genome.fa.s4.2.7.7.80.10.50.1000.28.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  28  of  31  ( 3628 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)
5533266--5533321	21	2.8	20	74	15	51	48	0	0	51	1.00
5533470--5533529	23	2.7	22	69	5	66	70	3	1	25	1.12
5533540--5533573	13	2.7	13	90	4	52	58	0	0	41	0.98
5533542--5533580	20	2.0	20	84	0	51	56	0	0	43	0.99
5533654--5533696	12	3.7	12	81	6	52	2	23	0	74	0.93
5533652--5533696	23	2.0	23	86	0	63	2	22	0	75	0.91
5533830--5533881	24	2.2	23	82	3	59	61	5	1	30	1.30
5537506--5537538	2	16.5	2	93	0	57	48	0	51	0	1.00
5545083--5545123	2	20.5	2	100	0	82	48	0	0	51	1.00
5547067--5547121	21	2.6	21	77	11	58	58	0	0	41	0.98
5547120--5547154	10	3.4	10	88	4	52	51	0	0	48	1.00
5548380--5548430	23	2.1	24	85	7	68	47	0	0	52	1.00
5549241--5549278	20	1.9	20	88	0	58	36	7	2	52	1.45
5550227--5550278	18	2.8	19	83	13	65	57	0	5	36	1.23
5550619--5550708	46	2.0	45	91	6	146	44	16	6	32	1.74
5550630--5550707	24	3.3	24	68	22	67	48	15	6	29	1.69
5551001--5551047	11	4.1	12	81	8	53	25	2	8	63	1.34
5560132--5560173	22	1.9	22	85	0	57	35	11	4	47	1.61
5562235--5562504	135	2.0	137	83	5	341	44	3	5	46	1.44
5562418--5562657	100	2.3	103	82	5	281	42	5	6	45	1.52
5562310--5563066	347	2.2	343	82	7	906	44	4	5	45	1.46
5562422--5563066	347	1.9	348	88	2	978	43	4	6	46	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5562769--5563009	104	2.4	101	86	6	308	43	2	5	48	1.37
5562769--5563063	104	2.8	103	80	9	271	44	2	5	47	1.37
5564375--5564418	17	2.9	15	78	15	54	54	0	0	45	0.99
5564378--5564438	31	2.0	31	90	0	95	55	0	0	44	0.99
5564372--5564448	24	3.3	23	79	12	68	57	0	0	42	0.99
5564557--5564595	20	2.0	20	89	0	60	61	2	5	30	1.31
5564960--5565017	19	3.0	18	69	16	53	46	0	0	53	1.00
5566869--5566917	18	2.7	18	77	0	53	4	18	6	71	1.23
5569055--5569104	17	2.8	18	82	11	59	36	0	2	62	1.07
5569046--5569116	25	2.9	25	79	12	76	40	0	1	57	1.07
5569331--5569391	22	3.0	21	77	13	65	37	0	0	62	0.96
5569331--5569389	21	2.7	23	77	12	63	37	0	0	62	0.95
5569400--5569467	19	3.3	21	68	24	54	32	5	0	61	1.20
5571887--5571926	18	2.3	17	91	4	62	57	0	0	42	0.98
5572086--5572130	11	3.9	11	77	11	54	77	2	0	20	0.87
5573271--5573315	23	2.0	23	82	4	56	44	0	6	48	1.29
5573961--5573986	2	13.0	2	100	0	52	50	0	0	50	1.00
5574159--5574201	14	3.2	13	81	18	52	58	0	0	41	0.98
5574881--5574960	32	2.6	32	74	20	82	47	0	0	52	1.00
5574928--5574962	17	2.0	18	88	5	54	51	0	0	48	1.00
5575408--5575453	19	2.6	17	77	12	56	56	0	2	41	1.11
5575412--5575450	19	2.0	20	90	5	62	56	0	2	41	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5577121--5577150	2	15.0	2	100	0	60	50	0	0	50	1.00
5578612--5578648	13	2.5	15	79	20	51	51	0	0	48	1.00
5578619--5578656	13	2.9	14	88	7	53	44	0	0	55	0.99
5578652--5578706	26	2.2	25	83	6	67	50	1	1	45	1.22
5578785--5578837	27	1.9	28	84	3	72	45	1	0	52	1.11
5579075--5579115	15	2.9	15	86	13	52	34	0	0	65	0.93
5585660--5585709	14	3.8	14	82	15	61	66	0	0	34	0.92
5585758--5585797	22	1.9	22	85	10	57	62	2	0	35	1.09
5592359--5592468	54	2.0	54	100	0	220	19	20	18	42	1.89
5600336--5600368	2	16.5	2	100	0	66	48	0	0	51	1.00
5600492--5600532	21	2.0	21	85	9	57	34	0	0	65	0.93
5600570--5600636	25	2.7	25	76	15	68	56	1	0	41	1.08
5600570--5600652	29	2.9	28	78	7	76	56	1	0	42	1.07
5600570--5600645	24	3.2	23	77	9	64	55	1	0	43	1.08
