genome.fa.s8.2.7.7.80.10.50.1000.22.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  22  of  33  ( 3942 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)
3520572--3520613	19	2.2	19	83	8	50	33	0	2	64	1.07
3524106--3524144	13	3.2	13	92	7	64	43	0	0	56	0.99
3524112--3524149	13	3.4	11	89	10	51	44	0	0	55	0.99
3525462--3525510	18	2.7	18	80	3	53	34	0	4	61	1.15
3528749--3528790	13	3.4	13	87	6	52	9	4	0	85	0.72
3529066--3529123	12	5.1	12	73	10	59	39	0	0	60	0.97
3529066--3529145	23	3.4	23	74	10	65	41	0	0	58	0.98
3529092--3529157	22	3.0	23	81	14	68	42	0	0	57	0.98
3529703--3529752	3	16.7	3	95	0	91	32	2	0	66	1.03
3536383--3536434	21	2.6	20	79	8	61	32	1	3	61	1.25
3542752--3542790	18	2.2	18	86	9	53	69	0	5	25	1.09
3544781--3544841	30	2.0	30	100	0	122	31	13	9	45	1.75
3547877--3547911	2	17.5	2	100	0	70	0	0	51	48	1.00
3549990--3550015	10	2.6	10	100	0	52	15	19	0	65	1.27
3554058--3554083	2	13.0	2	100	0	52	50	0	50	0	1.00
3555637--3555679	16	2.7	16	88	0	59	58	2	0	39	1.11
3556013--3556037	2	12.5	2	100	0	50	48	0	52	0	1.00
3556036--3556071	3	12.0	3	93	0	63	33	33	30	2	1.72
3556929--3556960	2	16.0	2	93	0	55	46	0	0	53	1.00
3556921--3556954	14	2.4	14	90	0	50	44	5	0	50	1.26
3556995--3557041	17	2.8	17	84	9	53	55	0	0	44	0.99
3557001--3557060	27	2.3	25	80	5	66	55	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3557663--3557687	2	12.5	2	100	0	50	48	0	0	52	1.00
3563054--3563084	2	15.5	2	100	0	62	48	0	0	51	1.00
3563679--3563732	2	28.0	2	82	14	69	53	0	1	44	1.11
3564201--3564239	6	6.2	6	82	11	51	56	0	0	43	0.99
3564194--3564236	20	2.2	19	91	4	68	62	0	0	37	0.95
3567532--3567569	13	3.0	13	92	3	60	92	7	0	0	0.40
3571310--3571348	20	2.0	20	84	0	51	53	0	0	46	1.00
3571316--3571376	20	2.8	20	83	14	61	49	0	0	50	1.00
3571313--3571377	22	2.9	22	79	11	69	50	0	0	49	1.00
3571625--3571657	2	16.5	2	100	0	66	48	0	0	51	1.00
3575232--3575263	6	5.3	6	92	0	55	0	21	15	62	1.32
3576077--3576102	2	13.0	2	100	0	52	50	0	0	50	1.00
3578398--3578438	14	2.8	15	81	7	57	48	4	2	43	1.37
3588766--3589308	270	2.0	272	94	1	948	40	25	13	20	1.89
3590148--3590232	42	2.0	42	100	0	170	16	14	28	41	1.87
3590151--3590217	21	3.2	21	64	16	57	14	14	28	41	1.86
3591186--3591215	14	2.1	14	93	0	51	26	6	6	60	1.47
3592062--3592087	3	8.7	3	100	0	52	30	0	0	69	0.89
3596217--3596252	2	18.0	2	94	0	63	50	2	0	47	1.15
3597042--3597072	2	15.5	2	100	0	62	48	0	0	51	1.00
3603214--3603279	34	1.9	34	90	0	105	45	16	15	22	1.85
3604240--3604316	30	2.6	30	91	0	127	44	15	15	24	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3604261--3604326	30	2.4	28	85	10	82	46	13	15	24	1.81
3606555--3606587	2	16.5	2	100	0	66	48	0	51	0	1.00
3617304--3617358	29	2.0	28	82	7	67	43	5	3	47	1.44
3619461--3619512	22	2.3	23	84	12	65	55	1	0	42	1.10
3624549--3624594	6	7.8	6	86	13	53	39	0	0	60	0.97
3624548--3624606	29	2.1	28	90	3	91	40	3	0	55	1.16
3624548--3624592	23	2.0	23	87	12	67	40	0	0	60	0.97
3628307--3628345	2	19.5	2	100	0	78	48	0	0	51	1.00
3628696--3628720	2	12.5	2	100	0	50	52	0	0	48	1.00
3629282--3629315	17	1.9	18	88	5	52	44	0	0	55	0.99
3629322--3629353	16	2.0	16	93	0	55	53	0	0	46	1.00
3629331--3629378	25	1.9	25	83	8	62	45	0	0	54	0.99
3629326--3629409	34	2.4	34	76	9	91	45	0	2	52	1.13
3629666--3629761	11	9.7	11	66	25	54	43	1	0	55	1.06
3630256--3630307	17	3.1	17	78	13	63	51	0	0	48	1.00
