genome.fa.s6.2.7.7.80.10.50.1000.161.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  161  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)
48262520--48262562	2	22.0	2	95	4	79	51	0	0	48	1.00
48266778--48266857	10	7.6	10	70	14	54	55	1	3	40	1.26
48270169--48270293	52	2.4	52	81	2	135	23	20	26	30	1.98
48274317--48274359	11	3.9	11	78	0	50	16	11	11	60	1.59
48285031--48285056	6	4.3	6	100	0	52	15	15	38	30	1.88
48285368--48285406	15	2.4	16	87	8	53	35	0	0	64	0.94
48285789--48285824	19	1.9	19	94	5	65	69	0	2	27	1.02
48290448--48290487	20	2.0	20	100	0	80	45	5	15	35	1.68
48291112--48291171	27	2.2	27	84	0	75	21	13	18	46	1.83
48291124--48291175	27	1.9	27	96	0	95	25	13	17	44	1.85
48294404--48294433	3	10.0	3	100	0	60	0	33	0	66	0.92
48296965--48297000	2	18.0	2	100	0	72	50	0	0	50	1.00
48302153--48302184	12	2.5	13	95	5	57	59	0	0	40	0.97
48303371--48303395	12	2.1	12	100	0	50	16	8	8	68	1.38
48308237--48308275	19	2.1	19	85	9	53	56	10	5	28	1.54
48327866--48327902	13	2.9	13	96	4	67	24	21	8	45	1.78
48343554--48343675	59	2.1	58	92	1	199	51	13	17	17	1.76
48344143--48344176	3	11.3	3	100	0	68	35	0	0	64	0.94
48346931--48346979	16	3.1	16	80	11	57	34	2	22	40	1.66
48349473--48349512	21	1.9	21	85	10	55	60	2	2	35	1.24
48351450--48351501	21	2.5	21	96	0	95	17	25	15	42	1.88
48351454--48351508	21	2.6	21	91	0	74	18	23	14	43	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48353433--48353476	2	22.0	2	100	0	88	50	0	0	50	1.00
48353633--48353677	2	22.5	2	90	0	72	51	44	0	4	1.21
48370088--48370144	9	6.2	9	74	10	53	14	5	1	78	0.99
48370208--48370239	16	2.0	16	93	0	55	71	0	9	18	1.12
48370208--48370246	15	2.5	16	87	4	53	71	0	10	17	1.12
48370294--48370343	24	2.1	24	81	7	57	76	0	10	14	1.03
48371918--48371950	15	2.2	15	94	0	57	69	6	24	0	1.10
48384117--48384142	2	13.0	2	100	0	52	50	0	0	50	1.00
48384261--48384291	11	2.8	11	95	0	53	32	0	25	41	1.56
48403363--48403424	3	20.7	3	96	0	115	64	0	1	33	1.03
48404836--48404869	18	1.9	18	88	5	52	29	0	5	64	1.17
48407447--48407471	12	2.1	12	100	0	50	32	12	32	24	1.91
48408453--48408504	21	2.5	21	81	6	61	30	0	1	67	1.02
48438217--48438275	29	2.0	30	93	3	102	35	22	16	25	1.95
48441519--48441546	2	14.0	2	100	0	56	50	0	0	50	1.00
48443719--48443794	38	2.0	38	100	0	152	42	13	21	23	1.88
48450507--48450563	26	2.2	26	87	0	78	21	14	8	56	1.65
48456359--48456390	14	2.2	15	94	5	57	56	6	12	25	1.59
48462325--48462385	17	3.5	17	77	8	70	36	1	1	60	1.16
48464194--48464283	31	2.9	32	85	5	121	36	3	11	48	1.55
48465500--48465531	14	2.1	16	88	11	50	68	0	0	31	0.90
48465500--48465532	15	2.1	16	88	5	50	69	0	0	30	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48466013--48466073	20	2.9	21	81	16	65	4	44	0	50	1.23
48476099--48476127	2	14.5	2	100	0	58	48	0	0	51	1.00
48481967--48481991	2	12.5	2	100	0	50	48	0	0	52	1.00
48493721--48494292	279	2.1	279	98	0	1117	32	18	10	37	1.86
48508675--48508754	29	2.8	28	73	17	74	63	3	3	28	1.29
48509204--48509248	22	2.0	22	87	8	65	33	2	0	64	1.06
48515824--48515880	28	2.1	27	86	3	78	49	7	3	40	1.47
48515877--48515916	17	2.4	17	87	8	55	45	7	15	32	1.74
48515934--48515990	16	3.6	16	90	0	87	45	3	3	47	1.37
48515964--48516025	22	2.7	23	90	5	90	48	1	1	48	1.21
48517282--48517392	57	1.9	57	89	7	172	29	18	27	25	1.98
48517803--48517959	20	7.8	20	66	19	76	19	20	10	49	1.78
48518020--48518057	20	1.9	20	88	0	58	23	21	7	47	1.77
48518052--48518107	20	2.8	19	78	10	51	26	14	12	46	1.80
48518417--48518463	22	2.1	23	84	4	60	14	12	8	63	1.50
48529568--48529634	27	2.5	27	95	0	116	31	23	31	13	1.93
