genome.fa.s4.2.7.7.80.10.50.1000.54.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  54  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)
15279358--15279401	23	1.9	24	86	9	65	61	4	27	6	1.41
15279356--15279407	22	2.3	22	78	12	61	63	3	26	5	1.34
15279367--15279410	23	1.9	22	81	9	52	61	4	27	6	1.41
15285284--15285368	37	2.3	37	85	0	107	30	29	16	23	1.96
15285353--15285403	25	2.0	25	100	0	102	35	19	15	29	1.93
15285468--15285935	49	9.7	49	93	3	776	29	29	7	33	1.86
15285468--15285935	96	4.9	94	92	4	756	29	29	7	33	1.86
15293905--15294637	47	15.3	47	90	4	1133	33	8	28	29	1.87
15293905--15294637	96	7.6	95	93	2	1148	33	8	28	29	1.87
15294603--15294670	33	2.1	33	97	0	127	29	10	30	29	1.90
15294556--15294717	80	2.0	80	98	0	315	32	9	29	29	1.88
15294636--15294879	47	5.2	47	91	0	380	32	8	29	29	1.87
15296325--15296541	40	5.4	40	91	0	335	23	22	28	26	1.99
15300385--15301073	47	14.7	47	88	6	1001	32	8	29	29	1.86
15300385--15301018	96	6.8	93	82	11	580	32	8	29	30	1.86
15301192--15301292	37	2.7	37	96	0	184	24	18	30	25	1.98
15307311--15307438	39	3.3	39	89	0	202	32	20	25	21	1.97
15307310--15307456	78	1.9	77	84	4	197	31	21	25	21	1.98
15311105--15311352	27	9.2	27	83	5	313	27	24	10	37	1.87
15311357--15311552	27	7.3	27	82	2	223	35	18	19	26	1.95
15311357--15311551	54	3.6	54	83	2	248	35	18	19	26	1.95
15311357--15311550	81	2.4	82	84	1	257	36	18	19	26	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15311751--15311833	27	3.1	26	86	5	103	20	21	21	36	1.96
15311921--15311979	22	2.7	22	78	0	55	22	25	20	32	1.98
15312152--15312217	27	2.5	27	85	7	82	16	22	22	37	1.93
15312341--15312515	6	28.8	6	71	17	130	21	16	13	48	1.80
15312341--15312449	49	2.2	49	86	3	148	22	18	12	46	1.82
15312341--15312515	67	2.6	67	85	9	225	21	16	13	48	1.80
15312366--15312536	30	5.9	30	75	10	149	21	16	13	49	1.79
15314643--15314819	27	6.6	27	81	6	171	29	28	15	26	1.96
15314643--15314819	54	3.3	54	80	5	196	29	28	15	26	1.96
15314664--15314818	81	1.9	81	85	5	215	29	28	16	26	1.97
15328374--15328398	11	2.3	11	100	0	50	24	0	12	64	1.27
15329329--15329591	30	8.8	30	83	1	294	31	17	18	33	1.94
15332962--15333029	33	2.0	34	82	2	84	27	25	22	25	1.99
15335251--15335428	27	6.6	27	79	6	153	28	29	16	25	1.97
15335251--15335427	54	3.3	54	80	6	187	28	29	16	24	1.96
15337934--15338091	40	4.0	40	91	0	244	23	18	27	29	1.98
15351433--15351476	21	2.1	21	82	0	52	29	6	29	34	1.83
15352880--15352916	18	2.1	18	100	0	74	32	16	16	35	1.91
15353568--15353938	46	7.9	47	75	14	247	27	20	29	22	1.98
15353802--15353933	47	2.8	47	84	5	176	25	19	29	25	1.99
15356699--15356964	46	5.7	46	71	11	193	21	18	28	30	1.97
15356748--15356910	47	3.5	47	72	14	165	21	19	28	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15356692--15356957	93	2.9	93	88	0	415	21	19	28	30	1.97
15363815--15363872	30	1.9	30	85	0	80	32	13	25	27	1.94
15364257--15364472	46	4.6	45	75	13	172	26	18	31	23	1.98
15364811--15364930	56	2.1	56	96	0	222	45	10	23	21	1.82
15366306--15366864	47	11.8	47	91	2	795	33	8	29	28	1.87
15366715--15366836	22	5.3	22	63	21	61	33	10	29	26	1.90
15369046--15369070	11	2.3	11	100	0	50	0	28	12	60	1.32
15373001--15373136	45	3.0	45	86	2	182	46	12	19	22	1.83
15373826--15373860	4	8.8	4	100	0	70	22	0	0	77	0.78
15379700--15379768	31	2.2	31	86	0	93	36	40	4	18	1.71
15382750--15382780	15	2.1	15	100	0	62	58	6	0	35	1.24
15387526--15387573	23	2.1	23	84	7	62	64	4	0	31	1.12
15387768--15387857	45	2.0	45	100	0	180	37	26	2	33	1.69
15389010--15389066	16	3.5	16	81	15	64	33	3	1	61	1.23
15392203--15392544	88	3.9	88	87	3	392	24	22	23	29	1.99
