genome.fa.s4.2.7.7.80.10.50.1000.118.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  118  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)
40292303--40292349	16	2.9	16	80	0	58	2	55	0	42	1.12
40292314--40292364	20	2.6	19	84	3	66	0	56	0	43	0.99
40292386--40292417	2	16.0	2	100	0	64	0	50	0	50	1.00
40294213--40294262	10	5.0	10	78	9	57	66	2	8	24	1.29
40295134--40295287	76	2.1	74	88	2	227	27	16	19	37	1.93
40296736--40296798	21	3.0	21	90	0	99	15	25	17	41	1.89
40300723--40300879	81	2.0	81	93	1	271	36	14	14	34	1.86
40301133--40301163	16	1.9	16	93	0	53	9	0	9	80	0.90
40301196--40301277	39	2.1	39	97	0	155	40	3	12	43	1.59
40307426--40307476	25	2.0	25	96	0	93	50	5	25	17	1.68
40315341--40315436	48	2.0	48	100	0	192	39	16	16	27	1.90
40324402--40324486	42	2.0	42	100	0	170	38	23	9	28	1.86
40329957--40330142	73	2.5	73	97	0	354	40	24	6	28	1.79
40334387--40334572	73	2.5	73	97	0	354	40	24	6	28	1.79
40342593--40342646	22	2.5	22	78	6	56	51	1	0	46	1.11
40346114--40346230	55	2.1	55	96	0	216	23	39	22	15	1.92
40347121--40347176	17	3.2	17	66	14	51	48	26	0	25	1.52
40347110--40347182	35	2.1	35	97	0	137	47	23	0	28	1.52
40352481--40352522	17	2.5	17	80	7	50	45	4	9	40	1.58
40353518--40353584	25	2.7	25	83	0	98	17	23	20	37	1.94
40353810--40353850	12	3.5	12	75	18	50	24	2	14	58	1.49
40353807--40353853	23	2.0	23	100	0	94	25	4	12	57	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40362348--40362398	25	2.0	25	92	0	84	39	5	17	37	1.74
40362351--40362398	12	3.9	12	75	5	51	39	4	18	37	1.70
40366050--40366100	25	2.0	25	92	0	84	39	5	17	37	1.74
40366053--40366100	12	3.9	12	75	5	51	39	4	18	37	1.70
40380486--40380536	24	2.1	24	92	0	84	21	11	23	43	1.85
40380518--40380808	74	3.9	74	100	0	582	28	17	18	35	1.94
40382094--40382160	7	9.6	7	78	12	66	29	25	0	44	1.54
40382098--40382159	21	3.0	21	85	0	79	29	27	0	43	1.55
40385643--40385703	21	2.8	21	72	5	59	14	22	27	34	1.94
40387656--40387717	22	2.9	21	75	2	61	24	20	19	35	1.96
40387676--40387732	22	2.6	22	75	2	62	21	17	19	42	1.90
40387656--40387740	43	2.0	43	80	0	98	23	20	18	37	1.94
40390822--40390861	20	2.0	21	85	9	57	32	0	5	62	1.17
40390827--40390867	20	2.2	20	82	8	50	31	2	4	60	1.30
40390914--40390981	31	2.3	31	87	5	95	63	1	2	32	1.18
40392451--40392538	41	2.1	41	89	0	131	28	13	21	36	1.92
40392463--40392563	41	2.4	41	88	4	141	26	13	22	36	1.92
40394454--40394502	19	2.3	23	80	13	61	48	0	12	38	1.41
40399395--40399423	14	2.1	14	93	6	51	48	13	6	31	1.69
40410943--40410985	16	2.7	16	85	0	50	55	0	0	44	0.99
40411776--40411829	28	1.9	28	88	0	81	50	3	0	46	1.19
40421761--40421841	32	2.6	31	80	2	90	29	3	16	50	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40422799--40422877	25	3.3	25	65	13	67	30	7	15	46	1.73
40423155--40423200	19	2.4	19	85	3	65	47	13	10	28	1.76
40423506--40423815	152	2.0	153	94	0	550	23	16	11	48	1.78
40431397--40431437	20	2.1	20	86	4	57	51	2	4	41	1.36
40434872--40434915	15	2.9	15	96	0	79	18	20	15	45	1.85
40434987--40435045	29	2.0	29	96	0	109	25	13	3	57	1.52
40447207--40447326	48	2.6	46	74	17	122	30	26	29	14	1.95
40447197--40447330	23	5.7	24	72	16	118	32	25	26	14	1.95
40449475--40449523	3	17.3	3	76	19	52	69	0	2	28	1.00
40449481--40449519	11	3.5	11	92	0	69	69	0	2	28	1.02
40449482--40449523	19	2.2	19	87	8	59	71	0	2	26	0.98
40449509--40449561	20	2.7	20	85	8	65	56	5	0	37	1.23
40451438--40451466	15	1.9	15	100	0	58	20	34	24	20	1.97
40452770--40452812	14	3.0	14	80	12	52	46	9	0	44	1.35
40454369--40454413	20	2.2	21	84	4	56	77	2	17	2	0.97
