genome.fa.s101.2.7.7.80.10.50.1000.4.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: Scaffold101
Parameters: 2 7 7 80 10 50 1000
Length:  827217

Tables:   1   2   3   4   5   6   

This is table  4  of  6  ( 650 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)
424293--424350	6	9.3	6	75	20	57	79	1	5	13	0.98
424293--424350	18	3.1	19	77	18	68	79	1	5	13	0.98
426936--426986	16	3.1	16	81	10	59	56	0	1	41	1.10
427785--427821	4	9.2	4	100	0	74	51	0	0	48	1.00
429851--429889	20	1.9	21	89	5	62	41	0	0	58	0.98
432079--432127	7	6.4	7	78	17	53	79	0	4	16	0.88
432077--432132	25	2.2	24	87	6	76	78	0	3	17	0.89
432785--432826	4	10.2	4	89	5	66	47	0	2	50	1.14
432786--432825	21	1.9	21	100	0	80	45	0	2	52	1.14
433079--433117	20	2.0	20	89	0	60	35	5	46	12	1.65
433201--433271	27	2.6	27	88	6	99	46	23	7	22	1.76
435155--435200	21	2.1	22	84	4	58	19	30	19	30	1.97
437653--437698	20	2.3	20	88	0	65	34	4	50	10	1.57
437775--437843	27	2.5	27	86	6	86	46	23	5	24	1.74
438429--438463	3	11.7	3	100	0	70	31	0	0	68	0.90
438508--438548	16	2.5	16	84	4	55	26	0	0	73	0.84
438487--438542	25	2.2	26	81	9	62	30	1	0	67	1.01
441020--441086	18	4.0	17	76	21	61	58	2	0	38	1.14
442523--442547	2	12.5	2	100	0	50	52	0	0	48	1.00
442928--442972	19	2.2	21	84	7	58	40	0	0	60	0.97
443230--443273	23	1.9	23	90	0	70	45	6	0	47	1.29
444951--444984	4	8.8	4	93	6	61	23	0	0	76	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
445233--445277	23	2.0	23	90	0	72	40	8	13	37	1.76
449396--449477	7	10.5	8	75	16	57	56	1	1	41	1.15
449378--449525	38	4.1	34	70	20	88	56	2	2	39	1.22
450381--450410	13	2.4	12	94	5	51	43	0	0	56	0.99
450750--450794	23	2.0	22	91	8	74	55	0	2	42	1.12
450873--450917	19	2.5	18	89	7	65	24	2	0	73	0.95
455223--455255	17	1.9	17	93	0	57	54	9	3	33	1.47
467624--467661	6	6.3	6	87	0	58	34	15	0	50	1.45
467633--467662	9	3.3	9	90	0	51	33	13	0	53	1.40
469970--470002	3	11.0	3	100	0	66	66	0	0	33	0.92
473983--474019	2	19.0	2	88	5	58	51	2	0	45	1.15
478218--478243	6	4.3	6	100	0	52	53	0	0	46	1.00
478347--478408	31	2.0	31	83	0	79	38	8	0	53	1.31
481124--481189	34	2.0	34	93	3	116	37	7	16	37	1.77
481474--481499	2	13.0	2	100	0	52	50	0	0	50	1.00
482328--482380	25	2.1	26	82	10	65	49	0	1	49	1.12
482335--482384	23	2.3	21	82	6	64	48	0	2	50	1.12
485970--485996	3	9.0	3	100	0	54	66	0	0	33	0.92
489241--489288	19	2.5	21	83	12	59	52	0	2	45	1.12
489241--489288	20	2.5	19	83	12	55	52	0	2	45	1.12
489401--489444	21	2.1	21	83	8	54	59	4	2	34	1.30
489508--489537	14	2.1	14	93	0	51	70	0	0	30	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
490422--490463	22	1.9	22	85	9	59	61	14	0	23	1.32
490518--490570	13	3.9	13	77	15	54	71	0	0	28	0.86
490598--490644	22	2.1	23	88	4	69	59	2	0	38	1.09
491926--491967	20	2.0	22	86	13	61	38	0	4	57	1.20
492491--492532	16	2.7	15	86	13	66	52	0	0	47	1.00
493417--493466	25	2.1	24	81	7	57	64	4	0	32	1.12
493415--493467	24	2.2	24	77	9	56	60	3	0	35	1.15
493878--493939	27	2.4	25	84	15	74	58	1	0	40	1.08
497999--498078	19	4.3	19	71	9	56	33	1	1	63	1.10
498043--498073	16	1.9	16	100	0	62	41	0	0	58	0.98
498233--498262	7	4.4	7	91	8	53	0	10	0	90	0.47
498231--498262	13	2.5	13	94	0	55	0	12	0	87	0.54
501174--501212	20	2.0	20	85	10	53	64	2	0	33	1.08
501209--501245	18	2.0	19	89	5	58	35	0	2	62	1.10
