genome.fa.s2.2.7.7.80.10.50.1000.11.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  11  of  38  ( 4457 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)
1698329--1698373	21	2.1	21	84	8	56	53	4	20	22	1.63
1702222--1702299	20	3.6	21	74	15	70	26	14	15	43	1.85
1702288--1702325	13	2.9	13	96	0	67	34	18	15	31	1.92
1704782--1704855	20	3.7	20	81	3	103	35	13	20	31	1.91
1704800--1704875	21	3.7	21	82	3	109	40	11	18	28	1.86
1704782--1704875	41	2.3	41	100	0	188	38	12	19	29	1.89
1709952--1710119	79	2.1	79	83	2	203	29	16	29	24	1.96
1710076--1710152	28	2.8	28	86	7	95	22	18	35	24	1.96
1710135--1710310	52	3.4	52	82	7	221	31	11	26	30	1.92
1712796--1712854	13	5.0	13	70	29	60	42	15	15	27	1.86
1712775--1712874	33	3.0	33	94	0	164	44	16	15	25	1.85
1712808--1712874	20	3.7	20	74	25	85	46	14	14	23	1.83
1712894--1712961	19	3.9	18	76	23	83	38	14	11	35	1.83
1712916--1712940	13	1.9	13	100	0	50	32	16	16	36	1.90
1712897--1712959	32	2.0	32	96	0	117	36	15	12	34	1.86
1712997--1713220	21	10.7	21	96	0	405	33	21	14	30	1.93
1713207--1738932	370	69.4	370	95	0	46029	32	20	14	32	1.93
1713207--1738932	739	34.7	740	95	0	46029	32	20	14	32	1.93
1741732--1765541	370	64.4	370	96	1	43204	32	21	14	32	1.93
1741732--1765541	739	32.2	740	96	1	43204	32	21	14	32	1.93
1766079--1768809	59	46.4	59	89	4	3765	25	20	28	25	1.99
1777007--1777185	79	2.3	79	84	1	225	29	16	30	24	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1777195--1777581	52	7.4	52	70	13	213	32	12	26	29	1.92
1777282--1777417	51	2.6	52	85	5	177	33	13	24	28	1.94
1777401--1777475	27	2.7	27	85	6	98	22	17	34	25	1.96
1779998--1780065	19	3.9	18	76	23	83	38	14	11	35	1.83
1780020--1780044	13	1.9	13	100	0	50	32	16	16	36	1.90
1780001--1780063	32	2.0	32	96	0	117	36	15	12	34	1.86
1780101--1780173	20	3.8	18	77	12	74	34	15	15	35	1.88
1781639--1781664	13	2.0	13	100	0	52	30	15	15	38	1.88
1781649--1781704	19	2.9	19	91	2	94	30	19	14	35	1.91
1783593--1783709	51	2.3	51	84	0	162	30	11	24	32	1.92
1783394--1783655	79	3.3	78	74	5	251	32	12	25	29	1.93
1786156--1786181	13	2.0	13	100	0	52	38	15	15	30	1.88
1786236--1786285	21	2.5	21	90	6	77	32	16	10	42	1.81
1786710--1786778	31	2.3	31	94	2	122	30	18	18	31	1.96
1790704--1790739	17	2.1	17	94	0	63	52	0	8	38	1.32
1805429--1805453	13	1.9	13	100	0	50	36	16	16	32	1.90
1805514--1805541	13	2.2	13	100	0	56	39	14	14	32	1.86
1805496--1805560	33	2.0	33	90	3	105	40	12	10	36	1.78
1809963--1810156	79	2.5	79	87	1	273	32	14	25	27	1.95
1810089--1810208	51	2.3	51	88	1	177	29	13	28	29	1.94
1810011--1810267	130	2.0	130	87	0	370	31	13	26	27	1.94
1814824--1815349	168	3.2	167	86	4	699	51	9	11	27	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1816664--1816941	150	1.9	149	86	2	396	31	8	6	53	1.58
1816807--1817179	165	2.3	165	80	6	420	30	10	7	50	1.66
1817371--1817404	14	2.4	14	90	9	52	35	2	0	61	1.11
1818748--1818849	50	2.0	51	90	1	161	28	6	12	51	1.65
1819432--1819728	156	1.9	154	79	7	332	23	17	20	39	1.92
1819450--1820018	155	3.7	157	74	8	405	24	17	19	38	1.93
1822930--1823029	51	2.0	51	85	0	137	46	10	16	28	1.78
1827295--1827354	10	5.8	10	72	20	52	15	3	1	80	0.93
1832001--1832033	11	2.8	12	90	9	59	0	18	0	81	0.68
1833079--1833254	42	4.2	41	73	7	131	40	18	24	15	1.90
1833106--1833192	41	2.1	42	82	2	104	41	21	22	13	1.89
1833255--1833393	40	3.5	40	79	5	138	37	20	24	17	1.94
1833253--1833596	42	8.3	42	72	12	187	42	19	22	15	1.88
1833369--1833597	84	2.7	83	79	4	244	46	19	20	13	1.84
1833939--1834031	42	2.2	42	82	0	114	39	18	26	15	1.90
