genome.fa.s1.2.7.7.80.10.50.1000.44.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  44  of  52  ( 6211 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)
7128746--7128815	19	3.3	21	75	15	56	41	0	2	55	1.14
7129699--7129723	2	12.5	2	100	0	50	52	0	0	48	1.00
7130083--7130151	31	2.2	32	81	5	77	55	1	0	43	1.08
7131617--7131657	21	2.1	18	86	13	55	43	4	0	51	1.23
7138735--7138763	2	14.5	2	100	0	58	51	0	0	48	1.00
7139157--7139187	16	1.9	16	93	0	53	83	9	3	3	0.86
7143343--7143394	25	2.1	24	82	3	59	42	0	0	57	0.98
7143388--7143422	18	1.9	18	88	0	52	42	5	0	51	1.25
7146257--7146281	3	8.3	3	100	0	50	32	68	0	0	0.90
7147846--7147930	36	2.4	34	74	14	82	32	1	4	61	1.24
7148082--7148127	10	4.6	10	78	10	58	71	0	0	28	0.86
7148707--7148767	17	4.0	15	79	16	63	62	1	0	36	1.05
7149789--7150061	146	1.9	148	82	7	351	48	15	6	29	1.70
7156175--7156218	17	2.6	16	82	7	52	72	6	0	20	1.07
7156173--7156218	16	2.7	18	83	10	60	71	6	0	21	1.08
7156813--7156851	20	1.9	21	84	5	53	41	5	7	46	1.55
7157778--7157808	11	2.8	11	95	0	53	41	0	0	58	0.98
7157787--7157822	16	2.2	16	90	0	54	36	0	2	61	1.11
7160102--7160142	2	20.5	2	100	0	82	51	0	48	0	1.00
7161063--7161087	2	12.5	2	100	0	50	48	0	0	52	1.00
7164382--7164413	16	2.0	16	93	0	55	59	0	40	0	0.97
7164375--7164420	22	2.1	22	88	8	67	58	0	41	0	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7164651--7164793	44	3.2	44	74	14	148	39	4	2	53	1.35
7164798--7164864	25	2.9	23	87	10	93	58	0	0	41	0.98
7165429--7165453	2	12.5	2	100	0	50	52	0	0	48	1.00
7166445--7166498	22	2.5	22	96	0	99	44	24	3	27	1.70
7166445--7166506	22	2.8	22	90	4	81	45	25	3	25	1.69
7169592--7169637	15	3.1	15	87	0	56	58	0	0	41	0.98
7169602--7169642	15	2.7	15	92	0	64	58	0	0	41	0.98
7177334--7177386	24	2.2	24	82	0	61	47	0	1	50	1.12
7177363--7177402	19	2.1	19	90	9	64	42	0	0	57	0.98
7178010--7178069	21	2.7	21	78	16	59	46	1	0	51	1.10
7178572--7178607	18	2.1	18	89	5	56	47	0	8	44	1.33
7178719--7178766	16	2.9	16	82	14	62	43	0	0	56	0.99
7180754--7180788	2	18.0	2	88	5	54	48	0	2	48	1.16
7182101--7182150	9	6.1	9	78	19	56	56	0	0	44	0.99
7182122--7182156	15	2.2	16	95	5	63	45	2	0	51	1.16
7182598--7182638	15	2.5	17	88	7	59	48	2	0	48	1.14
7184486--7184512	11	2.5	11	100	0	54	70	7	7	14	1.32
7185648--7185691	21	2.1	21	100	0	88	43	4	13	38	1.65
7185899--7185961	21	2.9	21	83	9	74	60	0	0	39	0.97
7185899--7185956	22	2.7	22	84	10	75	63	0	0	36	0.94
7185908--7185968	21	2.8	22	85	7	81	59	0	0	40	0.98
7186760--7186815	26	2.1	28	86	6	80	42	0	0	57	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7188277--7188311	17	2.0	17	88	5	52	45	0	5	48	1.26
7188466--7188521	17	3.3	16	80	9	58	50	3	1	44	1.29
7188477--7188542	9	7.8	8	75	21	55	51	1	0	46	1.10
7188591--7188625	2	17.5	2	87	0	52	45	2	2	48	1.32
7188993--7189035	21	2.0	21	82	8	52	48	0	0	51	1.00
7189064--7189103	17	2.4	17	78	0	53	50	0	2	47	1.14
7189497--7189588	30	3.0	32	75	21	83	40	0	0	59	0.97
7189566--7189629	22	3.0	23	78	13	75	37	0	0	62	0.95
7189597--7189645	22	2.1	24	82	17	59	32	0	0	67	0.91
7191306--7191357	14	3.7	14	80	10	70	40	1	0	57	1.10
7192503--7192561	15	3.9	14	77	14	55	44	1	3	50	1.28
7193432--7193456	13	1.9	13	100	0	50	56	0	4	40	1.18
7195340--7195380	9	4.2	10	79	14	50	29	0	0	70	0.87
7195342--7195380	20	2.0	20	94	0	69	30	0	0	69	0.89
7196148--7196225	18	4.1	18	67	27	54	55	0	0	44	0.99
7196319--7196388	35	2.0	35	86	5	97	61	1	1	35	1.14