40454469--40454495	12	2.2	12	100	0	54	7	7	33	51	1.58
40456800--40456932	48	2.8	48	85	10	173	30	21	16	32	1.95
40475378--40475420	19	2.3	19	83	0	50	48	0	0	51	1.00
40477258--40477316	30	2.0	30	93	0	100	30	25	5	38	1.77
40479046--40479088	18	2.4	18	88	0	59	20	25	9	44	1.81
40482545--40483065	126	4.1	125	86	2	670	28	16	17	37	1.92
40482545--40483065	251	2.1	253	85	4	705	28	16	17	37	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40483127--40483268	34	4.2	33	79	9	119	44	15	0	39	1.52
40483180--40483266	33	2.6	33	87	3	122	39	17	1	42	1.57
40483716--40483808	50	1.9	50	86	4	127	36	3	7	52	1.46
40496280--40497730	724	2.0	724	99	0	2884	31	18	26	23	1.97
40507627--40507659	17	1.9	17	93	0	57	51	0	0	48	1.00
40511903--40511942	19	2.1	19	85	4	53	45	2	0	52	1.14
40512049--40512100	6	9.2	6	77	12	56	76	0	0	23	0.78
40512039--40512100	16	3.9	16	79	8	65	75	0	0	24	0.80
40512038--40512100	22	2.8	21	81	11	63	74	0	0	25	0.82
40513198--40513232	14	2.4	15	95	4	63	60	0	37	2	1.12
40513239--40513273	13	2.7	13	90	0	52	77	0	22	0	0.78
40513686--40513715	11	2.7	11	94	0	51	50	10	0	40	1.36
40513990--40514046	27	2.1	27	96	0	105	17	38	26	17	1.92
40516283--40516341	20	2.9	21	80	12	70	81	0	1	16	0.78
40516293--40516342	6	8.0	6	88	6	73	82	0	0	18	0.68
40522748--40522800	26	2.0	26	92	0	88	30	28	9	32	1.88
40531614--40531653	21	1.9	21	89	0	62	62	2	0	35	1.09
40531589--40531652	26	2.5	25	77	5	65	64	4	0	31	1.14
40531689--40531779	46	2.0	46	84	4	121	62	1	1	35	1.10
40531720--40531769	20	2.4	21	87	12	77	66	0	0	34	0.92
40531724--40531762	19	2.0	20	95	5	71	66	0	0	33	0.92
40531750--40531803	17	3.3	16	80	12	56	62	3	0	33	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40531782--40531823	23	1.9	21	85	9	57	64	2	2	30	1.19
40531869--40531933	33	2.0	33	84	6	87	49	7	0	43	1.31
40531933--40531981	20	2.5	20	93	0	80	16	6	26	51	1.68
40536534--40536563	15	2.0	15	100	0	60	53	0	0	46	1.00
40541974--40542089	25	4.6	25	69	13	78	33	15	26	24	1.95
40541982--40542089	50	2.2	49	80	8	128	34	14	27	23	1.94
40545563--40545619	18	3.1	19	82	10	73	28	1	1	68	1.09
40549828--40549866	16	2.5	15	84	12	51	41	0	0	58	0.98
40550966--40550990	13	1.9	13	100	0	50	64	0	8	28	1.22
40561166--40561284	55	2.2	55	92	0	193	26	10	23	38	1.88
40566801--40566849	24	2.0	24	100	0	98	34	8	8	48	1.62
40569358--40569554	43	4.6	43	81	5	209	23	15	26	34	1.94
40569358--40569577	86	2.6	88	80	5	236	22	15	27	34	1.95
40583871--40583905	18	1.9	18	94	0	61	42	5	8	42	1.59
40584091--40584141	23	2.3	22	90	6	77	25	43	1	29	1.66
40584135--40584173	20	2.1	19	90	9	62	28	35	0	35	1.58
40586046--40586084	18	2.1	18	85	4	51	20	20	30	28	1.98
40591220--40591273	17	2.8	19	79	20	60	66	7	0	25	1.17
40591220--40591274	18	2.8	19	76	17	60	67	7	0	25	1.16
40592799--40592953	29	5.3	28	79	5	148	36	14	25	23	1.93
40592799--40592952	59	2.6	58	82	5	184	36	14	25	23	1.93
40595165--40595272	25	4.3	26	73	11	91	31	20	26	21	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40595165--40595282	50	2.4	50	80	8	125	31	20	27	20	1.97
40595211--40595299	25	3.6	25	78	3	90	32	19	28	20	1.96
40596767--40596826	27	2.2	27	82	5	68	26	1	8	63	1.32
40597030--40597055	9	2.9	9	100	0	52	34	0	11	53	1.37
40597342--40597383	23	1.9	21	90	9	66	30	7	4	57	1.47
40597328--40597389	27	2.3	25	79	15	70	30	6	3	59	1.38
40597459--40597518	26	2.3	26	82	8	77	33	5	6	55	1.48
40597533--40597572	20	2.0	20	90	9	64	32	0	5	62	1.17
40597843--40597895	27	2.0	27	81	7	63	28	5	1	64	1.27
40597931--40597956	3	8.7	3	100	0	52	30	0	0	69	0.89

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