genome.fa.s3.2.7.7.80.10.50.1000.31.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  31  of  32  ( 3795 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)
5828801--5828850	2	25.5	2	95	4	93	52	0	0	48	1.00
5842724--5842781	18	3.4	18	73	26	63	43	0	0	56	0.99
5842753--5842827	13	5.8	12	75	18	62	46	0	0	53	1.00
5842712--5842828	28	4.3	26	75	16	96	43	0	0	55	1.05
5842727--5842845	20	5.3	23	69	25	78	44	0	0	55	0.99
5842765--5842853	31	2.8	32	77	13	87	47	0	0	52	1.00
5844421--5844474	25	2.2	25	96	0	99	31	24	12	31	1.93
5846676--5846701	2	13.0	2	100	0	52	50	0	0	50	1.00
5849019--5849048	15	2.0	15	93	0	51	0	10	0	90	0.47
5849216--5849277	32	1.9	32	100	0	124	35	12	6	45	1.68
5858462--5858546	15	6.6	13	72	20	63	56	1	5	36	1.31
5864059--5864136	39	2.0	39	92	0	129	24	28	11	35	1.90
5867505--5868131	92	6.9	90	73	8	409	29	13	22	35	1.92
5875517--5875550	2	17.0	2	100	0	68	50	0	0	50	1.00
5876994--5877040	21	2.2	21	77	7	51	34	14	2	48	1.56
5878702--5878733	2	16.0	2	100	0	64	50	0	0	50	1.00
5883578--5883612	2	18.5	2	88	11	56	48	0	0	51	1.00
5884893--5884921	2	14.5	2	100	0	58	48	0	0	51	1.00
5884953--5884995	22	2.0	21	86	4	59	62	0	11	25	1.29
5885676--5885724	22	2.2	22	85	0	62	40	2	0	57	1.10
5897784--5897846	26	2.5	25	85	10	76	26	7	19	46	1.77
5905780--5905817	18	2.1	18	100	0	76	23	26	15	34	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5907631--5907671	3	13.7	3	100	0	82	0	31	0	68	0.90
5916307--5916354	20	2.3	20	89	10	71	66	0	0	33	0.92
5916311--5916363	15	3.6	14	78	16	54	66	0	0	33	0.92
5916739--5916770	15	2.1	15	94	0	55	56	0	0	43	0.99
5917410--5917447	19	2.0	19	90	10	60	68	0	2	28	1.03
5920091--5920123	2	16.5	2	100	0	66	51	0	0	48	1.00
5921446--5921481	19	1.9	19	88	5	56	58	2	2	36	1.27
5922943--5922974	15	2.1	15	94	0	55	31	3	0	65	1.08
5923164--5923218	18	3.1	18	78	5	58	69	3	1	25	1.15
5924454--5924541	16	5.6	16	71	11	65	35	2	7	54	1.42
5925937--5926154	34	6.5	34	84	5	273	40	26	7	25	1.82
5925935--5926154	67	3.3	67	87	1	314	40	26	7	25	1.82
5930570--5930785	34	6.4	34	84	5	269	40	26	7	25	1.83
5930568--5930785	67	3.2	67	87	1	310	40	27	7	24	1.82
5932597--5932642	23	2.0	24	82	4	58	65	0	2	32	1.05
5933070--5933099	2	15.0	2	92	0	51	53	0	46	0	1.00
5935799--5935939	70	2.0	70	100	0	282	31	9	21	37	1.86
5938830--5938859	10	3.0	10	95	0	51	20	13	46	20	1.83
5947720--5947777	22	2.8	20	72	25	50	62	1	13	22	1.41
5954355--5954392	10	3.5	11	86	13	53	55	0	0	44	0.99
5960877--5960918	6	7.2	6	91	5	68	16	80	0	2	0.81
5960877--5960919	11	3.7	11	90	9	68	18	79	0	2	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5964060--5964099	2	20.0	2	94	0	71	52	0	0	47	1.00
5964580--5964615	3	12.0	3	87	0	54	63	0	2	33	1.08
5965107--5965144	15	2.5	16	83	12	53	0	50	0	50	1.00
5967440--5967473	13	2.5	14	85	9	52	76	0	8	14	1.01
5971527--5971561	2	17.5	2	100	0	70	0	51	0	48	1.00
5985151--5985181	2	15.5	2	100	0	62	51	0	0	48	1.00
5985324--5985392	24	2.8	24	77	16	63	42	2	4	50	1.37
5985411--5985436	3	8.7	3	100	0	52	34	0	0	65	0.93
5986114--5986144	2	15.5	2	100	0	62	48	0	51	0	1.00
5987084--5987174	37	2.5	37	74	13	89	52	1	0	46	1.07
5988064--5988124	16	3.8	16	76	8	70	42	14	14	27	1.85
5988064--5988124	32	1.9	32	83	6	79	42	14	14	27	1.85
5989047--5989092	15	3.0	15	77	3	56	56	6	0	36	1.25
5990931--5990963	2	17.0	2	93	6	59	51	0	0	48	1.00
5991424--5991450	12	2.2	12	100	0	54	92	0	7	0	0.38
