genome.fa.s20.2.7.7.80.10.50.1000.17.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_chr2
Parameters: 2 7 7 80 10 50 1000
Length:  61750188

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   

This is table  17  of  186  ( 22216 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)
5238258--5238302	18	2.6	17	86	13	65	77	0	22	0	0.76
5240392--5241620	50	24.7	50	69	5	655	32	25	20	21	1.97
5240382--5241616	399	3.1	398	84	2	1604	32	24	20	22	1.97
5240382--5241620	100	12.5	100	86	1	1533	32	25	20	22	1.97
5243271--5243342	3	23.3	3	78	10	74	29	5	1	63	1.25
5243274--5243342	16	4.4	16	82	10	65	28	5	1	63	1.26
5243269--5243322	19	2.8	19	91	5	83	27	3	0	68	1.06
5243268--5243342	19	4.1	17	83	13	80	29	5	1	64	1.24
5244497--5244522	4	6.5	4	100	0	52	23	0	0	76	0.78
5246051--5246096	16	2.9	16	75	15	51	56	0	8	34	1.30
5246253--5246280	3	9.3	3	100	0	56	64	0	0	35	0.94
5253685--5253761	30	2.6	29	81	6	75	19	28	32	19	1.96
5255420--5255455	19	1.9	19	88	5	56	55	11	8	25	1.62
5256046--5256104	3	20.0	3	72	10	50	66	3	1	28	1.18
5257576--5257682	44	2.4	44	76	6	108	28	24	15	30	1.96
5257621--5257744	59	2.1	59	93	1	214	24	25	16	33	1.96
5257678--5257858	45	4.1	44	72	2	146	28	25	17	28	1.98
5257684--5257858	89	2.0	89	93	0	296	28	25	17	28	1.97
5257684--5257815	44	3.0	45	71	2	131	28	27	17	27	1.98
5257678--5257835	45	3.5	45	73	1	156	25	25	17	31	1.97
5257719--5257869	44	3.4	44	73	1	131	28	23	17	31	1.97
5262090--5262174	9	9.4	9	80	5	100	41	23	8	27	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5262090--5262174	18	4.7	18	85	5	118	41	23	8	27	1.83
5262090--5262174	27	3.1	27	84	0	116	41	23	8	27	1.83
5262276--5262342	18	3.9	18	70	20	63	16	1	41	40	1.57
5262282--5262316	13	2.7	13	95	0	61	14	0	45	40	1.45
5263831--5263858	14	2.0	14	100	0	56	14	42	21	21	1.88
5268615--5268654	20	2.0	20	95	0	71	32	15	22	30	1.94
5272039--5272075	19	1.9	19	88	0	56	56	10	8	24	1.60
5272666--5272724	3	20.0	3	72	10	50	66	3	1	28	1.18
5276183--5276448	103	2.6	104	91	0	426	19	20	30	29	1.97
5283675--5283940	103	2.6	104	90	3	419	19	20	29	29	1.97
5285272--5285301	13	2.2	14	94	5	53	43	0	6	50	1.28
5285938--5285973	17	2.1	17	94	0	63	22	25	5	47	1.73
5287600--5287645	21	2.2	21	84	3	58	56	2	2	39	1.24
5287608--5287655	21	2.3	21	85	0	60	64	4	0	31	1.12
5287738--5287782	21	2.1	21	84	8	56	51	2	2	44	1.26
5291533--5291571	19	2.1	19	95	0	69	35	10	0	53	1.35
5300716--5300742	6	4.5	6	100	0	54	48	0	51	0	1.00
5301631--5301678	23	2.1	23	100	0	96	33	20	18	27	1.96
5314113--5314152	21	2.0	20	85	5	53	42	5	20	32	1.73
5315711--5315772	24	2.6	24	82	10	81	14	27	24	33	1.94
5320290--5320366	33	2.4	31	77	10	82	33	5	1	59	1.28
5320312--5320400	29	3.0	29	74	9	81	34	5	1	58	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5320689--5320732	4	10.8	4	97	2	79	22	0	2	75	0.92
5320773--5320806	15	2.3	15	89	0	50	17	11	5	64	1.45
5329153--5329196	21	2.1	21	100	0	88	34	13	27	25	1.93
5331063--5331116	20	2.7	19	74	5	54	25	0	0	74	0.83
5335248--5335455	51	4.0	53	94	2	361	28	23	19	28	1.98
5335248--5335455	104	2.0	104	93	3	357	28	23	19	28	1.98
5337778--5338028	127	2.0	126	90	0	394	39	18	11	30	1.86
5339998--5340025	14	2.0	14	100	0	56	50	7	7	35	1.57
5340659--5340691	3	11.0	3	100	0	66	33	0	33	33	1.58
5340690--5340727	3	12.7	3	100	0	76	34	31	34	0	1.58
5340737--5340765	3	9.7	3	100	0	58	65	0	0	34	0.93
5347665--5348353	87	7.9	87	90	1	1035	36	19	16	27	1.93
5347666--5348353	346	2.0	348	90	1	1096	36	19	16	27	1.93
5349716--5349769	16	3.4	16	81	0	63	46	3	20	29	1.68
