genome.fa.s4.2.7.7.80.10.50.1000.52.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  52  of  198  ( 23681 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)
15553930--15553967	19	2.0	19	89	0	58	50	7	5	36	1.54
15554287--15554324	20	1.9	20	100	0	76	36	0	0	63	0.95
15555378--15555421	19	2.3	18	81	11	52	54	0	9	36	1.32
15555455--15555513	25	2.3	24	83	13	66	55	1	3	38	1.26
15559581--15559627	23	2.0	23	84	8	60	27	12	27	31	1.93
15560481--15560527	23	2.0	23	95	0	85	17	19	36	27	1.93
15562981--15563021	18	2.2	19	86	4	57	17	2	4	75	1.08
15572683--15572710	14	2.0	14	100	0	56	85	0	14	0	0.59
15572682--15572806	39	3.1	39	87	8	162	70	1	12	15	1.24
15583545--15583606	29	2.1	29	96	0	115	30	9	17	41	1.82
15589720--15589757	20	1.9	20	84	10	51	36	0	2	60	1.11
15593069--15593158	39	2.4	38	80	9	103	53	11	16	18	1.72
15593595--15593625	16	2.0	16	93	6	55	19	6	19	54	1.65
15596588--15596718	45	2.9	45	83	0	172	22	22	16	38	1.93
15596684--15596810	45	2.8	46	82	4	161	18	20	17	43	1.88
15598704--15598786	42	2.0	42	95	4	150	32	9	19	38	1.84
15599017--15599196	46	3.9	46	75	2	137	29	17	20	32	1.95
15606497--15606728	50	4.7	49	81	9	134	23	28	19	28	1.98
15606533--15606775	50	4.7	50	80	8	240	23	27	20	27	1.99
15616962--15617027	20	3.4	19	70	19	55	30	4	16	48	1.66
15616960--15617087	39	3.3	39	84	2	159	31	5	19	43	1.74
15626127--15626171	22	2.0	23	86	4	65	44	6	0	48	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15627474--15627505	15	2.0	17	88	11	50	62	9	0	28	1.26
15627665--15627704	19	2.0	20	85	4	55	47	0	15	37	1.45
15629701--15630134	44	9.9	44	67	12	185	30	21	17	30	1.96
15629741--15629998	46	5.8	46	71	12	182	29	21	18	31	1.97
15629593--15630124	175	3.0	175	93	0	902	30	21	17	31	1.96
15638666--15638711	19	2.4	19	85	7	58	45	10	19	23	1.82
15642575--15642614	19	2.0	20	85	4	55	47	0	15	37	1.45
15648528--15648583	25	2.2	25	83	0	67	26	28	14	30	1.95
15673127--15673898	43	18.0	43	77	3	629	40	21	14	23	1.90
15683137--15683424	146	2.0	143	87	2	414	45	11	10	32	1.75
15683576--15683745	91	1.9	91	87	7	256	34	21	12	30	1.91
15683804--15683892	20	4.7	20	78	8	71	67	2	4	25	1.21
15683845--15683896	19	2.9	17	78	13	59	65	0	5	28	1.16
15684037--15684082	20	2.2	22	84	7	60	60	13	0	26	1.32
15684070--15684127	17	3.3	18	79	9	57	65	3	1	29	1.19
15684150--15684183	11	3.2	11	91	4	52	76	2	0	20	0.92
15684173--15684227	17	3.3	17	74	2	58	63	1	0	34	1.05
15684212--15684253	21	2.0	21	86	9	59	54	2	0	42	1.13
15683804--15684349	9	58.0	9	65	20	126	61	4	2	31	1.29
15684781--15684814	16	2.2	16	89	5	52	82	0	0	17	0.67
15684980--15685071	29	3.2	28	75	14	80	31	1	5	61	1.25
15684980--15685041	20	3.2	19	80	13	65	29	1	4	64	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15684980--15685218	9	25.8	9	66	24	90	33	2	3	60	1.28
15685517--15685568	20	2.8	18	75	11	50	61	11	0	26	1.30
15701685--15701945	132	2.0	129	80	3	290	23	15	15	45	1.83
15711633--15711838	39	5.3	38	90	3	268	32	14	21	32	1.93
15718524--15718579	19	2.9	19	80	15	53	41	12	5	41	1.66
15734891--15734936	18	2.6	18	82	6	58	45	0	2	52	1.13
15735597--15735640	22	2.0	21	82	4	52	40	0	2	56	1.11
15739366--15739406	14	2.9	14	85	3	55	39	0	4	56	1.21
15745439--15745473	17	2.1	17	89	10	54	42	0	34	22	1.54
15745538--15745685	69	2.1	69	86	2	199	18	14	30	36	1.91
15750640--15750681	18	2.4	18	88	4	59	16	26	11	45	1.82
15751483--15751571	28	3.0	30	80	8	119	26	20	25	26	1.99
15751676--15751752	26	3.0	26	90	0	118	42	24	16	15	1.87
15751915--15752121	27	7.7	27	74	13	124	20	18	19	41	1.91
15751930--15752121	54	3.6	55	77	9	191	19	19	18	42	1.89
