genome.fa.s25.2.7.7.80.10.50.1000.3.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   53   54   55   56   

This is table  3  of  56  ( 6609 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)
333263--333293	15	2.1	15	100	0	62	12	61	6	19	1.53
333519--333576	18	2.9	21	68	19	52	24	55	10	10	1.65
333528--333562	18	1.9	18	94	0	61	25	51	5	17	1.67
337075--337139	2	32.5	2	90	0	85	49	7	0	43	1.31
337261--337321	2	30.5	2	89	0	86	49	6	0	44	1.28
337061--337456	182	2.2	183	97	1	749	36	10	13	38	1.80
339975--340030	23	2.3	24	78	12	60	53	5	0	41	1.24
340158--340191	1	34.0	1	87	0	50	0	94	2	2	0.38
341573--341609	15	2.3	17	90	9	60	45	0	0	54	1.00
341568--341611	17	2.5	19	75	24	51	47	0	0	52	1.00
342781--342810	2	15.5	2	93	6	53	50	0	0	50	1.00
345044--345080	18	2.0	19	94	5	67	43	0	0	56	0.99
345089--345125	19	2.0	19	94	5	67	64	0	0	35	0.94
345916--345943	2	14.0	2	100	0	56	0	50	0	50	1.00
345943--345980	2	19.0	2	100	0	76	50	0	0	50	1.00
348023--348069	23	2.1	23	88	4	69	51	4	0	44	1.21
348053--348107	27	2.0	28	83	16	71	50	0	0	49	1.00
348867--348900	2	17.0	2	87	0	50	47	5	0	47	1.26
349367--349415	2	24.5	2	95	0	89	48	0	51	0	1.00
350422--350453	3	10.7	3	100	0	64	31	0	0	68	0.90
370013--370041	2	15.0	2	92	7	51	51	0	0	48	1.00
378841--378873	13	2.4	14	85	5	50	72	0	0	27	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
385415--385448	2	17.0	2	100	0	68	50	0	0	50	1.00
390324--390367	23	1.9	23	90	0	70	61	0	2	36	1.09
390347--390387	21	2.0	20	85	4	55	65	2	2	29	1.18
390378--390451	32	2.3	32	84	13	91	58	1	2	37	1.21
390389--390449	18	3.5	18	71	28	60	55	1	1	40	1.19
404676--404717	3	14.0	3	100	0	84	0	33	0	66	0.92
404965--404994	5	6.0	5	100	0	60	40	0	0	60	0.97
411661--411718	29	2.0	29	86	0	80	41	3	1	53	1.28
413607--413639	2	17.0	2	93	6	59	48	0	0	51	1.00
414358--414391	2	17.0	2	87	0	50	52	2	0	44	1.16
414790--414824	14	2.5	14	90	0	52	48	0	2	48	1.16
416400--416431	2	16.0	2	100	0	64	50	0	0	50	1.00
416588--416625	2	19.0	2	100	0	76	50	0	0	50	1.00
422003--422039	2	18.5	2	100	0	74	48	0	0	51	1.00
422787--422833	20	2.3	21	79	17	55	36	2	2	59	1.21
422840--422870	16	2.0	16	93	6	55	38	0	0	61	0.96
422916--422943	13	2.2	13	100	0	56	60	14	0	25	1.34
427961--428003	16	2.7	16	89	10	70	55	9	4	30	1.52
427960--428052	32	2.9	31	76	10	89	55	10	6	26	1.58
431172--431208	2	18.5	2	100	0	74	0	51	0	48	1.00
432803--432836	17	2.0	17	94	0	59	32	5	23	38	1.79
436863--437027	82	2.0	82	98	0	321	46	20	8	24	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
441115--441188	32	2.4	29	80	20	89	31	0	1	67	0.99
441111--441189	29	2.6	31	77	14	78	31	0	1	67	0.99
441655--441684	6	4.8	6	95	4	51	20	0	0	80	0.72
445641--445679	21	1.9	20	84	5	51	23	43	5	28	1.75
449690--449729	6	7.2	6	91	2	50	12	0	87	0	0.54
449690--449732	14	3.2	13	83	9	50	13	0	86	0	0.58
449691--449732	20	2.1	20	90	0	66	14	0	85	0	0.59
450327--450359	16	2.0	17	88	5	50	18	15	21	45	1.85
454907--454941	2	17.5	2	100	0	70	51	0	0	48	1.00
461588--461627	14	2.7	15	78	21	57	50	0	0	50	1.00
462810--462856	17	2.7	18	78	21	55	55	4	2	38	1.31
462848--462886	16	2.4	17	83	8	55	64	2	0	33	1.08
463509--463563	2	27.5	2	100	0	110	50	0	0	49	1.00
465024--465072	25	2.0	25	87	0	71	36	14	6	42	1.70
468943--468994	26	2.0	26	100	0	104	30	30	3	34	1.76
