genome.fa.s39.2.7.7.80.10.50.1000.21.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: Scaffold39
Parameters: 2 7 7 80 10 50 1000
Length:  4724573

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   

This is table  21  of  27  ( 3195 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)
3517243--3517268	13	2.0	13	100	0	52	38	15	15	30	1.88
3519488--3519532	21	2.1	22	88	8	67	55	4	17	22	1.60
3521336--3521366	15	2.1	15	93	0	53	48	16	22	12	1.80
3523443--3523468	13	2.0	13	100	0	52	30	15	15	38	1.88
3523589--3523634	21	2.2	20	81	11	58	32	19	4	43	1.71
3530062--3530133	20	3.6	20	75	20	71	36	13	18	31	1.90
3531040--3531064	2	12.5	2	100	0	50	48	0	0	52	1.00
3534241--3534270	14	2.1	14	100	0	60	43	20	16	20	1.88
3536486--3536546	31	2.0	30	84	12	79	49	3	1	45	1.28
3539897--3539996	48	2.1	48	94	3	175	26	36	4	34	1.75
3543568--3543610	18	2.5	17	80	3	50	53	25	9	11	1.67
3544047--3544111	12	5.7	12	69	22	50	40	1	0	58	1.07
3544198--3544259	20	3.2	19	80	13	63	51	0	0	48	1.00
3546521--3546553	16	2.0	17	94	5	59	48	12	12	27	1.76
3547002--3547030	14	2.1	14	93	6	51	27	6	6	58	1.50
3547886--3547927	19	2.2	19	95	0	75	47	26	16	9	1.77
3548825--3548856	13	2.3	15	89	10	50	56	0	6	37	1.25
3554523--3554556	2	17.0	2	100	0	68	50	0	50	0	1.00
3555603--3555631	6	4.8	6	100	0	58	17	17	34	31	1.93
3555858--3555883	13	2.0	13	100	0	52	30	0	0	69	0.89
3555859--3555903	23	1.9	24	86	4	65	28	0	0	71	0.87
3556611--3556655	18	2.5	19	85	10	67	57	6	0	35	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3556916--3556956	12	3.0	14	75	17	50	46	0	9	43	1.36
3558375--3558400	13	2.0	13	100	0	52	38	15	15	30	1.88
3560618--3560667	21	2.3	21	80	10	57	56	4	18	22	1.58
3562465--3562495	15	2.1	15	93	0	53	48	16	22	12	1.80
3564575--3564599	13	1.9	13	100	0	50	32	16	16	36	1.90
3564720--3564765	21	2.2	20	81	11	58	32	19	4	43	1.71
3567051--3567076	13	2.0	13	100	0	52	38	15	15	30	1.88
3569206--3569230	13	1.9	13	100	0	50	36	16	16	32	1.90
3569299--3569352	20	2.7	20	85	8	74	38	12	14	33	1.85
3575495--3575519	13	1.9	13	100	0	50	36	16	16	32	1.90
3576997--3577063	33	2.0	33	91	0	107	23	31	17	26	1.97
3577434--3577459	3	8.7	3	100	0	52	34	0	34	30	1.58
3581340--3581463	20	6.6	19	73	20	100	27	13	15	43	1.84
3581378--3581447	33	2.1	33	89	0	104	27	14	15	42	1.86
3583720--3583885	80	2.1	78	78	7	174	24	25	15	34	1.95
3585875--3585914	20	2.0	20	85	14	55	32	22	0	45	1.53
3587230--3587296	33	2.0	33	82	0	80	28	31	13	26	1.94
3587492--3587522	16	1.9	16	100	0	62	9	19	6	64	1.45
3587640--3587689	21	2.4	21	93	3	84	38	4	26	32	1.75
3588268--3588292	13	1.9	13	100	0	50	36	16	16	32	1.90
3594054--3594096	17	2.5	17	100	0	86	67	11	6	13	1.41
3594456--3594509	20	2.7	21	85	8	76	31	18	14	35	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3594558--3594584	13	2.1	13	100	0	54	48	14	7	29	1.71
3595485--3595515	2	15.5	2	100	0	62	48	0	0	51	1.00
3596371--3596419	16	3.1	16	84	0	71	44	28	12	14	1.81
3597884--3598181	148	2.0	148	98	0	578	33	20	17	29	1.95
3609352--3609377	13	2.0	13	100	0	52	30	15	15	38	1.88
3611753--3611799	21	2.3	20	76	23	53	40	4	21	34	1.73
3611923--3611961	13	3.0	13	96	0	69	35	15	17	30	1.91
3611947--3612025	20	3.7	20	78	15	77	44	15	15	25	1.85
3614042--3614072	15	2.1	15	93	0	53	12	22	16	48	1.80
3615876--3615920	21	2.1	21	84	8	56	22	20	4	53	1.63
3618139--3618164	13	2.0	13	100	0	52	30	15	15	38	1.88
3619669--3619718	26	1.9	26	100	0	100	18	16	16	50	1.79
3619979--3620030	20	2.5	21	78	3	61	65	3	0	30	1.10
3624134--3624186	22	2.3	22	84	12	63	60	0	9	30	1.28
