genome.fa.s258.2.7.7.80.10.50.1000.16.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: Scaffold258
Parameters: 2 7 7 80 10 50 1000
Length:  5730937

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   

This is table  16  of  25  ( 2900 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)
3635185--3635246	21	3.0	20	81	9	70	58	8	0	33	1.28
3637245--3637285	21	2.0	21	90	4	66	36	2	0	60	1.10
3637453--3637502	18	2.7	18	82	11	57	40	2	0	58	1.10
3637936--3638014	38	2.1	38	100	0	158	54	7	5	32	1.51
3643960--3644029	27	2.7	25	75	14	70	52	0	0	47	1.00
3654069--3654229	79	2.0	79	95	0	286	32	19	23	24	1.98
3661472--3661501	2	15.0	2	92	0	51	53	0	0	46	1.00
3666860--3666894	4	8.8	4	100	0	70	77	0	0	22	0.78
3666864--3666911	8	6.0	8	90	0	51	72	10	0	16	1.10
3678005--3678035	2	15.5	2	100	0	62	0	48	0	51	1.00
3679849--3679883	17	2.1	17	89	10	54	45	0	0	54	0.99
3682215--3682265	22	2.3	22	83	6	59	50	5	1	41	1.37
3682215--3682276	21	2.8	22	80	4	72	48	4	1	45	1.33
3687352--3687433	40	2.0	40	97	0	155	42	9	17	30	1.81
3691731--3691770	6	6.7	6	94	0	71	12	67	2	17	1.33
3710823--3710885	28	2.4	28	84	7	78	42	0	1	55	1.09
3711484--3711509	2	13.0	2	100	0	52	0	50	0	50	1.00
3713858--3713905	24	2.0	24	95	0	87	39	12	14	33	1.84
3720084--3720140	22	2.6	22	71	17	57	52	0	0	47	1.00
3720673--3720712	18	2.2	18	86	8	55	0	22	20	57	1.41
3721247--3721281	3	11.7	3	100	0	70	31	0	0	68	0.90
3721394--3721433	19	2.1	20	86	9	57	55	0	5	40	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3724723--3724771	23	2.3	20	78	18	62	63	8	8	20	1.48
3724728--3724780	23	2.3	23	100	0	106	60	9	11	18	1.57
3725689--3725763	20	3.8	20	78	3	71	40	10	13	36	1.79
3725686--3725763	40	2.0	39	84	2	102	39	11	12	35	1.80
3726425--3727420	28	35.0	28	82	7	1034	21	18	32	27	1.97
3726377--3727419	56	18.3	56	84	6	1195	21	18	32	27	1.97
3726377--3727419	84	12.2	84	85	4	1282	21	18	32	27	1.97
3728356--3728407	23	2.2	24	82	3	61	5	13	11	69	1.35
3728342--3728413	37	2.0	35	86	5	99	6	12	11	69	1.36
3728363--3728408	23	2.0	23	86	4	65	4	13	10	71	1.27
3734520--3734568	22	2.2	22	100	0	98	67	8	8	16	1.40
3735484--3735558	20	3.8	20	80	3	80	40	12	13	34	1.81
3735481--3735558	40	2.0	39	87	2	111	39	12	12	34	1.82
3740717--3740756	18	2.1	20	86	9	57	32	0	0	67	0.91
3740710--3740753	12	3.8	11	85	8	61	36	0	0	63	0.95
3740711--3740757	23	2.1	22	88	11	69	31	0	0	68	0.90
3741691--3741750	24	2.6	24	84	7	72	55	0	1	43	1.10
3742154--3742188	4	8.8	4	100	0	70	22	0	0	77	0.78
3743346--3743374	6	5.0	6	91	8	51	65	0	0	34	0.93
3743974--3744037	20	3.4	18	68	21	51	59	1	4	34	1.28
3743974--3744071	11	8.5	11	67	24	51	59	1	3	36	1.20
3748064--3748107	23	2.0	22	90	4	70	38	2	2	56	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3748526--3748592	22	3.2	20	77	22	68	65	1	0	32	1.02
3748549--3748589	17	2.4	18	80	8	50	68	2	0	29	1.03
3749225--3749262	15	2.5	15	84	12	51	5	15	2	76	1.08
3751793--3751849	28	2.0	28	96	0	105	12	7	40	40	1.70
3755841--3755869	2	14.5	2	100	0	58	0	0	48	51	1.00
3767946--3767976	3	10.3	3	92	0	53	32	3	0	64	1.09
3772622--3772650	14	2.0	15	93	6	51	44	0	0	55	0.99
3778837--3778905	33	2.1	33	100	0	138	18	27	23	30	1.98
3779667--3779735	33	2.1	33	100	0	138	18	27	23	30	1.98
3778300--3779940	830	2.0	830	100	0	3282	28	16	24	30	1.96
3785449--3785482	16	2.1	17	88	5	52	41	2	5	50	1.42
3785504--3785535	2	16.0	2	100	0	64	50	0	0	50	1.00
3787212--3787249	2	19.0	2	100	0	76	0	50	0	50	1.00
3793646--3793671	13	2.0	13	100	0	52	53	23	15	7	1.67
