genome.fa.s5.2.7.7.80.10.50.1000.139.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  139  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)
42468007--42468078	36	2.0	36	100	0	144	22	19	5	52	1.66
42472670--42472697	13	2.2	13	100	0	56	39	0	0	60	0.97
42472879--42473024	40	3.7	40	82	3	186	16	27	16	39	1.90
42472939--42473004	20	3.3	20	70	8	62	15	25	16	42	1.87
42472958--42473124	20	8.4	20	80	7	196	18	32	14	33	1.92
42472958--42473107	60	2.5	60	92	2	239	18	33	14	33	1.91
42478098--42478191	46	2.0	46	100	0	188	35	25	4	35	1.76
42478115--42478187	22	3.2	22	63	14	58	34	24	4	36	1.75
42487044--42487132	25	3.6	25	81	3	99	32	22	17	26	1.97
42492596--42492630	17	2.1	17	94	0	61	48	8	5	37	1.58
42493612--42493650	10	4.1	9	86	6	51	61	2	0	35	1.10
42493813--42493874	29	2.1	29	100	0	124	46	24	3	25	1.67
42511245--42511320	38	2.0	39	94	2	136	51	27	2	18	1.59
42511491--42511530	9	4.4	9	83	0	53	27	10	22	40	1.86
42511491--42511530	18	2.2	18	95	0	71	27	10	22	40	1.86
42511595--42511650	24	2.3	24	75	0	67	39	5	17	37	1.73
42511754--42511852	38	2.6	38	83	1	99	31	18	26	24	1.97
42511804--42512249	72	6.1	73	79	5	433	38	16	20	25	1.93
42511804--42512305	35	13.9	35	77	6	349	38	16	20	25	1.92
42511797--42512244	109	4.1	106	77	9	384	38	16	19	25	1.92
42511768--42512249	38	13.2	36	79	7	370	37	16	20	24	1.93
42513854--42513895	22	1.9	22	95	0	75	9	21	28	40	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42513970--42514209	43	5.6	43	73	7	182	31	30	15	22	1.95
42513974--42514209	87	2.7	86	82	2	249	31	30	15	22	1.95
42514557--42514669	21	5.4	21	85	0	127	5	42	17	34	1.72
42514640--42514786	66	2.2	66	83	4	172	12	27	18	41	1.86
42514646--42514809	66	2.5	66	82	4	170	12	26	18	42	1.87
42520266--42520645	9	43.2	9	71	15	151	38	2	14	45	1.58
42520271--42520301	16	1.9	16	100	0	62	32	0	19	48	1.49
42520266--42520444	25	7.1	25	72	11	123	36	3	17	42	1.66
42520287--42520399	57	2.0	57	82	3	138	37	3	17	41	1.67
42520385--42520792	34	12.5	34	77	13	313	39	0	12	47	1.47
42520266--42520611	43	8.3	43	68	17	185	38	2	14	44	1.58
42520470--42520504	13	2.7	13	95	0	61	40	0	8	51	1.33
42520483--42520832	56	6.3	56	81	13	461	40	0	11	48	1.43
42520551--42520599	25	2.0	25	87	0	71	36	2	14	46	1.56
42520384--42520736	167	2.1	167	99	0	697	39	1	12	47	1.48
42520637--42520671	13	2.7	13	95	0	61	40	0	8	51	1.33
42520701--42520751	22	2.4	22	90	3	86	41	0	9	49	1.36
42520757--42520807	22	2.4	22	90	3	86	41	0	9	49	1.36
42520654--42520882	112	2.0	112	81	5	266	41	4	10	42	1.60
42520899--42520939	13	2.8	15	85	14	59	34	0	19	46	1.50
42522738--42522765	6	4.7	6	100	0	56	0	17	17	64	1.30
42523544--42523581	10	3.8	10	92	0	67	42	13	0	44	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42523544--42523581	20	1.9	20	100	0	76	42	13	0	44	1.43
42525272--42525304	16	2.1	16	94	5	59	39	30	0	30	1.57
42526093--42526517	114	3.7	114	88	1	620	26	22	19	31	1.98
42530792--42531136	45	7.6	45	73	13	179	29	22	18	29	1.97
42531218--42531345	45	2.8	45	75	3	123	26	17	19	35	1.94
42531280--42531514	105	2.2	105	87	4	357	29	20	18	32	1.96
42531570--42531686	44	2.7	43	88	3	166	29	23	20	26	1.99
42532913--42532959	21	2.2	21	84	0	58	29	25	17	27	1.97
42540111--42540146	18	1.9	19	88	5	56	38	0	27	33	1.57
42541620--42541655	18	1.9	19	88	5	56	38	0	27	33	1.57
42542180--42542292	41	2.9	41	77	9	144	28	19	19	32	1.96
42542184--42542288	37	2.7	38	79	5	122	27	20	20	31	1.97
42551384--42551737	40	8.7	40	85	7	489	29	24	21	24	1.99
42551384--42551737	82	4.3	82	94	2	601	29	24	21	24	1.99
42553683--42553727	2	22.5	2	100	0	90	48	0	0	51	1.00
