genome.fa.s1.2.7.7.80.10.50.1000.39.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  39  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)
6444400--6444435	17	2.1	17	89	0	54	44	0	0	55	0.99
6445114--6445146	13	2.5	14	85	14	52	75	0	12	12	1.04
6445588--6445612	13	1.9	13	100	0	50	44	0	0	56	0.99
6449712--6449778	4	17.8	4	85	11	70	50	16	0	32	1.45
6449712--6449810	26	3.8	26	93	0	135	50	11	0	38	1.38
6449732--6449810	4	19.8	4	94	0	104	50	7	0	41	1.31
6449724--6449810	22	4.0	22	93	0	138	50	9	0	40	1.34
6450302--6450335	17	2.0	17	88	11	52	58	2	0	38	1.13
6451397--6451493	50	1.9	50	89	0	149	25	5	25	43	1.75
6453550--6453627	30	2.6	30	79	0	84	47	3	16	32	1.65
6454921--6454964	11	4.3	11	76	23	51	29	0	0	70	0.88
6454932--6454964	11	2.9	12	82	17	52	27	0	0	72	0.85
6455169--6455233	20	3.2	20	85	8	80	32	0	0	67	0.91
6455168--6455226	13	4.6	12	76	19	57	35	0	0	64	0.94
6464428--6464488	29	2.1	29	87	0	86	44	1	6	47	1.39
6467784--6467832	19	2.6	19	80	9	55	79	0	16	4	0.88
6469521--6469551	14	2.2	14	94	0	53	38	0	6	54	1.26
6469562--6469610	16	3.3	15	72	18	50	48	0	2	48	1.12
6470180--6470220	21	1.9	22	85	5	57	48	0	0	51	1.00
6470913--6470937	2	12.5	2	100	0	50	52	0	48	0	1.00
6472677--6472716	21	1.9	21	90	10	64	40	0	0	60	0.97
6472705--6472772	34	2.0	34	82	5	84	55	2	1	39	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6473158--6473231	30	2.5	30	78	12	80	35	1	4	59	1.25
6479490--6479534	15	3.1	15	87	6	65	51	0	0	48	1.00
6479478--6479523	5	9.4	5	77	13	51	56	0	0	43	0.99
6481017--6481147	65	2.0	65	81	8	151	39	2	1	56	1.21
6480999--6481148	5	30.8	5	65	16	57	38	2	1	58	1.18
6483426--6483485	20	2.9	21	75	14	61	58	0	0	41	0.98
6483404--6483473	29	2.4	30	79	11	74	54	0	0	45	0.99
6483450--6483487	20	1.9	20	94	0	67	57	0	0	42	0.98
6483457--6483527	27	2.6	27	72	18	67	50	1	1	46	1.18
6483450--6483514	20	3.2	21	75	14	66	52	1	1	44	1.19
6483497--6483527	2	15.5	2	93	0	53	48	3	0	48	1.17
6483716--6483746	16	1.9	16	93	0	53	41	0	6	51	1.27
6484174--6484223	22	2.3	22	82	6	66	46	0	0	54	1.00
6485100--6485149	2	25.0	2	100	0	100	50	0	0	50	1.00
6485485--6485567	29	2.8	29	80	5	78	50	0	2	46	1.14
6485753--6485786	7	4.7	7	85	7	50	64	0	0	35	0.94
6488005--6488040	2	18.0	2	94	0	63	0	47	0	52	1.00
6488382--6488444	23	2.7	24	82	7	76	63	4	0	31	1.15
6488399--6488444	8	5.9	8	80	12	51	65	4	0	30	1.12
6491985--6492031	16	2.8	17	78	15	62	36	4	6	53	1.46
6491981--6492088	39	2.8	39	74	18	100	39	1	4	53	1.32
6491995--6492059	17	3.6	17	71	25	53	36	1	6	55	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6492591--6492641	24	2.1	24	88	0	75	11	43	7	37	1.71
6493123--6493251	41	3.2	40	78	13	115	31	2	0	65	1.05
6493338--6493387	23	2.2	23	86	10	68	48	0	0	52	1.00
6494163--6494210	19	2.4	20	83	16	64	64	0	0	35	0.94
6498671--6498895	114	2.0	114	95	0	405	36	20	14	28	1.92
6500822--6500846	13	1.9	13	100	0	50	56	0	8	36	1.29
6502493--6502526	17	2.0	17	88	0	50	70	0	11	17	1.16
6505487--6505536	2	25.5	2	76	11	50	48	6	0	46	1.27
6505995--6506038	23	2.0	23	86	13	65	25	11	0	63	1.27
6506166--6506200	18	1.9	18	88	0	52	48	0	0	51	1.00
6506822--6506862	21	2.1	21	86	13	61	36	2	2	58	1.24
6506829--6506867	20	2.0	20	85	10	53	38	2	2	56	1.27
6508374--6508403	2	14.5	2	93	6	51	50	0	3	46	1.18
6508907--6508941	18	1.9	18	88	0	52	54	0	0	45	0.99
6510237--6510312	23	3.3	23	74	7	66	34	5	14	46	1.67