1837994--1838734	370	2.0	370	99	0	1473	44	16	16	21	1.86
1843103--1843142	9	4.1	9	82	17	53	82	0	15	2	0.77
1843142--1843236	7	12.7	7	67	20	50	34	0	1	64	1.01
1843142--1843205	8	8.6	8	69	20	50	34	0	1	64	1.03
1843142--1843235	13	6.7	15	70	25	64	35	0	1	63	1.01
1844246--1844292	16	2.7	17	77	12	51	31	10	2	55	1.46
1844267--1844316	25	1.9	27	88	8	77	28	6	2	64	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1844704--1844784	37	2.2	38	84	6	103	30	2	1	65	1.13
1846261--1846523	79	3.3	78	83	3	314	32	14	25	27	1.94
1846477--1846551	28	2.7	28	89	4	107	26	18	32	22	1.97
1846587--1846658	28	2.5	30	89	8	107	27	20	27	23	1.99
1846418--1846700	107	2.6	108	83	2	365	31	13	28	26	1.94
1849769--1849886	52	2.3	52	89	2	175	28	16	19	34	1.94
1849873--1849899	13	2.1	13	100	0	54	29	14	14	40	1.86
1849959--1850015	13	3.9	13	72	24	51	33	17	12	36	1.87
1849936--1850035	32	3.1	32	91	2	148	37	16	10	37	1.82
1850424--1850746	49	6.8	48	84	6	362	30	19	25	23	1.98
1850585--1850653	22	3.2	22	63	19	54	31	18	27	21	1.97
1850763--1851059	28	10.4	28	83	5	337	18	17	31	32	1.94
1850763--1851068	58	5.3	58	85	4	347	19	16	31	32	1.94
1850804--1851067	86	3.0	86	90	2	395	20	17	31	30	1.96
1852512--1852603	1	92.0	1	75	0	76	1	1	10	86	0.67
1852500--1852600	7	13.7	7	76	19	91	0	0	12	85	0.71
1852509--1852602	23	4.1	23	82	10	104	1	1	11	86	0.69
1852500--1852584	31	2.8	31	89	5	129	0	1	11	87	0.61
1852500--1852605	38	2.8	37	86	12	130	0	0	13	84	0.71
1852512--1852584	24	3.2	23	88	5	112	0	1	9	89	0.56
1858621--1858671	18	2.7	19	87	6	68	27	11	15	45	1.81
1861234--1861271	13	2.9	13	96	0	67	31	15	18	34	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1867118--1867176	32	1.9	30	83	13	75	59	10	10	20	1.58
1867457--1867482	13	2.0	13	100	0	52	30	15	15	38	1.88
1869671--1869738	19	3.9	18	76	23	83	35	13	14	36	1.85
1869692--1869716	13	1.9	13	100	0	50	36	16	16	32	1.90
1869673--1869735	32	2.0	32	96	0	117	34	14	15	34	1.88
1869758--1869811	20	2.8	19	80	5	72	24	14	16	44	1.85
1872246--1872321	27	2.8	28	89	2	109	23	34	21	21	1.97
1872137--1872526	51	7.4	51	69	14	204	29	25	12	32	1.92
1872304--1872526	103	2.1	105	80	3	236	29	24	12	33	1.92
1874517--1874555	13	3.0	13	92	0	69	35	17	15	30	1.91
1874717--1874850	53	2.5	53	91	1	223	28	18	17	35	1.93
1874820--1874890	20	3.5	20	77	11	74	29	12	16	40	1.86
1880555--1880787	52	4.5	52	94	0	385	27	15	19	36	1.92
1880796--1880822	13	2.1	13	100	0	54	29	14	14	40	1.86
1880864--1880961	19	5.8	18	69	28	81	36	17	13	32	1.88
1880859--1880959	32	3.1	32	94	1	175	35	17	12	33	1.88
1880883--1880939	13	3.9	13	76	24	60	33	17	15	33	1.92
1884216--1884415	41	4.9	40	69	17	110	43	12	25	19	1.85
1884469--1884770	61	4.9	61	87	2	383	30	20	24	23	1.98
1884957--1885023	33	2.0	33	88	0	98	34	11	13	40	1.81
1884977--1885001	13	1.9	13	100	0	50	36	16	16	32	1.90
1885064--1885088	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1885097--1885224	52	2.5	52	94	3	224	33	17	17	30	1.94
1889357--1889414	1	58.0	1	75	0	53	3	0	8	87	0.64
1889336--1889395	28	2.1	28	81	6	68	1	8	5	85	0.81
1889357--1889414	9	6.3	9	81	15	66	3	0	8	87	0.64
1889357--1889414	18	3.2	18	87	7	82	3	0	8	87	0.64
1898943--1899188	79	3.1	77	82	6	280	32	14	24	27	1.95
1899146--1899218	28	2.6	27	82	4	101	27	16	31	24	1.96
1899256--1899324	28	2.5	28	83	11	88	27	17	30	24	1.97
1899067--1899337	107	2.5	107	82	5	334	30	14	27	27	1.95
1899314--1899476	51	3.2	51	79	7	179	35	10	22	31	1.88

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