genome.fa.s4.2.7.7.80.10.50.1000.9.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  9  of  31  ( 3628 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)
2167664--2167703	20	2.1	19	86	13	55	52	0	0	47	1.00
2167673--2167726	25	2.1	26	82	3	65	55	1	0	42	1.10
2168487--2168530	22	2.0	22	86	0	61	47	2	4	45	1.35
2168493--2168539	22	2.2	22	84	3	60	46	4	2	46	1.34
2169659--2169709	27	1.9	26	84	4	66	56	0	0	43	0.99
2169754--2169810	21	2.8	21	76	17	66	50	0	0	49	1.00
2169775--2169865	13	7.1	13	66	26	52	48	1	0	50	1.08
2171247--2171283	2	18.5	2	100	0	74	0	51	0	48	1.00
2180119--2180149	2	15.5	2	100	0	62	48	0	0	51	1.00
2180451--2180475	12	2.1	12	100	0	50	32	0	0	68	0.90
2183640--2183664	13	1.9	13	100	0	50	80	0	12	8	0.92
2187399--2187442	24	1.9	24	86	9	65	56	0	4	38	1.20
2187430--2187510	39	2.1	39	95	0	144	46	1	3	48	1.27
2187617--2187668	23	2.4	22	83	6	61	59	0	0	40	0.97
2187639--2187674	16	2.3	16	85	4	56	58	0	0	41	0.98
2188324--2188431	24	4.4	24	73	16	80	48	0	1	49	1.18
2190406--2190590	34	5.5	34	86	3	248	40	26	7	25	1.81
2195007--2195190	34	5.4	34	86	3	246	40	26	7	26	1.82
2197694--2197741	25	1.9	25	83	8	62	50	2	2	45	1.25
2197858--2197894	2	19.0	2	94	5	67	48	0	0	51	1.00
2206145--2206177	15	2.1	16	88	5	50	39	0	3	57	1.14
2207678--2207703	12	2.2	12	100	0	52	46	7	7	38	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2207674--2207716	14	3.2	14	83	12	63	51	6	6	34	1.56
2207881--2207979	47	2.1	47	88	1	146	35	7	4	53	1.47
2213425--2213451	13	2.1	13	100	0	54	40	22	7	29	1.81
2221923--2221983	16	3.8	16	80	2	59	31	0	8	60	1.26
2222846--2222889	16	2.8	16	76	13	54	20	15	20	43	1.88
2223466--2223496	16	2.0	16	93	6	55	29	0	6	64	1.18
2223584--2223615	14	2.3	15	89	10	50	62	3	0	34	1.11
2223685--2223748	30	2.1	30	82	5	76	37	6	0	56	1.25
2226522--2226556	2	17.5	2	93	0	61	45	0	2	51	1.16
2230694--2230734	2	21.0	2	95	5	75	51	0	0	48	1.00
2239972--2240001	1	30.0	1	93	0	51	0	96	0	3	0.21
2240187--2240251	32	2.0	32	85	5	87	30	3	4	61	1.31
2240205--2240251	16	2.9	16	75	12	51	29	4	4	61	1.34
2242566--2242607	21	2.0	22	85	4	59	28	16	9	45	1.79
2244943--2244998	29	1.9	29	88	0	85	48	0	3	48	1.19
2244986--2245031	11	4.7	10	77	22	53	43	0	2	54	1.12
2245014--2245088	34	2.2	34	87	0	114	40	2	2	54	1.28
2245020--2245085	15	4.0	16	72	18	55	39	3	0	57	1.14
2248885--2248920	10	3.6	10	92	0	63	16	0	2	80	0.83
2249419--2249528	37	2.9	37	72	17	93	53	1	2	41	1.25
2251533--2251580	12	4.1	11	76	12	51	45	2	6	45	1.40
2253840--2253918	11	7.2	11	71	16	56	36	0	2	60	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2253891--2253946	20	3.0	18	76	19	53	28	0	5	66	1.14
2257609--2257643	2	17.5	2	100	0	70	51	0	48	0	1.00
2262517--2262550	18	2.0	18	88	11	54	67	0	0	32	0.91
2262458--2262566	29	3.7	29	72	13	91	55	2	0	41	1.14
2264884--2264914	2	15.5	2	100	0	62	0	48	0	51	1.00
2264914--2264946	2	16.5	2	100	0	66	48	0	0	51	1.00
2265847--2265876	14	2.1	14	100	0	60	53	13	20	13	1.72
2272246--2272283	16	2.4	16	86	8	51	71	2	5	21	1.19
2275359--2275989	212	3.0	211	90	0	983	27	15	17	39	1.90
2282074--2282101	2	14.0	2	100	0	56	50	0	0	50	1.00
2286024--2286105	40	2.0	41	90	4	130	50	8	20	20	1.74
2287007--2287060	12	4.2	13	73	20	51	46	0	0	53	1.00
2288012--2288081	20	3.1	22	76	19	65	57	1	0	41	1.08
2288266--2288290	2	12.5	2	100	0	50	48	0	0	52	1.00
2288269--2288330	12	5.1	12	81	12	58	46	1	8	43	1.42
