	38	2.3	38	98	0	169	17	51	11	19	1.75
10891131--10891214	3	27.3	3	71	17	50	28	3	2	65	1.22
10891143--10891216	24	2.8	27	67	21	66	31	4	1	63	1.21
10891131--10891219	18	4.8	18	78	11	83	30	3	2	64	1.22
10891143--10891218	25	2.9	26	73	11	75	31	3	1	63	1.21
10891290--10891342	15	3.4	15	79	7	52	30	0	5	64	1.17
10891423--10891493	18	3.8	18	75	12	54	32	0	5	61	1.19
10891446--10891487	16	2.6	17	81	11	52	33	0	7	59	1.25
10891384--10891637	117	2.1	117	76	15	261	30	4	5	59	1.40
10891425--10891634	117	1.8	117	84	5	291	30	2	5	60	1.33
10895986--10896130	3	48.3	3	71	17	88	64	6	3	25	1.32
10895992--10896103	42	2.7	40	82	10	118	64	6	4	25	1.36
10897827--10898273	177	2.5	177	87	1	612	27	23	19	29	1.98
10902933--10902974	20	2.1	20	95	0	75	45	9	16	28	1.79
10919908--10919985	39	2.0	39	97	0	147	42	17	7	32	1.78
10932078--10932112	12	2.9	12	91	0	61	25	28	0	45	1.54
10932792--10932840	21	2.4	19	77	12	53	42	16	6	34	1.73
10934900--10935039	67	2.1	67	100	0	280	48	12	2	35	1.56
10935747--10935788	7	6.0	7	94	0	66	28	0	52	19	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10936246--10936309	30	2.1	31	97	2	121	37	3	0	59	1.13
10958776--10958806	10	3.1	10	100	0	62	38	41	9	9	1.71
10962772--10962889	39	3.0	39	89	0	164	23	27	20	27	1.99
10970106--10970208	52	2.0	52	92	3	172	33	6	19	40	1.78
10980766--10980837	18	4.0	17	75	22	67	36	18	5	40	1.74
11002676--11002962	29	9.9	29	82	3	281	40	12	26	21	1.88
11005037--11005223	40	4.7	40	95	0	320	22	27	21	27	1.99
11008054--11008119	29	2.2	30	82	12	75	37	0	3	59	1.13
11008097--11008121	8	3.1	8	100	0	50	24	0	0	76	0.80
11008165--11008198	2	17.0	2	100	0	68	50	50	0	0	1.00

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