genome.fa.s5.2.7.7.80.10.50.1000.127.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: A05
Parameters: 2 7 7 80 10 50 1000
Length:  100714657

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   311   312   313   314   315   316   317   318   

This is table  127  of  318  ( 38109 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)
39463503--39463546	20	2.2	20	84	8	54	43	2	0	54	1.12
39464041--39464086	13	3.4	14	85	8	60	52	0	0	47	1.00
39464045--39464084	14	2.8	16	78	21	52	47	0	0	52	1.00
39464089--39464148	22	2.8	22	85	5	70	51	0	0	48	1.00
39464864--39464898	18	1.9	18	88	0	52	34	14	14	37	1.86
39467011--39467148	66	2.1	66	80	0	159	31	21	12	35	1.90
39471734--39471778	20	2.2	20	88	4	63	42	2	2	53	1.25
39475491--39475542	21	2.4	22	90	6	79	34	26	25	13	1.93
39475468--39475554	21	4.0	23	76	10	74	37	25	21	14	1.92
39476045--39476164	51	2.4	51	83	4	136	25	22	12	40	1.89
39477363--39477401	19	2.0	20	90	5	62	23	25	23	28	1.99
39477424--39477460	18	2.1	18	85	14	51	24	21	5	48	1.71
39478750--39478792	22	2.0	22	85	0	59	72	2	4	20	1.14
39479559--39479627	30	2.3	30	82	5	77	52	15	24	7	1.68
39479616--39479648	14	2.3	15	94	5	59	54	15	27	3	1.55
39487499--39487557	27	2.2	27	100	0	118	52	8	10	28	1.64
39487925--39488000	35	2.2	34	79	6	82	27	11	14	46	1.80
39488630--39488663	14	2.4	14	90	0	50	64	5	5	23	1.38
39489883--39489922	18	2.2	19	86	13	57	77	15	0	7	0.98
39491373--39491411	21	1.9	20	89	5	60	25	2	10	61	1.41
39493513--39493776	31	8.5	31	88	1	368	29	17	25	27	1.98
39493814--39493939	47	2.7	48	85	2	157	30	15	25	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39498301--39498333	13	2.4	14	90	5	50	27	0	0	72	0.85
39498362--39498422	20	2.9	21	82	9	79	37	0	0	62	0.96
39498385--39498409	13	1.9	13	100	0	50	40	0	0	60	0.97
39498363--39498425	22	3.0	21	79	9	74	39	0	0	60	0.97
39498600--39498648	19	2.6	19	78	9	57	55	0	6	38	1.25
39498648--39498705	20	2.9	20	79	5	73	62	0	1	36	1.06
39498747--39498779	14	2.3	15	94	5	59	57	0	0	42	0.98
39498726--39498795	21	3.0	24	78	14	76	55	0	0	44	0.99
39498745--39498821	34	2.2	35	84	15	106	58	2	0	38	1.12
39498735--39498816	11	7.2	11	75	20	71	57	1	0	41	1.06
39498863--39498926	21	3.0	20	86	8	67	54	0	1	43	1.09
39498874--39498959	21	4.5	20	69	26	78	60	1	1	37	1.12
39498874--39498926	21	2.5	21	90	6	81	60	0	1	37	1.08
39498889--39498933	22	2.1	21	87	4	63	62	2	2	33	1.20
39498894--39498961	35	2.0	35	91	8	113	61	1	1	35	1.14
39500201--39500254	3	18.3	3	78	17	60	62	0	3	33	1.12
39500470--39500523	3	18.3	3	84	3	65	59	0	7	33	1.25
39500865--39500926	17	3.5	17	71	6	52	54	4	6	33	1.47
39501053--39501095	22	2.0	22	86	9	61	51	11	0	37	1.39
39501946--39501998	21	2.8	20	83	13	67	71	0	9	18	1.12
39501953--39501997	21	2.1	22	91	4	74	73	0	8	17	1.08
39502952--39502986	14	2.5	14	85	0	52	40	0	20	40	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39515235--39515266	17	1.9	17	93	6	57	62	0	0	37	0.95
39519613--39519641	4	7.2	4	100	0	58	75	0	24	0	0.80
39523662--39523686	5	5.0	5	100	0	50	80	0	0	20	0.72
39523911--39523944	18	1.9	18	94	5	61	26	5	0	67	1.13
39536869--39536926	25	2.3	26	85	8	75	12	12	17	58	1.63
39540233--39540262	14	2.1	14	100	0	60	66	0	26	6	1.16
39554749--39554927	39	4.6	39	90	0	277	13	26	21	37	1.91
39567802--39567861	24	2.4	26	77	8	70	61	6	0	31	1.22
39573330--39573360	15	2.0	16	93	6	55	51	9	0	38	1.35
39581229--39581284	21	2.6	22	75	11	53	28	3	5	62	1.34
39583567--39583624	31	1.9	30	82	10	73	37	0	1	60	1.07
39583656--39583701	22	2.0	22	83	8	56	36	0	2	60	1.09
39583793--39583834	22	1.9	22	90	0	66	52	4	0	42	1.22
39587628--39587666	18	2.2	18	95	0	69	46	7	12	33	1.71
39588772--39588806	3	11.7	3	100	0	70	34	0	0	65	0.93