501667--501712	24	2.0	24	83	8	60	34	4	0	60	1.16
502999--503059	31	2.0	31	83	6	79	34	9	13	42	1.77
506343--506368	2	13.0	2	100	0	52	50	50	0	0	1.00
507004--507040	19	1.9	19	88	0	56	45	0	0	54	1.00
507372--507434	29	2.2	28	78	15	76	55	3	0	41	1.16
508138--508178	13	3.1	13	82	6	55	36	7	0	56	1.27
508136--508181	14	3.4	14	84	6	67	39	6	0	54	1.26
511916--511963	3	16.0	3	100	0	96	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
512148--512191	18	2.3	20	81	11	58	50	0	4	45	1.22
512485--512509	2	12.5	2	100	0	50	48	0	0	52	1.00
512971--513016	21	2.2	21	88	0	65	52	0	4	43	1.21
513255--513288	2	17.0	2	100	0	68	0	50	0	50	1.00
513511--513545	16	2.2	16	94	0	61	54	0	8	37	1.31
514543--514570	14	2.0	14	100	0	56	35	0	0	64	0.94
514566--514601	13	2.8	13	82	0	54	41	0	2	55	1.14
514969--515002	13	2.6	13	85	0	50	61	2	0	35	1.11
515587--515652	27	2.4	27	87	7	89	46	18	7	27	1.75
520162--520227	27	2.4	28	89	2	98	48	21	6	24	1.72
524457--524542	22	4.0	22	77	4	86	47	4	3	44	1.40
525972--526007	16	2.2	17	90	5	56	55	0	8	36	1.30
526001--526052	18	2.7	20	82	14	56	55	1	1	40	1.22
531113--531138	2	13.0	2	100	0	52	50	0	0	50	1.00
531292--531355	28	2.2	28	89	8	94	67	0	0	32	0.91
531308--531364	21	2.6	22	78	16	64	64	0	0	35	0.93
531294--531363	21	3.5	20	74	14	63	67	0	0	32	0.91
531298--531386	32	2.8	33	80	6	96	62	1	2	33	1.15
532210--532325	54	2.1	55	88	1	180	50	4	7	37	1.51
533192--533225	15	2.1	17	89	10	54	55	0	0	44	0.99
533399--533443	20	2.4	19	88	7	65	62	0	2	35	1.08
534343--534384	20	2.1	20	86	8	59	21	2	14	61	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
539351--539504	81	1.9	81	91	0	254	27	20	22	29	1.98
546103--546128	12	2.2	12	100	0	52	19	7	19	53	1.68
549791--549875	20	4.0	21	77	13	77	49	0	1	49	1.08
550451--550482	2	16.0	2	100	0	64	50	0	50	0	1.00
551192--551232	17	2.5	17	80	7	50	36	0	0	63	0.95
551430--551474	20	2.2	21	84	11	58	26	4	6	62	1.39
560221--560245	13	1.9	13	100	0	50	56	0	16	28	1.41
562757--562785	2	14.5	2	100	0	58	48	0	0	51	1.00
564873--564926	26	2.1	26	89	3	83	37	3	5	53	1.42
568816--568873	20	3.1	18	76	13	55	50	0	1	48	1.11
570824--570885	11	5.1	11	77	21	61	41	0	1	56	1.09
570828--570880	14	4.0	14	85	14	85	43	0	0	56	0.99
570824--570885	25	2.5	25	97	0	115	41	0	1	56	1.09
570952--571008	30	1.9	29	86	10	80	47	12	7	33	1.68
571003--571054	27	1.9	27	88	0	77	42	3	0	53	1.19
572316--572341	12	2.2	12	100	0	52	57	7	0	34	1.27
575192--575225	11	3.1	11	86	0	50	73	0	0	26	0.83
575183--575225	22	2.0	22	85	0	59	69	2	0	27	1.00
575393--575441	24	2.0	24	100	0	98	38	16	8	36	1.78
575846--575922	19	3.8	18	75	21	64	62	0	0	37	0.96
575870--575916	24	2.0	23	87	4	67	65	0	0	34	0.93
576040--576082	19	2.3	18	85	14	61	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)
576520--576545	2	13.0	2	100	0	52	50	0	0	50	1.00
576627--576662	17	2.1	18	90	10	58	16	0	8	75	1.04
576752--576810	16	3.6	16	86	9	75	23	0	3	72	0.99
581838--581888	19	2.7	18	76	8	57	43	9	0	47	1.36
581981--582015	2	17.5	2	100	0	70	51	0	0	48	1.00
582281--582316	16	2.2	17	90	5	56	52	0	0	47	1.00
582351--582401	15	3.3	15	77	5	57	62	5	0	31	1.19
584093--584136	2	22.0	2	100	0	88	50	0	0	50	1.00
584229--584268	18	2.2	18	86	0	53	60	0	0	40	0.97
584312--584336	2	12.5	2	100	0	50	48	0	0	52	1.00

Tables:   1   2   3   4   5   6