genome.fa.s4.2.7.7.80.10.50.1000.95.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  95  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)
30474269--30474579	115	2.7	111	73	11	290	36	16	19	27	1.94
30474411--30474746	167	2.0	167	91	1	539	35	16	20	27	1.94
30474723--30474862	74	1.9	75	85	4	194	30	17	22	29	1.97
30474723--30474881	74	2.1	75	81	4	187	33	17	20	27	1.95
30474588--30474988	188	2.1	188	91	0	640	31	15	22	30	1.95
30475430--30475454	12	2.1	12	100	0	50	16	0	52	32	1.44
30475553--30475656	7	14.9	7	82	4	111	20	1	49	28	1.60
30475627--30475811	95	1.9	96	81	4	221	27	1	29	41	1.65
30475882--30475908	14	1.9	14	100	0	54	48	0	7	44	1.31
30475910--30475950	20	2.0	20	85	0	55	60	4	7	26	1.43
30475945--30475992	18	2.7	17	87	6	69	79	2	4	14	0.98
30476482--30476870	198	2.0	197	91	1	627	28	17	20	33	1.95
30477382--30477406	10	2.5	10	100	0	50	48	12	8	32	1.69
30478149--30478192	18	2.4	19	84	3	54	13	15	13	56	1.67
30478196--30478275	7	11.3	7	83	2	106	3	13	12	70	1.31
30478659--30479222	47	11.2	51	63	25	147	38	8	4	49	1.52
30478676--30479287	100	6.1	100	90	5	995	38	8	4	49	1.52
30478676--30479287	302	2.0	297	93	3	1039	38	8	4	49	1.52
30479357--30479410	13	4.0	13	88	7	72	46	9	1	42	1.46
30479378--30479513	53	2.6	53	84	0	191	38	11	5	44	1.64
30479658--30479907	9	28.8	9	70	10	155	45	20	3	31	1.67
30479817--30479875	24	2.4	24	83	11	75	47	18	3	30	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30485374--30485544	66	2.6	65	84	4	209	40	18	28	12	1.88
30485515--30485587	21	3.5	21	81	3	76	34	17	41	6	1.76
30486054--30486241	43	4.3	43	83	6	220	20	17	30	31	1.95
30486175--30486317	75	1.9	75	83	7	175	23	16	30	30	1.96
30488367--30488450	6	14.6	5	80	16	60	70	0	7	22	1.11
30488370--30488450	12	6.9	11	77	12	72	70	0	7	22	1.12
30488370--30488448	42	1.9	42	89	2	124	70	0	7	21	1.11
30490201--30490225	12	2.1	12	100	0	50	24	24	12	40	1.88
30492164--30492471	27	11.4	27	82	2	305	40	21	18	19	1.91
30498939--30498985	21	2.2	22	81	11	53	14	25	0	59	1.36
30502585--30502611	10	2.7	10	100	0	54	22	7	22	48	1.75
30504342--30504423	41	2.0	41	90	0	128	23	20	26	29	1.99
30504624--30504690	30	2.3	29	73	19	66	59	2	5	31	1.36
30504870--30504923	7	7.6	7	81	4	63	20	0	27	51	1.47
30504959--30504996	15	2.5	16	79	12	53	15	0	36	47	1.46
30504959--30504997	7	5.3	7	87	6	51	15	0	38	46	1.46
30508753--30509031	86	3.2	86	88	0	378	31	7	17	43	1.77
30508753--30509110	86	4.1	85	83	5	362	31	8	17	42	1.79
30508753--30509086	173	1.9	173	80	6	381	31	8	17	43	1.78
30509107--30509191	40	2.1	40	84	4	109	30	5	14	49	1.66
30510350--30510442	43	2.2	44	78	9	102	31	20	21	26	1.98
30510365--30510635	43	6.3	43	80	9	216	25	16	27	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30510373--30510619	129	1.9	129	81	6	304	26	16	27	29	1.97
30521044--30521467	173	2.5	172	92	3	710	27	19	24	28	1.99
30520917--30521592	217	3.1	216	83	7	741	27	19	23	28	1.98
30521140--30521420	84	3.3	84	70	15	268	26	19	24	29	1.98
30521004--30521601	44	13.7	44	71	13	316	28	19	24	27	1.98
30522977--30523001	11	2.3	11	100	0	50	32	0	16	52	1.44
30531563--30531597	17	2.1	17	100	0	70	22	11	34	31	1.90
30533022--30533058	19	2.1	18	90	10	58	40	16	0	43	1.48
30542134--30542318	51	3.7	49	77	7	185	23	18	28	29	1.98
30546873--30546921	21	2.3	21	89	0	71	28	16	0	55	1.42
30546882--30546922	21	2.0	21	100	0	82	24	14	0	60	1.34
30546889--30546935	21	2.2	21	85	7	60	25	17	2	55	1.53
30551630--30551663	2	17.0	2	100	0	68	50	0	0	50	1.00
30570542--30570594	25	2.1	26	85	3	72	41	1	22	33	1.65
30576945--30577079	49	2.8	49	91	0	216	23	22	21	31	1.98
