genome.fa.s4.2.7.7.80.10.50.1000.183.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  183  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)
57008027--57008112	42	2.0	42	95	0	154	25	16	24	33	1.95
57015216--57015267	24	2.2	24	89	0	77	36	3	9	50	1.54
57016211--57016260	26	1.9	26	95	0	91	44	16	14	26	1.85
57019655--57019706	24	2.2	24	89	0	77	36	3	9	50	1.54
57036100--57036197	23	4.3	23	94	2	171	32	26	20	20	1.97
57036100--57036197	45	2.2	46	92	3	171	32	26	20	20	1.97
57041412--57041509	23	4.3	23	96	2	180	31	26	21	20	1.98
57041412--57041509	45	2.2	46	94	3	180	31	26	21	20	1.98
57043564--57043643	11	6.9	11	70	19	56	42	1	0	56	1.07
57043544--57043639	38	2.5	38	89	1	138	37	1	0	61	1.03
57046370--57046461	19	4.8	19	91	0	148	38	14	8	39	1.77
57046347--57046461	38	2.9	38	84	5	140	39	14	7	38	1.76
57051787--57051828	20	2.1	20	86	0	57	47	0	7	45	1.30
57052223--57052266	19	2.3	19	88	0	61	6	20	29	43	1.78
57055949--57055983	6	5.8	6	100	0	70	31	0	51	17	1.45
57062060--57062202	72	2.0	72	88	1	216	35	19	17	27	1.94
57062797--57062858	26	2.3	26	81	8	72	58	0	6	35	1.24
57062966--57063012	8	5.3	9	87	7	53	59	0	2	38	1.09
57062962--57063016	17	3.2	18	82	12	62	60	0	1	38	1.08
57071758--57071792	17	2.1	16	89	5	52	25	2	2	68	1.17
57072718--57072756	11	3.4	11	80	13	51	51	0	2	46	1.14
57074177--57074220	23	2.0	22	86	4	61	50	34	2	13	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57074522--57074576	15	3.2	16	82	14	58	12	7	1	78	1.04
57074522--57074570	17	2.8	17	87	9	64	12	6	2	79	0.99
57074536--57074579	17	2.9	14	86	13	52	9	9	0	81	0.87
57080265--57080352	44	2.0	44	90	0	140	21	9	27	42	1.83
57087485--57087549	27	2.4	27	75	10	69	6	21	1	70	1.17
57089443--57089467	2	12.5	2	100	0	50	48	0	0	52	1.00
57095014--57095050	17	2.1	18	90	5	58	72	0	18	8	1.08
57095991--57096026	17	2.3	15	90	9	54	69	0	0	30	0.89
57097049--57097112	25	2.5	26	94	5	121	25	0	9	65	1.22
57098390--57098422	16	2.1	15	94	5	57	72	3	0	24	0.98
57098388--57098437	21	2.3	20	83	10	55	70	6	2	22	1.20
57098606--57098722	4	29.2	4	72	14	64	70	2	3	23	1.14
57098602--57098716	22	5.3	21	67	11	70	71	2	3	22	1.14
57098653--57098686	13	2.6	13	95	0	59	85	5	2	5	0.83
57100271--57100606	130	2.5	130	81	6	361	28	20	18	32	1.96
57100359--57100845	181	2.7	181	90	1	762	29	21	17	31	1.96
57100271--57100831	44	12.6	44	70	12	304	29	21	18	31	1.96
57103486--57103599	43	2.7	43	78	8	124	27	28	21	22	1.99
57104479--57104507	11	2.5	12	88	11	51	41	6	0	51	1.28
57105379--57105450	19	3.8	19	81	15	78	5	18	1	75	1.07
57105392--57105439	13	3.6	14	81	18	66	4	16	0	79	0.89
57105384--57105426	20	2.2	19	84	16	52	4	18	0	76	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57105381--57105453	34	2.2	33	83	9	87	5	17	1	75	1.07
57105378--57105441	13	5.0	12	75	17	58	4	18	0	76	0.95
57105378--57105461	27	3.2	24	79	18	80	7	15	1	76	1.06
57105396--57105460	34	1.9	34	84	6	87	7	13	1	76	1.06
57110458--57110490	16	2.1	15	94	5	57	72	3	0	24	0.98
57110456--57110509	21	2.6	21	82	11	58	68	5	1	24	1.21
57111309--57111334	12	2.2	12	100	0	52	7	34	46	11	1.69
57112905--57113192	151	1.9	151	89	1	452	24	17	29	27	1.97
57118933--57119051	45	2.8	42	83	7	157	31	22	20	26	1.98
57119503--57119572	21	3.3	21	89	0	104	4	42	20	32	1.71
57119503--57119592	21	4.3	21	86	0	99	4	42	20	33	1.72
57121839--57122555	365	2.0	365	92	0	1182	33	20	15	30	1.93
57122598--57122678	24	3.2	23	77	19	90	45	9	0	44	1.37
57122598--57122682	28	3.2	26	76	12	84	44	9	0	45	1.36
57123185--57123214	15	2.0	15	100	0	60	40	40	0	20	1.52
57123186--57123214	8	3.8	8	90	9	51	37	41	0	20	1.53