15751929--15752113	81	2.3	82	78	8	191	19	19	17	43	1.89
15758764--15758806	9	4.8	9	82	0	50	13	0	4	81	0.84
15773051--15773084	17	2.0	17	88	11	52	67	5	0	26	1.13
15792424--15792911	50	9.7	50	87	3	631	27	20	29	22	1.98
15797318--15797355	19	2.0	19	85	10	51	21	44	0	34	1.52
15807170--15807222	22	2.4	20	77	20	52	28	1	11	58	1.43
15807164--15807220	23	2.4	25	80	14	66	31	1	10	56	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15814887--15814930	20	2.2	20	87	0	61	54	6	9	29	1.58
15830063--15830247	44	4.2	44	65	18	114	28	20	25	25	1.99
15830014--15831366	132	10.2	132	93	0	2260	29	20	25	24	1.99
15835265--15835308	18	2.3	20	88	7	65	22	15	2	59	1.48
15835349--15835423	4	19.0	4	97	2	143	25	0	25	49	1.51
15844479--15844545	34	1.9	35	87	3	100	44	14	8	31	1.76
15846696--15846739	20	2.2	20	84	8	54	56	6	2	34	1.38
15859987--15860055	34	2.0	34	100	0	138	30	14	17	37	1.90
15872050--15872134	9	9.4	9	74	5	73	42	21	9	27	1.83
15872066--15872134	27	2.6	27	88	4	95	40	23	10	26	1.86
15872174--15872262	6	14.8	6	100	0	178	16	0	16	66	1.26
15872174--15872275	18	5.5	20	96	2	139	18	0	14	66	1.25
15872303--15872346	18	2.4	18	88	0	61	13	2	43	40	1.57
15872509--15872551	18	2.4	18	88	0	68	18	18	20	41	1.90
15875603--15875651	20	2.5	20	81	15	66	12	24	6	57	1.58
15875854--15875999	50	2.9	50	82	4	186	21	29	23	25	1.99
15878767--15878845	36	2.2	36	84	2	97	36	25	6	31	1.81
15879805--15879838	18	1.9	18	88	5	52	52	11	23	11	1.70
15883496--15883567	36	2.0	35	82	12	85	37	23	8	30	1.84
15884530--15884563	18	1.9	18	88	5	52	52	8	23	14	1.69
15885258--15885310	18	2.9	18	80	2	61	41	45	1	11	1.51
15887754--15887917	41	4.0	41	86	0	211	20	28	16	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15896807--15896893	9	9.7	9	83	5	104	22	6	21	48	1.74
15902261--15902323	19	3.3	18	77	14	65	57	6	1	34	1.34
15902260--15902330	20	3.6	19	80	14	74	57	7	1	33	1.34
15902472--15902542	20	3.6	19	83	11	90	54	8	1	35	1.39
15902475--15902552	39	2.0	41	87	10	117	48	7	2	41	1.45
15902168--15902575	212	1.9	210	91	3	667	47	11	5	35	1.63
15904668--15904742	39	1.9	39	89	5	116	54	1	0	44	1.08
15904913--15904971	29	2.1	28	87	3	82	50	3	0	45	1.18
15904979--15905019	19	2.1	20	86	4	57	41	0	0	58	0.98
15906154--15906226	34	2.1	34	82	0	83	26	10	12	50	1.72
15908230--15908269	18	2.3	18	82	4	55	60	5	17	17	1.54
15911103--15911165	29	2.2	28	82	5	72	30	14	14	41	1.85
15911407--15911688	125	2.3	125	90	4	435	29	15	22	31	1.95
15912175--15912212	19	2.0	19	94	0	67	31	28	21	18	1.97
15913368--15913977	29	20.6	29	82	7	681	32	0	23	43	1.60
15913615--15913643	6	4.8	6	100	0	58	13	0	51	34	1.42
15913590--15913672	41	2.0	41	90	0	130	26	0	32	40	1.56
15913560--15913701	70	2.0	70	93	0	239	29	0	27	42	1.61
15914214--15914245	7	4.6	7	100	0	64	59	12	0	28	1.34
15915201--15915234	15	2.3	15	90	5	52	67	5	0	26	1.13
15915419--15915471	22	2.4	23	81	6	65	35	0	30	33	1.58
15915476--15915531	22	2.5	22	94	2	94	42	0	28	28	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15915735--15915790	29	2.0	29	85	3	78	42	14	12	30	1.82
15918152--15918181	15	1.9	16	93	6	53	50	0	33	16	1.46
15919063--15919103	14	2.8	15	78	14	50	51	2	0	46	1.14
15921424--15921480	20	2.8	20	86	0	87	50	1	3	43	1.29
15921424--15921487	20	3.3	19	84	6	83	54	1	3	40	1.25
15921488--15921547	25	2.3	26	82	5	68	66	3	1	28	1.17
15929077--15929113	2	18.5	2	94	0	65	45	0	2	51	1.15
15929345--15929396	20	2.6	21	78	6	54	36	5	5	51	1.50
15929818--15929875	20	2.7	21	84	7	64	36	0	3	60	1.14
15932348--15932373	2	13.0	2	100	0	52	50	0	0	50	1.00

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