5991423--5991454	16	2.0	16	93	0	55	90	0	9	0	0.45
5991674--5991708	6	5.8	6	89	0	52	48	0	14	37	1.44
5992593--5992625	8	4.2	8	88	7	50	84	0	15	0	0.61
5994075--5994145	36	2.0	36	97	0	133	23	9	15	50	1.74
5995721--5995752	2	16.0	2	100	0	64	50	0	0	50	1.00
5997890--5997922	17	1.9	17	100	0	66	12	18	9	60	1.57
6001082--6001134	26	2.0	26	96	0	97	28	11	5	54	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6001084--6001142	26	2.2	26	90	3	91	30	13	5	50	1.63
6001390--6001423	17	1.9	18	88	5	52	35	0	0	64	0.94
6016603--6016796	108	1.8	104	82	8	250	31	27	13	27	1.94
6021127--6021163	15	2.5	15	86	0	56	35	0	0	64	0.94
6021126--6021172	23	2.1	22	84	11	60	40	0	0	59	0.97
6021321--6021369	21	2.5	19	86	6	62	40	0	0	59	0.98
6021321--6021370	19	2.5	20	78	18	59	40	0	0	60	0.97
6021331--6021369	19	2.1	19	90	4	62	41	0	0	58	0.98
6021378--6021435	29	2.1	27	83	6	71	58	0	1	39	1.08
6022181--6022213	13	2.5	13	90	9	50	30	0	0	69	0.88
6022995--6023036	2	21.5	2	95	4	77	50	0	0	50	1.00
6023571--6023598	2	14.0	2	100	0	56	0	50	0	50	1.00
6025601--6025646	23	2.0	23	87	8	67	28	4	8	58	1.47
6026065--6026092	2	14.0	2	100	0	56	50	0	0	50	1.00
6027657--6027704	2	24.0	2	100	0	96	50	0	0	50	1.00
6031373--6031407	3	11.7	3	100	0	70	65	0	0	34	0.93
6032112--6032143	2	16.0	2	100	0	64	50	0	0	50	1.00
6032357--6032468	56	2.0	55	83	11	140	52	2	2	41	1.29
6037555--6037592	2	19.0	2	100	0	76	50	0	0	50	1.00
6038297--6038429	65	2.0	67	94	4	234	27	16	12	42	1.85
6043453--6043488	17	2.1	18	89	5	56	36	19	0	44	1.51
6048385--6048415	2	15.5	2	100	0	62	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)
6051435--6051471	2	19.0	2	91	5	58	45	0	2	51	1.15
6054680--6054704	4	6.2	4	100	0	50	76	0	24	0	0.80
6057507--6057531	2	12.5	2	100	0	50	48	0	0	52	1.00
6059688--6059734	5	9.4	5	90	0	76	59	0	38	2	1.09
6060622--6060649	3	9.3	3	100	0	56	32	0	0	67	0.91
6060907--6060932	2	13.0	2	100	0	52	50	0	0	50	1.00
6061233--6061273	3	13.7	3	100	0	82	34	0	0	65	0.93
6065732--6065770	2	19.5	2	89	0	60	43	0	56	0	0.99
6065728--6065772	10	4.5	10	91	0	63	40	0	60	0	0.97
6067257--6067286	3	10.0	3	92	0	51	63	0	0	36	0.95
6067279--6067317	3	13.0	3	88	0	60	35	2	0	61	1.10
6067681--6067715	6	5.8	6	93	0	61	85	0	2	11	0.69
6070491--6070518	2	14.0	2	100	0	56	50	0	0	50	1.00
6071973--6072008	2	18.0	2	100	0	72	0	50	0	50	1.00
6073043--6073078	2	18.0	2	88	0	54	50	44	5	0	1.25
6076209--6076241	12	2.8	12	90	0	57	0	57	0	42	0.98
6076796--6076830	3	11.7	3	100	0	70	68	0	0	31	0.90
6077753--6077787	15	2.3	15	85	14	54	71	0	0	28	0.86
6077749--6077786	20	1.9	20	88	0	58	73	0	0	26	0.83
6078439--6078473	9	3.9	9	100	0	70	68	0	0	31	0.90
6081701--6081734	2	17.0	2	100	0	68	50	0	0	50	1.00
6081972--6082004	2	16.5	2	100	0	66	51	48	0	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6082004--6082036	2	16.5	2	100	0	66	51	0	0	48	1.00
6085031--6085059	2	15.0	2	92	7	51	48	0	0	51	1.00
6087861--6087900	2	20.0	2	94	0	71	0	47	0	52	1.00
6092173--6092208	2	18.0	2	100	0	72	50	0	0	50	1.00
6093223--6093252	2	15.0	2	100	0	60	50	0	0	50	1.00
6094191--6094243	22	2.4	22	90	6	81	37	0	11	50	1.38
6098032--6098072	2	20.5	2	100	0	82	0	51	0	48	1.00
6099528--6099560	7	4.7	7	92	0	57	60	0	0	39	0.97
6100149--6100178	3	10.0	3	100	0	60	66	0	0	33	0.92
6103231--6103258	2	14.0	2	100	0	56	50	0	50	0	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