genome.fa.s196.2.7.7.80.10.50.1000.4.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: Scaffold196
Parameters: 2 7 7 80 10 50 1000
Length:  7488280

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   

This is table  4  of  47  ( 5587 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)
454287--454437	68	2.2	68	83	0	176	31	11	25	30	1.92
461272--461322	22	2.4	21	90	6	84	54	3	23	17	1.59
461278--461321	22	2.0	22	100	0	88	54	4	22	18	1.61
461646--461701	12	4.4	12	78	12	58	51	0	0	48	1.00
461646--461690	14	3.3	14	81	6	65	48	0	0	51	1.00
461638--461690	27	2.0	26	96	3	97	50	0	0	49	1.00
464024--464071	2	24.0	2	79	8	53	45	2	6	45	1.40
467028--467071	19	2.3	19	84	4	52	50	2	0	47	1.13
467059--467110	16	3.2	16	75	5	50	42	3	0	53	1.19
467596--467653	16	3.6	16	78	0	62	41	6	1	50	1.39
476732--476771	2	20.0	2	100	0	80	50	0	0	50	1.00
477050--477094	2	22.5	2	86	0	63	2	46	2	48	1.26
479769--479806	16	2.3	17	90	4	60	65	7	0	26	1.19
479827--479852	3	8.7	3	100	0	52	34	0	0	65	0.93
480250--480288	20	2.0	20	89	0	60	46	0	2	51	1.14
480922--480984	25	2.5	26	80	10	78	44	1	1	52	1.20
480972--481017	18	2.4	19	89	7	67	54	0	0	45	0.99
480972--481017	19	2.4	18	82	10	56	54	0	0	45	0.99
482300--482344	15	2.7	18	76	16	51	73	0	2	24	0.95
484717--484757	13	3.2	13	82	0	55	39	12	12	36	1.80
485403--485456	21	2.6	21	75	13	58	59	3	1	35	1.26
485780--485874	43	2.2	44	82	1	111	55	0	8	35	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
486100--486131	14	2.4	14	94	5	57	43	0	0	56	0.99
486098--486182	35	2.4	35	80	11	93	52	1	0	45	1.08
488298--488346	22	2.3	22	78	3	55	32	6	10	51	1.61
489539--489572	2	17.0	2	100	0	68	50	0	50	0	1.00
490156--490187	2	16.0	2	93	0	55	46	0	3	50	1.17
493052--493089	19	2.0	19	89	0	58	36	2	0	60	1.11
496344--496370	2	13.5	2	100	0	54	48	0	0	51	1.00
497821--497895	39	1.9	39	91	0	123	32	16	21	30	1.95
504050--504079	2	15.0	2	100	0	60	50	0	0	50	1.00
505534--505571	15	2.4	16	82	8	51	36	2	0	60	1.11
505531--505597	21	3.2	20	72	18	55	40	1	0	58	1.07
506213--506255	18	2.4	18	80	0	50	25	0	4	69	1.07
506380--506423	19	2.3	19	96	0	79	20	0	0	79	0.73
506964--507006	18	2.4	18	80	3	52	74	6	4	13	1.19
507048--507085	16	2.4	16	86	4	51	68	13	0	18	1.21
507624--507709	24	3.5	24	84	7	93	66	1	1	31	1.07
507644--507673	15	2.0	15	93	0	51	63	0	3	33	1.11
507624--507777	17	8.8	17	72	18	111	63	1	1	32	1.16
507624--507711	26	3.5	26	84	9	103	65	1	1	31	1.07
507639--507798	59	2.8	55	77	14	162	64	2	1	31	1.17
507638--507776	9	15.4	9	71	19	103	64	2	2	31	1.18
507813--508013	9	23.1	9	67	21	83	31	3	1	62	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
507804--507853	26	1.9	26	84	8	66	30	8	0	62	1.24
507796--507931	40	3.4	38	73	18	91	30	3	1	63	1.20
507822--507939	40	2.9	39	76	16	107	29	2	2	65	1.19
507823--507933	16	6.9	16	68	23	63	30	2	1	64	1.17
508714--508764	19	2.7	20	78	9	61	45	0	0	54	0.99
510716--510813	18	5.1	17	68	22	52	32	0	0	67	0.91
510718--510813	19	4.9	19	75	10	86	33	0	0	66	0.92
510716--510820	42	2.7	39	80	15	128	33	0	0	66	0.92
511029--511084	22	2.6	21	75	8	58	37	1	0	60	1.07
511142--511193	14	3.6	14	76	10	52	73	0	1	25	0.94
511142--511193	22	2.3	23	80	9	63	73	0	1	25	0.94
511659--511741	23	3.8	23	66	21	61	46	0	0	53	1.00
511634--511695	30	2.0	31	90	3	99	43	0	0	56	0.99
511640--511712	30	2.4	29	80	10	85	46	0	0	53	1.00
