genome.fa.s60.2.7.7.80.10.50.1000.13.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: Scaffold60
Parameters: 2 7 7 80 10 50 1000
Length:  3815296

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   

This is table  13  of  21  ( 2419 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)
1932113--1932186	21	3.5	20	78	12	78	47	2	2	47	1.30
1932128--1932185	11	5.5	11	72	15	59	48	3	1	46	1.29
1932240--1932361	34	3.7	34	88	5	162	39	2	6	51	1.41
1932273--1932428	11	14.6	11	70	20	91	37	3	7	51	1.47
1932317--1932428	21	5.4	21	78	6	104	35	3	8	52	1.48
1932313--1932373	12	5.6	12	69	20	53	36	1	9	52	1.45
1932491--1932538	21	2.2	23	88	7	73	31	4	4	60	1.35
1934942--1934984	21	2.0	21	86	4	59	51	4	2	41	1.35
1939089--1939124	2	18.0	2	100	0	72	50	0	0	50	1.00
1944383--1944407	2	12.5	2	100	0	50	48	0	0	52	1.00
1947486--1947516	2	16.0	2	93	6	55	51	0	0	48	1.00
1948082--1948118	2	18.5	2	100	0	74	51	0	0	48	1.00
1949351--1949426	37	2.1	37	85	9	104	46	1	0	52	1.08
1961994--1962021	14	2.0	14	100	0	56	14	21	14	50	1.78
1966084--1966137	28	1.9	28	88	7	83	55	0	0	44	0.99
1966084--1966137	27	1.9	29	88	7	85	55	0	0	44	0.99
1966082--1966176	27	3.5	25	78	13	82	55	0	1	43	1.06
1966106--1966180	38	2.0	38	82	15	93	54	0	2	42	1.14
1967034--1967058	2	12.5	2	100	0	50	52	0	0	48	1.00
1967917--1967947	1	31.0	1	93	0	53	3	0	96	0	0.21
1968662--1968713	25	2.2	23	83	13	61	28	3	5	61	1.37
1969841--1969888	19	2.6	18	83	6	60	47	0	4	47	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1971747--1971779	2	16.5	2	100	0	66	48	0	51	0	1.00
1975151--1975179	2	14.5	2	100	0	58	51	0	0	48	1.00
1990032--1990095	22	3.0	21	75	8	58	43	0	1	54	1.09
1998841--1998920	27	3.1	26	76	16	69	45	0	1	53	1.08
1999144--1999186	23	1.9	22	86	13	61	58	0	0	41	0.98
1999295--1999363	22	3.1	22	75	17	63	63	0	0	36	0.94
1999327--1999396	15	4.2	16	70	18	54	62	0	1	35	1.04
1999281--1999403	30	4.2	29	73	13	99	60	0	0	39	1.03
1999281--1999396	53	2.3	53	82	8	134	62	0	0	37	1.02
1999386--1999424	19	2.1	19	90	9	62	43	0	0	56	0.99
1999386--1999429	18	2.4	18	88	7	63	47	0	0	52	1.00
1999392--1999435	19	2.4	18	85	11	54	47	0	0	52	1.00
1999448--1999499	26	2.0	27	84	3	70	61	1	0	36	1.07
1999485--1999521	12	3.2	12	78	21	51	48	0	0	51	1.00
1999503--1999540	16	2.3	16	82	17	51	52	0	0	47	1.00
2011126--2011160	15	2.3	15	90	0	52	51	0	42	5	1.25
2015077--2015126	20	2.4	22	77	12	61	44	0	4	52	1.20
2015625--2015649	11	2.3	11	100	0	50	60	0	0	40	0.97
2017246--2017299	2	27.5	2	96	3	101	50	0	0	50	1.00
2018722--2018756	2	17.5	2	100	0	70	48	0	51	0	1.00
2019585--2019614	2	15.0	2	100	0	60	50	0	0	50	1.00
2021463--2021491	2	14.5	2	100	0	58	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2025589--2025631	22	2.0	22	90	4	70	60	0	0	39	0.97
2028289--2028347	24	2.5	24	78	15	68	52	0	0	47	1.00
2028954--2029022	28	2.4	29	78	7	79	44	1	0	53	1.09
2028973--2029021	21	2.3	22	82	7	64	46	2	0	51	1.12
2029472--2029531	16	3.9	16	82	4	70	68	0	0	31	0.90
2029485--2029538	10	5.4	10	77	16	58	68	0	0	31	0.90
2029472--2029523	26	2.0	27	85	11	72	69	0	0	30	0.89
2029484--2029538	22	2.8	19	71	26	51	67	0	0	32	0.91
2029484--2029584	31	3.4	31	80	9	95	60	1	0	37	1.08
2029893--2029951	6	9.7	6	73	23	52	33	1	1	62	1.15
2031787--2031824	19	2.1	18	90	5	58	26	0	0	73	0.83
2031776--2031817	13	2.9	15	86	10	52	30	0	0	69	0.89
2031796--2031838	13	3.2	13	86	6	50	32	0	0	67	0.91
2034630--2034670	7	5.7	7	91	2	64	80	0	0	19	0.71
