genome.fa.s4.2.7.7.80.10.50.1000.158.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  158  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)
49881204--49881255	14	3.6	14	75	14	52	73	1	21	3	1.10
49883210--49883317	43	2.5	42	83	4	126	29	29	17	23	1.97
49885824--49885882	26	2.3	26	88	5	86	27	30	30	11	1.92
49886498--49886531	15	2.3	15	90	10	52	52	0	2	44	1.16
49887232--49887288	21	2.7	21	75	20	64	43	33	1	21	1.63
49887709--49887902	82	2.4	82	86	5	259	28	29	19	22	1.98
49887709--49887902	41	4.7	41	83	7	225	28	29	19	22	1.98
49887962--49888112	39	3.8	39	80	6	169	23	18	19	38	1.93
49887962--49888112	40	3.8	39	84	2	185	23	18	19	38	1.93
49889080--49889124	19	2.4	19	92	0	72	71	4	0	24	1.05
49892218--49892266	25	2.0	24	84	15	64	44	0	4	51	1.20
49893132--49893229	41	2.4	41	89	5	146	40	10	23	25	1.86
49897384--49897485	41	2.5	40	88	4	150	27	24	20	27	1.99
49898116--49898275	81	2.0	82	81	6	193	40	13	6	40	1.69
49901642--49901682	12	3.4	12	90	6	57	75	0	19	4	0.98
49905150--49905191	18	2.2	20	83	8	52	38	0	7	54	1.28
49909684--49909726	21	2.0	21	86	8	61	53	4	9	32	1.53
49910503--49910532	13	2.3	13	94	0	51	40	46	0	13	1.43
49910671--49910720	9	5.4	9	77	13	57	22	10	26	42	1.84
49913331--49913370	21	1.9	21	90	10	64	40	20	10	30	1.85
49929336--49929366	5	6.0	5	96	3	53	0	38	58	3	1.15
49930551--49930581	15	2.1	15	100	0	62	80	0	19	0	0.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49931932--49931974	21	2.1	21	87	8	63	20	4	18	55	1.60
49938890--49939074	101	1.8	102	90	3	302	23	17	27	31	1.97
49938882--49939072	51	3.8	52	80	7	223	24	17	27	30	1.97
49939277--49939349	37	1.9	38	88	2	112	41	2	24	31	1.69
49941934--49942123	37	4.9	37	81	11	206	26	21	16	35	1.94
49942045--49942400	46	7.5	46	87	7	489	28	21	14	34	1.93
49942047--49942400	98	3.7	98	91	4	585	28	21	14	34	1.94
49942002--49942400	144	2.8	142	85	9	525	28	21	15	34	1.94
49944425--49944584	4	39.8	4	97	1	293	25	1	25	48	1.59
49950171--49950252	41	2.0	41	100	0	164	46	7	24	21	1.77
49953273--49953409	40	3.4	40	82	4	152	37	22	21	18	1.94
49953446--49953760	41	7.6	41	90	1	441	21	20	24	32	1.98
49953446--49953760	124	2.5	123	87	2	436	21	20	24	32	1.98
49953446--49953760	165	1.9	165	87	1	461	21	20	24	32	1.98
49953787--49953966	89	2.0	89	96	0	333	42	3	6	47	1.48
49953949--49953999	26	2.0	26	84	0	66	56	5	11	25	1.57
49954259--49954291	14	2.3	15	94	5	59	30	0	33	36	1.58
49954385--49954535	82	1.8	82	95	0	275	27	1	26	44	1.62
49954786--49954824	7	5.6	7	84	0	51	20	2	48	28	1.62
49959937--49959981	20	2.2	20	80	11	56	53	0	4	42	1.21
49960006--49960098	43	2.2	43	82	3	107	21	21	31	25	1.98
49960190--49960234	22	2.1	21	91	4	72	42	28	17	11	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49965130--49965185	24	2.3	25	93	6	105	60	3	0	35	1.14
49965204--49965264	28	2.2	28	85	5	81	50	3	0	45	1.17
49965229--49965348	18	6.8	18	68	19	58	50	3	2	43	1.32
49965204--49965343	44	3.2	43	70	22	128	50	2	2	45	1.28
49965283--49965342	17	3.5	17	78	17	61	53	1	3	41	1.27
49965170--49965381	88	2.4	90	84	7	279	47	4	3	44	1.38
49968342--49968397	12	4.8	12	78	14	55	48	1	8	41	1.45
49969344--49969383	8	5.2	8	82	11	57	62	25	0	12	1.30
49971859--49971897	3	13.0	3	100	0	78	66	0	0	33	0.92
49974441--49974465	13	1.9	13	100	0	50	64	16	0	20	1.30
49975191--49975373	100	1.8	99	89	3	287	44	15	15	24	1.85
49975168--49975373	48	4.2	49	82	6	247	43	15	15	25	1.85
49975292--49975374	23	3.5	23	72	6	76	40	16	18	24	1.90
49979397--49979494	48	2.0	48	96	0	178	23	24	5	46	1.72
50004279--50004432	80	1.9	80	98	0	299	35	28	5	30	1.79
