genome.fa.s11.2.7.7.80.10.50.1000.23.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  23  of  29  ( 3461 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)
3696560--3696610	22	2.2	24	86	13	72	64	0	0	35	0.94
3697937--3698007	31	2.3	30	76	7	70	49	0	4	46	1.21
3703223--3703259	6	6.3	6	93	6	51	86	10	2	0	0.67
3704564--3704601	3	12.7	3	100	0	76	34	0	0	65	0.93
3704815--3704858	21	2.2	20	83	4	52	61	0	9	29	1.27
3705242--3705281	3	13.3	3	100	0	80	67	0	0	32	0.91
3705376--3705429	21	2.7	21	82	8	76	42	0	5	51	1.25
3705376--3705426	20	2.5	21	81	15	63	41	0	5	52	1.25
3705379--3705456	19	4.0	20	80	6	70	41	0	3	55	1.18
3709712--3709802	46	2.0	47	88	2	139	27	17	28	26	1.98
3712216--3712278	27	2.2	29	80	5	67	50	20	1	26	1.57
3715754--3715782	6	4.8	6	100	0	58	34	13	34	17	1.89
3716138--3716167	14	2.1	14	93	0	51	43	0	0	56	0.99
3720151--3720261	34	3.5	32	70	18	88	48	0	0	51	1.00
3720251--3720293	22	2.0	22	86	9	61	58	2	0	39	1.11
3721069--3721147	32	2.5	31	75	6	77	46	1	2	49	1.23
3721129--3721184	30	1.9	30	88	3	87	42	0	0	57	0.99
3723314--3723404	16	5.5	17	68	20	59	58	1	0	40	1.05
3723314--3723403	17	5.5	17	69	20	66	58	1	0	40	1.05
3723344--3723422	8	10.0	8	70	25	53	59	1	1	37	1.14
3723314--3723411	11	9.5	11	68	18	50	58	1	1	39	1.12
3725750--3725782	10	3.4	10	83	8	50	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)
3726419--3726482	29	2.4	27	82	14	87	53	3	0	43	1.16
3733591--3733666	25	3.0	24	71	16	64	40	0	1	57	1.07
3733606--3733666	18	3.5	18	72	20	58	39	0	1	59	1.08
3733591--3733664	33	2.2	33	81	15	89	40	0	1	58	1.07
3733626--3733672	24	2.0	24	83	8	60	38	2	2	57	1.23
3733624--3733679	25	2.3	24	78	9	60	35	1	1	60	1.17
3733601--3733679	32	2.4	33	81	12	90	36	1	1	60	1.13
3743719--3743777	32	1.9	31	86	10	86	38	0	3	57	1.15
3743856--3743924	28	2.5	26	86	6	84	60	2	1	34	1.20
3744228--3744262	2	17.5	2	100	0	70	0	48	0	51	1.00
3749973--3750013	20	2.0	20	86	9	57	53	4	0	41	1.22
3750405--3750430	2	13.0	2	100	0	52	50	0	0	50	1.00
3752027--3752080	24	2.3	23	79	14	67	38	0	0	61	0.96
3752819--3752856	18	2.1	19	90	5	60	52	2	0	44	1.14
3752819--3752865	19	2.6	18	89	3	67	55	2	0	42	1.12
3760524--3760552	2	14.5	2	100	0	58	51	48	0	0	1.00
3765311--3765340	4	7.5	4	92	0	51	46	23	3	26	1.68
3766170--3766204	2	17.5	2	100	0	70	51	0	0	48	1.00
3766914--3766938	3	8.3	3	100	0	50	68	0	0	32	0.90
3767402--3767455	23	2.4	22	71	3	54	61	0	0	38	0.96
3767420--3767477	29	2.0	29	82	0	71	56	0	0	43	0.99
3767440--3767490	22	2.3	23	79	3	59	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3767949--3768016	5	13.8	5	74	20	63	64	0	0	35	0.94
3767949--3768038	22	4.1	24	83	12	97	64	0	0	35	0.94
3767964--3768038	11	6.7	11	71	26	52	64	0	0	36	0.94
3768140--3768167	2	14.0	2	100	0	56	50	0	0	50	1.00
3771429--3771522	46	2.0	46	100	0	188	30	8	20	40	1.82
3776393--3776443	25	2.0	24	85	14	68	21	0	1	76	0.88
3776519--3776571	23	2.3	23	70	3	54	49	0	0	50	1.00
3776553--3776591	17	2.4	16	83	8	53	41	0	0	58	0.98
3777110--3777158	17	2.9	17	81	0	62	57	0	0	42	0.99
3778090--3778118	3	9.7	3	100	0	58	0	31	0	68	0.89
3778179--3778206	6	4.7	6	100	0	56	0	0	14	85	0.59
3793224--3793266	21	2.1	20	83	12	52	55	0	2	41	1.12
3793224--3793266	20	2.2	20	83	8	52	55	0	2	41	1.12
3793974--3794034	26	2.3	26	85	0	77	13	49	14	22	1.78
3807263--3807287	13	1.9	13	100	0	50	44	0	0	56	0.99