48529704--48529747	21	2.1	21	95	0	79	29	0	11	59	1.32
48530365--48530455	8	10.4	8	71	17	56	50	14	0	35	1.43
48530412--48530560	19	8.1	19	65	24	70	55	13	0	31	1.39
48530391--48530487	27	3.8	26	86	9	139	55	13	0	30	1.38
48530556--48530622	27	2.5	27	95	0	116	11	31	25	31	1.92
48533663--48534140	117	4.1	117	90	3	734	26	27	14	30	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48535454--48535490	11	3.3	12	85	14	53	54	0	5	40	1.24
48535461--48535559	10	9.9	10	69	18	55	57	0	3	39	1.14
48535465--48535649	38	5.0	39	79	15	198	62	0	3	34	1.11
48535465--48535605	68	2.1	68	93	5	241	62	0	2	34	1.10
48544563--48544618	19	3.1	18	78	12	60	60	0	3	35	1.14
48544563--48544614	20	2.7	19	80	16	63	61	0	3	34	1.14
48547652--48547711	23	2.4	24	83	13	77	40	10	1	48	1.47
48547668--48547711	23	1.9	23	95	0	79	34	6	2	56	1.38
48547780--48547857	27	2.9	27	86	0	111	30	21	29	17	1.97
48547933--48548001	19	3.7	18	79	12	86	36	10	1	52	1.44
48547933--48548007	18	4.1	18	78	13	82	36	10	1	52	1.45
48547937--48548007	37	1.9	37	97	0	133	38	11	1	49	1.48
48548203--48548264	19	3.3	19	81	4	90	40	11	0	48	1.39
48548211--48548270	18	3.3	18	81	4	84	38	11	0	50	1.39
48548211--48548281	18	3.9	17	77	14	70	39	11	0	49	1.39
48548203--48548281	37	2.1	37	92	0	131	40	11	0	48	1.39
48548278--48548352	18	4.1	18	76	6	71	53	0	8	38	1.31
48548278--48548349	37	2.0	36	91	2	117	51	0	8	40	1.32
48548284--48548352	19	3.7	19	80	5	88	53	0	8	37	1.32
48548578--48548647	19	3.7	19	78	3	88	55	1	7	35	1.36
48548233--48548826	295	2.0	292	93	3	1007	42	10	12	33	1.77
48549162--48549231	19	3.7	19	78	3	88	55	1	7	35	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48549304--48549382	27	2.9	27	94	0	131	15	31	22	30	1.95
48549471--48549520	26	2.0	25	88	11	75	54	0	10	36	1.34
48549457--48549520	28	2.4	28	86	5	87	50	1	9	39	1.44
48552567--48552615	25	2.0	25	84	8	64	36	32	4	26	1.75
48558735--48558763	13	2.2	13	100	0	58	68	0	0	31	0.89
48562082--48562130	2	24.5	2	100	0	98	51	0	0	48	1.00
48563969--48564118	73	2.1	73	100	0	300	28	11	27	32	1.91
48572597--48572665	29	2.3	30	80	12	79	49	14	14	21	1.79
48573199--48573248	21	2.4	21	83	9	59	34	2	18	46	1.60
48588453--48588479	13	2.1	13	100	0	54	22	14	14	48	1.81
48589650--48589690	3	13.7	3	100	0	82	34	34	31	0	1.58
48590826--48590852	2	13.5	2	100	0	54	51	0	0	48	1.00
48595102--48595152	22	2.5	21	84	12	70	58	0	1	39	1.09
48598381--48598411	16	1.9	16	93	0	53	54	3	3	38	1.32
48599369--48599431	13	4.8	13	88	0	99	31	6	25	36	1.81
48599838--48599876	16	2.5	16	95	4	71	43	15	10	30	1.80
48603241--48603304	17	3.7	17	74	16	60	67	1	1	29	1.09
48603376--48603434	29	2.0	30	86	3	84	57	3	0	38	1.15
48604794--48604915	23	5.3	23	88	0	190	21	22	27	29	1.99
48604796--48604915	46	2.6	46	95	0	213	20	22	27	29	1.99
48606670--48606725	10	5.9	9	82	12	60	32	3	1	62	1.23
48610870--48610916	24	2.0	24	84	12	62	48	4	4	42	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48612868--48613049	72	2.5	73	95	0	321	40	16	11	31	1.84
48614939--48614963	3	8.3	3	100	0	50	68	0	32	0	0.90
48631895--48632184	144	2.0	144	97	0	553	46	10	14	28	1.77
48633007--48633031	13	1.9	13	100	0	50	64	4	0	32	1.12
48633010--48633053	22	2.1	20	83	8	52	68	6	2	22	1.25
48645908--48645933	11	2.4	11	100	0	52	30	0	7	61	1.24
48646372--48646421	26	1.9	26	84	8	66	50	4	2	44	1.32
48646795--48646824	15	2.1	14	93	6	51	50	0	0	50	1.00
48669192--48669256	31	2.2	29	81	15	71	53	4	3	38	1.37
48673929--48673960	16	1.9	17	93	6	57	81	0	12	6	0.87

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