42554155--42554370	107	2.0	107	96	0	396	30	18	18	32	1.95
42556726--42556768	22	1.9	22	90	4	68	53	6	2	37	1.41
42557618--42557657	18	2.2	18	86	8	55	40	5	0	55	1.22
42564092--42564301	105	2.0	105	97	0	393	37	20	8	33	1.82
42588643--42588678	11	3.1	11	92	8	54	19	0	0	80	0.71
42590626--42590703	22	3.5	22	89	0	102	26	15	26	30	1.96
42593522--42593558	19	1.9	19	100	0	74	32	24	21	21	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42594889--42595026	68	2.0	71	85	5	192	51	5	3	39	1.43
42609584--42609644	28	2.2	27	91	2	95	29	22	24	22	1.99
42610007--42610204	27	7.3	27	84	5	231	24	17	19	38	1.92
42610008--42610204	81	2.4	81	85	1	261	24	16	19	39	1.92
42613202--42613272	25	2.9	23	82	14	79	28	18	12	40	1.87
42628878--42628919	15	2.5	17	88	11	61	40	0	0	59	0.97
42628890--42628916	10	2.7	10	100	0	54	40	0	0	59	0.98
42629783--42629820	16	2.4	16	86	8	51	47	2	28	21	1.64
42630095--42630140	23	2.0	23	95	0	83	19	21	19	39	1.93
42630094--42630180	23	4.1	21	75	17	81	20	20	20	37	1.94
42631227--42631276	24	2.1	24	92	0	82	14	34	32	20	1.92
42632655--42632720	5	13.2	5	100	0	132	59	0	0	40	0.98
42638790--42638853	26	2.5	24	80	11	83	34	7	12	45	1.71
42638792--42638844	26	2.0	26	96	0	97	35	5	11	47	1.63
42655533--42655996	27	17.1	27	83	4	414	18	17	23	40	1.91
42657383--42657419	16	2.2	18	85	9	51	75	2	13	8	1.13
42672382--42672418	9	4.1	9	92	0	65	45	13	10	29	1.77
42673442--42673467	5	5.2	5	100	0	52	19	19	19	42	1.90
42676578--42676611	2	17.0	2	100	0	68	50	0	0	50	1.00
42677710--42677747	18	2.2	18	90	9	62	71	2	5	21	1.19
42677902--42677967	33	2.0	33	96	0	123	27	22	10	39	1.87
42684742--42684780	6	6.5	6	87	0	60	79	5	0	15	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42688259--42688294	18	1.9	19	88	5	56	72	8	5	13	1.27
42691893--42691954	30	2.1	30	90	6	99	48	9	8	33	1.65
42701083--42701113	14	2.2	14	94	0	53	38	0	41	19	1.51
42716628--42716691	17	3.5	17	69	19	56	29	10	14	45	1.78
42716917--42717013	49	2.0	48	91	2	158	19	15	23	41	1.90
42721728--42721806	39	2.0	39	97	0	149	29	10	13	46	1.76
42721728--42721789	22	3.0	22	64	22	62	29	9	14	46	1.76
42722036--42722129	48	1.9	49	84	2	127	20	13	22	43	1.87
42722601--42722632	15	2.0	17	88	11	50	28	3	0	68	1.04
42735277--42735324	18	2.6	18	75	15	53	41	6	12	39	1.68
42754694--42755262	27	21.2	27	82	3	576	19	16	20	43	1.88
42765235--42765273	18	2.2	18	90	0	60	15	5	5	74	1.17
42769870--42769920	23	2.2	23	82	6	59	50	13	23	11	1.74
42775543--42775579	18	2.1	18	90	5	58	59	0	2	37	1.12
42778940--42779013	34	2.2	34	82	4	87	28	18	22	29	1.98
42779478--42779621	27	5.4	27	92	0	227	15	17	22	43	1.87
42782936--42783025	27	3.4	26	81	4	99	20	15	17	46	1.84
42788016--42788050	18	2.0	18	94	5	63	11	22	45	20	1.82
42792214--42792271	26	2.2	27	78	9	66	24	5	1	68	1.19
42793941--42793967	9	3.0	9	100	0	54	33	22	22	22	1.97
42798629--42798665	16	2.3	16	86	13	58	54	5	0	40	1.24
42799476--42799899	212	2.0	212	95	0	760	39	22	16	21	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42800307--42800378	36	2.0	36	97	0	135	40	13	11	34	1.81
42802184--42802267	22	4.0	21	79	13	84	19	7	0	73	1.05
42802292--42802360	28	2.3	32	80	16	85	21	1	8	68	1.25
42802617--42802665	23	2.2	23	81	3	55	18	2	6	73	1.14
42809223--42809296	13	4.9	16	69	30	56	13	32	33	20	1.91
42809211--42809371	30	5.4	30	84	5	209	16	30	32	20	1.94
42817888--42817957	33	2.1	34	94	5	124	18	12	5	62	1.49
42822906--42822970	28	2.3	28	97	0	121	15	6	16	61	1.53
42826129--42826172	5	9.0	5	80	5	54	18	4	2	75	1.09
42829624--42829745	23	5.3	23	81	2	129	13	12	27	46	1.78

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