7196338--7196417	21	3.6	22	69	21	69	63	1	0	35	1.02
7196438--7196473	18	2.0	19	89	10	58	44	0	0	55	0.99
7196555--7196594	18	2.3	18	87	12	57	45	2	0	52	1.14
7196829--7196911	41	2.0	40	81	6	96	48	1	0	50	1.08
7196976--7197031	18	3.1	17	82	12	58	41	0	0	58	0.98
7199425--7199479	26	2.1	26	100	0	110	69	12	0	18	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7202744--7202794	22	2.4	22	83	9	70	39	0	0	60	0.97
7210083--7210127	18	2.6	16	80	16	54	24	2	2	71	1.09
7214678--7214708	15	2.1	15	93	0	53	22	0	0	77	0.77
7214829--7214886	25	2.3	26	85	5	75	58	0	0	41	0.98
7214822--7214886	25	2.4	27	77	10	71	58	0	0	41	0.98
7214859--7214894	17	2.1	18	89	5	56	55	0	0	44	0.99
7214853--7214927	36	2.1	37	82	7	91	58	0	0	41	0.98
7221544--7221576	11	3.0	11	95	0	57	66	0	0	33	0.92
7222340--7222384	23	2.0	23	83	12	58	44	0	2	53	1.13
7222310--7222383	18	3.9	17	71	25	60	47	0	1	51	1.09
7222312--7222411	18	5.5	17	66	21	51	48	0	1	51	1.07
7222357--7222450	47	2.0	46	80	12	102	53	0	1	45	1.07
7232284--7232331	18	2.6	17	78	15	51	33	0	0	66	0.92
7234145--7234628	267	1.8	265	85	5	679	36	14	27	20	1.92
7235581--7235623	17	2.5	17	92	0	68	60	6	0	32	1.23
7237685--7237777	17	5.5	17	70	27	65	38	2	0	59	1.10
7237980--7238117	4	34.8	4	82	1	107	47	10	2	39	1.51
7237980--7238117	14	9.8	14	80	9	120	47	10	2	39	1.51
7238530--7238565	16	2.3	15	86	9	54	47	0	0	52	1.00
7239146--7239194	20	2.5	20	86	0	71	42	2	2	53	1.24
7239139--7239196	19	3.0	19	85	5	80	41	3	1	53	1.28
7239166--7239208	19	2.3	19	88	4	61	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7240095--7240144	9	5.6	9	77	17	59	34	0	0	66	0.92
7240607--7240642	2	18.5	2	88	5	56	47	0	2	50	1.15
7245459--7245519	13	4.7	13	79	6	52	45	0	0	54	1.00
7245459--7245511	27	2.0	27	81	7	63	45	0	0	54	0.99
7245484--7245546	32	2.0	32	81	6	74	53	1	0	44	1.10
7245844--7245878	17	2.1	17	94	0	61	57	0	0	42	0.99
7245854--7245909	25	2.2	25	78	6	60	48	0	0	51	1.00
7246070--7246122	24	2.2	24	79	0	61	37	0	1	60	1.08
7246535--7246581	22	2.2	22	85	7	62	61	0	0	38	0.96
7247280--7247304	6	4.2	6	100	0	50	84	0	0	16	0.63
7247591--7247620	2	15.0	2	100	0	60	50	0	0	50	1.00
7247674--7247727	14	3.9	13	76	11	54	40	1	0	57	1.09
7247878--7247902	12	2.1	12	100	0	50	36	24	8	32	1.84
7248018--7248056	17	2.3	18	82	13	55	30	0	2	66	1.05
7248081--7248136	21	2.6	22	80	5	71	55	0	0	44	0.99
7248676--7249039	183	2.0	179	95	2	656	26	10	19	43	1.83
7253582--7253642	23	2.7	23	81	0	77	52	1	0	45	1.10
7253641--7253683	10	4.4	10	88	2	61	48	0	2	48	1.14
7253641--7253687	15	3.2	14	84	3	58	46	0	2	51	1.13
7253639--7253676	5	7.8	5	82	5	51	52	0	0	47	1.00
7257205--7257302	42	2.3	43	81	15	105	58	1	0	40	1.05
7257226--7257270	17	2.6	18	80	16	51	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)
7257646--7257682	19	1.9	19	89	10	58	43	0	0	56	0.99
7258497--7258565	23	2.9	23	80	8	77	55	0	0	44	0.99
7261866--7261890	3	8.3	3	100	0	50	0	32	0	68	0.90
7263822--7263899	38	2.1	38	100	0	156	32	12	21	33	1.91
7264045--7264083	2	19.5	2	100	0	78	48	0	0	51	1.00
7265826--7265850	13	1.9	13	100	0	50	48	32	12	8	1.69
7268907--7269007	11	9.3	11	73	14	68	56	0	0	41	1.12
7268964--7269033	20	3.6	19	71	19	56	58	0	0	41	0.98
7268917--7269037	19	6.6	18	66	26	58	58	0	0	39	1.09
7269022--7269061	20	2.0	20	90	4	64	50	0	0	50	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   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52