genome.fa.s36.2.7.7.80.10.50.1000.25.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: Scaffold36
Parameters: 2 7 7 80 10 50 1000
Length:  4808052

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   

This is table  25  of  28  ( 3342 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)
3845726--3845816	16	5.8	16	68	17	64	43	0	0	56	0.99
3846985--3847027	20	2.2	20	86	0	59	34	0	2	62	1.08
3846982--3847042	32	1.9	31	83	12	79	32	1	1	63	1.13
3850733--3850869	69	2.0	69	91	0	220	29	7	11	51	1.65
3851062--3851094	17	2.0	16	94	5	57	75	0	0	24	0.80
3853447--3853487	14	2.9	14	85	0	55	41	4	0	53	1.22
3856053--3856228	80	2.2	80	89	0	271	34	23	8	34	1.85
3862592--3862648	21	2.7	21	94	0	96	36	12	12	38	1.80
3865082--3865125	16	2.6	17	85	7	63	50	2	0	47	1.13
3866043--3866067	12	2.1	12	100	0	50	24	0	8	68	1.16
3866029--3866077	16	3.1	17	85	8	59	24	0	6	69	1.11
3866114--3866205	33	2.6	36	78	13	111	56	0	0	43	0.99
3866144--3866208	17	3.2	20	70	22	64	53	0	0	46	1.00
3869593--3869650	9	6.6	9	74	20	52	36	0	5	58	1.20
3869622--3869651	16	1.9	15	93	6	51	40	0	0	60	0.97
3871154--3871189	13	2.8	14	84	16	51	63	2	0	33	1.08
3872788--3872827	21	1.9	21	85	10	55	25	5	5	65	1.34
3873104--3873382	108	2.6	110	84	5	370	40	13	11	34	1.81
3874465--3874491	2	13.5	2	100	0	54	48	0	0	51	1.00
3876555--3876589	2	18.0	2	88	5	54	51	2	0	45	1.16
3882131--3882157	4	6.8	4	100	0	54	51	0	0	48	1.00
3882978--3883041	23	2.9	23	77	9	71	46	1	0	51	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3882960--3883076	43	2.6	45	76	20	127	46	1	0	52	1.11
3883074--3883113	19	2.2	19	86	4	55	47	5	5	42	1.47
3883125--3883192	20	3.3	20	82	10	77	22	7	1	69	1.22
3883480--3883557	2	39.0	2	80	10	61	43	2	3	50	1.34
3883445--3883549	50	2.1	50	81	0	120	44	4	8	41	1.56
3884488--3884518	16	1.9	16	93	0	53	54	0	0	45	0.99
3885591--3885635	23	2.0	23	100	0	90	4	17	22	55	1.60
3886600--3886647	12	3.9	12	81	5	60	43	0	0	56	0.99
3886589--3886646	25	2.3	25	81	3	71	46	0	0	53	1.00
3886600--3886647	6	7.8	6	83	4	51	43	0	0	56	0.99
3887255--3887312	24	2.3	24	73	5	62	50	0	1	48	1.11
3887306--3887339	13	2.7	13	90	4	52	67	2	0	29	1.05
3887832--3887896	22	3.0	22	70	19	64	43	0	0	56	0.99
3887853--3887896	19	2.4	19	88	3	63	40	0	0	59	0.98
3892844--3892877	6	5.7	6	89	10	52	82	0	14	2	0.79
3892844--3892877	11	2.8	12	86	13	52	82	0	14	2	0.79
3893667--3893749	35	2.4	33	84	11	105	46	1	1	50	1.16
3893683--3893749	34	1.9	36	88	8	104	50	1	1	46	1.19
3893768--3893821	22	2.5	21	76	8	54	40	0	1	57	1.09
3893823--3893880	12	4.8	12	71	12	55	51	1	0	46	1.11
3893955--3893998	21	2.0	22	91	4	72	43	6	0	50	1.29
3894028--3894092	29	2.2	30	83	8	80	61	4	0	33	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3894110--3894146	11	3.8	10	80	20	51	70	0	0	29	0.88
3895400--3895470	24	3.3	20	84	13	81	64	0	1	33	1.02
3895415--3895462	9	5.1	9	78	9	51	64	0	2	33	1.05
3895423--3895470	20	2.4	19	93	6	78	66	0	2	31	1.03
3895411--3895503	15	5.9	15	70	20	57	59	0	1	39	1.05
3895464--3895524	15	4.1	15	78	4	61	49	0	0	50	1.00
3895520--3895554	18	2.1	18	89	10	56	62	0	2	34	1.10
3896089--3896161	15	4.8	15	72	20	62	45	0	0	54	0.99
3896089--3896132	22	2.0	21	91	4	70	43	0	0	56	0.99
3896089--3896153	15	4.2	15	77	14	69	44	0	0	55	0.99
3896120--3896193	37	1.9	39	83	5	98	41	1	1	55	1.17
3902101--3902141	21	1.9	21	85	14	57	58	0	2	39	1.11
3903491--3903533	22	2.0	22	85	0	59	53	0	4	41	1.21
3903938--3903976	17	2.4	16	86	4	51	38	0	0	61	0.96