3814200--3814239	20	2.0	20	90	0	62	50	2	0	47	1.14
3814336--3814369	15	2.1	17	89	10	54	41	8	0	50	1.34
3814413--3814472	27	2.3	26	82	8	68	40	5	1	53	1.33
3814742--3814805	25	2.6	24	73	9	58	59	1	1	37	1.16
3817873--3817977	42	2.5	42	79	13	110	32	4	7	55	1.49
3817873--3817977	21	5.0	21	72	13	90	32	4	7	55	1.49
3828722--3828811	32	2.8	33	80	13	98	52	0	1	46	1.07
3829691--3829772	43	1.9	42	90	2	128	21	30	6	41	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3830204--3830229	2	13.0	2	100	0	52	50	0	0	50	1.00
3837539--3837569	16	1.9	16	93	0	53	0	25	0	74	0.82
3840615--3840650	18	2.0	18	100	0	72	44	11	16	27	1.82
3844689--3844766	2	39.0	2	84	0	84	1	8	48	41	1.43
3850603--3850662	20	3.2	20	77	11	65	51	0	0	48	1.00
3850615--3850658	15	3.3	14	82	17	58	52	0	0	47	1.00
3850602--3850689	38	2.3	38	78	9	90	54	0	0	45	0.99
3850613--3850715	52	2.0	52	81	11	122	51	1	0	45	1.19
3850741--3850810	9	7.9	9	73	20	58	47	0	0	52	1.00
3850711--3850811	26	3.6	27	82	6	105	45	0	1	52	1.12
3850769--3850800	17	1.9	16	93	6	55	43	0	0	56	0.99
3850741--3850817	26	2.9	27	92	5	122	45	0	0	54	0.99
3850782--3850850	35	2.0	34	82	5	84	42	0	0	57	0.98
3852406--3852462	30	2.0	30	86	6	82	68	0	1	29	1.00
3852403--3852463	21	3.2	18	78	17	61	67	0	1	31	1.01
3852403--3852525	30	4.3	26	70	22	70	61	1	0	35	1.11
3852445--3852555	22	5.0	22	71	20	72	55	1	0	42	1.10
3852427--3852546	11	12.3	10	69	24	62	58	1	0	39	1.14
3852403--3852548	11	13.9	11	65	25	50	60	1	0	37	1.10
3860598--3860630	2	16.5	2	100	0	66	48	0	0	51	1.00
3863279--3863305	13	2.1	13	100	0	54	22	7	14	55	1.64
3871907--3871953	2	23.0	2	82	4	58	48	0	8	42	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3871907--3871953	12	4.2	12	89	8	64	48	0	8	42	1.33
3876406--3876444	12	3.2	12	85	0	51	20	0	2	76	0.90
3886810--3886871	31	2.0	31	96	0	115	29	20	22	27	1.99
3889879--3889928	20	2.5	20	84	9	68	54	0	0	46	1.00
3889869--3890149	106	2.7	105	94	2	501	48	0	2	47	1.21
3889993--3890034	20	2.2	20	91	8	70	50	0	2	47	1.14
3890094--3890140	20	2.4	19	82	13	60	51	0	2	46	1.13
3889873--3890131	33	7.5	34	63	25	91	47	0	3	48	1.23
3890099--3890140	20	2.2	20	87	8	61	52	0	2	45	1.13
3890983--3891012	15	2.0	15	93	0	51	43	0	10	46	1.37
3891259--3891294	3	12.0	3	100	0	72	66	0	0	33	0.92
3891293--3891324	3	10.7	3	100	0	64	34	0	0	65	0.93
3898109--3898138	14	2.1	14	100	0	60	30	20	0	50	1.49
3905140--3905184	2	22.5	2	86	0	63	46	4	2	46	1.35
3906922--3906987	31	2.0	34	88	8	102	30	6	0	63	1.18
3915271--3916617	335	4.0	335	87	1	1772	42	5	9	42	1.61
3916528--3916566	9	4.4	9	83	3	53	53	0	0	46	1.00
3924423--3924457	2	17.5	2	100	0	70	48	0	0	51	1.00
3926110--3926163	2	27.0	2	88	0	81	0	44	5	50	1.25
3943460--3943557	49	2.0	49	95	0	178	33	11	20	34	1.88
3955365--3955396	2	16.0	2	100	0	64	50	0	0	50	1.00
3957225--3957457	107	2.2	107	99	0	459	43	2	4	49	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3957807--3957833	2	13.5	2	100	0	54	51	48	0	0	1.00
3959933--3959977	2	22.5	2	86	0	63	46	0	6	46	1.29
3962851--3962923	33	2.1	35	82	9	89	42	2	0	54	1.14
3964996--3965045	24	2.1	24	88	7	75	42	2	2	54	1.23
3968343--3968397	23	2.4	23	90	0	83	60	0	0	40	0.97
3968384--3968444	32	2.0	31	84	12	81	44	0	0	55	0.99
3968384--3968445	30	2.1	30	81	6	72	45	0	0	54	0.99
3968466--3968536	22	3.2	22	69	11	56	63	5	0	30	1.17
3969891--3969940	21	2.3	23	86	6	68	52	0	0	48	1.00
3972141--3972205	2	32.5	2	96	0	121	50	0	0	49	1.00

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