genome.fa.s12.2.7.7.80.10.50.1000.6.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   

This is table  6  of  120  ( 14336 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)
1773872--1773926	28	2.0	28	85	7	76	49	0	1	49	1.11
1774055--1774111	20	2.8	21	81	7	64	61	1	1	35	1.17
1775058--1775119	27	2.2	28	91	2	99	56	0	3	40	1.15
1777456--1777526	31	2.3	31	82	4	81	12	11	4	71	1.27
1778318--1778349	15	2.1	15	94	0	55	46	3	12	37	1.57
1778507--1778531	7	3.6	7	100	0	50	48	0	0	52	1.00
1779215--1779247	16	2.1	16	88	11	50	75	12	9	3	1.14
1781076--1781118	19	2.3	19	88	4	61	67	0	6	25	1.15
1787188--1787231	23	1.9	23	95	0	79	50	4	0	45	1.22
1787189--1787238	23	2.2	23	88	0	73	48	8	0	44	1.32
1788250--1788283	13	2.6	13	80	0	50	41	0	5	52	1.25
1798060--1798103	21	2.1	21	91	8	72	43	4	0	52	1.22
1798314--1798338	2	12.5	2	100	0	50	52	0	0	48	1.00
1802863--1802896	5	7.2	5	93	6	54	20	0	0	79	0.73
1802866--1802899	13	2.6	14	90	9	54	17	0	0	82	0.67
1810247--1810304	23	2.6	21	79	17	55	43	3	5	48	1.42
1810847--1810889	22	2.0	22	90	0	68	51	0	0	48	1.00
1815148--1815185	15	2.5	15	83	8	51	39	2	0	57	1.12
1817293--1817372	21	4.2	19	73	17	60	72	2	1	23	1.04
1817293--1817373	18	4.3	18	75	17	76	71	2	1	24	1.05
1817583--1817634	26	2.0	26	84	0	68	42	1	3	51	1.31
1824408--1824444	19	1.9	19	89	10	58	45	10	0	43	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1825868--1825902	16	2.2	16	90	10	54	60	2	0	37	1.12
1826244--1826278	18	2.0	18	88	5	54	62	2	0	34	1.10
1826386--1826434	18	2.7	18	84	6	64	63	2	4	30	1.24
1826369--1826425	21	2.7	21	78	13	71	63	5	3	28	1.33
1827964--1828547	89	6.6	89	94	2	969	26	23	20	30	1.98
1827964--1828547	266	2.2	267	92	2	969	26	23	20	30	1.98
1831437--1831568	16	8.4	16	72	9	92	34	2	31	31	1.70
1831425--1831615	78	2.4	78	94	0	328	31	3	31	33	1.74
1831550--1831638	44	2.0	46	88	4	137	29	4	29	37	1.77
1831550--1831660	46	2.6	44	77	13	115	32	4	27	35	1.77
1831802--1831835	18	1.9	17	88	5	50	55	2	0	41	1.15
1831828--1831857	15	1.9	16	93	6	53	50	6	0	43	1.28
1836598--1836666	16	4.3	16	94	0	120	37	4	34	23	1.75
1836648--1836740	44	2.1	46	93	4	163	27	4	31	36	1.76
1836648--1836753	39	2.5	44	85	11	141	29	3	32	34	1.75
1836975--1837044	25	2.7	25	82	10	79	58	1	0	40	1.07
1837017--1837049	16	2.1	16	94	5	59	66	0	0	33	0.92
1836974--1837050	15	5.5	13	77	17	59	59	1	0	38	1.06
1836989--1837051	25	2.3	29	78	13	71	60	0	0	39	0.97
1836880--1837113	115	2.0	118	90	5	379	51	4	1	42	1.31
1838809--1838839	4	7.8	4	92	0	53	25	3	22	48	1.66
1849116--1849166	27	1.9	26	84	4	66	27	0	3	68	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1849848--1849880	13	2.3	15	90	10	52	33	0	0	66	0.92
1850954--1850995	18	2.4	18	92	4	68	61	0	2	35	1.09
1851035--1851068	17	2.0	17	88	11	52	47	0	0	52	1.00
1851964--1852125	46	3.6	46	93	4	269	27	24	14	33	1.95
1858250--1858279	2	15.0	2	100	0	60	50	0	0	50	1.00
1863457--1863894	44	9.8	44	70	13	216	28	22	19	29	1.98
1863647--1863894	131	1.9	131	80	8	290	28	23	21	27	1.99
1863565--1863892	87	3.8	87	74	9	274	28	21	20	29	1.98
1877152--1877200	22	2.1	24	82	14	59	55	2	8	34	1.41
1880430--1880455	12	2.2	12	100	0	52	23	30	15	30	1.95
1883057--1883126	31	2.3	31	97	0	131	38	15	10	35	1.81
1885289--1885391	37	2.7	39	77	14	101	39	2	3	53	1.34
1885370--1885486	62	1.9	59	87	5	171	40	3	3	52	1.35
1887765--1887818	20	2.7	20	82	11	65	62	0	0	37	0.95
1889346--1889425	33	2.4	33	93	0	133	20	22	17	40	1.92