511605--511741	65	2.1	63	80	12	156	47	0	0	51	1.05
511712--511752	16	2.5	17	81	14	50	39	0	0	60	0.96
512934--512966	12	2.5	13	85	14	50	27	0	12	60	1.32
512941--512966	12	2.2	12	100	0	52	30	0	7	61	1.24
513016--513077	22	2.8	22	85	0	79	37	1	17	43	1.59
517666--517731	25	2.9	22	78	12	78	40	1	18	39	1.60
517895--517977	42	2.0	42	97	2	159	24	26	4	44	1.73
519682--519719	20	1.9	20	84	10	51	63	0	5	31	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
526583--526783	102	2.0	101	91	1	323	38	6	2	52	1.41
526895--526945	20	2.5	19	84	12	66	72	1	0	25	0.95
526879--526939	28	2.1	28	82	14	72	68	1	0	29	0.99
526916--526974	15	3.9	15	72	16	50	64	1	0	33	1.04
526900--526978	40	2.1	35	82	13	88	67	1	0	31	0.99
526963--527010	22	2.2	21	85	3	60	58	0	0	41	0.98
526981--527010	11	2.9	10	90	9	51	56	0	0	43	0.99
528989--529039	21	2.5	21	84	9	61	50	7	0	41	1.31
530308--530352	21	2.1	22	87	4	65	53	0	0	46	1.00
530744--530803	21	3.0	20	74	13	61	51	1	8	38	1.42
530903--530950	18	2.5	20	80	13	55	47	0	4	47	1.21
530938--530979	20	2.1	20	82	8	50	42	0	0	57	0.99
530942--530997	24	2.4	23	80	13	69	42	1	0	55	1.10
530943--531031	34	2.6	33	85	5	108	43	1	1	53	1.15
531045--531094	24	2.0	25	96	3	93	58	0	4	38	1.17
531077--531113	18	2.2	17	90	9	58	72	0	2	24	0.97
531053--531106	24	2.2	24	83	6	65	66	0	3	29	1.09
531081--531116	9	4.0	9	86	13	56	66	0	2	30	1.06
531373--531462	45	2.0	45	87	8	130	50	1	2	46	1.21
531372--531461	22	4.0	22	71	8	74	51	1	2	45	1.21
531521--531574	28	2.0	27	81	3	63	53	1	0	44	1.11
532508--532546	17	2.2	19	86	9	55	33	2	0	64	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
532504--532552	16	3.1	15	77	13	53	38	2	0	59	1.09
533036--533101	14	4.4	15	73	16	57	57	3	1	37	1.23
533145--533192	25	1.9	24	84	16	62	43	2	0	54	1.12
533169--533216	17	2.8	17	78	12	62	56	0	0	43	0.99
539779--539826	25	2.0	25	87	4	71	41	2	0	56	1.11
539778--539824	22	2.1	22	84	7	60	40	2	0	57	1.11
540407--540439	17	2.0	16	94	5	57	15	0	6	78	0.93
540396--540454	21	2.8	21	80	12	59	15	0	5	79	0.89
541967--541995	2	14.5	2	100	0	58	48	0	0	51	1.00
542786--542820	6	5.8	6	90	10	54	62	0	0	37	0.95
544314--544346	2	17.0	2	90	6	50	45	0	3	51	1.16
546181--546242	11	5.6	10	75	25	54	46	3	1	48	1.28
546852--546898	15	3.0	15	84	9	58	48	2	2	46	1.25
547448--547606	74	2.1	74	81	9	180	55	2	3	38	1.29
547597--547634	13	2.8	14	84	4	51	73	0	0	26	0.83
547597--547634	7	5.6	7	84	6	51	73	0	0	26	0.83
547700--547791	47	2.0	47	88	0	139	28	2	15	54	1.53
547751--548002	74	3.5	73	79	6	269	32	2	11	53	1.50
548642--548773	63	2.1	63	85	4	185	48	12	11	28	1.75
549727--549936	74	2.9	72	80	11	227	56	10	0	31	1.38
549759--549947	69	2.6	71	78	9	199	56	10	0	32	1.38
550350--550517	75	2.2	76	85	6	225	43	1	0	54	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
550484--550517	14	2.3	14	90	10	50	35	0	0	64	0.94
550789--550845	15	3.7	14	74	19	51	80	0	19	0	0.71
550791--550844	10	5.3	9	78	22	54	81	0	18	0	0.69
550793--550845	11	4.9	11	84	9	65	81	0	18	0	0.70
551446--551489	23	1.9	23	90	0	70	15	4	13	65	1.41
551847--551907	9	6.5	10	71	17	51	81	0	14	3	0.80
551847--551907	19	3.3	19	82	11	81	81	0	14	3	0.80
551848--551907	8	6.8	8	75	20	57	81	0	15	3	0.81
551848--551907	27	2.2	27	85	5	77	81	0	15	3	0.81
552129--552179	26	1.9	26	84	11	68	47	0	0	52	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