genome.fa.s64.2.7.7.80.10.50.1000.21.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   

This is table  21  of  45  ( 5312 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)
3924903--3924955	23	2.4	22	78	6	61	45	0	1	52	1.11
3928855--3928905	27	2.0	27	85	14	72	50	0	0	49	1.00
3928942--3929010	12	5.3	12	73	20	50	42	0	0	57	0.98
3928959--3928997	15	2.5	16	83	8	53	35	0	0	64	0.94
3928954--3929015	28	2.2	28	83	16	76	40	0	0	59	0.97
3928997--3929063	24	2.7	26	78	17	72	47	0	0	52	1.00
3929020--3929052	15	2.1	16	88	5	50	51	0	0	48	1.00
3929048--3929101	22	2.5	21	82	8	63	33	1	1	62	1.16
3930045--3930070	3	8.7	3	100	0	52	69	0	0	30	0.89
3930474--3930501	12	2.3	12	100	0	56	57	0	0	42	0.99
3935579--3935665	30	2.9	30	81	8	104	54	1	2	42	1.20
3936401--3936456	13	4.1	14	74	21	57	41	0	1	57	1.09
3936404--3936456	7	8.0	7	74	19	51	41	0	1	56	1.10
3936779--3936832	24	2.2	24	83	6	65	57	0	0	42	0.98
3936779--3936829	23	2.2	24	85	3	68	58	0	0	41	0.98
3936834--3936886	22	2.6	21	80	11	56	52	0	1	45	1.11
3937849--3937885	14	2.6	15	87	8	51	62	0	0	37	0.96
3938229--3938254	12	2.2	12	100	0	52	80	0	19	0	0.71
3939147--3939219	25	2.6	30	67	22	68	58	1	0	39	1.06
3939112--3939236	65	1.9	66	80	12	150	56	0	0	43	1.05
3939184--3939246	33	1.9	31	84	9	81	55	1	0	42	1.09
3939173--3939269	40	2.4	41	78	15	94	55	1	0	43	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3941165--3941214	16	3.1	16	82	0	64	66	0	6	28	1.15
3942269--3942314	25	1.9	25	91	8	78	60	0	0	39	0.97
3942570--3942630	20	3.0	20	85	9	70	52	0	0	47	1.00
3942638--3942701	24	2.7	23	80	9	74	46	0	0	53	1.00
3944612--3944665	11	5.2	10	76	14	56	33	0	0	66	0.92
3944741--3944814	26	2.8	25	70	25	64	54	1	0	44	1.08
3946673--3946727	21	2.6	21	76	0	65	65	0	0	34	0.93
3946666--3946728	14	4.4	14	76	9	65	61	0	0	38	0.96
3946929--3946962	16	2.1	16	88	0	50	41	0	0	58	0.98
3953450--3953537	29	3.0	29	94	0	149	44	15	15	23	1.86
3954493--3954561	33	2.1	33	83	5	86	33	0	5	60	1.20
3954510--3954554	21	2.1	22	84	12	58	35	0	2	62	1.08
3954508--3954561	27	2.0	28	85	10	76	33	0	3	62	1.12
3954514--3954576	33	1.9	33	83	6	83	34	0	6	58	1.23
3956269--3956423	18	9.3	18	69	25	101	58	0	0	41	0.98
3956271--3956410	11	13.1	11	72	20	70	58	0	0	41	0.98
3956248--3956422	71	2.5	72	80	11	193	57	0	1	41	1.06
3956305--3956430	16	8.1	16	69	23	83	58	0	0	41	0.98
3956773--3956814	22	1.9	22	95	0	75	59	0	2	38	1.10
3956797--3956898	24	4.0	25	73	12	100	58	0	0	40	1.04
3956816--3956863	19	2.5	20	80	9	57	58	0	2	39	1.10
3956778--3956885	32	3.5	32	77	8	89	58	0	1	39	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3956775--3956885	52	2.3	47	84	13	136	58	0	1	39	1.09
3956844--3956917	32	2.3	32	86	11	98	59	0	0	40	0.97
3956853--3956918	18	3.9	17	73	26	59	59	0	0	40	0.98
3956797--3956929	27	4.9	27	69	24	86	60	0	0	38	1.02
3965107--3965186	41	2.0	41	97	0	151	42	5	8	43	1.57
3967069--3967107	19	2.0	20	85	5	53	25	0	2	71	0.98
3967104--3967191	31	3.3	26	77	16	74	42	1	0	56	1.06
3967089--3967168	31	2.5	33	84	11	114	38	0	0	61	0.96
3968859--3968899	15	2.8	14	85	10	55	39	0	0	60	0.96
3968862--3968914	16	3.2	16	80	15	54	45	0	0	54	0.99
3971427--3971459	14	2.3	15	89	5	50	36	0	9	54	1.32
3971765--3971827	18	3.4	18	72	20	67	22	3	3	71	1.14
3971752--3971832	37	2.2	37	97	0	153	25	2	2	69	1.14
3971759--3971829	24	2.9	24	79	10	63	22	2	2	71	1.12
3971851--3971897	17	2.8	17	84	12	62	46	4	4	44	1.42
3971851--3971885	16	2.1	16	89	5	52	45	5	5	42	1.51