50008973--50008997	2	12.5	2	100	0	50	52	0	0	48	1.00
50030219--50030276	14	4.1	14	84	2	71	37	3	20	37	1.70
50033286--50033313	2	14.0	2	100	0	56	50	0	0	50	1.00
50038824--50038859	18	2.0	18	94	0	63	22	2	33	41	1.68
50043496--50043587	31	3.1	31	75	4	100	43	13	9	33	1.76
50053799--50053837	19	2.1	19	100	0	78	61	0	5	33	1.18
50059991--50060037	19	2.4	19	82	3	58	46	4	0	48	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50060690--50060735	23	2.0	23	100	0	92	43	4	13	39	1.63
50066766--50066892	60	2.1	60	80	9	143	22	15	14	47	1.82
50068400--50068529	29	4.3	29	73	8	100	46	6	1	46	1.37
50068417--50068465	24	2.1	22	85	7	62	44	2	0	53	1.12
50070742--50070792	19	2.7	19	78	6	50	25	1	11	60	1.41
50071979--50072026	22	2.2	22	92	0	78	41	14	4	39	1.65
50071985--50072028	22	2.0	22	100	0	88	40	13	4	40	1.65
50076792--50076827	18	1.9	19	88	5	56	47	0	0	52	1.00
50078836--50078863	6	4.7	6	100	0	56	35	0	14	50	1.43
50078899--50078938	12	3.5	12	77	22	50	65	0	2	32	1.06
50081430--50081479	3	16.7	3	100	0	100	32	0	0	68	0.90
50081506--50081540	18	1.9	18	94	0	61	20	2	2	74	1.08
50082393--50082435	22	1.9	23	85	4	61	58	0	0	41	0.98
50085515--50085612	25	4.0	24	76	5	81	33	20	27	18	1.96
50085542--50085626	24	3.5	24	73	13	75	31	20	29	18	1.96
50085533--50085659	25	5.2	25	72	11	91	32	20	29	18	1.96
50088866--50088897	2	16.0	2	100	0	64	50	0	0	50	1.00
50089502--50089536	12	3.0	12	87	4	54	62	0	8	28	1.24
50090703--50090788	43	2.0	43	95	0	154	52	2	22	23	1.59
50090708--50090773	16	4.4	16	68	24	54	54	3	22	19	1.58
50096942--50097005	31	2.1	31	84	0	83	48	10	15	25	1.77
50107513--50107543	3	10.0	3	93	6	53	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50114237--50114345	28	3.4	29	65	24	76	38	2	4	54	1.36
50115574--50115650	31	2.6	28	70	24	68	57	10	7	24	1.59
50116073--50116104	15	2.2	15	94	5	57	34	0	3	62	1.11
50118667--50118957	107	2.7	109	91	2	453	29	14	20	35	1.92
50122792--50122835	10	4.5	10	83	13	56	81	0	15	2	0.78
50122813--50122847	6	5.8	6	89	0	52	85	0	5	8	0.73
50122813--50122848	18	2.0	18	94	0	63	83	0	8	8	0.82
50123650--50123686	8	4.6	8	90	10	58	75	0	13	10	1.04
50123650--50123695	15	3.0	15	87	9	58	71	0	15	13	1.14
50125225--50125274	25	2.0	25	84	0	64	36	20	18	26	1.95
50125473--50125522	25	2.0	25	88	0	73	38	20	16	26	1.92
50124976--50125610	124	5.1	125	93	1	1089	35	20	18	25	1.95
50127958--50128248	107	2.7	109	91	2	462	29	13	20	35	1.92
50129522--50129560	9	4.0	9	84	15	51	53	0	0	46	1.00
50129464--50129562	24	4.1	24	72	12	76	49	3	0	47	1.17
50129524--50129560	20	1.9	19	89	10	58	54	0	0	45	1.00
50139034--50139068	18	1.9	18	94	0	61	25	28	5	40	1.78
50139315--50139355	21	2.0	21	90	0	64	31	51	14	2	1.56
50142608--50142875	127	2.1	123	85	6	342	31	17	15	36	1.91
50145254--50145308	14	3.8	15	80	7	60	47	10	0	41	1.39
50145634--50145665	15	2.1	15	94	0	55	15	6	9	68	1.36
50147132--50147380	50	4.8	50	87	3	327	21	28	22	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50147475--50147506	13	2.5	13	94	0	55	56	12	0	31	1.37
50150534--50150558	13	1.9	13	100	0	50	8	0	24	68	1.16
50150649--50150739	44	2.1	44	100	0	182	30	8	20	39	1.83
50157495--50157538	23	1.9	23	86	9	63	54	0	0	45	0.99
50157659--50157686	2	14.0	2	100	0	56	50	0	0	50	1.00
50163395--50163466	28	2.6	28	84	8	85	44	0	4	51	1.20
50163545--50163743	66	3.2	63	68	19	175	41	2	6	49	1.42
50163507--50163804	120	2.5	120	93	1	508	42	2	5	50	1.37
50163577--50163767	61	3.2	60	69	16	187	42	2	6	48	1.41
50163632--50163683	15	3.6	15	80	12	56	44	0	1	53	1.11

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