genome.fa.s4.2.7.7.80.10.50.1000.14.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_chr8
Parameters: 2 7 7 80 10 50 1000
Length:  78745976

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   

This is table  14  of  235  ( 28198 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)
3847339--3847377	15	2.6	15	87	0	60	30	5	5	58	1.41
3847349--3847389	19	2.0	21	86	9	59	34	7	7	51	1.58
3855542--3855573	13	2.6	12	90	9	55	53	15	0	31	1.43
3858444--3858478	18	1.9	18	94	0	61	80	0	8	11	0.92
3862361--3862392	13	2.6	12	90	9	55	53	15	0	31	1.43
3866314--3866474	38	4.2	38	86	1	196	19	19	26	34	1.96
3866314--3866474	76	2.1	78	85	2	218	19	19	26	34	1.96
3866444--3866657	112	1.9	111	95	1	376	26	15	27	30	1.96
3873629--3873748	38	3.2	38	88	4	170	20	21	24	34	1.97
3878351--3878497	57	2.6	57	81	11	153	26	32	12	27	1.93
3878351--3878476	29	4.4	29	80	12	138	25	32	14	27	1.94
3878352--3878497	29	5.1	28	76	11	120	26	32	13	28	1.93
3879536--3879596	17	3.8	17	76	20	60	54	3	6	36	1.43
3880350--3880391	15	2.7	16	85	3	59	14	7	14	64	1.48
3880621--3880731	30	3.7	30	83	3	127	42	2	23	31	1.68
3880920--3881088	77	2.2	77	100	0	338	39	17	17	25	1.91
3880955--3881232	77	3.7	73	81	7	267	37	17	15	28	1.91
3881142--3881549	87	4.7	86	84	6	529	37	20	15	26	1.93
3881077--3881560	259	1.9	250	85	6	659	36	20	15	27	1.93
3881141--3881551	172	2.4	175	87	4	566	37	20	15	26	1.93
3881151--3881632	259	1.9	252	83	7	627	34	21	15	27	1.94
3896207--3897300	548	2.0	548	99	0	2170	28	19	16	35	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3901130--3901170	14	2.7	16	85	7	59	14	7	14	63	1.50
3901394--3901509	30	3.9	30	77	3	101	45	1	20	31	1.61
3901632--3901666	8	4.4	8	92	0	61	2	22	22	51	1.61
3903966--3903992	14	1.9	14	100	0	54	37	0	3	59	1.15
3903960--3904010	24	2.1	24	85	7	68	33	1	3	60	1.26
3903966--3904010	6	7.2	6	80	9	54	33	0	4	62	1.15
3907776--3907815	18	2.3	18	91	4	64	32	0	2	65	1.06
3907881--3907970	39	2.2	41	88	3	130	53	5	2	38	1.37
3908079--3908136	28	2.0	28	83	9	73	50	3	0	46	1.18
3915407--3915449	17	2.6	17	79	17	54	34	4	13	46	1.65
3919200--3919244	23	2.0	23	86	8	65	40	6	13	40	1.71
3926788--3927077	145	2.0	145	96	0	535	39	13	17	30	1.87
3933886--3933935	26	1.9	26	84	15	68	28	10	22	40	1.86
3942469--3942499	16	1.9	16	100	0	62	45	6	22	25	1.76
3944186--3944267	29	2.8	29	92	0	137	20	24	15	39	1.92
3953515--3953595	29	2.8	29	88	3	119	19	25	17	37	1.94
3960414--3960438	12	2.1	12	100	0	50	68	0	0	32	0.90
3962972--3963015	19	2.2	19	84	8	52	52	4	0	43	1.22
3964571--3964615	23	2.0	23	83	8	58	37	2	8	51	1.46
3965914--3965946	12	2.8	12	86	4	50	33	0	0	66	0.92
3966070--3966131	29	2.1	30	90	3	99	59	11	3	25	1.46
3972270--3972310	21	2.0	21	90	0	64	29	21	29	19	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3980172--3980216	22	2.0	22	83	8	56	37	4	13	44	1.64
3983888--3983944	25	2.3	25	85	8	73	71	3	17	7	1.22
3983896--3983967	29	2.4	29	80	11	76	73	4	19	2	1.12
3983896--3983960	34	1.9	33	84	3	85	75	3	18	3	1.07
3989197--3989231	9	3.8	9	96	3	61	45	0	11	42	1.40
3993383--3993459	31	2.6	29	79	8	91	42	11	3	41	1.59
3993916--3994010	47	2.0	47	100	0	190	51	8	12	27	1.68
3996875--3996913	20	2.0	20	85	10	53	48	2	2	46	1.29
4017301--4017346	20	2.2	21	88	3	67	28	0	4	67	1.10
4023839--4024063	40	5.7	40	85	4	249	25	28	21	24	1.99
4023995--4024072	40	1.9	41	82	10	97	26	28	21	23	1.99
4030563--4030711	42	3.5	43	76	9	126	28	24	20	26	1.99
4035616--4035985	54	6.9	54	91	2	555	36	17	24	22	1.94
4038138--4038174	18	2.1	18	100	0	74	27	0	21	51	1.48
4043437--4043503	31	2.2	31	97	0	125	53	28	0	17	1.44