3910183--3910268	27	3.1	27	81	11	86	45	0	0	54	0.99
3915397--3915451	29	2.0	27	82	13	67	45	0	0	54	0.99
3915431--3915457	6	4.5	6	100	0	54	37	0	0	62	0.95
3916327--3916361	2	17.5	2	100	0	70	48	0	0	51	1.00
3919687--3919718	12	2.6	13	85	14	50	75	0	0	25	0.81
3923767--3923795	2	14.5	2	100	0	58	48	0	51	0	1.00
3930439--3930486	23	2.0	23	84	11	62	43	0	0	56	0.99
3931471--3931534	31	2.1	31	96	0	119	28	15	7	48	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3931599--3931641	2	21.5	2	100	0	86	48	0	0	51	1.00
3931832--3931880	25	1.9	25	87	4	71	36	0	2	61	1.08
3934061--3934094	16	2.2	16	89	5	52	61	0	0	38	0.96
3936749--3936791	17	2.6	17	89	7	63	69	6	0	23	1.12
3936755--3936799	17	2.6	17	85	0	63	73	6	0	20	1.05
3937740--3937770	2	15.5	2	100	0	62	51	0	0	48	1.00
3941073--3941176	41	2.5	42	87	3	138	36	5	11	46	1.64
3948668--3948737	28	2.5	28	83	2	86	41	2	0	55	1.14
3948811--3948842	16	2.0	16	93	0	55	59	0	0	40	0.97
3948799--3948895	23	4.2	23	75	11	67	57	1	0	41	1.05
3949726--3949761	18	2.0	18	94	0	63	47	0	0	52	1.00
3950496--3950587	26	3.2	29	77	19	102	55	0	1	43	1.07
3952871--3952931	20	2.7	23	75	19	65	68	3	3	24	1.19
3956585--3956650	13	4.9	13	73	24	57	36	0	0	63	0.95
3956570--3956656	30	2.9	30	92	1	138	37	0	0	62	0.96
3956627--3956665	18	2.2	17	86	4	51	43	0	0	56	0.99
3956908--3956958	26	2.0	26	85	7	70	49	0	0	50	1.00
3956968--3957006	20	1.9	21	84	5	53	48	2	0	48	1.15
3956965--3957017	25	2.1	26	82	10	65	49	1	0	49	1.12
3961634--3961666	2	17.0	2	93	6	59	48	0	0	51	1.00
3962896--3962929	16	2.1	17	88	5	52	58	2	0	38	1.13
3963563--3963616	19	3.1	17	80	12	65	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3964067--3964155	47	1.9	47	84	15	123	53	0	0	46	1.00
3965059--3965084	4	6.5	4	100	0	52	50	0	0	50	1.00
3967546--3967570	2	12.5	2	100	0	50	48	0	0	52	1.00
3967930--3967960	2	15.5	2	100	0	62	51	0	0	48	1.00
3981013--3981055	2	21.5	2	100	0	86	51	0	0	48	1.00
3987252--3987281	14	2.1	14	93	0	51	46	3	13	36	1.60
3988266--3988620	175	2.0	176	93	0	604	25	18	16	39	1.91
3992010--3992055	8	6.0	8	77	10	51	43	0	2	54	1.12
3992011--3992064	12	4.1	13	79	15	58	42	1	1	53	1.22
3993864--3993903	19	2.3	18	84	16	57	47	0	0	52	1.00
3993870--3993910	19	2.2	19	86	8	57	51	0	2	46	1.14
4004468--4004518	16	3.1	16	80	5	57	66	11	21	0	1.23
4004970--4005013	22	2.0	23	90	4	72	50	0	2	47	1.13
4004958--4005013	22	2.6	22	83	8	71	50	1	1	46	1.22
4009484--4009524	16	2.6	16	81	14	57	34	0	2	63	1.08
4009449--4009527	37	2.1	39	80	4	90	43	1	2	53	1.22
4018462--4018494	2	17.0	2	87	6	50	54	0	0	45	0.99
4020737--4020870	71	1.9	72	82	13	170	52	4	1	41	1.30
4026187--4026369	92	2.0	92	100	0	366	31	14	19	34	1.92
4028455--4028505	26	2.0	26	84	3	68	1	15	0	82	0.76
4028457--4028507	25	2.0	27	84	7	70	1	15	0	82	0.76
4034500--4034551	11	5.0	11	79	13	65	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4034500--4034553	16	3.3	16	82	15	58	66	0	0	33	0.92
4034498--4034618	32	3.7	34	70	20	87	57	0	0	41	1.04
4035598--4035654	24	2.4	24	94	2	98	17	22	24	35	1.95
4038296--4038375	26	2.7	30	78	16	87	47	3	0	48	1.19
4038333--4038372	19	2.0	21	85	9	57	40	7	0	52	1.30
4038288--4038376	6	15.3	6	72	15	55	48	3	0	48	1.18
4042413--4042439	14	1.9	14	100	0	54	48	22	7	22	1.75
4043555--4043581	2	13.5	2	100	0	54	51	0	0	48	1.00
4045437--4045516	40	2.0	40	97	0	151	27	28	7	36	1.84
4051457--4051504	15	3.3	15	76	2	53	64	0	0	35	0.94

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