genome.fa.s4.2.7.7.80.10.50.1000.159.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  159  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)
50163507--50163789	59	4.7	60	68	14	199	42	2	4	49	1.37
50163761--50163802	15	2.7	16	82	14	52	45	0	2	52	1.13
50163941--50164030	45	2.0	44	82	6	110	34	27	5	32	1.80
50164397--50164426	2	15.0	2	100	0	60	50	0	0	50	1.00
50167011--50167048	10	3.7	10	92	3	58	47	0	0	52	1.00
50167822--50167898	29	2.6	29	83	4	91	48	14	12	24	1.79
50169335--50169378	21	2.1	21	100	0	88	27	15	31	25	1.96
50169641--50169671	16	1.9	16	93	0	53	48	0	9	41	1.36
50171279--50171426	43	3.4	43	83	0	179	27	15	18	39	1.90
50171284--50171484	43	4.8	42	77	10	155	25	14	19	39	1.90
50171398--50171468	36	2.0	36	94	0	124	28	8	18	45	1.78
50174585--50174699	3	38.3	3	96	0	212	33	0	1	65	1.03
50179204--50179351	7	20.4	7	74	16	74	77	3	6	12	1.07
50179208--50179298	42	2.2	42	86	4	121	79	5	1	14	0.97
50179208--50179298	6	15.2	6	75	11	80	79	5	1	14	0.97
50181603--50182276	43	15.2	42	66	9	205	30	22	22	24	1.99
50181569--50182277	91	8.0	90	89	3	1039	30	22	22	24	1.99
50181569--50182277	268	2.7	267	91	1	1152	30	22	22	24	1.99
50182555--50182704	76	2.0	76	82	5	187	28	27	22	21	1.99
50182638--50182919	89	3.2	87	82	6	316	29	25	23	20	1.99
50182468--50182795	165	2.0	164	79	3	354	28	25	24	21	1.99
50184882--50184913	2	16.0	2	100	0	64	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50185228--50185303	3	25.3	3	97	0	143	32	1	0	65	1.01
50187303--50187417	46	2.5	46	85	0	158	29	24	21	24	1.99
50187296--50187416	23	5.2	24	77	11	128	30	24	20	23	1.99
50194234--50194305	35	2.0	37	86	7	105	36	1	0	62	1.04
50194267--50194317	26	2.0	24	85	7	66	31	0	1	66	1.03
50199388--50199430	14	3.1	14	82	0	50	2	39	2	55	1.25
50202083--50202116	17	1.9	17	88	5	50	23	26	0	50	1.50
50208851--50208896	24	2.0	24	83	12	60	13	4	34	47	1.62
50208974--50209194	94	2.4	94	85	1	282	26	20	21	32	1.98
50215244--50215273	6	5.0	6	100	0	60	33	0	16	50	1.46
50215371--50215532	64	2.6	64	78	17	189	56	2	6	33	1.39
50215669--50215712	22	2.2	21	84	15	58	50	2	6	40	1.42
50217375--50217549	95	1.8	95	83	1	233	28	20	18	33	1.96
50217375--50217559	96	1.9	95	82	3	228	28	20	17	34	1.95
50217480--50217589	45	2.5	45	86	1	141	29	25	18	27	1.98
50218806--50218850	11	3.9	11	80	11	54	0	17	0	82	0.68
50218802--50218844	18	2.4	18	88	0	68	0	16	0	83	0.64
50218805--50218868	32	2.1	32	88	8	98	0	20	0	79	0.73
50218806--50218868	18	3.7	17	85	6	65	0	20	0	79	0.73
50218794--50218868	29	2.6	28	81	8	98	0	22	0	77	0.77
50223499--50223692	8	25.9	8	69	22	57	56	1	8	33	1.37
50223568--50223693	2	65.0	2	72	12	75	54	0	6	38	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50223493--50223678	81	2.3	80	77	12	198	56	1	9	32	1.39
50223498--50223733	73	3.2	73	78	16	243	57	1	8	33	1.37
50223467--50223754	71	4.1	68	72	21	220	56	1	8	33	1.38
50227648--50227698	23	2.2	23	89	0	75	39	17	9	33	1.83
50228180--50228206	8	3.4	8	100	0	54	22	0	0	77	0.76
50230632--50230879	25	10.4	25	84	8	270	19	25	18	36	1.94
50230759--50230795	19	1.9	19	100	0	74	21	29	16	32	1.95
50230815--50230883	22	3.1	22	89	0	111	17	23	17	42	1.89
50230638--50230877	69	3.4	68	83	11	184	20	25	18	36	1.95
50230632--50230879	94	2.6	95	81	12	260	19	25	18	36	1.94
50235489--50235539	23	2.2	23	86	6	68	39	19	9	31	1.84
50243781--50243857	38	2.0	38	94	0	136	49	22	16	11	1.78
50245147--50245211	29	2.2	31	89	8	100	53	7	7	30	1.57
50246783--50246823	20	2.0	20	86	9	57	58	2	14	24	1.49
50246965--50247057	27	4.2	22	65	28	54	49	3	13	33	1.59