30576945--30577121	49	3.6	49	86	3	214	22	23	21	32	1.98
30576945--30577188	49	4.9	50	83	2	170	21	25	22	30	1.99
30581666--30581740	3	25.0	3	97	0	141	33	1	0	65	1.01
30590259--30590382	42	3.0	42	82	14	159	58	0	1	39	1.08
30590284--30590350	29	2.3	29	94	2	118	59	0	0	40	0.97
30590259--30590329	18	3.5	19	81	12	72	59	0	1	39	1.06
30590274--30590382	11	10.4	11	72	19	90	59	0	1	38	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30591125--30591156	17	1.9	17	93	6	57	28	31	0	40	1.57
30599800--30599913	42	2.7	42	81	0	129	27	20	32	20	1.97
30599838--30599923	42	2.0	42	84	0	109	25	16	36	22	1.94
30600366--30600648	61	4.6	62	82	6	310	32	12	27	28	1.92
30603556--30603623	25	2.7	25	88	0	100	30	19	22	27	1.97
30609549--30609585	19	1.9	19	88	0	56	10	10	5	72	1.25
30621400--30621441	20	2.1	20	95	0	75	28	16	4	50	1.66
30621424--30621497	32	2.4	31	91	6	123	33	9	10	45	1.71
30625882--30625975	47	2.0	47	100	0	188	25	10	10	53	1.68
30627861--30627901	15	2.7	16	77	11	50	48	0	7	43	1.30
30627942--30627975	2	17.5	2	93	6	61	50	0	0	50	1.00
30629769--30630056	84	3.4	85	71	15	252	29	22	19	28	1.98
30629764--30630142	173	2.2	168	88	2	542	30	21	19	29	1.97
30629860--30630137	84	3.2	84	69	14	242	31	21	19	27	1.98
30629932--30630361	217	2.0	217	89	1	666	29	21	19	29	1.98
30638478--30638542	24	2.7	24	77	11	62	16	20	18	44	1.87
30642269--30642303	17	2.1	17	89	10	54	71	5	2	20	1.19
30642458--30642498	15	2.7	16	77	11	50	48	0	7	43	1.30
30642539--30642569	2	15.5	2	100	0	62	51	0	0	48	1.00
30651055--30651106	15	3.3	15	81	10	59	7	7	0	84	0.77
30651033--30651106	23	3.1	24	86	9	89	6	12	0	81	0.88
30651037--30651106	6	11.7	6	77	11	54	5	12	0	81	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30654172--30654262	37	2.3	40	85	11	125	31	9	6	51	1.61
30654301--30654330	2	15.0	2	100	0	60	50	0	0	50	1.00
30660794--30661140	50	6.9	50	68	3	232	30	19	23	25	1.98
30660790--30661148	100	3.6	100	94	0	628	29	20	23	26	1.99
30661222--30661708	132	3.7	132	88	0	742	29	18	24	27	1.98
30663336--30663426	37	2.3	39	85	11	123	31	10	6	50	1.63
30663516--30663549	2	17.0	2	93	0	59	47	2	0	50	1.16
30672358--30672399	17	2.5	17	88	0	57	21	35	26	16	1.94
30674652--30674686	7	5.1	7	96	3	63	42	0	0	57	0.99
30677225--30677286	19	3.4	19	66	20	60	32	3	1	62	1.20
30677227--30677320	35	2.7	35	93	4	156	30	5	3	60	1.34
30677327--30677383	9	6.7	9	82	9	66	42	14	1	42	1.55
30677330--30677381	16	3.1	16	86	8	68	40	15	1	42	1.58
30677426--30677462	19	1.9	19	94	0	65	45	0	0	54	1.00
30677464--30677527	23	3.0	22	72	21	64	48	20	0	31	1.50
30677588--30677628	12	3.4	12	82	0	55	51	21	2	24	1.60
30677588--30677646	24	2.5	24	83	5	68	50	18	3	27	1.62
30677595--30677646	12	4.5	11	79	13	52	50	17	3	28	1.64
30677636--30677942	34	9.4	34	68	15	144	51	18	1	28	1.55
30677603--30677804	95	2.1	95	93	0	341	53	16	1	28	1.52
30677695--30677734	12	3.3	12	89	0	62	50	12	0	37	1.41
30677783--30678126	9	41.2	9	74	14	258	45	21	2	30	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30677787--30678126	25	13.6	25	82	4	265	45	21	2	30	1.63
30677803--30678033	108	2.1	108	96	0	428	45	21	2	30	1.63
30677786--30678117	108	3.2	104	79	12	342	45	21	2	30	1.63
30677901--30678137	34	7.1	33	67	16	100	44	21	2	30	1.66
30683599--30683666	21	3.2	21	82	0	82	30	19	45	4	1.70
30689624--30689778	43	3.7	43	86	10	212	26	18	25	29	1.98
30689616--30689778	83	2.0	84	87	3	240	27	17	25	29	1.98
30692908--30693069	39	4.2	39	88	7	224	32	3	0	63	1.12
30692908--30693069	40	4.2	38	89	9	213	32	3	0	63	1.12
30692915--30693076	38	4.2	39	88	4	220	33	3	0	62	1.12

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