3807332--3807382	22	2.4	22	86	3	68	45	0	0	54	0.99
3807396--3807471	27	2.8	27	75	17	68	38	0	2	59	1.12
3807784--3807812	3	9.7	3	100	0	58	0	31	0	68	0.89
3810112--3810159	25	1.9	25	82	0	60	20	12	22	43	1.86
3814576--3814607	2	16.0	2	100	0	64	50	0	0	50	1.00
3816241--3816322	42	1.9	43	87	2	121	36	1	2	59	1.18
3816275--3816351	36	2.1	36	86	9	104	37	0	2	59	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3816249--3816343	42	2.3	42	83	8	115	37	0	2	60	1.09
3816353--3816423	22	3.2	21	77	15	72	39	2	2	54	1.29
3816372--3816419	20	2.4	20	75	0	51	41	2	2	54	1.24
3828078--3828110	3	11.0	3	100	0	66	66	0	0	33	0.92
3828715--3828744	3	9.7	3	92	7	51	63	0	0	36	0.95
3828712--3828743	10	3.3	10	91	8	57	62	0	0	37	0.95
3830087--3830115	3	9.7	3	100	0	58	65	0	0	34	0.93
3830644--3830685	19	2.2	19	83	8	50	33	0	4	61	1.17
3830699--3830735	17	2.2	17	100	0	74	70	10	0	18	1.16
3830878--3830907	3	10.0	3	100	0	60	33	0	0	66	0.92
3831324--3831382	16	3.7	16	73	22	52	44	0	3	52	1.17
3832734--3832763	4	7.5	4	92	0	51	46	0	23	30	1.52
3836559--3836628	36	2.0	35	82	2	86	48	5	4	41	1.46
3836924--3836969	11	4.4	10	78	10	56	73	0	0	26	0.83
3836924--3836969	21	2.2	21	84	7	58	73	0	0	26	0.83
3849629--3849658	2	15.0	2	100	0	60	50	0	0	50	1.00
3850715--3850794	34	2.4	34	83	8	92	65	5	7	22	1.38
3854015--3854055	18	2.3	17	84	12	55	34	24	7	34	1.83
3856157--3856186	15	1.9	16	93	6	53	46	3	6	43	1.46
3861325--3861359	18	1.9	18	94	0	61	65	0	14	20	1.26
3863940--3863972	2	16.5	2	93	0	57	0	48	3	48	1.17
3864122--3864183	21	2.8	21	73	21	56	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3866884--3866926	21	2.0	21	82	8	52	34	11	25	27	1.91
3868242--3868296	20	2.6	22	75	16	62	49	0	0	50	1.00
3868242--3868294	22	2.5	21	69	6	54	49	0	0	50	1.00
3868264--3868336	32	2.2	34	87	9	114	45	0	0	54	0.99
3871821--3871849	6	4.8	6	100	0	58	48	17	34	0	1.47
3874509--3874533	2	12.5	2	100	0	50	52	0	48	0	1.00
3874595--3874623	2	15.0	2	92	7	51	51	0	48	0	1.00
3874800--3874832	13	2.5	13	81	18	50	66	0	0	33	0.92
3874800--3874859	28	2.2	26	82	11	68	61	1	0	36	1.06
3874895--3874938	22	1.9	24	90	9	74	31	2	0	65	1.05
3875003--3875048	20	2.3	20	85	3	58	28	0	4	67	1.10
3875973--3876007	17	2.0	17	88	5	52	54	0	0	45	0.99
3875973--3876035	18	3.8	18	72	23	57	60	0	0	39	0.97
3879972--3880010	15	2.7	15	88	4	53	51	0	2	46	1.14
3879937--3880012	19	4.0	19	72	19	52	50	1	2	46	1.24
3880167--3880215	9	5.4	9	78	7	55	55	0	0	44	0.99
3880166--3880213	17	2.7	17	81	12	53	56	0	0	43	0.99
3881236--3881275	17	2.4	16	83	4	53	50	0	0	50	1.00
3882206--3882280	17	4.7	17	71	14	61	44	0	0	56	0.99
3891542--3891601	15	4.0	16	77	18	67	53	0	0	46	1.00
3891542--3891601	13	4.0	14	77	18	59	53	0	0	46	1.00
3891589--3891641	24	2.2	23	80	6	61	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3892541--3892570	14	2.2	14	94	5	53	40	0	0	60	0.97
3892597--3892629	16	2.1	16	88	11	50	57	0	0	42	0.98
3892791--3892823	16	2.0	17	88	5	50	51	0	3	45	1.16
3893739--3893777	3	13.0	3	83	0	51	30	28	5	35	1.79
3902376--3902402	2	13.5	2	100	0	54	0	48	0	51	1.00
3902988--3903041	25	2.2	25	83	6	65	53	1	0	44	1.11
3903147--3903261	32	3.6	31	83	6	151	42	6	1	49	1.37
3904606--3904644	14	2.9	14	84	3	53	51	0	0	48	1.00
3904782--3904834	22	2.2	25	87	12	85	58	1	1	37	1.20
3906280--3906307	13	2.2	13	100	0	56	35	7	7	50	1.57

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