genome.fa.s60.2.7.7.80.10.50.1000.19.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  19  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)
3225210--3225235	6	4.3	6	100	0	52	30	15	19	34	1.93
3234890--3234972	37	2.2	39	83	12	102	36	1	0	62	1.03
3234927--3234985	5	11.4	5	73	20	50	35	0	0	64	0.94
3234926--3234976	17	3.0	17	77	8	59	33	0	0	66	0.92
3234927--3234976	22	2.3	22	93	6	84	34	0	0	66	0.92
3237115--3237172	22	2.6	23	81	15	68	51	0	0	48	1.00
3237133--3237178	7	6.4	7	79	20	51	52	0	0	47	1.00
3237117--3237186	22	3.1	22	76	17	63	48	0	0	51	1.00
3237215--3237268	24	2.3	24	84	15	69	50	0	5	44	1.25
3251664--3251727	2	32.0	2	100	0	128	50	0	0	50	1.00
3256995--3257072	37	2.1	37	100	0	156	33	7	16	42	1.77
3263173--3263358	41	4.5	41	91	0	291	30	16	29	23	1.96
3269173--3269199	3	9.0	3	100	0	54	0	0	33	66	0.92
3272590--3272671	38	2.2	38	95	0	146	31	19	6	42	1.76
3273399--3273439	2	20.5	2	84	0	55	46	2	0	51	1.14
3274989--3275016	3	9.3	3	100	0	56	0	35	32	32	1.58
3275233--3275275	3	14.0	3	90	4	68	65	2	0	32	1.06
3275241--3275272	16	2.0	16	100	0	64	62	0	0	37	0.95
3275239--3275275	19	1.9	19	100	0	74	64	0	0	35	0.94
3275332--3275369	2	19.0	2	100	0	76	0	50	0	50	1.00
3275591--3275624	2	17.0	2	87	0	50	50	0	5	44	1.26
3276455--3276505	20	2.5	20	79	17	61	70	0	0	29	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3276476--3276565	19	5.1	18	71	20	75	57	1	1	40	1.13
3276479--3276576	19	5.3	18	71	22	62	57	2	1	39	1.17
3278466--3278492	2	13.5	2	100	0	54	48	0	0	51	1.00
3279864--3279888	8	3.1	8	100	0	50	88	0	0	12	0.53
3280600--3280637	2	19.0	2	100	0	76	50	0	50	0	1.00
3283174--3283199	3	8.7	3	100	0	52	0	30	0	69	0.89
3294362--3294391	2	15.0	2	100	0	60	50	0	0	50	1.00
3295439--3295468	4	7.5	4	92	0	51	20	0	3	76	0.92
3296185--3296236	27	1.9	27	81	14	63	50	1	0	48	1.12
3303921--3303970	26	1.9	26	88	8	75	58	2	0	40	1.10
3306033--3306106	27	2.4	32	72	19	77	47	0	2	50	1.15
3307411--3307461	24	2.1	24	85	7	68	52	1	1	43	1.23
3314119--3314158	2	20.0	2	89	0	62	50	5	0	45	1.23
3314203--3314237	2	17.5	2	87	0	52	42	0	5	51	1.25
3314739--3314771	6	5.5	6	100	0	66	18	36	15	30	1.91
3314769--3314795	6	4.5	6	100	0	54	18	66	0	14	1.25
3316676--3316703	2	14.0	2	100	0	56	50	0	0	50	1.00
3319166--3319198	2	17.0	2	93	6	59	48	0	0	51	1.00
3322716--3322743	2	14.0	2	100	0	56	50	0	0	50	1.00
3323541--3323572	2	16.0	2	100	0	64	50	0	0	50	1.00
3326625--3326657	12	2.8	12	86	4	50	33	0	3	63	1.10
3326828--3326888	28	2.1	30	84	6	81	65	1	8	24	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3327449--3327473	12	2.1	12	100	0	50	44	16	0	40	1.47
3331719--3331761	3	14.3	3	100	0	86	32	0	0	67	0.91
3346771--3346835	32	2.0	33	87	3	96	53	12	7	26	1.64
3348789--3348917	60	2.2	60	92	2	215	34	24	5	35	1.79
3349096--3349155	22	2.8	22	71	16	54	43	0	5	51	1.23
3349470--3349496	2	13.5	2	100	0	54	48	0	0	51	1.00
3377417--3377453	20	1.9	18	89	10	56	48	2	21	27	1.63
3380100--3380134	2	17.5	2	100	0	70	0	0	48	51	1.00
3380406--3381061	344	1.9	339	81	5	786	31	15	13	38	1.87
3384573--3384604	2	16.0	2	100	0	64	50	0	50	0	1.00
3384982--3385017	18	2.0	18	88	0	54	30	13	13	41	1.84
3387046--3387080	2	17.5	2	87	0	52	45	0	5	48	1.26
3388536--3388598	2	32.0	2	88	3	83	49	4	1	44	1.33
3390252--3390277	2	13.0	2	100	0	52	50	0	50	0	1.00
3390879--3390918	18	2.2	18	86	8	55	60	0	0	40	0.97
