genome.fa.s4.2.7.7.80.10.50.1000.12.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  12  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)
3972840--3972866	2	13.5	2	100	0	54	48	0	0	51	1.00
3973234--3973298	32	2.0	33	93	3	114	12	3	15	69	1.31
3976343--3976434	43	2.1	43	87	0	130	23	17	30	28	1.97
3980540--3980587	2	24.0	2	100	0	96	50	0	0	50	1.00
3982354--3982444	23	4.1	23	72	11	100	20	27	6	45	1.76
3982341--3982424	42	2.0	42	95	0	150	23	22	9	44	1.82
3983873--3983996	46	2.8	45	91	3	198	28	22	16	33	1.95
3983958--3984097	37	3.8	37	94	0	235	27	20	12	40	1.88
3992263--3992402	37	3.8	37	95	0	244	27	20	12	39	1.89
3996680--3996721	21	2.0	21	81	9	50	19	35	14	30	1.91
3997706--3997754	23	2.1	23	100	0	98	20	30	4	44	1.70
3998644--3998676	6	5.3	6	96	3	57	48	0	0	51	1.00
4001493--4001538	23	2.0	23	86	4	65	23	2	8	65	1.32
4001728--4001797	22	3.5	22	66	22	62	50	4	1	44	1.30
4001720--4001795	38	2.0	38	92	0	125	48	5	1	44	1.33
4003907--4003963	26	2.2	26	84	9	71	0	29	3	66	1.08
4004019--4004082	5	13.0	5	96	3	121	59	0	0	40	0.97
4016122--4016160	15	2.6	14	84	11	51	84	0	5	10	0.76
4019409--4019514	53	2.0	53	94	0	185	34	21	15	28	1.94
4026932--4026982	13	3.9	13	75	10	59	31	5	25	37	1.80
4027760--4027807	22	2.2	22	100	0	96	27	14	4	54	1.59
4028513--4028706	41	4.7	41	80	5	214	16	22	22	38	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4028511--4028706	82	2.4	82	96	1	358	16	22	21	38	1.92
4028845--4029021	82	2.2	81	95	2	318	28	15	20	35	1.93
4030014--4030057	10	4.7	9	84	15	54	45	0	9	45	1.35
4030122--4030173	27	1.9	27	88	0	77	40	0	9	50	1.35
4032677--4032747	29	2.4	29	95	0	133	42	12	7	38	1.70
4032995--4033886	9	105.1	9	67	23	97	46	13	2	37	1.57
4033025--4033079	25	2.2	25	86	0	74	47	20	1	30	1.60
4033163--4033749	31	19.0	31	81	13	601	47	10	2	38	1.54
4033163--4033709	120	4.5	120	83	12	647	47	10	2	38	1.53
4033588--4033639	16	3.1	16	88	5	77	46	21	0	32	1.52
4033754--4033884	16	7.8	16	69	16	70	42	18	1	37	1.60
4040155--4040330	43	4.1	43	86	4	248	32	28	18	20	1.96
4040144--4040330	86	2.2	86	94	0	320	33	28	19	19	1.96
4040777--4040834	19	2.7	22	84	10	68	36	8	17	37	1.80
4041454--4041502	27	1.9	26	84	12	66	38	4	4	53	1.39
4050547--4050649	50	2.1	50	96	3	190	49	10	16	23	1.77
4055702--4055802	39	2.7	35	71	21	87	55	1	5	36	1.36
4056514--4056540	11	2.5	11	100	0	54	40	7	0	51	1.30
4056505--4056650	40	4.0	37	85	10	187	37	2	0	59	1.12
4056867--4056902	18	2.1	18	89	5	56	33	25	0	41	1.55
4057505--4057529	7	3.6	7	100	0	50	72	0	0	28	0.86
4058635--4058758	63	2.0	63	80	0	140	29	8	32	29	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4058970--4059011	13	3.2	13	80	6	57	47	9	7	35	1.64
4061358--4061514	69	2.3	68	80	5	192	38	23	21	17	1.93
4061377--4061502	23	5.5	23	91	0	189	38	23	22	15	1.92
4063993--4064020	6	4.7	6	100	0	56	64	0	0	35	0.94
4065320--4065344	4	6.2	4	100	0	50	0	0	24	76	0.80
4066148--4066308	72	2.2	72	78	2	171	35	14	22	26	1.94
4066249--4066371	60	2.0	60	92	3	203	41	13	21	22	1.89
4066318--4066556	75	3.2	75	78	4	182	40	11	24	24	1.88
4066373--4066554	75	2.4	75	81	5	208	39	11	25	24	1.89
4073024--4073078	7	7.7	7	76	11	58	5	0	40	54	1.23
4073016--4073058	13	3.2	13	83	6	59	6	0	46	46	1.30
4073104--4073374	96	2.8	94	84	3	344	36	2	17	43	1.63
4073823--4073865	18	2.4	18	88	0	59	44	9	27	18	1.80
4073920--4073977	30	1.9	30	85	0	80	3	13	48	34	1.60
4074483--4074508	7	3.7	7	100	0	52	57	15	0	26	1.38
4075666--4075712	11	4.3	11	82	17	62	42	0	31	25	1.55