3971872--3971931	25	2.2	27	77	20	70	50	3	3	43	1.35
3971884--3971940	25	2.3	25	84	6	71	54	1	1	42	1.21
3973135--3973165	3	10.3	3	100	0	62	67	0	32	0	0.91
3976530--3976601	22	3.2	22	71	11	65	68	1	2	27	1.12
3976529--3976564	17	2.1	17	90	10	56	75	0	0	25	0.81
3976848--3976876	2	14.5	2	100	0	58	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)
3983084--3983134	20	2.3	23	83	12	72	35	0	0	64	0.94
3984699--3984769	28	2.4	32	80	17	91	39	0	0	60	0.97
3985983--3986020	14	2.9	14	84	11	53	55	0	0	44	0.99
3985991--3986048	29	2.0	30	82	3	73	48	0	0	51	1.00
3986471--3986512	22	2.0	21	85	4	57	64	0	0	35	0.94
3997178--3997202	2	12.5	2	100	0	50	52	0	0	48	1.00
3997188--3997243	28	2.0	27	93	3	94	53	7	12	26	1.64
4003445--4003478	2	17.0	2	100	0	68	50	0	0	50	1.00
4005643--4005726	29	2.9	29	72	11	84	54	0	0	45	0.99
4005719--4005780	20	3.0	21	81	9	74	41	0	0	58	0.98
4005753--4005794	20	2.1	20	91	8	68	47	0	0	52	1.00
4005786--4005825	17	2.4	17	87	4	55	57	5	0	37	1.21
4006200--4006234	8	4.4	8	86	13	54	25	0	0	74	0.82
4007939--4008873	465	2.0	465	92	0	1566	35	14	11	38	1.82
4009441--4009495	16	3.4	17	75	25	64	43	0	0	56	0.99
4009438--4009501	32	2.0	33	90	3	103	46	0	0	53	1.00
4009451--4009502	14	3.4	14	73	19	50	50	0	0	50	1.00
4009451--4009504	16	3.4	16	72	10	56	50	0	0	50	1.00
4009997--4010053	12	4.8	12	74	18	57	1	15	0	82	0.75
4009994--4010045	18	2.7	21	79	8	58	3	15	0	80	0.85
4009991--4010053	24	2.7	23	80	4	81	4	14	0	80	0.86
4010003--4010053	8	6.2	8	73	13	50	1	15	0	82	0.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4015456--4015519	18	3.5	20	74	21	68	39	0	1	59	1.07
4015457--4015558	17	6.2	16	71	19	59	37	0	0	61	1.03
4015427--4015517	35	2.6	34	83	10	103	40	0	1	58	1.05
4015457--4015526	17	3.8	18	74	14	63	38	0	1	60	1.06
4015435--4015536	23	4.5	22	72	17	82	38	0	0	60	1.03
4015771--4015805	17	1.9	18	88	11	54	42	0	0	57	0.99
4015826--4015879	17	3.0	18	83	8	65	38	0	0	61	0.96
4024178--4024219	15	2.6	16	92	7	68	57	0	0	42	0.99
4024658--4024709	15	3.4	15	78	5	59	55	1	1	40	1.22
4025407--4025441	18	2.1	17	89	10	54	28	0	0	71	0.86
4025397--4025438	21	2.1	20	91	8	68	33	0	0	66	0.92
4025397--4025450	20	2.7	20	80	8	56	33	0	0	66	0.92
4027483--4027521	16	2.5	15	88	8	60	53	0	0	46	1.00
4027767--4027805	17	2.2	19	86	9	55	25	0	7	66	1.18
4028063--4028103	16	2.6	16	80	3	57	73	2	0	24	0.96
4029290--4029335	20	2.2	21	85	14	60	52	0	0	47	1.00
4031891--4031962	37	1.9	37	85	0	99	27	25	6	40	1.81
4038230--4038367	71	1.9	71	91	0	222	49	8	2	39	1.49
4043098--4043176	33	2.5	31	82	13	92	53	0	0	46	1.00
4043122--4043188	20	3.1	22	73	16	61	50	0	0	49	1.00
4043470--4043495	5	5.2	5	100	0	52	23	19	38	19	1.93
4044884--4044914	16	1.9	16	93	0	53	64	0	0	35	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4046472--4046512	22	1.9	21	95	5	73	24	21	0	53	1.46
4046578--4046630	16	3.4	16	78	5	63	62	0	3	33	1.13
4046850--4046885	17	2.1	17	94	0	63	58	8	0	33	1.28
4047013--4047040	2	14.0	2	100	0	56	50	0	50	0	1.00
4047251--4047292	15	3.3	12	79	20	50	52	0	0	47	1.00
4047230--4047292	27	2.2	28	83	10	76	47	0	1	50	1.10
4047550--4047596	16	2.9	16	78	12	60	40	0	4	55	1.19
4048003--4048055	27	2.0	27	100	0	106	33	3	1	60	1.26
4048336--4048365	15	1.9	16	93	6	53	36	6	10	46	1.64
4048798--4048844	17	2.7	18	77	9	53	31	2	0	65	1.04

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   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45