2288338--2288418	15	5.4	16	69	20	68	49	0	0	50	1.00
2290938--2290975	2	19.0	2	100	0	76	50	0	0	50	1.00
2291400--2291438	20	1.9	21	84	5	53	35	0	7	56	1.28
2293119--2293221	52	2.0	52	90	7	165	29	15	16	38	1.89
2294563--2294605	18	2.6	16	85	7	50	34	2	2	60	1.22
2300347--2300394	14	3.1	14	73	21	51	56	0	0	43	0.99
2300347--2300393	17	2.9	17	76	17	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)
2300352--2300428	41	2.0	40	82	12	97	54	0	0	45	0.99
2300361--2300433	6	11.0	7	75	16	50	54	0	0	45	0.99
2300361--2300438	40	2.0	40	82	10	97	56	0	0	43	0.99
2307950--2307995	24	2.0	23	84	12	60	47	6	2	43	1.41
2308013--2308052	20	2.0	21	86	13	59	60	0	0	40	0.97
2308386--2308441	17	3.4	17	78	7	62	32	0	0	67	0.91
2309042--2309078	2	18.5	2	94	0	65	48	2	0	48	1.15
2309494--2309608	11	10.5	11	69	19	62	33	1	0	63	1.11
2309693--2309733	11	3.6	12	80	9	50	26	0	2	70	0.99
2309908--2309993	36	2.4	37	80	7	97	41	3	4	50	1.40
2310187--2310227	16	2.5	15	85	14	55	53	0	0	46	1.00
2310187--2310234	17	2.9	16	87	9	62	56	0	0	43	0.99
2310250--2310303	26	2.0	27	89	3	83	46	0	0	53	1.00
2320744--2320778	17	2.1	17	100	0	70	22	17	28	31	1.96
2323340--2323390	10	4.7	11	76	18	54	49	0	0	50	1.00
2323373--2323401	14	2.1	14	93	6	51	48	0	0	51	1.00
2323432--2323469	20	1.9	20	94	0	67	60	2	0	36	1.11
2326124--2326408	144	2.0	144	85	0	381	37	12	10	39	1.78
2329305--2329345	21	2.0	21	90	0	64	51	0	0	48	1.00
2336031--2336067	18	2.1	17	95	5	65	29	0	0	70	0.88
2336050--2336132	14	5.6	14	70	20	53	39	1	0	59	1.05
2336051--2336124	14	4.9	15	73	20	57	40	1	0	58	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2336021--2336138	34	3.5	32	71	24	93	36	0	0	61	1.08
2342348--2342375	2	14.0	2	100	0	56	50	0	0	50	1.00
2344864--2344941	11	7.1	11	77	17	65	34	0	0	65	0.93
2344875--2344940	24	2.8	23	82	13	73	31	0	0	68	0.90
2351637--2351794	80	2.0	79	93	1	271	39	16	17	25	1.90
2354761--2354863	10	10.0	10	69	19	52	41	7	2	47	1.47
2354723--2354863	21	6.8	21	73	9	76	39	6	4	49	1.50
2354814--2354881	10	6.9	9	76	18	64	44	2	1	51	1.25
2355293--2355331	2	19.0	2	84	5	51	48	7	0	43	1.31
2355738--2355848	54	2.1	54	92	0	186	12	10	50	26	1.73
2355792--2355884	42	2.2	42	82	0	114	12	7	53	25	1.65
2355979--2356004	6	4.3	6	100	0	52	0	0	84	15	0.62
2355931--2356058	60	2.1	60	94	0	220	13	6	65	14	1.44
2355919--2356126	108	1.9	108	87	3	303	15	7	60	16	1.57
2355991--2356109	48	2.5	48	90	2	177	15	6	61	16	1.54
2355919--2356166	108	2.3	108	81	4	232	15	8	57	18	1.62
2360077--2360121	12	3.8	12	96	0	81	53	0	0	46	1.00
2360071--2360128	24	2.4	24	82	0	80	46	0	0	53	1.00
2360234--2360276	21	2.1	21	86	4	61	58	4	0	37	1.19
2360774--2360800	2	13.5	2	100	0	54	48	0	0	51	1.00
2363727--2363788	21	3.0	21	77	20	60	38	0	1	59	1.07
2363741--2363779	20	2.0	20	90	5	62	35	0	2	61	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2369817--2369856	16	2.6	16	88	4	55	37	0	0	62	0.95
2369842--2369888	13	3.8	12	81	13	60	29	0	0	70	0.88
2369845--2369888	11	3.8	12	82	14	56	29	0	0	70	0.88
2369841--2369906	18	3.6	17	74	11	51	34	1	0	63	1.04
2378315--2378415	31	3.2	31	70	25	77	51	0	2	45	1.16
2379407--2379436	13	2.2	14	94	5	53	73	0	0	26	0.84
2389815--2389864	25	2.0	26	84	4	66	36	0	4	60	1.16
2390788--2390824	3	12.3	3	100	0	74	67	0	0	32	0.91
2393612--2393711	8	11.9	8	71	19	53	56	0	0	44	0.99
2393596--2393734	22	7.2	20	76	22	79	54	0	0	45	0.99

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