genome.fa.s11.2.7.7.80.10.50.1000.129.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   

This is table  129  of  210  ( 25152 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)
39254205--39254323	50	2.4	51	84	5	161	24	15	29	31	1.95
39262256--39262297	20	2.2	19	83	12	50	64	2	16	16	1.40
39262747--39262776	16	1.9	16	93	6	53	30	0	20	50	1.49
39270233--39270312	20	3.9	21	77	6	74	40	7	8	43	1.64
39272263--39272321	23	2.6	22	84	12	84	35	3	16	44	1.65
39276206--39276241	15	2.5	14	86	8	54	44	8	0	47	1.33
39278903--39279319	140	3.0	140	95	0	744	20	17	25	35	1.95
39281869--39281898	13	2.3	13	94	0	51	50	0	0	50	1.00
39281872--39281902	15	2.1	14	94	5	53	45	0	0	54	0.99
39285497--39285533	2	18.5	2	100	0	74	51	0	0	48	1.00
39285638--39285775	40	3.5	40	76	10	138	38	18	21	21	1.94
39285776--39285943	84	2.0	84	96	0	309	14	19	29	36	1.92
39285860--39286268	122	3.5	114	86	5	586	21	18	28	31	1.96
39286117--39286142	9	2.9	9	100	0	52	7	11	46	34	1.69
39286808--39287740	389	2.4	391	90	3	1447	29	5	23	41	1.76
39288471--39288525	28	2.0	28	92	0	92	54	7	5	32	1.51
39289320--39289431	42	2.7	42	94	0	197	30	23	23	23	1.99
39293451--39293826	185	2.0	185	96	0	689	47	6	29	16	1.71
39293993--39294101	40	2.7	40	80	2	121	44	16	13	24	1.84
39294640--39294684	14	3.2	14	84	6	56	20	0	31	48	1.49
39294652--39294691	7	5.7	7	84	0	53	20	0	32	47	1.50
39294645--39294691	21	2.2	21	92	0	76	19	0	31	48	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39299245--39299333	41	2.2	41	84	8	110	35	23	24	15	1.94
39300843--39301016	74	2.4	74	90	1	260	27	17	20	35	1.95
39312428--39312610	87	2.1	87	88	4	271	37	16	32	12	1.87
39312566--39312656	21	4.3	21	90	0	74	32	14	43	8	1.76
39312961--39313311	43	8.1	43	91	0	522	22	20	27	29	1.98
39314014--39314061	18	2.7	18	96	0	87	35	12	12	39	1.81
39314491--39314729	72	3.3	71	87	4	338	25	7	14	53	1.65
39315838--39315880	21	2.0	21	100	0	86	37	4	27	30	1.77
39316799--39316836	13	2.9	13	84	0	58	34	26	7	31	1.85
39319232--39319276	23	2.0	23	90	0	72	28	6	22	42	1.79
39320764--39321050	50	5.6	50	76	7	224	22	29	20	26	1.99
39324075--39324118	23	1.9	23	90	0	70	25	4	25	45	1.72
39325163--39325214	21	2.5	21	87	0	68	44	3	0	51	1.19
39325168--39325433	120	2.2	120	94	0	460	45	6	1	46	1.40
39325044--39325301	108	2.4	106	94	2	462	45	8	1	44	1.44
39325496--39325567	9	8.0	9	78	6	65	48	18	0	33	1.48
39325622--39325924	9	32.8	9	69	17	126	46	15	2	34	1.59
39325639--39325780	38	3.6	39	88	6	189	47	16	1	34	1.56
39325664--39325913	43	5.9	43	74	13	205	47	14	2	35	1.58
39325688--39326006	132	2.4	134	93	2	534	47	15	3	34	1.61
39327734--39327794	19	2.9	21	83	11	72	37	8	16	37	1.78
39327747--39327804	22	2.7	23	78	7	59	37	5	15	41	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39327991--39328035	23	2.0	23	81	0	54	22	0	15	62	1.33
39328185--39328233	23	2.2	22	82	10	55	36	2	0	61	1.08
39328326--39328402	37	2.1	37	80	11	86	37	9	1	51	1.42
39328711--39328764	3	18.0	3	100	0	108	33	0	0	66	0.92
39331079--39331209	69	1.9	71	85	3	185	23	7	25	42	1.80
39336363--39336398	16	2.2	16	100	0	72	38	36	0	25	1.56
39336429--39336731	27	11.3	27	85	4	355	19	16	22	41	1.90
39340264--39340336	32	2.2	33	90	2	112	36	6	31	24	1.82
39343825--39343855	15	2.1	14	94	5	53	35	9	0	54	1.33
39350107--39350174	30	2.3	31	84	5	86	23	10	2	63	1.40
39350509--39350533	11	2.3	11	100	0	50	48	8	0	44	1.32
39355966--39356036	3	23.7	3	88	0	70	35	0	8	56	1.30
39357685--39357794	54	2.0	54	87	0	157	47	8	20	24	1.77
39359845--39359893	2	24.5	2	87	0	71	51	0	6	42	1.27
39359937--39360160	113	2.0	115	95	1	407	37	8	19	34	1.83
