genome.fa.s1.2.7.7.80.10.50.1000.116.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  116  of  187  ( 22383 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)
34819658--34819963	29	10.6	29	78	6	259	23	14	24	37	1.92
34819653--34819963	58	5.4	58	81	5	294	23	14	24	37	1.92
34819658--34819912	87	2.9	86	80	5	291	21	14	24	38	1.91
34819800--34820051	58	4.4	58	72	10	173	25	14	23	36	1.93
34820000--34820065	29	2.3	29	75	0	69	31	15	19	33	1.93
34820693--34821036	29	12.0	29	72	8	204	23	15	22	38	1.93
34821701--34822066	29	12.8	29	75	5	251	22	16	24	36	1.94
34821996--34822096	29	3.5	29	86	1	123	25	18	24	30	1.98
34822685--34823046	29	12.7	29	76	6	274	21	16	24	38	1.93
34822981--34823062	29	2.8	29	88	3	94	28	13	21	36	1.91
34824184--34824315	64	2.1	64	98	0	255	30	21	11	36	1.89
34828356--34828556	50	3.9	50	79	8	215	24	21	29	24	1.99
34828466--34828581	50	2.3	50	78	0	133	27	25	25	21	1.99
34829153--34829264	55	2.0	55	100	0	224	33	5	23	38	1.77
34835034--34835224	50	3.7	50	79	9	222	27	20	28	23	1.99
34838323--34838464	40	3.5	40	86	0	176	33	22	14	30	1.93
34847937--34847968	16	2.0	16	100	0	64	18	25	18	37	1.94
34856268--34856310	17	2.5	17	78	14	52	51	11	4	32	1.59
34860469--34860709	120	2.0	120	93	0	410	34	27	9	27	1.88
34861127--34861171	20	2.2	20	80	0	54	20	20	22	37	1.94
34861182--34861221	20	2.0	20	85	0	53	27	20	12	40	1.88
34864016--34864092	27	2.9	28	75	21	83	18	20	18	42	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34866180--34866236	17	3.5	17	72	11	57	36	1	1	59	1.18
34866163--34866223	11	5.2	11	73	21	52	37	1	3	57	1.25
34866163--34866238	37	2.1	36	85	11	102	39	1	2	56	1.21
34867698--34867809	43	2.6	43	82	0	134	23	36	25	15	1.93
34870992--34871131	50	2.8	50	84	5	176	25	14	27	32	1.94
34877149--34877335	44	4.3	44	64	14	116	24	21	22	31	1.99
34877457--34877926	44	10.7	43	70	8	252	28	20	18	32	1.96
34877323--34877851	219	2.5	208	86	6	753	29	19	18	32	1.96
34877439--34877926	219	2.2	219	93	0	825	29	20	18	31	1.96
34900557--34900586	7	4.3	7	100	0	60	40	46	0	13	1.43
34913103--34913137	15	2.3	15	100	0	70	34	17	22	25	1.96
34925758--34925993	50	4.6	50	86	3	274	21	30	22	26	1.98
34931748--34932037	51	5.7	51	77	7	295	28	15	25	30	1.96
34931748--34932042	102	2.9	102	87	1	405	29	15	25	29	1.96
34933745--34933778	12	2.8	12	81	0	50	61	0	23	14	1.33
34940502--34940547	14	3.4	14	80	20	62	47	0	8	43	1.34
34942799--34942849	16	3.4	16	77	17	56	80	0	11	7	0.90
34942816--34942866	26	1.9	27	84	11	70	78	0	7	13	0.96
34942800--34942865	17	4.0	16	75	15	55	80	0	9	10	0.91
34944981--34945022	16	2.7	16	85	3	50	19	50	4	26	1.67
34951991--34952017	14	1.9	14	100	0	54	7	7	3	81	0.97
34952008--34952195	101	1.9	102	88	4	292	26	26	16	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34952988--34953030	16	2.7	16	85	10	61	72	0	2	25	0.97
34952988--34953030	11	4.0	11	84	6	61	72	0	2	25	0.97
34967501--34967550	19	2.7	19	82	14	61	54	0	4	42	1.19
34969403--34969484	44	1.9	43	87	7	123	62	2	20	14	1.43
34969401--34969501	44	2.3	44	81	13	120	62	1	22	12	1.40
34970993--34971036	20	2.2	20	84	8	54	36	9	4	50	1.55
34974082--34974269	50	3.6	50	81	4	160	26	27	19	26	1.99
34985672--34985786	22	5.1	22	78	14	117	42	19	22	15	1.88
34985672--34985797	47	2.7	46	86	6	175	42	18	23	16	1.89
34986886--34986972	5	17.6	5	75	13	74	55	2	2	40	1.25
34987623--34987696	35	2.1	35	84	0	94	21	25	24	28	1.99
34990786--34990814	9	3.2	9	100	0	58	34	31	0	34	1.58
34998217--34998272	28	2.0	28	100	0	112	25	17	10	46	1.80
34999986--35000061	27	2.7	28	89	6	102	60	1	2	35	1.19
34999999--35000062	27	2.4	27	94	2	112	60	1	3	34	1.22
