genome.fa.s4.2.7.7.80.10.50.1000.160.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  160  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)
53925175--53925213	19	2.1	19	95	0	69	43	2	10	43	1.52
53949139--53949488	56	6.6	54	77	9	364	27	21	27	23	1.99
53949139--53949491	106	3.3	106	99	0	697	27	21	27	23	1.99
53949808--53949838	15	2.1	15	100	0	62	45	19	6	29	1.75
53953256--53953545	50	5.7	50	82	3	314	27	22	28	21	1.99
53953862--53953892	15	2.1	15	93	0	53	41	19	9	29	1.83
53960259--53960314	28	2.0	28	100	0	112	28	10	28	32	1.90
53970761--53970793	17	1.9	17	100	0	66	18	30	9	42	1.81
53975485--53975517	17	1.9	17	93	0	57	21	27	9	42	1.83
53983831--53983868	17	2.2	17	100	0	76	39	5	28	26	1.78
53986100--53986214	51	2.3	51	96	0	212	27	30	0	41	1.56
53990972--53991196	123	1.8	123	94	0	396	32	21	16	29	1.95
53992661--53992885	123	1.8	123	95	0	405	32	21	17	29	1.96
54009463--54009640	27	6.6	26	82	6	178	26	15	28	29	1.96
54009464--54009619	82	1.9	81	86	3	224	26	16	28	28	1.97
54009460--54009640	82	2.2	81	82	2	220	27	16	27	29	1.97
54009545--54009651	27	3.9	27	85	1	70	26	14	28	30	1.95
54011061--54011106	24	1.9	24	86	0	65	30	10	15	43	1.81
54011320--54011411	31	3.0	31	100	0	184	29	9	13	47	1.74
54014648--54014747	38	2.6	39	83	1	121	40	3	7	50	1.45
54021397--54021474	25	3.2	24	81	1	84	14	14	26	44	1.83
54021453--54021529	40	1.9	40	89	5	120	12	15	28	42	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54021463--54021540	40	2.0	40	87	5	113	14	16	29	39	1.88
54021576--54021895	110	2.9	111	82	3	387	25	17	26	31	1.97
54024716--54024761	18	2.6	18	82	3	58	15	41	28	15	1.87
54027872--54027919	20	2.2	22	78	14	55	39	20	14	25	1.91
54030932--54031004	26	2.8	25	83	6	92	35	16	8	39	1.78
54032996--54033083	38	2.3	40	83	11	105	39	0	2	57	1.11
54033165--54033190	13	2.0	13	100	0	52	76	0	0	23	0.78
54036339--54036395	30	1.9	29	89	3	87	22	26	35	15	1.94
54037405--54037430	2	13.0	2	100	0	52	50	0	0	50	1.00
54037867--54037909	16	2.6	17	81	7	52	39	0	0	60	0.97
54037902--54037977	32	2.4	32	82	10	93	36	2	0	60	1.11
54037945--54037984	21	1.9	21	89	0	62	37	2	0	60	1.11
54037944--54037998	21	2.5	20	80	13	56	38	1	3	56	1.28
54038352--54038402	22	2.4	22	83	6	61	27	1	7	62	1.33
54038384--54038418	19	1.9	17	88	11	52	20	2	11	65	1.37
54047758--54047829	36	1.9	39	86	8	105	55	5	8	30	1.52
54047900--54047945	19	2.4	19	92	0	74	32	2	34	30	1.70
54049631--54049670	6	6.7	6	100	0	80	70	15	15	0	1.18
54055956--54056041	38	2.2	39	87	4	129	45	11	10	32	1.75
54064067--54064142	38	2.0	39	92	2	127	42	9	9	39	1.69
54064617--54064650	16	2.1	17	88	5	52	50	0	11	38	1.39
54067911--54068030	56	2.1	56	98	0	231	45	9	23	22	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54069201--54069344	40	3.6	40	79	12	145	25	23	27	24	2.00
54069253--54069351	39	2.5	39	86	4	110	25	22	28	24	1.99
54069200--54069350	79	1.9	80	81	6	182	25	23	27	23	2.00
54080803--54080896	47	2.0	47	97	0	179	42	18	10	28	1.83
54082410--54082453	23	1.9	22	82	17	54	36	25	0	38	1.56
54082499--54082591	45	2.1	45	89	0	141	31	21	20	26	1.98
54082588--54082723	50	2.7	51	86	5	179	30	27	17	24	1.97
54083874--54083915	21	2.0	21	85	0	57	28	40	14	16	1.88
54084649--54084693	21	2.1	22	83	4	56	37	4	0	57	1.19
54091243--54091405	43	3.8	43	79	8	161	31	28	18	21	1.97
54096409--54096524	54	2.1	54	83	0	142	20	24	25	29	1.99
54115190--54115234	23	2.0	23	82	8	56	44	4	15	35	1.67
54115994--54116119	58	2.2	58	89	2	191	53	2	0	44	1.13
54115994--54116134	58	2.5	56	86	7	171	53	2	0	43	1.17
54117806--54117881	38	2.0	38	97	0	143	15	19	23	40	1.90
54125975--54126014	18	2.2	18	100	0	80	50	15	5	30	1.65