6512853--6512895	2	21.5	2	100	0	86	48	0	0	51	1.00
6513114--6513146	2	17.0	2	93	6	59	51	0	0	48	1.00
6514342--6514387	23	2.0	23	87	8	67	32	0	8	58	1.28
6514476--6514508	2	16.5	2	100	0	66	51	0	0	48	1.00
6515698--6515724	2	13.5	2	100	0	54	48	0	0	51	1.00
6516523--6516576	22	2.4	23	79	14	67	27	0	1	70	0.98
6527256--6527319	14	4.8	13	75	17	51	71	0	1	26	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6527255--6527310	15	3.7	15	80	7	69	71	0	1	26	0.96
6527255--6527319	15	4.6	14	81	9	62	72	0	1	26	0.94
6527394--6527462	22	3.0	22	67	26	54	66	4	0	28	1.10
6527389--6527432	13	3.5	12	81	6	52	68	6	0	25	1.14
6527428--6527508	14	6.0	14	73	20	50	61	0	0	38	0.96
6527973--6528017	17	2.6	18	92	3	74	33	2	0	64	1.06
6528050--6528078	12	2.3	13	94	5	51	44	0	0	55	0.99
6531030--6531072	22	2.0	21	86	13	61	39	0	0	60	0.97
6532385--6532426	18	2.3	19	84	8	61	40	0	0	59	0.97
6532570--6532602	2	17.0	2	93	6	59	51	0	0	48	1.00
6532845--6532884	19	2.2	19	86	13	57	37	0	0	62	0.95
6532881--6532921	21	2.1	19	86	13	57	53	0	0	46	1.00
6533100--6533145	12	4.1	12	78	13	53	34	0	0	65	0.93
6533123--6533169	18	2.4	21	80	20	57	42	0	2	55	1.12
6533157--6533213	30	1.9	29	86	10	80	45	3	0	50	1.18
6534341--6534424	23	3.6	23	78	10	73	48	1	0	50	1.08
6534365--6534424	22	2.7	23	84	7	70	45	1	0	53	1.10
6535008--6535050	19	2.2	20	80	16	54	44	0	0	55	0.99
6535013--6535064	18	3.1	16	81	13	59	44	1	1	51	1.23
6535563--6535589	2	13.5	2	100	0	54	51	0	0	48	1.00
6538438--6538483	23	2.0	23	83	8	58	47	6	4	41	1.49
6538509--6538553	16	2.8	16	86	3	54	66	4	0	28	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6539467--6539660	63	3.1	63	89	0	262	44	10	30	14	1.78
6541287--6541326	21	1.9	21	90	10	64	60	0	0	40	0.97
6541314--6541362	18	2.7	17	78	9	53	46	0	0	53	1.00
6543737--6543761	9	2.8	9	100	0	50	44	8	24	24	1.80
6544961--6545018	22	2.6	23	78	13	66	43	1	0	55	1.10
6545438--6545482	22	2.0	23	86	4	65	57	4	4	33	1.38
6547046--6547104	29	2.0	29	90	0	91	40	15	6	37	1.74
6547046--6547114	29	2.4	29	85	4	77	43	14	5	36	1.70
6552397--6552736	171	2.0	171	98	0	662	39	10	9	41	1.71
6555468--6555508	20	2.1	20	86	4	57	68	2	4	24	1.22
6559684--6559746	19	3.1	21	77	20	64	39	1	0	58	1.07
6561906--6561944	20	1.9	20	84	5	51	43	5	2	48	1.38
6562562--6562586	2	12.5	2	100	0	50	52	0	0	48	1.00
6564082--6564122	3	13.7	3	94	0	73	68	0	31	0	0.90
6564083--6564127	9	5.0	9	94	0	54	68	0	28	2	1.01
6564170--6564206	16	2.3	16	90	0	56	78	0	0	21	0.75
6565035--6565074	20	2.1	19	86	13	55	40	0	0	60	0.97
6574504--6574557	2	29.0	2	85	14	80	50	0	50	0	1.00
6574530--6574573	20	2.2	20	83	0	52	56	0	40	2	1.11
6575056--6575080	2	12.5	2	100	0	50	52	0	0	48	1.00
6577160--6577188	4	7.2	4	100	0	58	75	0	0	24	0.80
6577969--6578008	14	2.6	16	80	15	57	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6580992--6581047	27	2.1	27	90	3	87	57	1	0	41	1.09
6583596--6583622	2	13.5	2	100	0	54	48	0	0	51	1.00
6585133--6585165	13	2.4	14	90	5	50	15	6	0	78	0.93
6585289--6585355	15	4.5	15	77	21	61	50	0	1	47	1.10
6585294--6585369	27	3.0	25	78	16	77	50	0	1	48	1.09
6588952--6588988	17	2.2	16	90	4	56	78	0	5	16	0.93
6590114--6590175	23	2.7	22	83	11	72	62	0	0	37	0.95
6590114--6590163	22	2.2	24	85	7	68	60	0	0	40	0.97
6594438--6594493	24	2.5	22	81	16	69	60	3	3	32	1.31
6594961--6595040	24	3.1	26	70	15	76	41	2	0	56	1.13

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