genome.fa.s5.2.7.7.80.10.50.1000.33.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  33  of  208  ( 24913 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)
9381015--9381679	51	14.0	46	71	18	368	13	6	49	30	1.67
9381003--9381374	51	7.5	51	84	8	446	12	6	49	31	1.66
9381000--9381698	99	7.3	98	81	11	579	14	6	48	30	1.69
9381341--9381497	36	3.9	36	71	22	125	19	7	44	28	1.78
9381144--9381750	324	1.9	324	90	1	984	15	6	47	31	1.70
9386720--9386755	16	2.3	16	90	4	56	33	0	2	63	1.08
9388868--9389109	122	2.0	122	93	0	412	42	11	19	26	1.86
9393128--9393172	9	4.9	9	79	15	56	31	0	0	68	0.89
9393131--9393173	10	4.5	10	80	8	54	27	0	0	72	0.85
9406585--9406627	19	2.3	19	96	4	79	55	9	18	16	1.67
9406919--9406960	21	2.0	21	86	9	59	66	14	4	14	1.40
9407133--9407174	22	1.9	22	85	0	57	30	19	28	21	1.97
9408745--9408799	24	2.3	24	80	0	65	38	16	25	20	1.92
9419083--9419148	26	2.6	27	79	11	68	36	15	25	22	1.93
9421134--9421399	140	1.9	140	87	3	392	27	20	20	31	1.98
9425120--9425162	21	2.0	21	86	0	59	55	30	2	11	1.48
9427685--9427839	35	4.5	35	81	0	168	25	21	14	38	1.92
9427685--9427839	70	2.2	69	82	5	188	25	21	14	38	1.92
9429605--9429681	3	25.7	3	100	0	154	66	0	0	33	0.92
9432687--9432795	50	2.2	50	81	0	128	29	23	21	25	1.99
9432729--9433556	94	8.9	94	79	4	841	26	20	19	33	1.97
9433151--9433493	44	7.4	44	68	21	173	25	22	20	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9440403--9440453	23	2.2	23	92	0	84	19	21	35	23	1.96
9444221--9444254	15	2.3	15	89	0	50	2	8	17	70	1.25
9444504--9444537	18	1.9	17	88	5	50	20	58	11	8	1.59
9445088--9445117	11	2.6	11	94	5	51	36	3	0	60	1.14
9445053--9445137	30	2.8	29	87	10	116	34	4	0	61	1.17
9445100--9445140	21	2.0	21	85	9	57	31	4	0	63	1.15
9445100--9445139	20	2.0	20	85	14	55	32	5	0	62	1.17
9445941--9446042	47	2.1	52	81	9	124	30	7	2	58	1.41
9446062--9446186	27	4.7	27	76	8	89	31	4	2	62	1.26
9446165--9446214	22	2.3	22	86	10	75	30	6	2	62	1.31
9445953--9446316	26	14.2	26	74	14	186	29	7	3	59	1.42
9446062--9446291	52	4.5	50	79	12	218	30	4	3	61	1.33
9446262--9446312	24	2.2	23	85	3	66	29	11	3	54	1.54
9446085--9446316	102	2.3	101	81	10	251	29	6	3	60	1.40
9449085--9449140	3	18.7	3	100	0	112	33	0	0	66	0.92
9453281--9453411	26	5.3	24	79	10	140	31	3	2	63	1.22
9453281--9453411	50	2.6	50	84	4	158	31	3	2	63	1.22
9453281--9453421	24	5.6	25	80	7	146	31	3	2	63	1.23
9453439--9453558	25	4.9	24	71	12	93	27	3	5	64	1.30
9453439--9453527	25	3.6	24	79	8	99	25	2	3	68	1.17
9458635--9458667	14	2.4	14	100	0	66	30	18	30	21	1.97
9461371--9461532	26	6.3	26	78	11	147	30	3	2	62	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9461371--9461512	51	2.8	51	86	7	175	31	4	1	62	1.23
9461371--9461512	24	5.7	24	77	13	119	31	4	1	62	1.23
9461528--9461618	25	3.6	25	71	19	73	28	4	3	63	1.29
9461906--9461957	23	2.2	24	79	3	61	23	5	3	67	1.29
9462079--9462105	14	1.9	14	100	0	54	51	33	0	14	1.43
9468938--9468969	15	2.1	15	100	0	64	62	12	18	6	1.50
9475501--9475526	5	5.2	5	100	0	52	42	19	19	19	1.90
9476434--9476473	5	8.0	5	100	0	80	20	0	80	0	0.72
9476573--9476609	9	4.1	9	92	0	65	29	10	13	45	1.77
9476662--9476692	9	3.4	9	90	0	53	38	22	12	25	1.90
9481403--9481696	43	6.8	43	92	2	466	28	33	19	19	1.96
9482731--9482761	15	2.1	15	100	0	62	51	12	29	6	1.65
9485650--9485696	25	1.9	24	87	12	69	38	8	4	48	1.53
9486374--9486491	22	5.4	22	88	0	164	33	14	25	27	1.94
9486536--9486578	21	2.0	21	86	0	59	39	39	0	20	1.53
9486697--9486786	14	6.5	14	83	2	110	28	46	1	23	1.59
