genome.fa.s25.2.7.7.80.10.50.1000.20.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  20  of  56  ( 6609 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)
3605175--3605210	18	2.0	18	100	0	72	44	16	16	22	1.86
3609810--3609875	34	2.0	33	81	3	78	22	27	28	21	1.99
3611697--3611722	2	13.0	2	100	0	52	50	0	50	0	1.00
3612796--3612844	26	1.9	26	83	4	64	12	8	8	71	1.31
3613729--3613815	11	8.1	11	73	16	58	36	1	6	55	1.34
3613730--3613813	32	2.7	30	80	14	98	36	1	7	54	1.35
3614315--3614402	10	9.3	10	67	16	62	38	0	0	61	0.96
3614316--3614402	37	2.3	37	88	5	122	39	0	0	60	0.97
3615583--3615609	7	3.9	7	100	0	54	25	0	0	74	0.83
3616079--3616119	21	2.0	20	86	13	57	43	0	0	56	0.99
3616079--3616122	22	2.0	21	83	12	54	45	0	0	54	0.99
3616628--3616720	8	10.8	8	76	16	71	56	0	0	43	0.99
3616604--3616690	26	3.7	23	71	21	65	52	0	1	45	1.08
3616629--3616720	27	3.6	25	74	20	91	57	0	0	42	0.98
3617259--3617298	21	2.1	18	86	13	53	55	5	5	35	1.44
3617304--3617340	17	2.1	18	90	5	58	40	0	0	59	0.97
3617317--3617359	15	2.9	14	83	10	50	37	2	0	60	1.10
3619178--3619234	26	2.2	25	90	3	87	57	0	0	42	0.98
3619901--3619962	22	2.8	21	80	14	63	46	0	0	53	1.00
3621351--3621410	30	2.0	30	87	6	86	63	0	1	35	1.05
3621372--3621540	25	6.4	25	68	18	69	57	0	1	41	1.06
3621358--3621519	11	15.3	11	63	21	69	58	0	1	40	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3621359--3621519	30	5.4	29	69	19	93	57	0	1	40	1.06
3621418--3621469	15	3.2	16	79	17	63	57	0	0	42	0.98
3621418--3621488	16	4.5	16	72	20	53	54	0	0	45	0.99
3621418--3621502	31	2.8	30	84	8	100	57	0	0	42	0.98
3621478--3621519	5	8.2	5	82	15	50	64	0	0	35	0.94
3621431--3621520	47	1.9	46	82	10	112	60	0	0	40	0.97
3621352--3621514	19	8.4	20	63	18	67	58	0	1	40	1.06
3621730--3621798	31	2.2	30	82	10	77	42	0	5	52	1.25
3621880--3621929	19	2.7	18	80	17	57	50	2	0	48	1.12
3623841--3623930	42	2.1	42	86	6	128	51	4	3	41	1.39
3624429--3624465	13	2.6	14	91	8	58	27	0	0	72	0.84
3624616--3624675	27	2.3	26	72	16	63	55	0	0	45	0.99
3624824--3624855	10	3.1	11	86	13	50	75	0	0	25	0.81
3624780--3624843	30	2.2	28	79	17	69	53	0	3	43	1.16
3627125--3627149	12	2.1	12	100	0	50	76	0	0	24	0.80
3634142--3634180	13	3.0	12	82	17	51	41	0	0	58	0.98
3634141--3634193	16	3.8	13	75	18	52	41	0	0	58	0.98
3635557--3635625	26	2.6	26	95	2	120	65	0	0	34	0.93
3635613--3635644	11	2.9	11	95	0	55	68	3	0	28	1.04
3635547--3635655	55	1.9	57	82	14	138	64	0	0	34	1.00
3635804--3635853	26	1.9	27	84	8	68	46	0	2	52	1.12
3641023--3641051	7	4.3	7	95	4	51	0	0	10	89	0.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3641143--3641177	2	17.5	2	100	0	70	51	0	0	48	1.00
3641574--3641603	13	2.4	13	94	5	53	70	0	0	30	0.88
3644810--3644845	3	12.0	3	100	0	72	66	0	0	33	0.92
3645866--3645922	22	2.6	22	80	8	62	47	0	1	50	1.11
3645924--3645948	2	12.5	2	100	0	50	52	0	48	0	1.00
3646333--3646365	16	2.0	17	94	5	59	57	6	0	36	1.23
3647588--3647637	2	26.0	2	76	8	50	42	2	6	50	1.38
3647594--3647637	8	5.6	8	86	5	63	40	2	6	50	1.42
3647786--3647864	19	4.1	20	67	22	51	35	0	1	63	1.03
3649458--3649498	21	1.9	22	85	5	57	60	4	0	34	1.18
3649949--3649984	2	18.5	2	88	5	56	52	2	0	44	1.15
3653664--3653727	12	5.4	12	75	15	62	34	0	0	65	0.93
3653671--3653728	11	5.2	11	75	8	55	37	0	0	62	0.96
3653671--3653742	23	3.1	23	83	16	87	41	0	0	58	0.98
3654744--3654844	8	12.9	8	68	24	56	59	0	0	40	0.97
3654752--3654789	11	3.5	11	79	13	51	65	0	0	34	0.93