4081056--4081083	13	2.2	13	100	0	56	82	0	0	17	0.68
4081890--4081927	20	1.9	20	88	0	58	44	0	10	44	1.38
4085366--4085402	18	2.1	17	90	5	56	78	2	0	18	0.87
4092368--4092510	42	3.4	42	76	10	132	28	14	16	39	1.88
4095794--4095820	12	2.2	12	100	0	54	70	0	0	29	0.88
4096449--4096497	22	2.3	21	82	10	55	69	6	2	22	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4100293--4100344	25	2.0	26	88	3	79	21	7	9	61	1.51
4102968--4103261	50	5.7	50	88	2	345	26	21	29	22	1.99
4112456--4112527	4	18.0	4	88	11	96	0	22	2	75	0.94
4112448--4112521	22	3.3	22	84	7	96	0	24	2	72	0.97
4113518--4113613	30	3.2	29	71	12	77	25	18	9	46	1.79
4114164--4114283	19	6.8	16	74	16	69	61	1	3	33	1.22
4114275--4114350	21	3.6	21	77	10	66	60	3	1	34	1.23
4114151--4114409	9	27.6	9	69	14	96	61	3	3	31	1.29
4118073--4118139	8	7.9	8	72	18	55	35	0	2	61	1.12
4118077--4118243	18	9.1	18	70	21	82	33	2	2	61	1.24
4118081--4118124	17	2.6	17	79	13	54	38	0	2	59	1.10
4118074--4118206	55	2.4	52	78	17	137	33	1	3	61	1.23
4118114--4118210	36	2.6	35	78	15	97	30	2	4	62	1.25
4118114--4118229	55	2.1	54	81	12	130	31	2	3	62	1.26
4118526--4118571	14	3.4	14	70	11	51	4	45	13	36	1.63
4118518--4118580	26	2.4	26	100	0	126	3	47	9	39	1.52
4124434--4124535	4	26.0	4	82	11	113	47	28	2	21	1.65
4126973--4127000	12	2.3	12	100	0	56	42	17	14	25	1.87
4131883--4131914	6	5.3	6	92	0	55	0	46	3	50	1.17
4132450--4132508	24	2.5	24	82	0	73	18	16	30	33	1.94
4138838--4138888	3	16.7	3	79	4	57	25	0	3	70	1.04
4139369--4139398	15	1.9	16	93	6	53	20	6	6	66	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4141144--4141182	20	2.0	20	94	0	69	33	10	17	38	1.84
4143817--4143843	2	13.5	2	100	0	54	51	0	48	0	1.00
4144347--4144407	27	2.3	26	88	2	95	27	11	22	37	1.89
4147215--4147304	45	2.0	45	91	0	144	28	15	6	48	1.70
4147460--4147537	38	2.1	38	97	0	147	30	12	25	30	1.93
4151204--4151321	40	3.0	38	81	7	148	38	18	18	24	1.93
4151377--4151498	41	3.0	42	87	3	169	21	20	30	27	1.98
4151382--4151498	40	2.9	41	88	3	166	21	20	29	29	1.98
4153498--4153537	17	2.4	17	95	0	71	47	15	22	15	1.82
4155120--4156681	23	68.3	23	74	11	1039	29	6	24	39	1.81
4155103--4156010	160	5.7	160	92	2	1380	29	7	24	39	1.82
4155142--4155991	137	6.2	136	79	8	590	29	7	24	39	1.82
4155784--4156149	137	2.7	137	90	1	545	29	6	25	38	1.82
4155775--4156309	160	3.3	160	85	4	589	29	6	25	38	1.81
4156220--4156604	160	2.4	158	90	1	601	30	6	23	40	1.79
4156091--4156431	137	2.5	137	94	0	583	28	7	23	40	1.81
4156106--4156683	137	4.2	137	87	4	484	29	6	23	40	1.80
4156380--4156683	135	2.2	134	90	2	457	30	5	22	41	1.77
4157331--4157494	43	3.8	43	92	0	247	19	20	34	26	1.96
4157793--4157868	9	8.4	9	86	0	98	42	25	9	23	1.83
4157793--4157860	18	3.8	18	94	0	118	41	25	10	23	1.86
4157892--4157918	8	3.4	8	100	0	54	22	11	11	55	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4157981--4158024	18	2.4	18	88	0	61	13	2	43	40	1.57
4159326--4159404	35	2.3	35	93	0	131	43	21	12	22	1.86
4160448--4160494	24	2.0	24	83	8	60	21	2	8	68	1.27
4160459--4160493	11	2.9	12	87	12	54	20	0	11	68	1.20
4165971--4166010	19	2.1	19	100	0	80	20	32	10	37	1.85
4167893--4167919	11	2.5	11	100	0	54	40	0	0	59	0.98
4169598--4169750	57	2.6	56	81	10	162	32	18	24	24	1.97
4169879--4170008	67	1.9	67	96	0	242	20	17	34	26	1.95
4178097--4178146	24	2.1	24	88	7	75	50	10	20	20	1.76
4178216--4178293	38	2.1	38	100	0	156	35	5	24	34	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