57123225--57123264	7	6.0	7	85	11	57	30	52	0	17	1.45
57123225--57123263	12	3.1	12	82	13	51	30	51	0	17	1.46
57123256--57123330	14	5.1	14	75	10	60	38	32	1	28	1.65
57123379--57123422	21	2.1	21	87	4	63	45	25	0	29	1.54
57123876--57124339	115	4.0	115	89	1	671	29	23	22	25	1.99
57124252--57124394	73	2.0	73	95	0	259	27	21	23	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57124137--57124508	188	2.0	187	87	2	541	26	23	23	26	2.00
57124252--57124411	73	2.2	73	91	0	257	28	22	22	26	1.99
57124314--57124642	114	2.9	111	84	5	408	27	26	22	24	2.00
57124022--57124639	302	2.0	302	85	3	814	27	24	23	24	2.00
57128549--57129334	88	9.0	86	87	6	893	24	23	22	28	1.99
57129089--57129240	77	2.0	78	97	1	288	25	23	22	28	1.99
57130555--57130604	20	2.6	18	84	15	64	14	16	0	70	1.18
57130562--57130604	19	2.2	20	88	12	63	11	16	0	72	1.13
57130957--57131057	50	2.0	49	86	1	139	10	7	6	74	1.22
57130991--57131068	27	2.8	26	71	9	66	6	10	5	78	1.09
57132367--57132496	22	5.9	22	89	0	188	26	26	14	32	1.95
57135446--57135471	12	2.2	12	100	0	52	7	34	46	11	1.69
57136163--57136209	2	23.5	2	100	0	94	48	0	0	51	1.00
57136546--57136584	15	2.7	15	88	4	53	51	0	5	43	1.24
57137404--57137722	110	2.9	112	93	1	527	32	20	16	30	1.95
57140793--57140836	16	2.6	16	82	13	52	70	2	0	27	0.99
57140806--57140866	30	2.1	31	82	14	76	70	3	3	22	1.17
57161235--57161291	29	2.0	27	83	6	69	66	1	22	8	1.29
57169406--57169438	2	17.0	2	93	6	59	51	0	0	48	1.00
57170765--57170861	43	2.3	42	79	8	110	53	1	1	44	1.14
57170797--57170858	8	8.4	8	77	10	53	50	1	0	48	1.10
57170876--57170935	4	15.0	4	81	13	70	75	0	25	0	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57172306--57172428	41	3.1	41	73	12	132	28	14	19	37	1.91
57172306--57172409	37	2.7	38	80	5	120	27	15	21	35	1.93
57176880--57177019	46	3.0	46	93	0	235	28	27	9	34	1.88
57184158--57184228	34	2.1	34	100	0	142	43	11	16	28	1.83
57187265--57187325	21	3.0	20	78	7	68	65	1	1	31	1.12
57190292--57190325	18	1.9	17	94	5	59	14	0	5	79	0.91
57192235--57192353	43	2.8	43	82	8	152	31	27	18	21	1.97
57197152--57197185	7	4.9	7	100	0	68	14	0	11	73	1.10
57197152--57197192	21	2.0	21	90	0	64	17	2	9	70	1.25
57198910--57198973	25	2.5	25	76	20	62	18	6	6	68	1.32
57199912--57199945	18	1.9	17	88	5	50	76	14	5	2	1.09
57208822--57208864	17	2.5	17	88	0	59	30	27	30	11	1.92
57209117--57209655	114	4.7	113	74	8	425	31	20	23	25	1.98
57209115--57209650	228	2.3	227	78	5	569	31	20	23	24	1.98
57209715--57209753	21	1.9	20	89	5	60	20	0	35	43	1.52
57214608--57214716	36	3.0	36	95	0	200	37	12	20	29	1.90
57214636--57214701	21	3.5	20	64	31	54	33	13	19	33	1.91
57214680--57214788	46	2.4	46	93	1	184	33	17	19	30	1.95
57215487--57215543	21	2.7	21	91	0	87	35	21	42	1	1.63
57215508--57215567	12	5.2	12	78	11	72	38	20	40	1	1.62
57216001--57216179	85	2.1	85	85	9	240	23	24	20	32	1.98
57216001--57216167	42	4.0	42	88	4	223	23	23	19	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57219272--57219317	18	2.6	17	83	12	58	0	30	0	69	0.89
57221322--57221440	44	2.8	42	71	23	122	56	1	3	38	1.26
57221702--57221741	14	2.9	14	84	0	53	32	7	17	42	1.77
57221725--57221764	20	2.0	20	90	0	62	27	10	12	50	1.72
57221710--57221776	34	1.9	35	87	3	100	32	8	11	46	1.72
57222704--57222815	19	6.0	17	67	24	57	59	3	2	33	1.28
57222755--57222816	20	3.3	19	78	8	65	59	4	0	35	1.19
57222984--57223023	20	2.1	19	85	4	53	25	0	2	72	0.97
57223912--57224028	61	1.9	61	86	8	168	52	12	11	23	1.72
57223915--57224056	61	2.3	59	82	8	144	50	13	13	23	1.77

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