3630262--3630319	17	3.4	17	80	4	64	51	0	3	44	1.18
3630299--3630341	22	2.0	22	85	0	59	55	2	4	37	1.33
3632355--3632393	20	1.9	21	94	5	71	28	2	0	69	1.02
3632823--3632953	41	3.0	41	75	18	133	45	0	1	52	1.15
3632971--3633014	22	2.0	22	82	8	54	47	4	0	47	1.22
3633141--3633168	2	14.0	2	100	0	56	50	0	50	0	1.00
3634317--3634342	3	8.7	3	100	0	52	34	0	30	34	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3636009--3636038	13	2.3	13	94	0	51	53	0	3	43	1.17
3641619--3641654	3	12.0	3	100	0	72	66	0	0	33	0.92
3642016--3642065	2	25.5	2	95	4	93	50	0	0	50	1.00
3649347--3649392	21	2.2	21	88	7	67	50	0	0	50	1.00
3649626--3649683	25	2.2	27	84	9	84	50	0	0	50	1.00
3650081--3650129	17	2.8	17	80	19	57	51	0	0	48	1.00
3650245--3650279	17	2.1	16	89	5	52	71	0	0	28	0.86
3655282--3655315	3	11.3	3	100	0	68	64	0	0	35	0.94
3656978--3657018	2	20.5	2	100	0	82	0	51	0	48	1.00
3657833--3657872	19	2.2	18	86	4	53	62	5	15	17	1.49
3658812--3658842	2	16.0	2	93	6	55	48	0	0	51	1.00
3659231--3659256	2	13.0	2	100	0	52	50	0	0	50	1.00
3660032--3660077	22	2.0	23	87	12	67	54	0	0	45	0.99
3660032--3660079	24	2.0	25	84	12	64	56	0	0	43	0.99
3661989--3662057	20	3.6	20	69	15	56	44	0	0	55	0.99
3661978--3662044	32	2.1	32	83	5	82	46	0	0	53	1.00
3670485--3670518	2	17.0	2	100	0	68	50	0	0	50	1.00
3672313--3672822	255	2.0	255	99	0	1011	29	10	22	37	1.87
3686220--3686257	2	19.0	2	94	0	67	52	0	0	47	1.00
3689263--3689299	3	12.3	3	100	0	74	67	0	0	32	0.91
3690675--3690704	2	15.0	2	100	0	60	50	0	0	50	1.00
3692860--3693050	96	2.0	96	88	0	283	29	14	15	40	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3696401--3696452	20	2.6	20	85	11	63	51	0	0	48	1.00
3706319--3706343	2	12.5	2	100	0	50	48	0	0	52	1.00
3718881--3718959	23	3.3	23	79	10	63	41	0	0	58	0.98
3718911--3718955	16	2.7	18	86	13	69	35	0	0	64	0.94
3721528--3721571	2	22.0	2	100	0	88	50	0	0	50	1.00
3724020--3724052	2	16.0	2	93	6	57	48	0	3	48	1.17
3724113--3724147	2	17.5	2	100	0	70	51	0	0	48	1.00
3724794--3724833	21	1.9	21	89	0	62	45	0	0	55	0.99
3725544--3725610	30	2.2	31	84	7	84	34	1	0	64	1.03
3725751--3725781	2	15.5	2	100	0	62	48	0	0	51	1.00
3728256--3728321	13	5.1	13	76	10	64	39	0	1	59	1.07
3728769--3728817	26	1.9	26	87	4	73	44	0	4	51	1.20
3728784--3728829	17	2.6	17	86	3	65	39	0	0	60	0.97
3728782--3728829	9	5.6	8	76	13	51	39	0	0	60	0.97
3728779--3728831	26	2.0	26	85	7	72	43	0	0	56	0.99
3729476--3729530	16	3.4	16	74	25	53	40	0	0	60	0.97
3729477--3729529	21	2.7	21	80	11	58	39	0	0	60	0.97
3730502--3730537	3	12.0	3	100	0	72	33	0	0	66	0.92
3730677--3730722	21	2.1	23	84	8	60	43	6	2	47	1.41
3732236--3732261	2	13.0	2	100	0	52	50	0	0	50	1.00
3732364--3732391	12	2.3	12	100	0	56	50	7	7	35	1.57
3736112--3736141	13	2.4	13	94	5	53	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3736112--3736141	6	4.8	6	92	8	51	53	0	0	46	1.00
3744106--3744139	16	2.1	17	94	5	61	41	8	0	50	1.34
3744385--3744413	2	14.5	2	100	0	58	51	0	0	48	1.00
3745128--3745154	2	13.5	2	100	0	54	0	48	0	51	1.00
3752556--3752598	21	2.0	21	82	8	52	62	2	0	34	1.08
3752591--3752629	20	1.9	21	94	5	71	51	0	0	48	1.00
3754100--3754144	23	2.0	23	91	8	76	66	0	0	33	0.92
3754124--3754205	32	2.6	32	79	11	98	52	1	0	46	1.08
3754125--3754229	32	3.8	28	70	20	78	51	1	0	46	1.12
3755366--3755396	2	15.5	2	100	0	62	48	0	0	51	1.00

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