genome.fa.s8.2.7.7.80.10.50.1000.12.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: At_chr9
Parameters: 2 7 7 80 10 50 1000
Length:  91122320

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   

This is table  12  of  279  ( 33431 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)
3862679--3862732	28	1.9	28	96	0	99	31	3	11	53	1.53
3867754--3867802	16	3.1	16	87	0	80	48	28	6	16	1.69
3869044--3869202	27	5.9	27	80	11	166	35	20	24	20	1.96
3869065--3869206	54	2.6	55	88	9	213	35	20	24	19	1.95
3870800--3870907	26	4.2	26	93	0	189	36	24	7	32	1.83
3875725--3875880	27	5.8	27	78	10	149	35	19	23	21	1.96
3875742--3875880	54	2.6	54	93	4	228	35	20	23	20	1.96
3878389--3878637	39	6.4	39	88	3	358	28	30	21	18	1.97
3886472--3886687	39	5.5	39	90	1	317	29	29	22	18	1.98
3889215--3889374	26	6.2	26	94	0	284	35	24	7	32	1.83
3890479--3890524	8	5.8	8	80	10	58	50	21	21	6	1.71
3890479--3890524	24	1.9	24	90	0	74	50	21	21	6	1.71
3890478--3890530	16	3.4	15	82	7	61	50	20	20	7	1.72
3890740--3890854	29	4.0	28	81	2	113	26	15	28	28	1.96
3896087--3896294	46	4.5	46	76	12	151	25	28	17	27	1.98
3897760--3897932	46	3.7	46	80	13	219	21	21	28	28	1.98
3897757--3897927	93	1.8	93	96	0	315	21	21	29	28	1.98
3899902--3899984	41	2.0	41	97	0	157	42	6	16	34	1.73
3906043--3906260	46	4.7	46	97	1	359	29	28	21	20	1.98
3911542--3911949	204	2.0	204	92	1	676	37	11	14	36	1.83
3912067--3912191	60	2.1	60	92	0	205	31	11	8	49	1.67
3912882--3912921	20	2.0	20	100	0	80	45	10	10	35	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3916006--3916191	93	2.0	93	98	0	363	36	14	31	17	1.90
3917602--3917641	18	2.2	18	86	8	55	20	0	12	67	1.22
3917643--3917675	11	2.9	12	86	13	52	66	0	0	33	0.92
3922745--3922805	31	2.0	31	96	0	113	27	27	9	34	1.89
3924884--3924935	24	2.0	27	82	14	65	61	0	3	34	1.14
3929019--3929055	12	3.0	13	88	11	60	37	8	40	13	1.74
3931455--3931535	26	3.1	26	75	8	76	55	4	6	33	1.46
3931999--3932054	21	2.7	22	78	15	57	55	5	7	32	1.50
3935661--3935731	36	2.1	35	86	7	101	50	5	15	28	1.66
3936717--3936768	7	7.0	7	80	10	59	23	0	0	76	0.78
3937647--3937720	5	13.8	5	78	10	51	77	0	4	18	0.93
3937649--3937720	30	2.4	29	81	9	92	77	0	4	18	0.92
3937648--3937715	20	3.5	19	75	23	61	77	0	4	17	0.92
3944101--3944128	10	2.8	10	100	0	56	60	0	7	32	1.24
3949660--3949692	11	2.9	12	86	13	52	33	0	0	66	0.92
3949908--3949950	22	2.0	22	85	0	59	58	11	11	18	1.63
3949915--3949955	11	3.7	11	80	0	55	56	9	14	19	1.66
3952750--3952795	23	2.0	23	86	0	65	47	19	2	30	1.61
3954663--3954704	19	2.2	19	83	8	50	30	2	0	66	1.04
3963069--3963120	24	2.2	24	89	0	77	55	9	1	32	1.43
3965038--3965089	24	2.2	24	89	0	77	55	9	1	32	1.43
3967772--3967865	47	2.0	47	100	0	188	34	17	17	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3969307--3969442	68	2.0	66	90	2	209	45	10	13	30	1.77
3969506--3969569	29	2.2	30	83	8	78	56	4	3	35	1.36
3970690--3970823	51	2.5	53	87	6	209	24	50	11	14	1.75
3970798--3970873	33	2.3	33	90	0	116	18	56	11	13	1.66
3970837--3970933	42	2.3	42	92	0	167	23	53	8	14	1.67
3970897--3970964	30	2.3	30	84	5	93	27	51	5	14	1.65
3973932--3973969	15	2.4	16	86	4	51	10	10	0	78	0.95
3973935--3973974	21	2.0	20	85	9	55	10	10	0	80	0.92
3974697--3974744	12	3.8	12	76	10	51	27	6	4	62	1.38
3974898--3974939	22	1.9	22	85	9	59	26	9	0	64	1.24
3975097--3975153	28	2.0	30	82	6	73	28	5	3	63	1.33
3975537--3975592	26	2.2	26	96	0	103	30	7	25	37	1.82
3983126--3983181	26	2.2	26	93	6	96	37	23	7	32	1.82
3987910--3987972	33	1.9	32	90	3	99	22	14	7	55	1.64
