genome.fa.s6.2.7.7.80.10.50.1000.115.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  115  of  168  ( 20060 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)
33592445--33592469	2	12.5	2	100	0	50	52	0	0	48	1.00
33593536--33593644	55	2.0	55	94	0	191	40	9	11	39	1.72
33596142--33596305	43	3.9	42	77	15	185	21	18	28	31	1.97
33596466--33596497	16	1.9	17	93	6	57	40	0	21	37	1.54
33600090--33600130	20	2.0	20	100	0	82	48	24	4	21	1.69
33604215--33604244	14	2.1	14	93	0	51	30	0	23	46	1.52
33607277--33607437	80	2.0	80	90	2	252	26	15	19	39	1.91
33608583--33608617	13	2.7	13	100	0	70	25	5	28	40	1.78
33608796--33608857	24	2.6	23	75	12	63	46	0	1	51	1.10
33613483--33613524	21	2.0	21	95	0	75	54	21	0	23	1.44
33613669--33613707	20	2.0	20	85	10	53	58	5	0	35	1.20
33613925--33613975	25	1.9	26	84	11	68	58	0	1	39	1.09
33614177--33614291	9	11.4	9	68	18	50	61	1	0	35	1.12
33614178--33614229	19	2.9	17	80	8	59	61	1	0	36	1.07
33614564--33614605	18	2.4	17	80	11	57	2	19	2	76	1.01
33625635--33625700	29	2.3	30	82	12	84	51	3	1	43	1.26
33626698--33626786	31	2.9	31	81	0	106	40	15	14	29	1.87
33626929--33627024	50	1.9	50	93	0	165	35	18	10	35	1.85
33627896--33628585	136	5.2	131	77	9	623	30	14	13	41	1.84
33629889--33629922	2	17.0	2	100	0	68	50	0	0	50	1.00
33646649--33646873	51	4.4	52	80	3	217	30	28	16	24	1.97
33649926--33650043	50	2.4	50	81	2	130	31	20	29	18	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33649926--33650043	25	4.7	25	79	0	110	31	20	29	18	1.96
33650331--33650375	22	2.0	22	100	0	90	35	13	17	33	1.89
33662810--33662900	44	2.1	44	93	0	155	47	13	12	27	1.78
33665526--33665566	18	2.3	18	88	12	59	65	7	14	12	1.45
33667830--33667878	25	2.0	25	100	0	98	28	10	28	32	1.90
33670298--33670541	41	6.0	40	88	7	262	33	27	19	20	1.96
33670298--33670541	82	3.0	82	85	5	316	33	27	19	20	1.96
33691409--33691462	25	2.2	25	82	0	63	40	20	25	12	1.88
33693041--33693108	35	2.0	35	91	2	111	41	11	8	38	1.73
33700195--33700243	14	3.4	14	91	2	80	22	0	0	77	0.77
33700195--33700242	15	3.3	15	88	5	80	20	0	0	79	0.74
33700804--33700844	19	2.1	20	95	4	75	26	19	4	48	1.69
33702312--33702347	6	6.0	6	93	0	54	66	5	0	27	1.13
33702312--33702346	18	1.9	18	94	0	61	68	5	0	25	1.11
33702750--33702774	6	4.2	6	100	0	50	84	0	16	0	0.63
33719723--33719751	1	29.0	1	100	0	58	100	0	0	0	0.00
33720795--33720874	40	2.0	40	83	9	101	35	3	2	58	1.29
33723078--33723103	12	2.2	12	100	0	52	76	0	7	15	0.99
33723374--33723416	3	14.3	3	100	0	86	32	0	0	67	0.91
33728729--33728843	42	2.7	42	82	5	124	27	18	26	27	1.98
33728769--33728865	42	2.3	43	87	1	133	26	14	24	34	1.94
33729154--33729272	30	4.0	28	80	6	103	34	20	3	42	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33729170--33729306	30	4.6	30	80	5	127	30	23	5	40	1.76
33729586--33729629	17	2.6	17	85	0	52	18	50	13	18	1.79
33729665--33729708	14	3.1	14	76	0	52	75	15	6	2	1.12
33729801--33729850	3	16.0	3	87	8	73	70	0	30	0	0.88
33729802--33729869	6	11.3	6	79	16	52	75	0	25	0	0.81
33729801--33729855	10	5.7	10	93	6	80	70	0	29	0	0.87
33729820--33729871	13	4.0	13	80	12	54	78	0	21	0	0.74
33729830--33729868	16	2.4	16	86	4	51	79	0	20	0	0.73
33730691--33731015	17	17.8	18	72	14	213	31	15	10	42	1.81
33730700--33730781	20	4.2	20	75	13	89	37	10	9	41	1.73
33730772--33731016	55	4.5	54	74	12	177	31	15	10	42	1.81
33730692--33731016	38	8.9	36	76	12	168	32	15	10	42	1.81
33731110--33731172	33	1.9	33	87	6	92	36	9	7	46	1.66
33733704--33733749	17	2.9	17	81	9	53	36	8	8	45	1.66
33733775--33733816	20	2.1	20	91	8	68	42	11	9	35	1.74