39360700--39360769	37	1.9	37	91	2	115	37	7	2	52	1.44
39363347--39363450	11	8.6	12	72	12	70	62	1	34	0	1.13
39363347--39363450	3	34.3	3	70	12	70	62	1	34	0	1.13
39363695--39363819	30	4.1	30	75	15	130	24	6	8	60	1.49
39363719--39363796	12	6.3	12	69	16	61	25	3	7	62	1.39
39363753--39363819	26	2.4	29	87	9	95	22	2	8	65	1.34
39363753--39363819	14	4.8	14	72	20	68	22	2	8	65	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39363713--39363849	64	2.2	64	85	6	181	24	4	9	62	1.44
39363949--39363987	17	2.5	15	87	8	51	71	2	10	15	1.23
39363983--39364510	157	3.3	158	90	4	794	53	7	9	29	1.60
39364443--39364471	15	1.9	15	100	0	58	72	0	0	27	0.85
39366170--39366224	25	2.2	25	80	6	67	21	7	10	60	1.55
39366964--39367005	8	5.4	8	80	5	50	50	23	0	26	1.50
39366963--39367011	16	3.1	16	82	5	55	51	22	2	24	1.59
39369868--39370080	41	5.3	40	70	15	136	48	11	6	33	1.64
39369895--39370036	76	1.9	76	86	2	205	50	12	7	30	1.67
39369966--39370220	135	1.9	133	81	9	304	53	12	3	30	1.54
39370249--39370304	20	2.8	21	76	15	64	1	28	0	69	0.98
39377440--39377484	3	15.0	3	100	0	90	33	0	0	66	0.92
39378785--39378829	21	2.1	21	88	8	65	73	0	17	8	1.08
39384644--39384686	21	2.0	21	86	8	61	27	18	20	32	1.96
39385478--39385524	12	3.5	13	81	18	53	31	2	12	53	1.51
39389005--39389038	16	2.1	16	88	5	50	55	0	32	11	1.36
39390550--39390637	21	4.3	20	73	20	67	22	3	4	69	1.22
39397783--39397825	16	2.5	18	88	7	63	34	2	2	60	1.22
39398735--39398916	84	2.1	86	80	11	205	32	4	12	50	1.61
39398871--39398986	59	2.0	58	89	1	178	44	1	12	41	1.51
39398875--39399002	59	2.2	59	84	6	163	46	1	12	39	1.51
39409076--39409137	31	2.0	31	83	0	79	25	22	25	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39422846--39422875	13	2.3	13	100	0	60	53	6	20	20	1.67
39424833--39424918	30	2.9	30	96	1	156	19	31	11	37	1.88
39424836--39425110	58	4.7	58	75	10	213	21	28	13	37	1.91
39424930--39425233	87	3.5	87	80	4	344	22	27	15	34	1.94
39424930--39425224	29	10.2	29	82	2	283	22	28	14	34	1.94
39427114--39427201	45	2.0	45	83	0	113	28	17	20	34	1.95
39429873--39429923	23	2.2	23	86	6	68	43	19	7	29	1.79
39437917--39437964	22	2.2	22	96	0	87	27	4	12	56	1.54
39440401--39440437	15	2.4	17	82	17	53	35	16	0	48	1.46
39441155--39441567	133	3.1	133	78	8	424	33	14	21	31	1.92
39441920--39441969	21	2.5	20	83	6	64	24	4	32	40	1.73
39450948--39451114	43	3.9	42	81	4	174	25	17	28	29	1.97
39450923--39451114	86	2.2	86	80	6	210	23	16	28	31	1.96
39452236--39452274	16	2.5	15	88	8	60	41	0	5	53	1.23
39452346--39452458	9	12.7	9	71	12	81	45	17	2	34	1.63
39452437--39452480	22	2.0	23	86	4	63	54	13	0	31	1.39
39453095--39453123	15	1.9	15	100	0	58	27	6	0	65	1.18
39454112--39454246	66	2.0	66	89	0	207	39	17	28	14	1.90
39454646--39454868	42	5.3	42	87	0	266	30	23	21	25	1.99
39455375--39455410	8	4.4	8	86	6	54	58	0	0	41	0.98
39455363--39455411	17	2.8	17	81	9	55	59	0	0	40	0.98
39464671--39464709	21	2.0	20	90	10	62	5	30	7	56	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39466689--39466724	19	1.9	18	88	5	54	30	0	8	61	1.26
39469495--39469528	4	8.5	4	100	0	68	23	0	0	76	0.79
39469498--39469545	8	6.0	8	90	0	51	22	8	2	66	1.29
39469602--39469645	3	14.7	3	85	0	61	27	4	2	65	1.23
39476493--39476716	89	2.5	90	83	3	265	36	14	19	29	1.92
39476404--39477060	45	14.1	46	72	12	288	35	15	18	30	1.92
39476663--39476766	52	2.0	52	100	0	208	46	15	13	25	1.82
39476581--39476851	142	1.9	142	80	1	310	38	15	15	29	1.89
39477061--39477157	44	2.2	43	98	0	149	28	17	28	24	1.97
39477126--39477378	96	2.6	95	85	4	339	35	18	17	27	1.94

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