9486698--9486797	7	14.4	7	75	10	71	32	43	1	24	1.61
9486697--9486786	7	13.0	7	75	6	76	28	46	1	23	1.59
9486817--9486848	14	2.2	15	94	5	57	37	31	0	31	1.58
9487227--9487331	41	2.6	41	87	0	147	26	25	23	23	2.00
9487310--9487351	20	2.1	20	95	0	75	21	35	23	19	1.96
9487270--9487392	61	2.0	61	91	0	201	26	27	21	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9487228--9487434	102	2.0	103	87	0	299	28	26	21	23	1.99
9487330--9487488	42	3.8	41	90	2	246	29	25	20	24	1.99
9489376--9491949	543	4.7	543	93	0	4202	33	21	14	29	1.94
9495199--9496447	541	2.3	541	96	0	2297	32	21	15	30	1.94
9498550--9500330	543	3.3	543	97	0	3346	33	21	14	29	1.94
9500872--9506197	543	9.8	543	76	0	5469	30	19	13	26	1.89
9503027--9506197	542	5.8	542	76	0	3455	30	20	13	26	1.89
9510961--9511146	98	1.9	98	94	0	327	37	24	10	26	1.88
9512592--9512659	21	3.0	24	77	14	72	39	14	5	39	1.71
9512615--9512677	21	3.0	21	95	0	108	39	12	7	39	1.73
9512903--9513480	44	13.1	45	76	8	494	29	26	16	27	1.97
9512902--9513478	132	4.4	131	93	1	958	28	26	16	27	1.97
9513482--9513780	44	6.9	44	74	11	219	27	22	21	29	1.99
9513576--9513731	84	1.8	85	85	9	221	27	23	21	27	1.99
9513859--9514043	44	4.2	44	64	17	114	24	24	21	29	1.99
9513747--9514073	131	2.5	131	88	3	476	23	26	19	30	1.98
9528839--9529035	98	2.0	98	95	0	358	37	24	9	28	1.87
9530476--9530564	21	4.0	24	84	10	75	39	14	6	39	1.73
9530499--9530616	21	5.7	21	91	4	195	37	13	10	38	1.79
9531436--9531476	19	2.1	20	86	4	57	31	9	2	56	1.45
9531879--9531950	16	4.2	17	75	12	51	0	18	6	75	1.02
9540464--9540509	24	1.9	24	82	8	58	21	10	8	58	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9540702--9540737	17	2.1	17	89	0	54	19	0	5	75	1.00
9542923--9542975	25	2.3	23	81	15	65	7	16	1	73	1.15
9543406--9543432	6	4.5	6	100	0	54	18	0	81	0	0.69
9544213--9544258	24	2.0	23	82	4	56	54	0	4	41	1.20
9545316--9545412	26	3.6	27	75	5	99	25	19	24	29	1.98
9547673--9547705	16	2.1	16	88	5	50	6	9	12	72	1.26
9553206--9553315	1	110.0	1	70	0	76	85	4	7	2	0.81
9553219--9553315	33	2.9	30	77	18	95	85	5	6	3	0.82
9553218--9553301	42	2.0	43	86	6	118	85	4	5	3	0.81
9553206--9553314	55	2.0	55	85	7	150	85	4	7	2	0.82
9553801--9553833	16	2.1	15	94	5	57	72	0	15	12	1.12
9553796--9553839	23	2.0	22	90	4	70	68	0	18	13	1.22
9555098--9555801	132	5.3	132	84	3	891	28	18	23	29	1.98
9555375--9555566	44	4.4	44	67	10	113	28	18	22	30	1.98
9555097--9555914	396	2.1	395	79	6	868	28	18	23	30	1.97
9555867--9556104	40	5.7	41	70	15	155	27	21	22	28	1.99
9555853--9556105	127	2.0	127	91	1	409	29	20	22	27	1.99
9568593--9568622	11	2.7	11	89	0	51	23	0	0	76	0.78
9580711--9580933	85	2.6	85	83	4	261	27	26	18	27	1.98
9580685--9580933	85	2.9	85	81	4	223	27	25	18	28	1.98
9580685--9580948	43	6.1	42	74	9	228	26	25	18	29	1.98
9581257--9581306	21	2.4	21	96	0	91	0	44	18	38	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9581277--9581433	66	2.4	66	92	0	260	13	26	18	41	1.87
9584421--9584463	22	2.0	22	90	0	68	9	18	27	44	1.80
9584569--9584658	42	2.1	43	85	2	119	23	22	30	24	1.99
9584787--9584923	43	3.2	43	89	5	179	32	28	18	21	1.96
9585272--9585383	21	5.3	21	78	4	100	6	42	16	34	1.73
9585272--9585373	42	2.4	42	79	6	116	5	43	15	35	1.71
9585355--9585501	66	2.2	66	86	4	199	13	28	18	39	1.89
9585394--9585524	66	2.0	66	86	3	183	14	25	19	41	1.89
9590912--9591386	9	54.8	9	66	22	198	32	1	21	44	1.61
9590912--9591085	43	4.2	42	76	16	141	32	1	20	45	1.61

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