1893634--1893677	17	2.6	17	89	7	63	63	0	4	31	1.14
1895476--1895586	24	4.7	24	81	8	122	30	2	9	56	1.46
1895520--1895598	24	3.3	24	84	7	72	31	3	7	56	1.45
1899292--1899434	50	3.1	43	89	8	187	31	13	22	32	1.93
1899347--1899460	50	2.3	50	89	3	158	37	12	21	28	1.90
1902093--1902136	16	2.7	16	89	3	61	68	11	20	0	1.20
1902892--1902986	11	8.7	11	66	11	52	42	2	0	55	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1902883--1902950	32	2.1	32	97	0	127	36	2	0	60	1.12
1902892--1903019	44	3.0	43	84	10	156	39	2	0	57	1.11
1902935--1903019	32	2.7	32	87	3	109	38	2	0	58	1.11
1903304--1903338	3	11.7	3	100	0	70	34	0	0	65	0.93
1903390--1903467	29	2.7	30	82	5	81	50	0	15	34	1.45
1906603--1906730	39	3.3	39	97	0	238	14	34	14	37	1.86
1913612--1913731	33	3.7	33	87	6	183	17	25	14	42	1.87
1913617--1913711	30	3.1	30	90	4	145	13	28	13	44	1.82
1921911--1921963	25	2.1	25	85	0	70	52	1	1	43	1.23
1925419--1925467	19	2.6	17	79	17	53	51	4	2	42	1.32
1926576--1926610	2	17.5	2	100	0	70	51	0	0	48	1.00
1927704--1927752	24	2.1	23	84	3	62	30	14	16	38	1.88
1929333--1929373	21	2.0	21	95	0	73	26	14	39	19	1.90
1929267--1929410	78	1.8	78	95	0	261	23	15	41	19	1.89
1931135--1931332	99	2.0	98	96	1	360	28	12	13	45	1.80
1948335--1948383	2	24.5	2	100	0	98	51	0	0	48	1.00
1950210--1950272	17	3.6	17	80	16	76	49	12	12	25	1.76
1950210--1950278	18	3.9	18	77	7	70	47	11	11	28	1.75
1950787--1950828	10	4.3	10	82	11	52	0	19	0	80	0.70
1950869--1950927	23	2.6	23	91	0	100	3	25	44	27	1.70
1951041--1951112	21	3.3	21	90	5	108	5	18	50	26	1.68
1951527--1951673	30	5.0	29	75	8	109	40	4	19	36	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1951541--1951653	59	1.9	59	81	3	138	43	3	15	37	1.65
1951548--1951635	29	3.0	30	75	12	92	39	1	19	39	1.59
1951670--1951712	8	4.9	8	81	18	50	18	0	2	79	0.85
1951664--1951712	17	2.7	19	78	15	68	24	0	2	73	0.94
1951891--1952045	75	2.1	75	92	0	256	23	20	27	29	1.98
1952017--1952073	28	2.0	28	100	0	114	31	21	26	21	1.98
1951946--1952148	103	2.0	103	98	0	388	26	21	26	26	1.99
1952049--1952278	75	3.1	74	86	6	329	23	20	26	29	1.99
1951891--1952223	178	1.9	178	89	2	526	23	19	27	29	1.98
1965912--1965974	17	3.6	17	80	16	76	49	12	12	25	1.76
1965912--1965980	18	3.9	18	77	7	70	47	11	11	28	1.75
1965913--1965981	35	2.0	35	85	5	95	46	11	11	30	1.76
1966084--1966126	22	2.0	21	86	8	61	41	9	13	34	1.77
1966141--1966181	17	2.3	19	87	8	59	31	4	4	58	1.40
1967281--1967337	28	2.0	28	100	0	114	31	21	26	21	1.98
1967217--1967412	103	1.9	103	97	0	374	26	19	26	27	1.99
1967313--1967531	75	2.9	74	87	5	316	23	19	27	30	1.98
1968436--1968472	19	2.0	18	89	5	56	24	2	2	70	1.14
1970530--1970599	25	2.9	24	85	10	90	61	0	2	35	1.11
1970512--1970599	24	3.4	26	82	16	96	60	1	2	36	1.17
1970557--1970608	11	4.5	11	83	11	68	55	0	5	38	1.24
1973655--1973703	20	2.7	18	79	14	55	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1973659--1973699	20	2.0	21	90	4	66	58	0	0	41	0.98
1975205--1975281	39	2.0	39	82	5	93	35	18	29	16	1.93
1978836--1978872	16	2.2	17	95	4	67	32	0	0	67	0.91
1986134--1986257	59	2.1	60	85	7	164	24	24	4	46	1.71
1986653--1986677	4	6.2	4	100	0	50	76	0	24	0	0.80
1986778--1986861	29	2.7	31	76	7	73	55	2	19	22	1.54
1986922--1986962	19	2.0	21	86	9	59	36	0	48	14	1.44
1990401--1990521	61	2.0	60	98	1	233	44	13	20	21	1.85
2004970--2005021	26	2.0	26	88	7	79	40	7	13	38	1.73
2015239--2015346	45	2.4	45	75	9	121	41	17	18	22	1.90

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