genome.fa.s64.2.7.7.80.10.50.1000.3.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  3  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)
455344--455384	18	2.2	19	86	4	57	60	0	0	39	0.96
456723--456755	12	2.5	13	90	9	50	0	30	0	69	0.88
457035--457066	3	10.7	3	100	0	64	31	0	0	68	0.90
457455--457491	15	2.5	14	87	12	56	86	0	13	0	0.57
458902--458948	21	2.2	21	92	0	76	27	6	31	34	1.82
460875--460913	18	2.2	18	85	0	51	41	2	2	53	1.28
460986--461040	21	2.6	21	79	2	56	69	7	1	21	1.23
462407--462439	3	11.0	3	100	0	66	33	33	33	0	1.58
475925--476024	45	2.2	45	81	0	110	24	32	18	26	1.97
478630--478663	17	1.9	18	88	5	52	29	0	2	67	1.05
478616--478670	26	2.0	27	82	10	67	32	0	1	65	1.03
479734--479771	11	3.1	13	81	14	53	50	2	0	47	1.15
484315--484345	2	15.5	2	100	0	62	48	0	0	51	1.00
485534--485597	5	12.4	5	73	18	51	62	0	3	34	1.11
485534--485597	11	6.2	11	74	20	66	62	0	3	34	1.11
485617--485655	14	2.9	14	84	3	53	53	0	0	46	1.00
486508--486533	2	13.0	2	100	0	52	50	0	0	50	1.00
490186--490214	7	4.3	7	95	4	51	48	27	13	10	1.75
491448--491486	21	2.0	21	85	10	55	17	10	15	56	1.66
495620--495660	2	20.5	2	100	0	82	51	0	0	48	1.00
496187--496225	12	3.2	12	85	0	60	41	0	5	53	1.23
496183--496218	6	6.0	6	86	0	54	44	0	2	52	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
499884--499937	24	2.2	24	93	0	90	37	14	7	40	1.74
505647--505693	23	2.0	23	100	0	94	25	17	4	53	1.62
505742--505772	2	15.5	2	93	0	53	48	0	3	48	1.17
507225--507255	5	6.2	5	96	0	53	77	3	19	0	0.90
508092--508188	47	2.1	47	96	0	176	54	7	22	15	1.65
510008--510048	19	2.4	17	84	15	57	53	0	0	46	1.00
510351--510376	5	5.2	5	100	0	52	80	0	0	19	0.71
511155--511197	23	2.0	23	86	9	63	55	2	2	39	1.25
511932--511962	2	15.5	2	100	0	62	48	0	0	51	1.00
512597--512648	20	2.6	20	79	8	61	46	1	0	51	1.12
512597--512650	21	2.6	21	80	13	60	46	1	0	51	1.11
512877--512923	11	4.3	11	78	10	51	36	4	0	59	1.17
512895--512923	10	2.7	11	94	5	51	27	6	0	65	1.18
513344--513372	2	14.5	2	100	0	58	48	0	0	51	1.00
519174--519253	33	2.3	35	74	6	83	62	2	1	33	1.16
519268--519315	18	2.7	17	75	9	51	47	8	6	37	1.59
519459--519493	3	11.7	3	100	0	70	65	0	0	34	0.93
519525--519559	16	2.1	17	89	5	54	45	0	0	54	0.99
524092--524179	29	3.1	28	77	11	90	62	0	1	36	1.03
524110--524158	24	2.1	23	84	3	62	63	0	2	34	1.06
524655--524691	2	19.0	2	88	5	58	2	48	0	48	1.15
528517--528546	2	15.0	2	92	0	51	46	0	3	50	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
529051--529084	17	2.1	17	88	5	52	50	0	0	50	1.00
529831--529855	2	12.5	2	100	0	50	52	0	0	48	1.00
530753--530826	31	2.4	30	80	10	80	48	0	1	50	1.09
530818--530857	21	1.9	20	90	10	62	40	0	0	60	0.97
533616--533659	5	8.8	5	89	0	52	4	54	15	25	1.60
536305--536345	6	6.8	6	97	0	64	39	0	9	51	1.35
536303--536348	2	23.0	2	81	0	56	41	0	8	50	1.33
542334--542366	2	16.5	2	93	0	57	48	3	0	48	1.17
543679--543720	2	21.0	2	95	0	75	50	47	0	2	1.14
544372--544434	12	5.3	13	77	14	57	52	3	6	38	1.43
544360--544421	12	5.5	11	79	12	63	48	0	6	45	1.28
544370--544432	22	2.7	24	76	14	69	52	3	6	38	1.43
545211--545265	22	2.5	23	82	8	69	38	0	0	61	0.96
545215--545265	21	2.5	21	81	9	52	37	0	0	62	0.95
545254--545313	13	4.7	13	78	12	61	45	1	0	53	1.10
545267--545313	24	2.0	23	87	4	67	48	0	0	51	1.00