15392322--15392542	44	5.0	45	65	8	139	24	21	22	31	1.98
15392315--15392542	88	2.6	88	95	2	406	24	21	23	30	1.99
15394763--15394795	15	2.1	16	88	5	50	6	9	6	78	1.08
15397263--15397311	19	2.5	20	80	6	57	40	12	20	26	1.87
15399271--15399350	36	2.2	36	80	8	92	52	2	8	36	1.46
15399482--15399549	3	22.7	3	85	5	93	63	1	4	30	1.23
15401304--15401355	25	2.1	25	96	0	95	44	15	25	15	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15401457--15401725	137	2.0	138	90	2	434	47	14	13	24	1.80
15403923--15403965	12	3.4	12	82	14	52	34	48	13	2	1.56
15404594--15404640	20	2.2	22	85	11	62	48	0	21	29	1.50
15404942--15405015	30	2.6	27	77	10	76	10	20	10	58	1.62
15407100--15407128	3	9.7	3	100	0	58	31	0	34	34	1.58
15423544--15423570	12	2.2	12	100	0	54	51	7	0	40	1.30
15424050--15424200	27	5.6	27	84	6	162	28	14	27	29	1.95
15424049--15424200	55	2.8	54	83	4	171	28	15	27	28	1.96
15424050--15424200	82	1.8	82	81	5	189	28	14	27	29	1.95
15428139--15428322	40	4.6	40	83	6	205	23	21	27	27	1.99
15428139--15428319	80	2.3	81	84	9	230	23	21	27	27	1.99
15441945--15441986	22	1.9	22	90	0	66	54	4	0	40	1.21
15441981--15442022	20	2.1	20	100	0	84	26	9	9	54	1.63
15458566--15458735	93	1.8	93	94	0	304	28	28	21	21	1.98
15458559--15458734	46	3.8	46	79	12	207	29	28	21	20	1.98
15466108--15466232	46	2.7	46	94	0	214	29	28	23	19	1.98
15479662--15479729	31	2.2	31	86	5	93	41	8	16	33	1.79
15480234--15480278	25	1.9	24	86	13	67	46	0	0	53	1.00
15480319--15480349	16	2.0	16	93	6	55	29	0	0	70	0.87
15480435--15480480	18	2.7	18	83	6	60	56	8	0	34	1.30
15482886--15482963	38	2.0	39	92	2	131	28	14	7	50	1.70
15483039--15483102	27	2.4	27	92	2	103	51	6	3	39	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15487383--15487425	22	2.0	22	81	9	52	53	16	11	18	1.72
15488098--15488236	63	2.2	63	77	1	136	30	28	19	21	1.98
15490819--15490885	29	2.3	29	81	0	80	25	35	19	19	1.95
15494603--15494645	20	2.0	20	82	8	50	32	11	11	44	1.77
15500169--15500222	21	2.6	21	80	8	58	44	16	3	35	1.66
15522782--15522818	19	1.9	19	94	0	65	70	2	0	27	1.01
15523311--15523368	25	2.5	22	83	8	71	55	1	0	43	1.10
15531145--15531180	10	3.5	11	85	14	58	22	0	0	77	0.76
15531136--15531180	20	2.3	20	92	3	74	24	0	0	75	0.80
15537825--15537946	27	4.5	27	81	0	118	28	28	15	27	1.96
15545828--15546005	27	6.6	27	83	3	196	29	28	14	26	1.95
15545849--15546004	82	1.9	81	86	3	224	29	28	14	26	1.95
15552640--15552685	24	2.0	23	86	4	65	13	21	26	39	1.90
15557032--15557059	12	2.3	12	100	0	56	25	14	28	32	1.94
15558346--15558389	17	2.6	16	86	10	61	34	0	20	45	1.51
15558790--15558838	25	2.0	25	100	0	98	40	8	18	32	1.80
15560224--15560301	38	2.1	38	100	0	156	34	17	17	29	1.94
15561665--15561764	42	2.3	43	79	5	114	29	18	22	31	1.97
15561930--15561964	18	1.9	18	94	0	61	31	8	25	34	1.86
15568562--15568611	20	2.5	20	86	0	64	34	10	32	24	1.88
15570978--15571360	50	7.8	50	78	6	324	26	20	29	23	1.99
15574212--15574263	27	2.0	26	84	3	68	34	21	26	17	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15584471--15584754	50	5.8	49	80	4	270	27	18	30	23	1.97
15587354--15587408	24	2.3	24	81	15	69	16	27	0	56	1.40
15594622--15594750	48	2.8	46	80	4	152	31	27	20	19	1.97
15600861--15601375	47	10.8	47	95	1	877	32	8	29	29	1.87
15600861--15601375	241	2.2	239	95	2	912	32	8	29	29	1.87
15621082--15621203	27	4.5	27	88	0	172	29	20	8	41	1.81
15621063--15621175	54	2.1	54	81	0	127	31	23	7	37	1.83
15621101--15621231	54	2.4	54	83	2	165	32	21	7	38	1.82
15621082--15621230	81	1.8	81	79	2	174	32	20	7	40	1.80
15621182--15621512	54	6.1	54	73	9	244	39	20	9	31	1.84

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