3990126--3990228	23	4.7	23	76	11	92	24	8	0	66	1.26
3990117--3990229	43	2.6	42	77	6	109	23	7	1	66	1.28
3990128--3990208	29	2.8	28	78	12	67	24	9	1	64	1.32
3990175--3990220	15	2.9	15	90	6	65	26	6	0	67	1.15
3990358--3990437	25	3.2	24	74	15	63	33	10	0	56	1.33
3992633--3992683	20	2.4	21	83	9	59	56	0	7	35	1.28
3993297--3993378	27	3.0	27	79	13	80	52	7	8	31	1.59
3993562--3993763	3	70.0	3	66	18	65	61	2	6	29	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3993527--3993588	31	1.9	31	81	12	72	51	8	4	35	1.53
3993692--3993772	33	2.4	33	80	11	94	64	2	2	30	1.20
3993702--3993786	15	5.4	15	77	13	73	63	3	3	29	1.28
3993736--3993788	18	2.8	19	80	13	56	64	1	5	28	1.27
3995843--3995950	26	4.2	26	93	0	189	36	24	7	32	1.83
3998636--3998660	12	2.1	12	100	0	50	16	20	24	40	1.91
3999568--3999917	177	2.0	177	100	0	700	22	27	18	31	1.97
4002869--4002976	26	4.2	26	91	0	171	37	24	7	31	1.83
4003533--4003557	7	3.6	7	100	0	50	28	0	72	0	0.86
4004238--4004276	20	2.0	20	89	0	60	15	0	25	58	1.37
4004271--4004316	22	2.1	22	87	0	65	23	0	36	39	1.55
4007766--4007833	30	2.2	33	79	15	81	42	7	4	45	1.52
4007767--4007833	32	2.2	30	84	10	82	43	7	4	44	1.52
4008108--4008160	26	2.1	26	89	3	81	39	3	0	56	1.17
4012160--4012184	10	2.5	10	100	0	50	40	8	0	52	1.31
4025967--4026006	21	2.0	20	85	5	53	17	0	27	55	1.43
4038130--4038298	90	1.9	90	85	2	232	25	14	18	40	1.89
4043579--4043622	20	2.2	20	100	0	88	50	6	4	38	1.50
4046684--4046735	28	2.0	27	85	14	74	48	5	5	40	1.51
4047018--4047436	3	140.7	3	66	15	140	60	2	6	30	1.35
4047069--4047151	22	3.9	21	74	16	73	65	0	7	27	1.19
4047306--4047421	47	2.4	47	80	8	128	60	0	6	31	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4047399--4047436	14	2.6	15	91	8	69	63	0	5	31	1.17
4050074--4050237	57	2.9	57	80	8	208	39	18	10	31	1.84
4053366--4053399	15	2.3	15	89	0	50	44	0	20	35	1.52
4053372--4053406	15	2.3	15	95	0	61	45	2	14	37	1.59
4053376--4053413	15	2.7	14	88	8	51	44	2	13	39	1.57
4058889--4058924	10	3.7	10	92	3	56	50	0	16	33	1.46
4069298--4069888	296	2.0	296	99	0	1173	30	20	16	31	1.95
4075271--4075309	6	6.2	6	82	11	51	30	2	0	66	1.05
4077093--4077135	19	2.3	18	84	15	52	37	18	0	44	1.50
4078652--4078712	23	2.7	23	92	0	104	32	18	24	24	1.97
4078652--4078758	47	2.2	49	80	12	116	32	17	22	27	1.96
4084976--4085035	25	2.4	25	91	2	95	40	1	0	58	1.08
4085050--4085084	17	2.1	17	100	0	70	28	17	17	37	1.92
4091701--4091725	12	2.1	12	100	0	50	20	8	0	72	1.10
4099819--4099895	32	2.4	31	81	10	93	49	1	9	40	1.43
4103139--4103194	18	3.1	18	66	19	53	50	1	8	39	1.44
4103154--4103212	18	3.3	18	66	17	50	54	1	6	37	1.37
4103139--4103214	36	2.1	36	97	0	143	51	1	7	39	1.39
4105757--4105787	15	2.1	15	100	0	62	25	6	25	41	1.79
4112180--4112222	21	2.0	21	91	8	70	37	6	4	51	1.50
4116187--4116234	22	2.2	22	88	7	71	18	2	66	12	1.33
4117280--4117338	22	2.7	21	82	10	64	45	1	8	44	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4117280--4117343	21	2.9	23	81	9	71	46	1	10	40	1.48
4125000--4125044	22	2.0	22	83	8	56	26	11	0	62	1.29
4131136--4131300	35	4.7	34	81	4	161	33	24	12	30	1.91
4131136--4131300	70	2.4	70	82	4	190	33	24	12	30	1.91
4134932--4135020	31	2.8	32	78	6	92	46	2	6	44	1.42
4138966--4139008	21	2.0	21	86	0	59	34	9	6	48	1.62
4142546--4142587	17	2.5	17	84	3	59	61	0	0	38	0.96
4142774--4142799	4	6.5	4	100	0	52	50	0	0	50	1.00
4153196--4153245	25	2.0	25	100	0	100	32	16	16	36	1.90
4179265--4179297	10	3.0	11	86	13	50	69	3	0	27	1.03

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