546747--546779	3	11.0	3	100	0	66	33	0	0	66	0.92
546894--546923	12	2.4	13	94	5	53	43	0	0	56	0.99
546982--547020	17	2.5	15	80	15	51	46	0	0	53	1.00
546986--547020	17	2.1	17	94	0	61	45	0	0	54	0.99
549648--549690	2	21.5	2	100	0	86	0	51	0	48	1.00
551294--551329	2	18.0	2	100	0	72	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
552391--552454	29	2.2	29	86	5	94	32	12	28	26	1.93
552620--552674	25	2.2	26	83	6	69	16	3	14	65	1.41
552619--552674	24	2.2	26	84	6	71	16	3	14	66	1.39
557547--557578	2	16.0	2	100	0	64	50	0	50	0	1.00
557984--558103	57	2.1	57	81	6	136	57	8	5	29	1.49
558073--558120	17	3.0	15	82	11	51	54	0	0	45	0.99
558073--558113	16	2.5	17	88	4	57	51	0	0	48	1.00
558090--558155	21	3.0	22	71	15	55	62	0	1	36	1.05
559904--559949	14	3.6	13	83	11	60	32	0	2	65	1.05
563594--563623	15	2.1	14	93	6	51	66	0	0	33	0.92
563665--563739	18	4.2	18	71	6	64	46	1	0	52	1.09
563678--563764	35	2.3	35	78	9	93	50	1	0	48	1.08
564672--564910	117	2.0	120	94	3	421	41	8	10	40	1.70
566442--566477	6	6.0	6	93	0	63	33	33	2	30	1.72
566444--566483	18	2.2	18	86	0	53	40	25	2	32	1.69
571211--571261	17	3.2	17	81	15	56	66	0	0	33	0.92
576639--576667	3	9.7	3	100	0	58	34	31	0	34	1.58
578508--578562	28	2.0	28	100	0	110	21	18	27	32	1.96
585433--585470	20	1.9	20	89	10	60	50	0	0	50	1.00
587819--587853	2	17.5	2	100	0	70	48	0	0	51	1.00
587825--587945	58	2.1	58	96	0	224	42	9	4	43	1.58
596541--596588	16	3.1	16	78	6	53	37	0	0	62	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
598364--598397	13	2.8	12	91	8	52	5	8	2	82	0.93
598826--598872	2	24.0	2	78	4	51	44	4	4	46	1.42
599256--599298	2	21.5	2	100	0	86	48	0	0	51	1.00
601946--601982	2	18.5	2	100	0	74	48	0	0	51	1.00
603230--603264	2	17.5	2	100	0	70	51	0	0	48	1.00
609273--609312	16	2.6	15	88	4	53	80	0	20	0	0.72
609274--609312	17	2.3	16	86	8	51	82	0	17	0	0.68
610558--610638	39	2.1	38	86	6	110	55	0	1	43	1.07
611780--611821	12	3.4	12	78	18	50	61	0	0	38	0.96
611780--611827	25	2.0	24	87	4	69	60	0	0	39	0.97
612847--612877	15	2.1	15	100	0	62	25	6	19	48	1.72
613919--614030	51	2.2	51	84	9	140	50	0	0	48	1.13
616183--616290	54	2.0	54	96	0	198	27	16	22	33	1.95
617271--617339	36	1.9	36	82	5	86	44	0	1	53	1.09
623383--623407	3	8.3	3	100	0	50	32	0	0	68	0.90
627678--627721	22	2.0	22	90	0	70	40	31	15	11	1.83
629334--629360	2	13.5	2	100	0	54	51	48	0	0	1.00
637359--637402	22	2.0	22	90	0	70	40	31	15	11	1.83
639016--639044	2	14.5	2	100	0	58	51	48	0	0	1.00
642895--642934	2	20.0	2	100	0	80	50	0	50	0	1.00
644344--644389	23	1.9	25	82	8	60	23	4	19	52	1.64
645473--645498	13	2.0	13	100	0	52	0	15	0	84	0.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
650236--650275	15	2.5	16	84	12	55	47	0	0	52	1.00
650402--650426	2	12.5	2	100	0	50	48	0	0	52	1.00
655941--655978	2	19.0	2	100	0	76	50	0	0	50	1.00
657602--657635	17	2.1	16	88	5	50	67	8	20	2	1.31
660258--660436	89	2.0	89	93	0	304	31	24	11	32	1.91
668029--668101	36	2.0	36	97	0	137	8	12	24	54	1.64
669743--669781	18	2.2	18	86	4	53	51	0	0	48	1.00
669796--669821	6	4.3	6	100	0	52	46	0	0	53	1.00
674772--675069	145	2.1	145	95	1	544	25	12	23	38	1.90
680028--680059	2	16.0	2	100	0	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