54127221--54127246	11	2.4	11	100	0	52	84	0	7	7	0.77
54134789--54134951	42	3.9	42	86	0	193	31	22	19	26	1.98
54135019--54135052	14	2.4	14	95	0	59	58	20	8	11	1.59
54135276--54135346	21	3.4	21	82	7	90	2	46	18	32	1.63
54141385--54141489	25	4.2	25	81	11	133	33	1	20	44	1.62
54141400--54141617	18	13.8	16	63	24	56	32	1	20	45	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54141453--54141783	26	13.1	26	82	12	399	32	0	19	46	1.56
54141504--54141781	77	3.7	76	86	9	401	32	0	19	47	1.55
54141686--54141764	18	4.4	18	70	25	69	35	0	18	45	1.50
54141453--54141783	51	6.6	51	84	11	393	32	0	19	46	1.56
54142043--54142113	13	5.5	13	86	0	106	50	2	7	39	1.44
54142042--54142113	26	2.8	26	100	0	144	50	2	6	40	1.44
54142118--54142634	17	27.6	17	70	20	259	42	2	11	43	1.54
54142085--54142497	57	7.1	57	91	5	619	43	2	10	43	1.54
54142448--54142520	23	3.4	23	67	21	68	47	4	5	42	1.45
54142511--54142634	57	2.2	57	95	0	221	41	1	12	45	1.51
54142568--54142643	40	1.9	40	97	0	143	44	1	10	43	1.47
54144681--54144874	84	2.2	86	91	4	320	30	19	19	30	1.96
54146793--54147607	112	7.3	112	95	0	1443	26	26	18	28	1.98
54147554--54147710	40	3.9	40	94	0	251	20	29	15	34	1.94
54149220--54149244	12	2.1	12	100	0	50	28	0	0	72	0.86
54158242--54158666	44	9.6	44	75	6	320	31	24	14	29	1.94
54158236--54158666	88	4.8	89	78	5	408	31	24	14	29	1.94
54158295--54158663	133	2.8	134	87	2	528	31	24	15	28	1.95
54159532--54159580	26	1.9	26	88	12	75	61	8	14	16	1.56
54164267--54164296	16	1.9	15	93	6	51	50	13	0	36	1.42
54164787--54164840	21	2.6	20	74	14	56	51	7	3	37	1.48
54173440--54173470	15	2.1	15	93	0	53	67	16	0	16	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54173593--54173638	14	3.2	14	87	6	65	80	8	0	10	0.91
54173600--54173646	7	6.6	7	76	13	51	80	4	2	12	0.94
54173600--54173646	15	3.3	14	85	11	60	80	4	2	12	0.94
54174839--54174890	18	3.0	18	72	8	54	76	1	5	15	1.05
54193026--54193130	1	105.0	1	100	0	210	0	0	0	100	0.00
54220545--54220821	48	5.7	48	91	4	448	35	6	26	31	1.83
54220550--54220840	98	3.0	97	87	5	421	34	7	26	31	1.84
54220957--54221058	37	2.8	37	87	3	143	28	17	26	27	1.98
54225978--54226015	19	2.0	19	100	0	76	21	5	15	57	1.57
54225980--54226022	19	2.3	19	91	0	68	20	4	9	65	1.40
54242052--54242163	43	2.6	43	98	0	215	9	25	33	30	1.88
54242031--54242176	43	3.4	43	90	1	197	13	23	33	29	1.92
54245844--54245875	3	10.7	3	100	0	64	68	0	0	31	0.90
54256783--54256835	25	2.1	25	100	0	106	41	7	16	33	1.77
54272174--54272219	23	2.0	23	83	8	58	41	4	17	36	1.69
54272188--54272233	21	2.1	23	84	8	60	36	4	15	43	1.66
54284447--54284599	28	5.6	27	73	12	132	30	15	28	25	1.96
54284529--54284632	28	3.7	27	78	10	95	29	21	25	23	1.99
54284447--54284606	54	2.9	56	85	5	245	30	16	27	25	1.97
54284447--54284634	56	3.4	56	83	7	179	30	17	27	24	1.97
54288119--54288295	96	1.8	96	91	0	291	25	25	20	28	1.99
54320284--54320315	16	2.0	16	100	0	64	18	25	25	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54320426--54320483	30	1.9	31	85	3	82	25	24	12	37	1.90
54328524--54328667	40	3.6	40	79	12	145	25	23	27	24	2.00
54328576--54328674	39	2.5	39	86	4	110	25	22	28	24	1.99
54328523--54328673	79	1.9	80	81	6	182	25	23	27	23	2.00
54335129--54335248	56	2.1	56	98	0	231	45	9	23	22	1.81
54336418--54336569	40	3.8	41	89	3	211	24	21	28	25	1.99
54336418--54336589	80	2.2	80	84	3	213	23	20	27	27	1.99
54340377--54340408	16	1.9	17	93	6	57	31	9	3	56	1.47
54353611--54353653	16	2.7	16	82	13	61	27	13	6	51	1.67
54353611--54353656	17	2.8	17	83	9	69	28	15	6	50	1.69

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