469036--469145	32	3.6	29	83	9	139	36	19	11	32	1.88
469028--469145	61	1.9	62	91	3	193	36	18	13	31	1.90
469025--469145	31	3.9	31	86	6	174	36	19	13	30	1.90
469188--469218	16	1.9	16	93	0	53	38	12	12	35	1.82
472938--472966	2	14.5	2	100	0	58	51	0	48	0	1.00
475694--475724	2	15.5	2	93	0	53	51	0	0	48	1.00
481723--481759	19	2.0	19	89	5	58	32	0	5	62	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
481879--481943	7	9.9	7	79	14	50	44	0	0	55	0.99
481976--482026	20	2.6	20	78	9	52	52	0	0	47	1.00
482527--482564	20	1.9	20	88	0	58	34	2	0	63	1.09
483082--483133	20	2.6	20	87	6	70	76	0	19	3	0.93
483172--483205	9	3.8	9	85	14	52	52	0	0	47	1.00
483378--483436	27	2.1	28	81	9	68	23	1	5	69	1.18
484146--484179	17	2.1	16	88	5	50	61	0	0	38	0.96
484572--484601	10	3.0	10	95	0	51	0	43	0	56	0.99
491995--492019	2	12.5	2	100	0	50	0	0	48	52	1.00
493011--493050	15	2.6	16	88	4	55	80	2	17	0	0.83
497661--497709	3	16.7	3	91	4	82	32	0	2	65	1.04
499488--499536	7	6.2	8	82	15	50	40	0	0	59	0.98
500870--500955	19	4.8	17	72	17	57	59	0	1	39	1.05
500858--500939	11	7.0	12	69	22	50	62	0	1	36	1.03
500884--500935	10	5.3	10	73	13	54	59	0	1	38	1.08
500879--500966	17	5.1	16	70	17	59	57	0	1	40	1.06
500884--500982	38	2.6	36	80	16	103	56	0	1	42	1.06
501249--501273	5	5.0	5	100	0	50	20	0	0	80	0.72
501560--501599	21	1.9	21	84	0	53	40	2	12	45	1.56
501712--501868	35	4.4	35	76	11	149	58	0	1	38	1.14
501729--501859	34	3.8	33	80	10	145	54	0	2	41	1.18
503549--503588	17	2.4	17	87	4	55	42	2	0	55	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
503544--503607	15	4.3	16	69	28	52	48	1	0	50	1.10
505045--505088	8	5.5	8	86	0	52	40	2	9	47	1.48
505045--505089	12	3.6	12	84	6	54	42	2	8	46	1.47
507340--507383	15	2.7	17	80	20	58	68	4	25	2	1.20
515779--515811	2	17.0	2	93	6	59	51	0	0	48	1.00
517228--517258	2	15.5	2	100	0	62	51	0	0	48	1.00
522302--522348	23	2.0	24	87	4	69	44	4	0	51	1.21
523113--523170	25	2.2	26	78	9	64	22	5	8	63	1.42
523274--523303	2	15.0	2	100	0	60	50	0	0	50	1.00
526014--526038	2	12.5	2	100	0	50	48	0	0	52	1.00
531653--531678	2	13.0	2	100	0	52	50	0	0	50	1.00
533868--533905	2	19.0	2	100	0	76	50	0	0	50	1.00
543420--543448	12	2.3	13	94	5	51	68	0	0	31	0.89
551040--551069	2	15.0	2	100	0	60	50	0	50	0	1.00
552618--552674	17	3.7	16	80	15	59	36	1	0	61	1.07
552618--552674	27	2.0	29	83	10	73	36	1	0	61	1.07
557535--557583	21	2.3	21	89	0	71	20	22	26	30	1.98
563426--563509	42	2.0	42	95	4	152	34	21	8	35	1.84
573656--573685	2	15.0	2	92	0	51	50	3	0	46	1.18
575444--575480	6	6.2	6	93	0	56	27	35	37	0	1.57
576849--576893	22	2.0	22	86	0	63	26	2	46	24	1.64
576851--576891	20	2.0	20	90	0	64	26	2	46	24	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
576881--576940	2	30.0	2	93	0	102	50	0	50	0	1.00
576847--576895	24	2.0	24	84	0	62	26	2	46	24	1.63
581021--581060	21	1.9	21	85	10	55	42	0	0	57	0.98
581804--581851	20	2.4	21	79	6	55	56	4	0	39	1.19
581939--581981	18	2.3	19	84	11	54	60	0	0	39	0.97
582954--582992	2	19.5	2	89	0	60	2	46	2	48	1.29
591086--591149	33	2.0	33	87	6	96	56	0	0	43	0.99
591376--591439	28	2.2	30	83	13	80	56	1	0	42	1.09
591390--591444	27	2.1	26	83	10	67	60	0	1	38	1.08
591817--591862	18	2.5	17	83	13	56	41	0	4	54	1.20

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   53   54   55   56