genome.fa.s4.2.7.7.80.10.50.1000.177.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  177  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)
55442591--55442702	37	3.0	37	92	0	179	26	20	15	37	1.92
55447767--55447808	10	4.0	11	81	9	52	2	16	2	78	0.96
55454938--55454966	12	2.3	13	94	5	51	72	3	0	24	1.00
55455486--55455510	2	12.5	2	100	0	50	0	0	48	52	1.00
55459118--55459146	7	4.1	7	100	0	58	27	0	0	72	0.85
55463797--55463938	72	2.0	72	94	0	248	35	16	18	29	1.92
55464479--55464518	3	13.3	3	100	0	80	67	0	0	32	0.91
55465735--55465771	7	5.1	7	87	6	56	5	0	40	54	1.24
55468837--55468871	7	5.0	7	92	0	61	60	14	0	25	1.35
55468837--55468878	21	2.0	21	95	0	75	61	11	2	23	1.42
55472101--55472138	19	2.0	20	89	5	60	28	13	7	50	1.69
55472423--55472450	6	4.7	6	100	0	56	50	0	0	50	1.00
55472434--55472491	22	2.6	23	86	8	84	39	0	1	58	1.08
55472436--55472493	23	2.5	24	83	13	68	39	0	1	58	1.08
55477716--55477757	22	1.9	22	85	0	57	42	2	4	50	1.36
55479970--55480009	16	2.5	15	84	11	53	57	0	5	37	1.21
55482848--55482887	3	13.0	3	84	5	53	32	2	2	62	1.22
55483786--55483983	109	1.8	108	89	3	310	29	17	20	32	1.96
55486063--55486218	83	1.9	84	84	10	212	46	5	4	42	1.47
55488153--55488238	21	4.2	21	81	8	88	17	25	16	40	1.90
55492315--55492486	86	2.0	86	90	4	276	39	7	15	37	1.75
55492966--55493064	21	4.8	21	77	2	83	20	21	17	41	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55493857--55493915	25	2.3	27	80	16	72	28	23	1	45	1.63
55495387--55495426	14	3.0	14	82	10	57	0	25	0	75	0.81
55495646--55495678	5	6.6	5	100	0	66	60	0	0	39	0.97
55495656--55495719	28	2.2	30	78	13	71	56	3	0	40	1.15
55500940--55501028	44	2.0	44	93	0	151	31	7	25	34	1.85
55507778--55507823	17	2.8	16	86	6	56	32	0	2	65	1.05
55508245--55508326	22	3.6	22	85	11	78	39	24	1	35	1.63
55508257--55508326	22	3.2	21	88	9	97	34	27	1	37	1.66
55508266--55508327	22	2.8	23	92	4	101	35	25	1	37	1.66
55508298--55508356	30	2.0	30	89	0	91	33	32	0	33	1.58
55508401--55508463	29	2.2	28	85	2	90	41	0	1	57	1.08
55508554--55508587	15	2.3	15	90	5	52	26	0	5	67	1.13
55510732--55511252	28	19.7	28	77	15	477	47	18	0	33	1.55
55510751--55511218	23	18.3	23	71	22	269	47	18	0	33	1.52
55510763--55510803	18	2.3	18	95	0	73	48	21	0	29	1.50
55514453--55514718	125	2.1	123	89	2	408	30	22	16	30	1.96
55529269--55529328	30	2.0	31	86	3	86	40	0	38	21	1.54
55529613--55529643	9	3.4	9	90	0	53	38	22	12	25	1.90
55529853--55529905	23	2.3	23	96	0	97	32	26	18	22	1.97
55531425--55531500	25	3.0	25	92	3	127	22	21	19	36	1.95
55531425--55531520	50	2.0	47	86	10	131	20	21	18	38	1.93
55531428--55531542	25	4.9	24	83	7	114	20	22	18	39	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55531488--55531546	22	2.7	23	80	15	70	13	23	18	44	1.86
55532011--55532048	13	2.9	13	92	0	67	28	7	23	39	1.83
55540444--55540496	23	2.2	24	83	9	65	50	7	5	35	1.54
55541586--55541733	51	2.9	51	82	1	170	22	26	27	22	2.00
55544749--55544841	4	23.2	4	97	0	159	24	3	25	46	1.68
55545405--55545442	2	19.5	2	83	5	51	55	0	0	44	0.99
55545626--55545684	25	2.4	23	73	18	57	45	3	6	44	1.47
55545626--55545691	23	2.7	25	81	9	75	42	3	7	46	1.47
55549474--55549515	15	2.6	17	81	11	61	66	0	0	33	0.92
55549474--55549542	24	3.0	23	78	8	68	57	1	0	40	1.07
55549474--55549536	22	2.7	23	80	4	65	60	1	0	38	1.07
55551675--55551699	11	2.3	11	100	0	50	40	0	0	60	0.97
55560478--55560513	18	1.9	19	94	5	65	44	0	0	55	0.99
55582571--55582599	3	9.7	3	100	0	58	65	0	34	0	0.93
55588747--55588806	28	2.1	28	87	0	84	25	20	13	41	1.88