4045545--4045727	40	4.6	39	78	9	183	24	20	27	27	1.99
4067444--4067485	22	1.9	22	85	9	59	38	4	19	38	1.73
4067440--4067492	22	2.3	23	78	18	58	33	9	18	37	1.83
4069001--4069194	47	4.1	47	89	0	280	32	11	29	26	1.91
4069030--4069101	22	3.1	22	64	24	58	33	13	29	23	1.93
4069075--4069150	23	3.2	25	62	24	63	28	13	34	23	1.92
4069164--4069350	48	3.8	48	86	8	277	36	6	26	31	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4069165--4069350	100	1.9	96	89	6	284	36	6	26	30	1.82
4069513--4069540	13	2.2	13	100	0	56	25	14	39	21	1.91
4069527--4069617	37	2.5	37	90	0	137	24	16	29	29	1.96
4072209--4072241	17	1.9	17	88	11	50	18	33	15	33	1.92
4077516--4077597	41	2.0	41	97	0	155	35	7	23	34	1.82
4084504--4084693	54	3.5	54	73	7	204	37	16	21	24	1.94
4084555--4084958	55	7.4	55	73	5	381	38	19	19	22	1.94
4084504--4085011	108	4.7	108	97	0	818	37	19	20	22	1.94
4084496--4085024	55	9.8	53	72	3	320	37	18	20	22	1.94
4087611--4087786	50	3.5	49	77	7	158	24	18	28	28	1.98
4087604--4087797	49	3.9	49	75	6	167	24	19	28	27	1.99
4094039--4094072	16	2.1	17	88	5	52	32	17	0	50	1.47
4094252--4094549	43	7.1	43	79	4	365	33	27	13	24	1.93
4094238--4094549	84	3.7	84	98	0	597	34	27	13	24	1.93
4097373--4097540	46	3.6	46	75	12	139	29	19	28	22	1.98
4109495--4109678	40	4.6	40	91	2	282	23	22	27	26	2.00
4109492--4109678	79	2.3	80	92	2	315	24	22	26	26	2.00
4109491--4109701	79	2.7	79	87	7	304	25	21	26	26	2.00
4114908--4115037	46	2.8	46	79	8	131	25	30	10	33	1.89
4118294--4118393	28	3.6	27	74	6	83	29	30	18	23	1.97
4118294--4118423	57	2.3	57	84	6	158	28	28	19	23	1.98
4118322--4118421	28	3.6	27	76	10	85	30	27	20	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4118433--4118548	40	2.9	40	96	0	205	25	25	21	26	2.00
4125404--4125473	25	2.8	25	85	8	81	38	24	18	18	1.93
4132980--4133053	31	2.4	31	95	0	130	25	31	27	16	1.96
4140939--4140986	17	3.1	17	74	17	50	37	2	25	35	1.68
4152018--4152124	53	2.0	53	98	0	205	34	23	16	25	1.95
4156976--4157043	28	2.7	23	74	20	64	17	5	32	44	1.73
4156949--4157028	28	2.8	28	90	1	124	17	3	32	46	1.66
4160958--4161193	48	4.9	48	81	7	264	27	17	28	26	1.98
4160968--4161193	95	2.4	96	84	3	305	27	18	28	25	1.98
4166099--4166211	27	4.2	26	84	9	138	19	23	21	35	1.96
4166098--4166204	55	2.0	54	88	5	162	20	24	19	35	1.96
4169918--4169979	26	2.3	26	89	8	90	37	29	6	27	1.82
4170084--4170165	27	3.0	27	92	1	128	18	24	20	36	1.95
4173371--4173525	42	3.7	42	66	12	102	27	16	25	29	1.97
4183602--4183639	19	2.0	20	89	5	60	26	21	15	36	1.93
4189903--4190047	72	2.0	72	97	0	272	31	4	17	47	1.66
4193633--4193809	27	6.5	27	83	3	194	27	15	27	29	1.96
4193634--4193784	82	1.9	81	88	4	232	27	15	27	29	1.96
4193787--4194043	129	2.0	129	98	0	496	27	16	26	29	1.97
4198142--4198522	190	2.0	190	99	0	753	27	20	24	27	1.99
4203210--4203282	37	2.0	37	97	0	137	23	20	19	36	1.95
4206026--4206051	12	2.2	12	100	0	52	50	7	0	42	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4206533--4206710	27	6.6	27	83	3	205	26	15	28	29	1.96
4206534--4206689	82	1.9	81	88	3	233	26	15	28	29	1.96
4206530--4206710	82	2.2	81	83	2	229	27	15	27	29	1.96
4218816--4218941	63	2.0	63	100	0	252	25	26	19	28	1.98
4220232--4220766	176	3.0	176	90	2	822	35	19	19	25	1.96
4220752--4220807	24	2.3	24	100	0	112	44	16	28	10	1.80
4223485--4223938	82	5.5	82	98	0	867	36	17	15	30	1.92
4224512--4224740	123	1.9	119	90	5	361	29	19	15	36	1.92
4225431--4226238	324	2.5	324	97	0	1535	34	19	14	31	1.92
4226550--4226642	34	2.8	31	87	11	114	18	16	22	43	1.88

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