33733939--33733968	5	6.0	5	100	0	60	60	0	0	40	0.97
33734129--33734196	8	7.8	8	80	19	66	1	17	0	80	0.78
33734129--33734200	18	3.9	18	79	12	83	1	18	0	80	0.78
33734129--33734200	10	7.6	10	79	16	73	1	18	0	80	0.78
33734294--33734363	25	3.0	23	82	10	79	0	25	7	67	1.16
33734449--33734504	14	4.3	13	78	13	53	0	25	0	75	0.81
33734449--33734495	14	3.5	14	85	8	62	0	25	0	74	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33734440--33734510	33	2.2	32	85	9	101	0	23	0	76	0.79
33734445--33734510	6	10.3	6	80	11	69	0	24	0	75	0.80
33735090--33735119	4	7.5	4	100	0	60	23	0	0	76	0.78
33735074--33735139	27	2.4	27	82	12	73	24	0	3	72	0.98
33735612--33735948	160	2.1	153	85	7	435	41	17	14	27	1.87
33735625--33735932	81	3.9	78	89	5	419	39	18	14	27	1.89
33736779--33736826	6	8.7	6	82	13	59	0	0	12	87	0.54
33736779--33736826	11	4.7	10	82	12	62	0	0	12	87	0.54
33739306--33739363	30	2.0	29	90	10	91	43	1	18	36	1.61
33739306--33739383	29	2.6	30	84	9	90	38	5	20	35	1.75
33739380--33739438	19	3.1	19	83	11	59	25	0	3	71	1.02
33744933--33744962	10	3.0	10	90	0	51	30	23	0	46	1.52
33744925--33744962	20	1.9	19	94	5	67	31	23	0	44	1.54
33748478--33748554	13	6.1	13	82	10	79	83	12	2	1	0.82
33748478--33748554	8	9.9	8	72	19	65	83	12	2	1	0.82
33748477--33748563	26	3.2	26	80	13	95	81	11	4	2	0.93
33748479--33748552	12	6.3	12	80	13	75	83	12	2	1	0.81
33748482--33748561	17	4.9	16	77	20	69	81	12	5	1	0.91
33749405--33749602	74	2.6	74	88	4	272	27	19	20	32	1.97
33749413--33749690	77	3.7	73	82	7	281	26	19	23	31	1.98
33749405--33749690	149	1.9	149	82	6	351	26	19	22	32	1.97
33749891--33750006	30	3.9	31	80	7	141	32	24	3	39	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33750502--33750595	3	31.0	3	90	6	145	70	0	29	0	0.88
33750502--33750614	9	12.1	10	89	8	127	72	0	27	0	0.85
33750563--33750610	14	3.5	14	83	11	64	81	0	18	0	0.70
33750512--33750620	15	7.6	13	85	9	67	74	0	25	0	0.82
33750714--33750763	21	2.4	21	76	3	57	64	14	20	2	1.39
33751435--33751738	17	16.8	18	72	13	198	32	15	10	41	1.82
33751451--33751696	36	6.8	36	74	13	166	32	15	9	42	1.80
33751462--33751504	20	2.1	21	86	4	61	46	11	9	32	1.72
33751435--33751627	89	2.2	88	82	10	223	32	15	9	42	1.80
33751531--33751738	36	5.8	35	78	11	154	32	15	10	41	1.82
33751517--33751631	55	2.1	55	80	3	142	34	15	8	40	1.78
33751437--33751699	74	3.6	74	78	12	251	32	15	9	41	1.80
33751580--33751739	37	4.4	35	74	9	135	32	16	11	40	1.84
33751458--33751739	74	3.9	74	77	12	230	33	15	10	40	1.81
33751602--33751911	38	8.1	38	70	18	173	34	13	9	42	1.77
33757484--33757564	41	2.0	40	82	7	99	37	7	4	50	1.52
33759630--33759659	15	1.9	16	93	6	53	46	0	0	53	1.00
33766426--33766590	43	3.9	43	79	7	176	30	27	15	26	1.96
33767905--33767947	18	2.4	18	85	11	54	4	23	0	72	1.04
33768606--33768731	64	2.0	64	91	0	207	31	23	25	19	1.98
33771187--33771213	11	2.5	11	100	0	54	66	33	0	0	0.92
33772036--33772103	32	2.1	32	81	10	77	25	35	23	16	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33778841--33778886	8	6.1	8	75	14	53	23	2	10	63	1.38
33779731--33779850	42	2.9	42	87	5	197	50	5	3	41	1.41
33782302--33782356	9	6.1	9	89	0	65	36	12	36	14	1.84
33782398--33782462	22	3.2	22	70	20	77	30	3	16	49	1.61
33782409--33782470	19	3.2	19	70	20	65	35	1	12	50	1.51
33782392--33782485	39	2.4	39	100	0	188	36	2	17	44	1.60
33782392--33782504	39	2.9	38	89	5	120	36	1	16	45	1.58
33785113--33785226	55	2.1	55	86	3	158	26	27	28	17	1.98
33791907--33792140	25	9.5	25	74	7	174	35	18	27	18	1.94
33794483--33794547	31	2.1	31	85	0	85	38	15	6	40	1.72

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