genome.fa.s220.2.7.7.80.10.50.1000.17.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: Scaffold220
Parameters: 2 7 7 80 10 50 1000
Length:  3999181

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   

This is table  17  of  19  ( 2201 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)
3559334--3559372	18	2.1	18	90	4	60	48	0	2	48	1.15
3559343--3559405	30	2.0	32	85	11	87	42	0	1	55	1.09
3559568--3559618	20	2.5	21	80	6	59	52	0	0	47	1.00
3560581--3560631	17	2.8	19	83	16	65	60	0	0	39	0.97
3563118--3563158	19	2.2	19	86	8	57	2	14	2	80	0.92
3563684--3564036	190	1.8	194	81	6	450	39	12	6	41	1.69
3565217--3565253	11	3.5	11	89	10	51	83	0	16	0	0.64
3571012--3571070	17	3.6	17	76	10	54	33	0	0	66	0.92
3573844--3574125	99	2.8	99	93	0	483	37	20	27	14	1.91
3589993--3590072	28	2.9	26	76	12	70	23	26	21	28	1.99
3590058--3590174	51	2.3	51	84	10	159	32	23	11	33	1.90
3590031--3590272	131	1.9	130	81	7	303	28	23	13	34	1.92
3592399--3592495	4	24.2	4	91	0	86	37	0	11	51	1.38
3594065--3594093	2	14.5	2	100	0	58	48	0	0	51	1.00
3594972--3595032	22	2.7	22	79	16	70	49	0	1	49	1.10
3594972--3595030	23	2.5	24	82	12	70	49	0	1	49	1.11
3598341--3598392	2	26.0	2	100	0	104	0	50	0	50	1.00
3601161--3601192	10	2.8	12	90	9	50	50	12	37	0	1.41
3601161--3601192	6	5.7	6	85	14	50	50	12	37	0	1.41
3601752--3601785	14	2.4	14	85	0	50	50	0	0	50	1.00
3601842--3601913	21	3.3	21	67	17	65	48	0	1	50	1.09
3602325--3602368	13	3.4	12	84	12	52	68	2	0	29	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3604009--3604158	23	6.0	23	69	21	90	39	0	1	59	1.06
3604165--3604198	10	3.4	10	83	0	50	73	2	0	23	0.97
3605940--3605974	17	2.1	17	94	0	61	45	8	20	25	1.79
3606228--3606277	21	2.3	22	82	3	57	70	0	18	12	1.17
3609477--3609520	2	22.0	2	100	0	88	50	0	0	50	1.00
3610580--3610650	28	2.6	28	78	14	76	52	0	0	47	1.00
3611147--3611173	14	1.9	14	100	0	54	37	3	0	59	1.15
3611305--3611368	33	1.9	33	81	12	78	65	1	0	32	1.02
3612377--3612423	20	2.5	20	86	10	64	38	0	0	61	0.96
3612693--3612749	22	2.5	22	86	8	71	31	8	8	50	1.64
3613343--3613383	21	2.0	20	85	4	55	41	7	0	51	1.30
3613512--3613556	21	2.0	23	83	8	58	37	0	2	60	1.09
3614008--3614046	20	2.0	20	85	10	53	48	0	0	51	1.00
3614046--3614092	21	2.2	21	81	7	60	42	0	0	57	0.98
3615325--3615352	14	2.0	14	100	0	56	42	7	0	50	1.30
3624453--3624499	2	24.0	2	89	4	69	53	2	44	0	1.12
3624883--3624952	24	3.0	23	80	15	72	62	0	0	37	0.95
3625993--3626026	2	17.0	2	100	0	68	50	0	0	50	1.00
3627453--3627607	76	2.0	76	93	2	267	38	2	27	31	1.70
3633656--3633722	25	2.7	24	79	4	71	43	0	0	56	0.99
3634934--3635014	24	3.5	23	75	14	69	62	2	0	34	1.08
3634974--3635041	19	3.3	21	79	8	59	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3636522--3636554	5	6.6	5	100	0	66	78	0	21	0	0.75
3637940--3637973	13	2.6	13	95	0	59	50	0	0	50	1.00
3638729--3638774	23	2.0	22	84	12	58	52	2	4	41	1.33
3639095--3639142	21	2.2	23	85	7	64	56	2	0	41	1.11
3639594--3639668	30	2.4	31	78	14	84	46	4	2	46	1.35
3639651--3639735	19	4.4	18	73	17	66	58	1	0	40	1.05
3639692--3639740	23	2.1	22	82	14	55	63	0	0	36	0.95
3639979--3640027	25	2.0	25	83	0	62	53	0	2	44	1.12
3647022--3647046	2	12.5	2	100	0	50	0	48	0	52	1.00
3647334--3647389	23	2.4	23	78	3	58	12	30	7	50	1.67
3650626--3650713	28	3.1	28	96	0	167	39	20	7	31	1.81
3651388--3651425	2	19.0	2	94	0	67	47	0	2	50	1.15
3654455--3654509	25	2.2	25	96	3	103	32	14	12	40	1.84
3658100--3658141	22	1.9	22	85	9	59	33	0	4	61	1.17