2034688--2034729	19	2.2	20	87	8	61	45	0	0	54	0.99
2034884--2034930	8	5.5	8	82	12	58	29	0	0	70	0.88
2036819--2036875	16	3.5	16	76	11	53	68	1	1	28	1.09
2036825--2036879	17	3.3	17	78	19	62	67	0	1	30	1.01
2038972--2039006	2	17.5	2	100	0	70	51	0	0	48	1.00
2042471--2042606	65	2.0	66	86	8	186	36	16	8	38	1.80
2042634--2042666	2	16.5	2	100	0	66	51	0	0	48	1.00
2043159--2043208	8	6.2	8	76	17	50	50	2	2	46	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2043159--2043210	17	3.1	17	81	10	63	50	1	1	46	1.23
2043103--2043241	72	1.9	73	80	1	163	46	5	5	42	1.51
2043911--2043944	2	17.0	2	100	0	68	50	0	0	50	1.00
2045538--2045566	2	14.5	2	100	0	58	51	0	0	48	1.00
2046716--2046751	2	18.0	2	100	0	72	50	0	0	50	1.00
2048863--2048895	3	11.0	3	100	0	66	66	0	0	33	0.92
2051837--2052016	6	29.3	6	69	18	86	46	2	3	47	1.35
2051837--2051903	26	2.6	25	82	17	93	47	4	4	43	1.43
2051899--2051955	11	5.1	10	76	19	51	45	1	1	50	1.22
2051895--2051955	25	2.7	23	81	18	74	45	1	1	50	1.21
2051885--2051968	42	2.0	43	83	6	109	44	3	2	50	1.32
2051978--2052041	20	2.9	21	79	11	67	53	3	0	43	1.16
2052092--2052148	22	2.6	23	83	8	75	49	8	3	38	1.51
2052464--2052488	2	12.5	2	100	0	50	48	0	0	52	1.00
2056012--2056188	87	2.0	87	94	0	309	36	20	12	30	1.89
2063226--2063255	15	2.0	15	93	0	51	16	0	63	20	1.31
2063969--2064041	20	3.7	20	68	22	55	43	0	0	56	0.99
2063981--2064055	32	2.3	35	86	9	104	42	1	0	56	1.08
2063958--2064060	44	2.4	44	80	15	108	39	0	0	59	1.04
2064229--2064416	93	2.0	94	90	2	297	41	7	14	36	1.75
2064457--2064597	23	6.1	23	70	25	93	34	2	0	61	1.16
2064540--2064617	40	2.0	40	86	0	111	28	8	1	61	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2064479--2064599	16	7.7	16	69	26	73	33	3	0	62	1.17
2064775--2064832	25	2.4	25	80	16	68	51	0	0	48	1.00
2064775--2064823	24	2.0	25	84	15	66	53	0	0	46	1.00
2065030--2065060	2	15.5	2	100	0	62	48	0	0	51	1.00
2065789--2065847	23	2.5	22	78	10	64	25	0	5	69	1.09
2065783--2065831	19	2.6	20	78	15	52	24	0	4	71	1.03
2066734--2066793	26	2.3	27	80	11	72	46	0	3	50	1.18
2066927--2066980	13	4.2	13	86	11	67	24	0	1	74	0.92
2066928--2066984	7	8.4	7	80	7	64	26	0	1	71	0.95
2066944--2067001	19	2.9	19	87	5	71	32	0	1	65	1.03
2066934--2067004	26	2.7	25	80	10	70	29	0	2	67	1.05
2067074--2067124	6	8.0	6	77	18	50	31	0	1	66	1.03
2067074--2067122	13	3.7	13	81	5	53	28	0	2	69	1.00
2067339--2067374	18	2.0	18	89	10	56	25	0	2	72	0.98
2077657--2077724	27	2.5	28	87	2	93	47	0	2	50	1.16
2077841--2077894	27	2.0	28	85	10	76	48	1	0	50	1.11
2077959--2077997	17	2.2	17	86	4	51	53	0	0	46	1.00
2082033--2082064	3	10.7	3	100	0	64	68	0	0	31	0.90
2082906--2082951	3	15.7	3	90	4	76	63	0	2	34	1.07
2083008--2083052	21	2.2	21	88	4	65	53	22	4	20	1.63
2083982--2084058	16	4.6	16	74	16	57	37	1	3	57	1.26
2083977--2084063	37	2.4	36	88	3	120	36	1	4	57	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2083993--2084063	21	3.3	21	84	2	88	39	0	2	57	1.13
2084026--2084068	21	2.0	21	95	0	77	41	2	0	55	1.12
2084030--2084107	21	3.6	21	76	11	68	48	2	2	46	1.29
2084174--2084230	28	2.0	29	90	10	91	50	1	0	47	1.11
2084174--2084250	29	2.7	29	82	13	88	48	3	0	48	1.20
2093840--2093890	19	2.8	18	74	11	50	49	0	0	50	1.00
2103780--2103815	17	2.1	17	89	0	54	33	0	0	66	0.92
2103802--2103874	24	3.0	25	82	11	80	43	1	0	54	1.08
2106417--2106486	28	2.5	28	81	6	72	45	0	1	52	1.09
2106709--2106760	28	1.9	26	84	7	68	53	1	0	44	1.11

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21