55588938--55588996	31	1.9	31	92	0	100	49	6	8	35	1.60
55589022--55589046	13	1.9	13	100	0	50	48	20	0	32	1.50
55590236--55590336	31	3.3	31	82	0	112	32	13	13	39	1.85
55594952--55594995	21	2.1	21	95	4	81	75	0	0	25	0.81
55600375--55600430	29	1.9	29	85	0	76	37	7	14	41	1.73
55604082--55604301	109	2.0	108	85	6	293	37	15	29	16	1.90
55613930--55613969	11	3.6	11	79	0	53	20	12	10	57	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55614006--55614068	30	2.1	30	93	0	108	23	3	17	55	1.56
55614188--55614219	11	2.9	11	95	0	55	68	0	0	31	0.90
55614187--55614226	11	3.2	13	80	20	50	67	0	0	32	0.91
55614458--55614531	13	5.4	13	71	16	60	32	1	2	63	1.17
55614545--55614588	21	2.0	22	83	12	56	54	2	2	40	1.25
55616804--55616830	14	1.9	14	100	0	54	59	0	0	40	0.98
55622785--55622826	11	3.5	12	84	15	52	40	0	0	59	0.97
55629091--55629152	21	2.8	23	73	11	58	48	6	1	43	1.38
55629852--55629901	21	2.4	22	76	10	59	12	28	0	60	1.32
55637869--55637934	33	2.0	33	100	0	132	48	15	6	30	1.69
55645364--55645411	19	2.5	19	86	10	62	60	6	4	29	1.40
55645516--55645573	21	2.8	20	82	7	62	56	3	1	37	1.26
55645557--55645610	19	2.9	18	76	15	56	62	1	3	31	1.23
55645557--55645611	9	5.9	9	75	8	56	63	1	3	30	1.22
55645480--55645622	10	14.2	10	66	17	55	60	3	2	33	1.28
55645947--55646004	9	6.4	9	78	6	64	41	0	0	58	0.98
55645953--55646005	19	2.8	19	86	8	65	39	0	0	60	0.97
55645944--55646002	26	2.3	26	82	5	75	42	0	0	57	0.98
55647875--55647916	20	2.0	21	86	13	61	83	2	4	9	0.88
55662545--55662579	16	2.2	16	89	0	52	14	2	14	68	1.32
55662732--55662816	25	3.2	25	64	15	62	34	22	9	34	1.86
55662732--55662839	55	2.0	55	96	0	198	32	25	8	33	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55664827--55664857	2	15.5	2	93	0	53	51	3	0	45	1.17
55669471--55669530	31	1.9	31	86	0	84	35	10	10	45	1.71
55675791--55675828	19	2.0	19	100	0	76	42	26	5	26	1.76
55676775--55676817	19	2.3	19	87	0	68	44	11	0	44	1.40
55683781--55683839	31	2.0	30	83	6	75	33	5	3	57	1.37
55696937--55696975	2	19.5	2	100	0	78	51	0	0	48	1.00
55705680--55705704	6	4.2	6	100	0	50	16	0	0	84	0.63
55706839--55706901	31	2.0	31	93	0	108	38	3	0	58	1.14
55706847--55706911	31	2.1	31	88	0	94	38	3	1	56	1.24
55708145--55708172	2	14.0	2	100	0	56	50	0	0	50	1.00
55710738--55710773	14	2.5	14	95	4	63	5	5	8	80	1.01
55710733--55710774	15	2.7	15	88	3	66	7	4	7	80	1.00
55712489--55712531	22	2.0	22	100	0	86	23	25	13	37	1.92
55720945--55720991	22	2.1	23	92	4	78	40	0	2	57	1.11
55721094--55721130	15	2.4	16	90	4	58	64	0	0	35	0.94
55723833--55723880	5	9.4	5	80	13	53	41	14	22	20	1.89
55726742--55726784	20	2.2	20	95	0	77	65	0	0	34	0.93
55727881--55727929	23	2.2	22	83	16	66	22	6	30	40	1.78
55736299--55736439	25	5.6	25	65	13	76	34	21	24	19	1.97
55736369--55736439	26	2.8	26	76	2	72	36	21	23	18	1.95
55744535--55744631	35	2.8	35	88	0	158	25	13	17	43	1.86
55753094--55753120	2	13.5	2	100	0	54	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55777338--55777362	10	2.5	10	100	0	50	60	0	20	20	1.37
55777357--55777386	4	7.5	4	100	0	60	50	0	26	23	1.50
55778790--55778856	20	3.2	20	74	12	71	43	1	1	53	1.19
55779863--55779900	17	2.2	18	86	9	53	42	0	0	57	0.98
55779858--55779900	17	2.5	17	82	10	52	41	0	0	58	0.98
55786491--55786553	3	21.3	3	96	3	119	65	0	0	34	0.93
55789726--55789800	31	2.4	31	86	6	98	18	13	10	57	1.64
55795582--55795629	2	24.0	2	91	0	78	45	4	0	50	1.21
55801010--55801043	14	2.3	15	90	5	52	5	14	2	76	1.09
55801166--55801202	7	5.3	7	100	0	74	72	0	0	27	0.84

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