genome.fa.s4.2.7.7.80.10.50.1000.21.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  21  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)
6112880--6112920	21	2.0	21	90	9	66	51	0	9	39	1.35
6128497--6128541	23	2.0	23	81	0	54	22	0	15	62	1.33
6128828--6128903	36	2.1	37	82	7	93	39	9	0	51	1.34
6130653--6130699	18	2.6	19	80	10	62	23	8	2	65	1.31
6130863--6130953	30	3.0	29	76	6	83	14	53	9	21	1.69
6130874--6130915	21	2.0	21	86	9	59	14	57	9	19	1.64
6132698--6132753	21	2.7	21	81	10	69	21	58	5	14	1.55
6132671--6132868	72	2.8	72	91	0	315	19	56	8	16	1.65
6132827--6132987	66	2.4	66	92	2	279	21	54	9	14	1.68
6132902--6132940	15	2.6	15	83	0	51	28	58	5	7	1.47
6132865--6132976	18	6.6	18	67	10	74	22	54	9	13	1.68
6132794--6133018	30	7.1	30	68	14	94	20	54	9	15	1.69
6132953--6133234	72	4.1	72	81	10	363	20	55	9	15	1.67
6132935--6133240	132	2.3	132	92	2	472	20	55	9	15	1.67
6133076--6133119	15	2.9	15	82	0	61	22	59	9	9	1.56
6133046--6133149	30	3.5	30	71	15	97	18	56	9	15	1.65
6133067--6133164	30	3.3	30	70	16	94	20	55	11	13	1.68
6133253--6133338	42	2.0	42	86	0	118	16	53	11	18	1.72
6133181--6133317	30	4.4	30	66	10	85	18	53	9	18	1.71
6133244--6133455	72	3.0	70	74	14	204	16	54	11	17	1.71
6133313--6133365	24	2.2	24	89	0	79	13	58	13	15	1.64
6133313--6133376	24	2.7	24	85	0	65	14	59	12	14	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6133136--6133365	96	2.4	93	80	6	280	18	54	10	16	1.70
6133343--6133425	42	2.0	42	85	0	112	18	56	8	16	1.64
6133373--6133436	30	2.1	30	91	0	101	18	53	7	20	1.69
6133412--6133483	30	2.4	30	85	0	108	16	51	9	22	1.73
6135361--6135396	19	1.9	18	88	5	54	58	8	2	30	1.42
6135485--6135525	17	2.5	17	92	4	66	51	7	4	36	1.51
6135512--6135554	22	2.0	21	86	4	59	55	2	0	41	1.12
6143565--6143619	25	2.2	25	93	3	94	47	12	7	32	1.69
6144563--6144733	60	2.9	60	87	6	235	25	12	22	39	1.89
6150788--6150836	21	2.4	20	83	6	62	38	14	2	44	1.56
6150802--6150844	21	2.0	21	100	0	86	44	18	0	37	1.50
6150809--6150858	21	2.4	20	83	12	57	38	18	2	42	1.61
6153917--6153966	24	2.0	25	84	3	66	30	2	2	66	1.14
6158633--6158670	2	19.0	2	100	0	76	50	0	0	50	1.00
6162738--6162766	2	14.5	2	100	0	58	51	0	0	48	1.00
6166204--6166353	33	4.5	33	71	12	119	28	20	16	34	1.95
6169687--6169715	14	2.1	14	100	0	58	58	13	0	27	1.36
6186971--6187032	27	2.3	27	91	0	106	30	22	32	14	1.94
6187960--6188099	49	2.9	48	82	8	178	32	1	12	52	1.48
6187960--6188046	27	3.4	27	81	15	130	35	1	11	51	1.46
6188142--6188179	19	2.0	19	89	0	58	36	5	7	50	1.54
6202339--6202371	5	6.4	5	96	3	57	78	0	0	21	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6208929--6208966	3	12.7	3	94	0	67	0	28	34	36	1.58
6221647--6221679	13	2.3	15	90	10	52	48	6	6	39	1.53
6239810--6239943	45	3.0	45	90	2	198	26	20	9	42	1.83
6244657--6244715	20	3.1	19	71	14	50	38	16	15	28	1.89
6252858--6252922	19	3.3	19	72	12	60	66	4	1	27	1.20
6252858--6252945	39	2.2	40	84	9	110	65	4	2	27	1.23
6262336--6262469	68	2.0	69	87	1	198	29	10	20	39	1.86
6266602--6266638	17	2.1	18	85	14	51	16	13	27	43	1.85
6273096--6273160	17	3.9	16	71	15	51	44	6	9	40	1.61
6273622--6273659	16	2.2	19	86	13	55	55	0	5	39	1.23
6278152--6278193	17	2.3	18	80	12	50	33	0	9	57	1.31
6303105--6303146	21	2.1	20	86	8	59	40	0	19	40	1.51
6306182--6306213	3	10.7	3	100	0	64	34	0	65	0	0.93
6306604--6306728	65	1.9	65	88	3	189	23	14	18	44	1.86
6307463--6307517	21	2.6	21	82	0	65	12	12	38	36	1.82
6308285--6308602	82	4.0	81	88	2	421	47	26	6	20	1.73