5350205--5350239	13	2.8	12	83	8	52	57	0	11	31	1.34
5352204--5352268	28	2.3	30	76	15	84	60	1	29	9	1.37
5355967--5356039	18	4.1	18	83	0	83	31	23	12	32	1.91
5355961--5356035	36	2.1	36	92	0	123	29	25	13	32	1.93
5361978--5362048	34	2.1	34	91	0	115	39	23	11	25	1.88
5363545--5363590	24	1.9	24	81	0	56	30	10	15	43	1.81
5365971--5366040	28	2.5	28	93	2	115	40	10	1	48	1.45
5366427--5366461	3	11.7	3	100	0	70	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5367191--5367235	18	2.5	18	85	0	63	28	4	46	20	1.69
5369551--5369589	14	2.7	15	84	8	53	61	5	5	28	1.39
5369563--5369591	14	2.1	14	100	0	58	55	0	6	37	1.27
5371870--5371897	11	2.5	11	100	0	56	7	7	0	85	0.73
5371916--5371983	27	2.5	28	95	4	122	48	0	10	41	1.37
5371987--5372012	13	2.0	13	100	0	52	23	0	0	76	0.78
5372021--5372056	19	1.9	18	88	5	54	72	5	2	19	1.17
5372773--5372928	10	16.0	10	63	24	57	0	32	0	66	1.01
5372815--5372925	18	6.1	18	73	15	86	0	32	0	65	1.05
5372846--5372925	34	2.8	28	73	24	76	0	32	1	66	1.00
5372778--5372894	38	3.1	38	89	7	168	0	32	0	66	0.98
5372886--5372928	22	1.9	23	85	4	61	0	30	2	67	1.03
5372747--5372929	28	6.2	30	66	21	84	0	33	0	65	1.01
5372977--5373053	27	2.9	27	88	0	109	16	31	25	25	1.97
5373083--5373153	29	2.5	28	88	8	101	49	1	9	39	1.45
5374671--5374705	7	5.1	7	96	3	63	57	14	0	28	1.38
5374671--5374713	21	2.1	20	82	4	50	60	11	2	25	1.43
5374832--5374862	16	1.9	16	93	0	53	29	9	22	38	1.86
5376339--5376683	87	4.0	87	87	0	485	36	17	16	29	1.91
5380573--5380616	21	2.1	21	91	0	70	20	29	20	29	1.98
5387707--5387737	15	2.1	15	93	0	53	38	0	0	61	0.96
5388821--5389476	170	3.9	170	87	2	897	35	17	7	39	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5390011--5390074	30	2.2	30	86	8	87	56	10	4	28	1.54
5391227--5391260	16	2.1	16	88	0	50	50	0	2	47	1.16
5391391--5391437	23	2.0	24	83	4	60	57	0	0	42	0.98
5409024--5409058	6	5.8	6	100	0	70	0	51	14	34	1.42
5409027--5409070	18	2.4	18	88	0	61	2	52	11	34	1.50
5412773--5412821	15	3.2	15	77	11	55	65	0	6	28	1.16
5413222--5413305	3	27.3	3	71	13	55	61	3	4	29	1.33
5414153--5414191	20	2.0	20	89	0	60	12	15	48	23	1.79
5432368--5432570	46	4.3	48	88	7	265	35	14	21	28	1.92
5432302--5432570	98	2.7	98	93	0	457	34	14	22	28	1.93
5432534--5432679	37	4.0	37	93	1	242	36	16	21	24	1.94
5437883--5438105	83	2.7	83	87	5	326	29	13	16	41	1.86
5438253--5438280	14	2.0	14	100	0	56	50	0	0	50	1.00
5438785--5438822	14	2.7	15	88	12	62	42	31	0	26	1.56
5439115--5439162	22	2.2	21	81	3	60	47	29	0	22	1.51
5439395--5439852	41	11.2	41	80	2	447	29	26	20	22	1.98
5440210--5440278	14	5.0	14	72	10	52	49	2	0	47	1.16
5440273--5440319	23	2.1	22	88	4	67	46	0	2	51	1.13
5440268--5440335	11	6.7	10	76	15	68	42	0	1	55	1.08
5445333--5445375	19	2.3	21	74	25	51	67	0	4	27	1.10
5447162--5447204	3	14.3	3	100	0	86	34	0	0	65	0.93
5470280--5470311	15	2.1	15	94	0	55	62	3	0	34	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5471774--5471814	20	2.0	20	90	0	64	17	58	9	14	1.62
5487190--5487254	25	2.5	25	82	7	67	33	23	26	16	1.96
5488795--5488825	12	2.6	12	94	0	53	54	3	0	41	1.16
5489102--5489202	40	2.5	40	93	0	166	28	23	19	27	1.99
5493649--5493695	18	2.5	18	86	13	60	46	6	10	36	1.64
5494488--5494524	16	2.4	16	90	4	58	59	5	2	32	1.34
5494642--5494763	60	2.0	60	88	3	183	54	13	0	31	1.45
5494757--5494898	23	5.8	23	87	9	185	53	15	0	30	1.42
5494775--5494925	8	19.0	8	70	21	68	54	13	0	31	1.39
5494756--5495306	19	27.3	19	66	23	135	56	13	0	29	1.41

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