3627640--3627678	11	3.3	11	89	10	51	2	0	10	87	0.65
3627640--3627687	18	2.7	18	81	12	62	6	0	8	85	0.74
3627640--3627685	7	6.9	7	85	5	51	4	0	8	86	0.68
3631841--3631909	27	2.6	27	95	0	120	21	18	39	20	1.93
3633687--3633729	20	2.2	20	87	4	61	25	13	13	46	1.81
3640368--3640416	23	2.2	23	85	3	64	61	14	4	20	1.49
3641326--3641351	13	2.0	13	100	0	52	30	23	15	30	1.95
3641441--3641492	21	2.4	22	93	6	97	38	11	23	26	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3641538--3641674	53	2.6	53	95	1	247	27	17	18	37	1.93
3641644--3641714	20	3.5	20	77	11	74	29	14	16	39	1.88
3641754--3641794	21	2.0	21	85	9	57	39	9	12	39	1.76
3642588--3642645	20	3.2	19	76	16	52	3	18	12	65	1.39
3642664--3642719	19	2.8	19	71	15	51	5	12	12	69	1.34
3642976--3643051	31	2.5	31	88	0	107	10	17	14	57	1.64
3643177--3643206	12	2.5	12	88	0	51	43	13	23	20	1.86
3643834--3644147	42	7.5	42	79	7	210	42	16	24	16	1.89
3643916--3644147	127	1.8	127	85	1	331	41	16	25	16	1.89
3643874--3644315	42	10.5	42	79	3	363	40	15	25	18	1.90
3644489--3644715	44	5.2	44	76	8	210	40	14	21	23	1.90
3644492--3644715	88	2.5	87	77	5	236	40	14	21	23	1.90
3658989--3659043	22	2.5	22	77	11	58	1	20	34	43	1.62
3659045--3659104	20	3.1	19	77	15	59	0	23	16	60	1.36
3659425--3659516	31	3.1	31	84	4	109	11	19	15	53	1.72
3659733--3659773	3	13.7	3	100	0	82	31	0	0	68	0.90
3663143--3663180	20	1.9	20	94	0	67	31	15	15	36	1.90
3665084--3665228	72	2.0	72	89	0	218	41	15	13	29	1.85
3665257--3665664	155	2.6	156	77	6	360	37	18	16	26	1.92
3666194--3666237	3	14.7	3	100	0	88	31	0	0	68	0.90
3667107--3667147	20	2.0	20	86	9	57	7	17	0	75	1.02
3667139--3667168	11	2.7	11	100	0	60	0	23	0	76	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3668860--3669107	84	3.0	81	80	9	277	41	12	26	19	1.86
3669329--3669818	44	11.2	43	75	9	334	37	14	24	22	1.92
3670020--3670334	88	3.6	87	78	10	302	30	14	26	29	1.95
3670084--3670333	84	2.9	83	80	9	261	28	15	26	30	1.96
3673185--3673228	21	2.2	20	83	4	52	0	11	4	84	0.77
3676345--3676824	155	3.2	153	79	9	517	37	16	18	27	1.92
3678340--3678387	19	2.6	18	83	16	62	4	20	0	75	0.97
3678353--3678402	25	2.0	25	84	7	66	6	24	0	70	1.10
3679037--3679078	20	2.1	21	86	8	61	66	4	9	19	1.38
3678757--3679558	166	4.9	165	80	7	841	50	8	10	30	1.67
3678757--3679558	328	2.4	328	84	5	1005	50	8	10	30	1.67
3680938--3681162	42	5.3	40	74	11	159	48	12	20	18	1.79
3680887--3681203	43	7.4	43	69	11	168	48	11	20	18	1.80
3680740--3681210	85	5.5	84	78	7	387	45	11	22	21	1.83
3681220--3681388	80	2.1	79	80	7	189	43	17	21	17	1.88
3681251--3681390	41	3.5	39	75	16	126	43	17	24	15	1.86
3682128--3682731	91	6.6	91	84	4	684	31	11	24	31	1.91
3682128--3682730	181	3.3	182	84	4	727	32	11	24	32	1.91
3690030--3690055	13	2.0	13	100	0	52	38	15	15	30	1.88
3694584--3694609	13	2.0	13	100	0	52	38	15	15	30	1.88
3701861--3701895	10	3.4	10	92	4	52	2	14	0	82	0.77
3712625--3712650	3	8.7	3	100	0	52	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3714243--3714285	19	2.3	19	91	0	68	51	9	4	34	1.55
3716196--3716233	19	2.0	21	85	15	55	47	2	0	50	1.15
3716539--3716572	16	2.2	16	89	5	52	44	0	2	52	1.16
3717028--3717067	21	2.0	21	85	14	57	62	7	7	22	1.47
3717496--3717549	20	2.7	20	88	0	81	42	12	14	29	1.83
3717601--3717626	13	2.0	13	100	0	52	30	15	15	38	1.88
3717581--3717648	33	2.1	32	94	2	118	36	17	13	32	1.89
3718785--3718824	20	2.0	20	90	5	62	82	0	17	0	0.67
3721812--3721849	20	1.9	20	88	0	58	71	2	2	23	1.12
3721985--3722047	23	2.7	22	78	21	74	50	1	7	39	1.41

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