35000866--35000917	24	2.2	24	85	0	68	38	3	7	50	1.50
35002664--35002944	50	5.6	50	84	0	330	22	28	20	28	1.98
35009806--35009835	16	1.9	15	93	6	51	43	33	3	20	1.68
35010323--35010356	6	5.7	6	85	0	50	2	20	0	76	0.92
35010323--35010362	18	2.5	15	88	12	53	2	20	0	77	0.88
35013380--35013431	24	2.2	24	82	0	59	40	3	5	50	1.45
35019165--35019229	20	3.3	20	70	12	62	55	7	16	20	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35019154--35019234	39	2.1	39	92	0	135	53	6	19	20	1.67
35019869--35019917	3	16.7	3	87	4	73	32	0	0	67	0.91
35020071--35020139	28	2.5	27	77	9	68	30	1	5	62	1.27
35020870--35021066	98	2.0	98	94	2	342	29	10	23	36	1.89
35024702--35024736	12	2.8	13	87	12	56	88	11	0	0	0.51
35026084--35026843	132	5.8	132	93	0	1268	28	17	23	29	1.97
35027281--35027345	20	3.3	20	70	12	62	55	7	16	20	1.65
35027270--35027350	39	2.1	39	92	0	135	53	6	19	20	1.67
35028064--35028260	98	2.0	98	96	2	360	28	10	23	37	1.88
35033278--35033385	29	3.7	29	70	1	81	26	16	18	37	1.92
35038126--35038154	7	4.1	7	100	0	58	31	0	27	41	1.56
35038311--35038360	21	2.3	22	82	6	66	28	12	14	46	1.79
35039867--35039920	24	2.3	24	87	3	74	11	18	22	48	1.79
35057240--35057280	20	2.0	20	85	0	55	46	21	0	31	1.52
35071287--35071357	35	2.0	35	100	0	142	33	8	25	32	1.86
35092853--35093113	27	9.7	27	82	0	308	34	19	19	26	1.96
35093347--35093441	32	3.0	32	85	0	136	21	23	21	34	1.97
35094417--35094469	27	2.0	27	100	0	106	37	15	20	26	1.92
35095537--35095597	27	2.2	26	77	11	68	50	8	9	31	1.65
35105964--35106024	22	2.6	22	77	17	61	60	3	4	31	1.34
35108037--35108077	21	2.0	21	95	0	73	43	7	21	26	1.79
35112436--35112476	21	1.9	22	85	5	57	12	21	26	39	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35114045--35114165	57	2.1	58	84	1	154	28	19	5	46	1.73
35115097--35115160	32	2.0	32	100	0	128	46	12	6	34	1.67
35131571--35131703	66	2.0	66	85	2	178	27	15	13	43	1.84
35135726--35135781	25	2.2	26	84	9	80	44	3	1	50	1.29
35140434--35140500	9	7.4	9	93	0	80	37	25	11	25	1.90
35140698--35140810	39	2.9	39	89	6	167	22	2	23	52	1.60
35150578--35150652	36	2.1	36	95	2	134	77	5	9	8	1.12
35152801--35152826	5	5.2	5	100	0	52	42	19	19	19	1.90
35153578--35153637	30	2.0	30	83	3	75	41	0	38	20	1.52
35153940--35153970	9	3.4	9	90	0	53	38	22	12	25	1.90
35156459--35156543	40	2.1	40	91	4	136	32	3	0	63	1.11
35156499--35156586	31	2.8	31	96	3	158	36	3	0	60	1.14
35156549--35156601	20	2.5	21	90	9	90	35	3	0	60	1.15
35156491--35156611	31	4.0	29	86	6	125	37	2	0	60	1.10
35164875--35164938	27	2.4	27	81	0	74	29	26	17	26	1.97
35164982--35165431	27	16.7	27	79	3	390	26	23	14	34	1.94
35164997--35165431	81	5.4	81	82	4	479	26	22	14	35	1.93
35178044--35178073	12	2.5	12	94	0	51	26	16	33	23	1.96
35184525--35184769	50	4.8	50	77	7	201	23	27	20	28	1.99
35190269--35191571	435	3.0	435	96	0	2396	31	23	14	30	1.94
35194839--35195074	50	4.7	50	81	1	251	22	28	20	27	1.99
35198886--35198965	27	3.0	27	86	0	115	22	26	15	36	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35199005--35199269	27	9.8	27	78	4	124	27	23	17	32	1.97
35199045--35199269	54	4.2	52	77	9	195	28	22	16	32	1.96
35199024--35199264	81	3.0	81	79	4	227	28	21	17	32	1.96
35199003--35199269	108	2.5	108	85	6	328	27	23	17	31	1.97
35201594--35201757	35	4.7	35	90	0	220	17	11	30	40	1.85
35205631--35205664	17	2.0	17	94	0	59	55	0	8	35	1.31
35211996--35212215	104	2.1	104	88	6	324	34	13	22	29	1.93
35215414--35215465	20	2.8	18	73	21	54	53	3	1	40	1.30
35220719--35220762	23	1.9	23	90	9	72	34	0	20	45	1.51
35221176--35221220	21	2.1	22	83	4	56	37	8	8	44	1.67

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