50247327--50247380	3	18.0	3	96	0	99	64	0	0	35	0.94
50249334--50249391	3	19.3	3	100	0	116	67	0	0	32	0.91
50253260--50253326	29	2.3	30	79	7	75	34	4	2	58	1.34
50253818--50253864	16	3.1	15	80	14	53	57	0	8	34	1.29
50256464--50256524	20	3.1	19	72	9	50	24	24	16	34	1.95
50259700--50259743	22	2.0	22	95	0	79	27	2	18	52	1.57
50267097--50267246	54	2.7	53	78	12	144	43	0	34	22	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50267998--50268050	27	2.0	27	85	7	72	41	5	7	45	1.56
50276284--50276310	7	3.9	7	100	0	54	55	0	0	44	0.99
50286181--50286222	20	2.2	19	86	4	57	71	4	0	23	1.05
50290106--50290255	42	3.6	42	80	3	151	19	22	17	41	1.90
50297994--50298028	17	2.1	18	89	10	56	34	22	5	37	1.78
50298586--50298624	16	2.4	16	82	0	51	46	10	10	33	1.72
50299614--50299645	3	10.7	3	93	0	55	65	3	0	31	1.08
50301824--50301862	20	1.9	21	89	5	62	69	0	7	23	1.14
50305417--50305450	6	5.7	6	92	0	59	14	35	50	0	1.44
50317640--50317699	29	2.0	31	84	12	81	46	3	1	48	1.28
50323883--50323937	2	27.5	2	100	0	110	50	0	0	49	1.00
50329037--50329064	13	2.2	13	100	0	56	64	0	14	21	1.29
50329607--50329679	26	2.8	26	83	6	78	19	19	21	39	1.92
50329694--50329745	25	2.1	25	82	7	61	19	26	23	30	1.98
50332804--50332894	39	2.3	39	92	0	146	45	20	4	29	1.71
50340670--50340715	19	2.4	19	85	10	58	52	8	0	39	1.33
50340665--50340721	18	3.1	19	82	12	66	52	7	0	40	1.28
50340727--50340755	2	14.5	2	100	0	58	51	0	0	48	1.00
50342428--50342464	9	4.1	9	92	0	65	45	13	10	29	1.77
50343433--50343462	6	5.0	6	100	0	60	66	0	0	33	0.92
50354843--50354878	16	2.2	16	100	0	72	25	0	36	38	1.56
50355108--50355142	18	2.0	18	88	5	54	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50355179--50355209	16	1.9	16	100	0	62	32	0	9	58	1.31
50355196--50355252	27	2.0	27	86	10	78	47	0	3	49	1.18
50355348--50355389	15	2.7	16	82	14	52	52	2	0	45	1.13
50355357--50355398	15	2.9	15	82	10	52	52	0	0	47	1.00
50355467--50355509	15	2.9	15	83	10	54	53	2	0	44	1.13
50366331--50366363	2	16.5	2	100	0	66	48	0	0	51	1.00
50368811--50368859	18	2.8	17	85	11	64	32	2	0	65	1.04
50368990--50369056	20	3.3	20	77	6	55	37	1	2	58	1.23
50369140--50369169	15	2.0	15	93	0	51	50	0	0	50	1.00
50369841--50369876	2	18.0	2	100	0	72	50	0	0	50	1.00
50381053--50381159	25	4.3	25	75	7	83	32	21	20	25	1.97
50381053--50381159	50	2.1	50	84	3	135	32	21	20	25	1.97
50385745--50385784	21	2.0	20	85	5	53	22	32	0	45	1.53
50393778--50393803	13	2.0	13	100	0	52	0	0	23	76	0.78
50394003--50394724	95	7.8	95	82	6	540	30	19	15	33	1.93
50393960--50394812	44	18.6	45	74	9	550	30	20	15	33	1.94
50393995--50394814	89	8.9	89	80	6	576	30	20	15	33	1.93
50401927--50401961	9	3.9	9	88	0	52	71	0	5	22	1.07
50403942--50403994	21	2.5	21	77	17	56	22	3	18	54	1.59
50404061--50404124	28	2.3	28	78	5	67	25	3	25	46	1.67
50404559--50404599	19	2.2	19	91	8	66	21	0	24	53	1.46
50404631--50404668	14	2.7	15	80	12	53	10	2	23	63	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50404631--50404675	20	2.2	21	84	4	56	13	2	24	60	1.45
50411823--50412136	166	1.8	167	83	6	407	24	15	21	38	1.92
50415190--50415219	6	5.0	6	100	0	60	33	33	0	33	1.58
50419759--50419788	13	2.3	13	100	0	60	36	26	6	30	1.82
50425345--50425402	3	19.0	3	92	3	98	32	1	0	65	1.03
50427651--50427693	19	2.3	18	84	15	52	20	23	13	41	1.88
50428955--50428991	17	2.1	18	90	5	58	29	24	0	45	1.53
50430632--50430684	16	3.5	14	82	14	61	71	0	15	13	1.14
50431919--50432860	353	2.7	350	94	1	1618	26	22	25	25	2.00
50431919--50432860	88	10.7	88	94	1	1613	26	22	25	25	2.00

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