39589176--39589212	19	1.9	19	89	10	58	56	8	5	29	1.51
39590519--39590596	34	2.3	34	91	2	122	35	12	7	43	1.72
39595523--39595655	47	2.8	47	94	0	230	39	22	13	24	1.90
39596158--39596201	14	3.1	14	81	15	54	54	2	0	43	1.12
39597110--39597152	22	2.0	22	90	0	68	34	2	16	46	1.60
39610843--39610885	22	2.0	22	90	0	68	34	2	16	46	1.60
39611364--39611411	20	2.4	21	82	10	64	70	6	4	18	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39617248--39617285	17	2.2	17	100	0	76	63	10	5	21	1.46
39619191--39619269	40	2.0	40	89	0	122	32	31	18	16	1.94
39626362--39626452	40	2.3	38	76	7	92	37	31	16	14	1.89
39627752--39627880	35	3.5	36	81	12	138	33	10	23	32	1.89
39629026--39629094	30	2.3	30	85	9	88	17	34	24	23	1.96
39630055--39630130	40	1.9	40	91	0	125	36	32	14	15	1.88
39634243--39634372	47	2.8	47	83	0	161	33	25	14	26	1.94
39635055--39635092	18	2.1	19	90	5	60	52	15	2	28	1.56
39637753--39637821	29	2.4	29	95	0	120	34	11	28	24	1.91
39640848--39640875	11	2.5	11	100	0	56	14	25	0	60	1.34
39641766--39641824	30	2.0	30	82	0	73	77	1	13	6	1.03
39643246--39643281	3	12.0	3	100	0	72	33	0	0	66	0.92
39649465--39649525	31	2.0	31	100	0	122	36	13	19	31	1.90
39651319--39651347	7	4.1	7	100	0	58	13	31	13	41	1.84
39653053--39653091	12	3.2	12	88	0	60	12	15	41	30	1.85
39660705--39660730	13	2.0	13	100	0	52	30	0	15	53	1.42
39662487--39662545	30	2.0	30	100	0	118	28	20	23	27	1.99
39662742--39662779	18	2.1	18	90	0	58	39	47	2	10	1.52
39662757--39662781	13	1.9	13	100	0	50	32	48	0	20	1.50
39662808--39662851	6	7.0	6	85	10	61	77	4	0	18	0.94
39662808--39662845	20	1.9	20	88	0	58	76	5	0	18	0.97
39662871--39662929	9	6.6	9	78	7	57	28	8	16	45	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39665504--39665632	61	2.1	61	84	2	161	26	31	20	20	1.98
39666480--39666505	13	2.0	13	100	0	52	30	0	15	53	1.42
39667286--39667362	40	1.9	40	83	0	100	14	15	32	37	1.88
39667374--39667418	22	2.0	23	82	4	56	24	8	44	22	1.81
39670310--39670408	40	2.5	39	77	6	110	17	11	33	38	1.85
39672278--39672340	20	3.2	20	100	0	126	30	19	15	34	1.93
39672356--39672412	13	4.1	14	74	24	50	54	3	0	42	1.17
39674041--39674084	20	2.1	20	83	8	52	70	6	4	18	1.27
39676236--39676268	8	4.1	8	92	7	50	87	0	12	0	0.53
39677367--39677401	18	1.9	18	88	0	52	25	0	0	74	0.82
39680205--39680248	23	1.9	23	85	0	61	59	2	11	27	1.44
39681504--39681594	43	2.1	43	97	0	173	21	28	4	45	1.71
39681653--39681698	5	9.0	5	81	13	58	80	2	0	17	0.81
39683945--39684001	30	1.9	29	82	10	71	42	15	5	36	1.70
39684872--39684960	43	2.1	43	100	0	178	34	21	8	34	1.85
39692851--39692904	22	2.5	22	75	0	54	20	27	25	25	1.99
39693283--39693326	22	1.9	24	90	9	74	0	13	15	70	1.17
39697689--39697738	20	2.5	19	87	9	73	42	8	0	50	1.32
39697710--39697746	15	2.4	16	86	13	60	37	10	0	51	1.37
39698089--39698152	20	3.2	20	70	18	53	43	4	1	50	1.32
39698487--39698531	15	2.9	15	81	15	56	46	0	11	42	1.39
39698503--39698557	20	2.8	19	84	10	74	49	0	9	41	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39702569--39702714	71	2.1	71	92	0	238	28	15	24	30	1.96
39704889--39704951	21	3.1	20	73	15	58	61	14	14	9	1.55
39705366--39705422	24	2.4	24	93	0	96	42	0	3	54	1.17
39710898--39710950	16	3.3	16	79	10	63	18	28	0	52	1.46
39712598--39712634	17	2.2	17	90	9	58	18	29	32	18	1.96
39714788--39714890	43	2.5	39	81	13	102	35	0	4	58	1.26
39718415--39718492	39	2.0	39	100	0	156	33	30	7	28	1.85
39723796--39723835	20	2.0	20	85	0	53	22	7	2	67	1.28
39727510--39727552	20	2.0	20	82	8	50	41	16	2	39	1.61
39728607--39728644	18	2.1	18	90	0	58	31	2	0	65	1.06

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   311   312   313   314   315   316   317   318