3654735--3654796	27	2.4	25	83	8	70	61	0	0	38	0.96
3654737--3654856	33	3.5	34	78	11	95	58	0	0	41	0.98
3654777--3654857	14	5.1	16	71	20	55	58	0	0	41	0.98
3654758--3654854	32	3.2	32	76	9	96	58	0	0	41	0.98
3655211--3655246	18	2.1	17	89	5	54	52	5	0	41	1.24
3655218--3655249	16	2.0	16	93	0	55	53	6	0	40	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3656804--3656864	30	2.0	31	87	6	88	63	0	13	22	1.28
3663103--3663132	2	15.0	2	100	0	60	0	0	50	50	1.00
3667216--3667254	18	2.2	17	86	4	51	43	2	0	53	1.14
3667306--3667335	11	2.6	11	94	5	51	30	3	0	66	1.07
3667724--3667759	2	18.0	2	100	0	72	50	0	50	0	1.00
3668313--3668354	18	2.4	17	80	11	50	61	0	2	35	1.09
3668324--3668377	26	2.0	28	83	16	71	55	0	3	40	1.17
3668802--3668852	10	5.4	9	75	15	50	29	0	0	70	0.87
3668801--3668861	20	3.0	21	81	11	74	31	0	0	68	0.89
3668801--3668864	21	3.1	22	80	13	82	31	0	0	68	0.90
3668802--3668878	38	2.0	39	82	12	97	31	0	1	67	0.99
3668872--3668916	21	2.0	23	84	16	60	35	0	6	57	1.25
3668871--3668921	23	2.2	24	77	22	56	37	0	5	56	1.23
3668891--3668951	32	1.9	32	86	0	86	37	0	1	60	1.07
3668918--3668996	28	2.8	29	79	14	76	37	1	1	59	1.14
3668997--3669052	21	2.8	20	81	7	69	48	0	0	51	1.00
3668992--3669061	20	3.5	20	75	16	72	44	0	1	54	1.09
3670968--3671041	25	3.0	25	73	11	71	39	0	0	60	0.97
3670959--3671035	15	4.8	16	75	17	70	36	0	0	63	0.95
3671235--3671305	30	2.5	28	82	11	74	42	1	0	56	1.08
3671254--3671302	18	2.6	18	81	12	55	46	0	0	53	1.00
3676339--3676401	19	3.3	19	79	14	67	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3676397--3676454	23	2.5	23	76	18	66	62	0	1	36	1.06
3676864--3676894	16	1.9	16	93	0	53	58	0	0	41	0.98
3677054--3677083	2	15.0	2	100	0	60	50	0	0	50	1.00
3677504--3677540	14	2.6	14	91	0	56	0	21	0	78	0.75
3682864--3682911	25	1.9	25	86	0	69	0	22	6	70	1.09
3683304--3683337	16	2.1	16	89	10	52	82	2	2	11	0.89
3684015--3684065	19	2.5	21	81	12	61	49	0	1	49	1.12
3684015--3684071	21	2.8	21	79	10	57	47	0	1	50	1.11
3684591--3684661	29	2.7	26	81	16	83	38	0	2	59	1.12
3684713--3684753	13	3.2	13	89	3	57	46	0	0	53	1.00
3684714--3684753	12	3.3	12	86	10	55	45	0	0	55	0.99
3684735--3684787	23	2.3	22	75	9	52	43	0	0	56	0.99
3684701--3684804	43	2.3	44	79	15	117	50	0	0	49	1.00
3684784--3684854	17	3.9	17	71	20	54	61	0	2	35	1.10
3685319--3685361	22	1.9	23	90	4	70	53	0	0	46	1.00
3686197--3686239	15	2.6	17	85	10	63	58	0	0	41	0.98
3686257--3686306	18	2.6	19	81	9	57	50	0	2	48	1.12
3687188--3687248	22	2.8	20	81	13	68	67	4	1	26	1.20
3687329--3687370	12	3.4	13	80	9	52	7	14	0	78	0.95
3687329--3687379	26	2.0	26	88	3	77	5	13	0	80	0.89
3687345--3687390	22	2.0	23	87	4	67	4	15	0	80	0.86
3687324--3687375	12	4.2	12	76	9	50	5	13	0	80	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3687344--3687373	16	1.9	16	93	6	53	3	10	0	86	0.67
3687344--3687390	23	2.0	23	88	8	69	4	14	0	80	0.85
3687538--3687589	23	2.2	22	90	10	77	65	0	0	34	0.93
3689806--3689849	2	22.0	2	95	0	79	50	0	2	47	1.13
3698967--3698997	5	6.2	5	92	0	53	58	0	3	38	1.15
3699705--3699786	31	2.7	28	72	18	67	59	3	2	34	1.28
3706911--3706979	25	2.8	25	78	12	79	37	0	0	62	0.96
3707357--3707413	21	2.8	21	91	2	89	59	3	0	36	1.14
3708141--3708172	2	16.0	2	100	0	64	50	0	0	50	1.00
3715105--3715226	60	2.1	59	95	1	217	36	9	23	30	1.87

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   46   47   48   
          49   50   51   52   53   54   55   56