3658961--3659010	12	4.0	12	80	10	55	40	2	0	58	1.10
3658968--3659010	6	6.8	6	82	10	50	41	0	0	58	0.98
3658968--3659012	20	2.4	19	88	7	65	42	0	0	57	0.98
3658983--3659034	17	3.2	17	82	15	58	44	0	0	55	0.99
3659009--3659042	17	2.0	17	100	0	68	41	0	0	58	0.98
3659616--3659645	8	3.9	8	95	4	53	36	0	0	63	0.95
3659617--3659667	16	3.1	16	78	13	50	37	0	0	62	0.95
3666708--3666774	29	2.4	28	80	12	75	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3666747--3666781	18	1.9	18	88	0	52	40	2	0	57	1.14
3666788--3666816	2	14.5	2	100	0	58	51	0	0	48	1.00
3667713--3667768	20	2.8	20	71	10	53	62	0	0	37	0.95
3668603--3668673	36	2.0	36	94	0	124	47	8	2	40	1.48
3671276--3671306	2	15.5	2	100	0	62	48	0	0	51	1.00
3671791--3671821	14	2.2	14	94	0	53	54	0	0	45	0.99
3674405--3674454	17	3.1	16	80	11	57	52	0	0	48	1.00
3674412--3674454	15	2.6	16	82	10	52	48	0	0	51	1.00
3676391--3676423	13	2.4	14	85	10	50	63	6	0	30	1.18
3677157--3677239	34	2.4	33	82	11	96	55	2	1	40	1.21
3678324--3678362	20	2.0	20	84	0	51	69	0	0	30	0.89
3684782--3684863	38	2.2	37	95	4	146	52	9	7	30	1.61
3684790--3684855	22	3.3	22	63	30	56	54	6	9	30	1.56
3690889--3690955	33	2.0	33	94	0	116	17	13	17	50	1.77
3695936--3695970	3	11.7	3	100	0	70	34	0	0	65	0.93
3696989--3697025	2	18.5	2	94	0	56	43	0	5	51	1.24
3703825--3703858	2	16.5	2	93	6	59	50	2	0	47	1.16
3704337--3704362	2	13.0	2	100	0	52	0	0	50	50	1.00
3705203--3705255	18	3.2	18	74	20	69	49	0	0	50	1.00
3707363--3707453	44	2.0	46	83	8	116	46	0	1	52	1.07
3707363--3707435	23	3.2	23	73	16	71	39	0	1	58	1.06
3707539--3707607	22	3.0	23	79	16	63	57	0	1	40	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3707572--3707605	13	2.5	13	90	4	50	58	0	0	41	0.98
3707542--3707610	35	2.0	34	86	8	95	59	0	1	39	1.06
3714604--3714649	22	2.1	22	100	0	92	34	0	15	50	1.44
3714739--3714786	14	3.4	14	75	8	53	60	2	0	37	1.09
3716289--3716342	14	3.9	14	80	4	56	50	1	1	46	1.23
3725085--3725148	30	2.1	30	83	11	78	40	4	7	46	1.53
3726979--3727134	40	4.0	39	72	21	109	57	0	1	41	1.07
3727032--3727116	30	2.8	28	82	12	89	56	0	1	42	1.07
3727036--3727134	10	9.6	10	69	12	58	55	0	2	42	1.11
3728133--3728433	150	2.0	150	92	2	498	33	5	13	46	1.68
3730942--3730971	2	15.0	2	100	0	60	50	0	0	50	1.00
3732192--3732479	146	2.0	144	84	1	378	37	11	22	28	1.89
3734828--3734865	18	2.1	19	90	5	60	55	0	0	44	0.99
3734842--3734889	22	2.1	23	92	3	80	50	0	0	50	1.00
3735016--3735049	16	2.2	16	89	5	52	17	5	8	67	1.37
3735581--3735614	2	17.0	2	100	0	68	50	0	0	50	1.00
3742610--3742638	2	15.0	2	92	7	51	48	0	0	51	1.00
3744296--3744329	17	1.9	18	88	5	52	38	0	2	58	1.13
3746601--3746669	28	2.5	28	71	17	72	59	0	1	39	1.06
3746654--3746693	17	2.3	18	83	12	57	62	0	0	37	0.95
3746694--3746751	18	3.3	17	74	11	55	50	3	0	46	1.18
3746743--3746808	33	2.0	34	87	3	98	34	1	0	63	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3747987--3748019	2	16.5	2	100	0	66	0	48	0	51	1.00
3749525--3749567	2	21.5	2	100	0	86	48	0	0	51	1.00
3752127--3752153	2	13.5	2	100	0	54	48	0	0	51	1.00
3753295--3753332	2	19.5	2	94	5	69	50	0	0	50	1.00
3753926--3753957	16	1.9	17	93	6	57	56	0	0	43	0.99
3769375--3769412	19	2.0	20	84	5	51	63	5	0	31	1.17
3770427--3770485	25	2.2	27	80	17	70	37	1	3	57	1.25
3772623--3772661	2	19.5	2	83	0	51	46	2	0	51	1.14
3773869--3773910	16	2.6	17	78	21	54	42	0	0	57	0.99
3773870--3773910	9	5.1	8	81	18	50	41	0	0	58	0.98

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19