6308304--6308637	82	4.2	77	88	3	308	49	25	5	19	1.71
6311469--6311509	22	1.9	22	90	5	66	39	0	19	41	1.52
6320954--6321095	27	5.3	27	84	0	194	42	21	16	18	1.88
6321259--6321365	26	4.1	26	90	0	151	21	22	21	34	1.97
6330371--6330421	19	2.6	19	78	6	57	13	27	23	35	1.93
6335282--6335331	2	25.0	2	95	0	91	48	0	2	50	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6339936--6340001	29	2.2	30	86	5	89	53	9	9	28	1.63
6340190--6340228	2	19.5	2	100	0	78	51	0	0	48	1.00
6346328--6346359	2	16.0	2	93	0	55	53	0	0	46	1.00
6348516--6348553	19	2.0	20	84	5	51	60	5	5	28	1.40
6350757--6350801	22	2.0	22	82	4	54	42	4	4	48	1.43
6365696--6365816	53	2.2	53	76	12	122	47	2	1	48	1.25
6365761--6365807	21	2.3	21	85	3	69	48	0	2	48	1.13
6365679--6365789	25	4.1	27	70	13	93	46	2	2	47	1.30
6365679--6365842	80	2.0	83	80	10	187	46	1	3	48	1.28
6373178--6373229	26	2.0	26	92	0	86	34	23	23	19	1.96
6377925--6377957	16	2.0	17	88	5	50	51	9	0	39	1.34
6378051--6378107	21	2.8	20	76	7	62	63	12	0	24	1.29
6393507--6393574	29	2.3	29	82	0	82	63	1	7	27	1.30
6393756--6393828	28	2.6	28	86	0	110	46	5	21	26	1.73
6396524--6396550	3	9.0	3	100	0	54	33	0	0	66	0.92
6402628--6403029	88	4.6	88	87	1	538	26	20	27	25	1.99
6402748--6402985	43	5.4	43	67	13	144	25	18	29	26	1.98
6402694--6402997	44	6.9	44	65	10	154	25	19	28	26	1.99
6404429--6404463	3	11.3	3	87	6	52	37	0	0	62	0.95
6407405--6407446	2	21.0	2	100	0	84	50	0	0	50	1.00
6415900--6415962	28	2.2	28	85	0	81	53	23	7	14	1.66
6417606--6417676	35	2.0	35	100	0	142	43	5	28	22	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6418977--6419097	61	2.0	60	85	1	161	37	14	6	41	1.73
6422075--6422104	6	5.2	6	96	4	53	46	0	53	0	1.00
6425172--6425204	14	2.4	14	94	0	57	72	3	0	24	0.98
6426700--6426904	102	2.0	102	95	0	365	42	11	13	32	1.80
6431325--6431371	17	2.8	17	79	20	62	36	2	6	55	1.37
6434974--6435006	18	1.9	17	88	11	50	54	6	3	36	1.41
6440916--6441259	32	10.8	32	84	2	343	40	16	11	31	1.83
6440916--6441259	64	5.4	64	87	1	440	40	16	11	31	1.83
6440916--6441259	96	3.6	95	83	5	383	40	16	11	31	1.83
6441462--6441519	30	2.0	30	82	3	73	25	22	6	44	1.77
6446158--6446201	22	2.0	22	100	0	88	27	13	22	36	1.92
6447606--6448207	32	18.8	32	83	2	681	40	16	11	31	1.84
6447606--6448207	64	9.4	64	93	1	960	40	16	11	31	1.84
6447606--6448207	96	6.3	96	83	1	760	40	16	11	31	1.84
6449218--6449243	11	2.4	11	100	0	52	61	0	0	38	0.96
6454635--6454690	26	2.2	26	83	6	69	25	3	3	67	1.22
6459458--6459608	56	2.7	56	85	0	203	27	22	12	37	1.90
6467690--6467737	21	2.1	23	85	11	64	22	14	6	56	1.61
6486225--6486267	16	2.6	16	79	17	52	2	20	0	76	0.89
6487094--6487183	42	2.1	42	89	0	135	21	25	38	14	1.91
6492827--6492984	43	3.7	43	86	2	203	31	26	13	29	1.94
6497019--6497140	42	2.9	43	84	4	151	24	19	36	19	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6513319--6513369	22	2.3	23	80	13	61	29	1	7	60	1.36
6516864--6516893	2	15.0	2	100	0	60	50	0	0	50	1.00
6519034--6519170	38	3.6	38	85	4	177	27	13	21	37	1.91
6523922--6523964	21	2.0	22	90	4	70	65	0	0	34	0.93
6523922--6523969	21	2.3	21	82	10	64	62	0	0	37	0.95
6526892--6526936	20	2.3	19	88	3	63	31	2	0	66	1.04
6528631--6528733	46	2.2	46	93	3	172	45	19	2	32	1.65
6533197--6533294	46	2.2	46	94	1	171	43	19	3	33	1.66
6537955--6538053	33	3.0	33	79	2	119	18	16	17	48	1.81
6539221--6539277	30	1.9	30	88	0	87	35	21	22	21	1.96

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