3390895--3390946	25	2.1	26	85	7	72	48	0	1	50	1.12
3392479--3392504	2	13.0	2	100	0	52	50	0	0	50	1.00
3393514--3393548	3	11.7	3	100	0	70	65	0	0	34	0.93
3396433--3396486	2	27.5	2	82	17	69	50	0	3	46	1.19
3397555--3397585	3	10.3	3	100	0	62	67	0	32	0	0.91
3399271--3399314	2	22.0	2	100	0	88	50	0	0	50	1.00
3404087--3404115	11	2.5	12	94	5	51	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3405712--3405773	24	2.6	24	84	5	72	3	24	19	53	1.60
3407276--3407306	15	2.0	16	93	6	55	64	25	3	6	1.33
3410422--3410459	18	2.1	18	95	0	67	52	13	15	18	1.74
3425723--3425753	6	5.2	6	92	0	53	83	12	0	3	0.75
3426020--3426056	2	18.0	2	88	5	56	51	2	0	45	1.15
3426535--3426563	2	14.5	2	100	0	58	0	48	0	51	1.00
3426563--3426588	2	13.0	2	100	0	52	50	0	0	50	1.00
3442040--3442065	2	13.0	2	100	0	52	50	0	0	50	1.00
3444948--3445189	120	2.0	121	94	0	423	36	12	14	35	1.84
3454033--3454137	31	3.3	31	65	19	81	34	13	9	42	1.76
3454024--3454152	64	2.0	64	93	0	222	33	15	10	41	1.81
3460817--3460858	12	3.5	12	83	0	57	83	0	16	0	0.65
3461034--3461082	7	6.9	7	76	4	53	63	4	28	4	1.31
3463951--3463988	19	2.0	19	100	0	76	0	47	0	52	1.00
3466197--3466254	24	2.4	23	77	8	71	20	15	12	51	1.75
3466625--3466669	2	22.5	2	100	0	90	0	48	0	51	1.00
3478082--3478154	36	2.0	36	91	0	119	26	12	19	42	1.86
3482978--3483015	20	1.9	20	89	10	60	2	18	13	65	1.37
3487651--3487683	6	5.5	6	100	0	66	18	33	15	33	1.92
3487653--3487695	18	2.4	18	88	0	59	18	27	23	30	1.98
3488663--3488703	2	21.0	2	90	5	66	0	46	2	51	1.14
3489340--3489369	2	15.0	2	100	0	60	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3496176--3496203	2	14.0	2	100	0	56	50	0	0	50	1.00
3497753--3497797	2	22.5	2	100	0	90	48	0	0	51	1.00
3499232--3499316	20	4.4	20	72	10	70	45	11	0	42	1.40
3499239--3499308	18	3.7	18	70	17	52	38	14	0	47	1.44
3499279--3499316	18	2.2	18	85	4	51	47	13	0	39	1.42
3503101--3503531	215	2.0	215	99	0	853	23	16	14	44	1.85
3517885--3517918	17	1.9	18	88	5	52	38	11	0	50	1.39
3521741--3521790	24	2.0	25	92	3	84	58	0	2	40	1.10
3522819--3522860	23	2.0	22	86	13	61	47	2	4	45	1.36
3522819--3522875	24	2.4	23	88	8	80	47	1	7	43	1.40
3522899--3522943	17	2.6	17	80	10	56	37	11	0	51	1.38
3522899--3522938	18	2.3	17	86	4	53	40	12	0	47	1.41
3526484--3526539	2	28.5	2	96	3	105	51	0	48	0	1.00
3531701--3531743	13	3.1	13	75	18	50	44	0	0	55	0.99
3531699--3531746	17	3.1	17	77	22	61	41	0	0	58	0.98
3537670--3537723	28	2.0	28	92	7	94	31	3	18	46	1.67
3539463--3539503	2	20.5	2	100	0	82	48	0	0	51	1.00
3548956--3548985	2	15.0	2	92	0	51	50	3	0	46	1.18
3560259--3560291	2	16.5	2	93	0	57	45	0	3	51	1.16
3578063--3578101	12	3.2	12	96	0	69	17	0	0	82	0.68
3583446--3583475	2	15.0	2	92	0	51	50	3	0	46	1.18
3594778--3594824	3	15.7	3	100	0	94	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3602922--3602954	5	6.6	5	100	0	66	81	0	0	18	0.68
3602922--3602960	15	2.6	15	91	0	51	79	0	5	15	0.90
3607066--3607126	5	12.6	5	74	22	51	62	0	0	37	0.96
3607077--3607164	37	2.3	40	80	11	103	57	1	0	40	1.06
3607141--3607190	16	3.1	17	73	23	54	58	0	0	42	0.98
3611330--3611359	3	10.0	3	100	0	60	66	0	0	33	0.92
3614492--3614540	20	2.5	20	83	6	64	48	2	0	48	1.12
3626720--3626745	5	5.2	5	100	0	52	0	0	23	76	0.78
3629088--3629166	22	3.4	23	84	5	97	46	1	0	51	1.08
3629195--3629225	15	2.1	15	93	0	53	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