5600579--5600656	20	4.1	19	69	14	52	58	1	0	39	1.06
5602917--5602953	2	18.5	2	94	0	65	48	2	0	48	1.15
5604271--5604324	11	4.7	11	77	8	63	33	0	1	64	1.04
5604264--5604310	24	2.0	24	82	0	58	36	0	4	59	1.17
5604360--5604417	18	3.2	18	72	18	57	43	0	0	56	0.99
5604334--5604426	20	4.4	22	70	22	74	39	1	0	59	1.05
5604330--5604426	32	3.0	33	73	23	107	41	1	0	57	1.05
5606478--5606533	26	2.2	26	83	6	69	42	0	5	51	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5606503--5606663	74	2.2	72	88	5	241	42	1	3	52	1.30
5606644--5606702	21	2.9	22	78	14	63	40	1	1	55	1.20
5607700--5607823	21	5.7	21	71	21	78	59	0	0	39	1.03
5607735--5607778	17	2.6	16	89	7	61	61	0	0	38	0.96
5607699--5607788	22	4.3	21	74	16	73	63	0	0	36	0.95
5607762--5607826	26	2.6	25	76	21	66	58	1	0	40	1.07
5607717--5607804	39	2.2	39	80	9	99	61	1	0	37	1.04
5607840--5607895	30	1.9	28	85	7	76	53	5	0	41	1.24
5610721--5610746	2	13.0	2	100	0	52	50	0	0	50	1.00
5611186--5611220	3	11.7	3	100	0	70	31	0	0	68	0.90
5611611--5611663	20	2.7	20	80	11	56	41	1	7	49	1.42
5612643--5612682	14	2.7	15	84	7	55	50	2	0	47	1.14
5613086--5613120	17	2.2	15	90	10	52	60	0	11	28	1.32
5613365--5613432	18	3.5	20	75	17	63	64	0	0	35	0.94
5613393--5613443	5	10.2	5	76	16	52	62	0	0	37	0.95
5613393--5613431	16	2.4	16	95	0	69	66	0	0	33	0.92
5613404--5613443	11	3.5	11	90	10	55	60	0	0	40	0.97
5613363--5613471	46	2.4	44	81	10	112	59	0	0	40	0.97
5613391--5613503	53	2.1	54	79	9	115	57	0	0	40	1.11
5613426--5613501	16	4.5	16	70	22	57	52	1	1	44	1.17
5613571--5613612	2	21.0	2	100	0	84	50	0	0	50	1.00
5613738--5613848	30	3.7	30	78	2	107	49	2	3	44	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5614113--5614156	17	2.6	18	85	10	65	56	0	0	43	0.99
5614083--5614184	46	2.2	47	86	10	138	57	1	0	39	1.16
5614131--5614196	29	2.4	27	87	7	105	66	0	0	33	0.92
5615035--5615088	18	3.1	19	82	17	64	44	0	0	55	0.99
5615035--5615091	17	3.3	17	81	16	64	45	0	0	54	0.99
5615204--5615232	13	2.1	14	93	6	51	44	0	0	55	0.99
5615461--5615495	16	2.1	17	89	5	54	34	0	0	65	0.93
5615750--5615787	11	3.5	11	82	7	51	86	0	13	0	0.56
5618619--5618668	22	2.3	22	82	6	57	50	0	0	50	1.00
5618626--5618668	22	1.9	23	85	4	61	51	0	0	48	1.00
5619248--5619340	19	5.2	18	71	18	61	51	0	0	48	1.00
5621533--5621567	18	1.9	18	88	0	52	37	8	42	11	1.72
5625635--5625669	12	2.8	12	91	4	52	88	0	11	0	0.51
5625634--5625669	17	2.2	17	90	5	56	88	0	11	0	0.50
5626128--5626155	2	14.0	2	100	0	56	50	0	0	50	1.00
5626768--5626818	23	2.3	22	82	3	57	21	3	1	72	1.11
5626894--5626995	43	2.4	42	83	1	123	40	6	5	47	1.55
5628580--5628615	2	18.0	2	100	0	72	50	0	0	50	1.00
5629391--5629433	16	2.7	16	85	0	59	37	0	2	60	1.10
5631333--5631387	20	2.8	20	75	10	67	40	12	3	43	1.60
5635421--5635463	14	2.9	14	78	21	52	53	0	0	46	1.00
5636094--5636131	15	2.4	17	86	8	53	47	2	2	47	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5636863--5636900	16	2.5	15	91	8	67	60	15	0	23	1.35
5637634--5637672	18	2.1	19	90	4	62	51	0	5	43	1.24
5637645--5637698	17	3.1	18	76	17	60	50	0	3	46	1.19
5637719--5637765	23	2.1	23	85	14	64	36	0	2	61	1.08
5639510--5639574	19	3.5	18	77	12	60	55	1	0	43	1.09
5640687--5640724	16	2.4	16	86	8	51	55	5	0	39	1.23
5640901--5640929	2	14.5	2	100	0	58	51	48	0	0	1.00
5641164--5641202	14	2.8	14	85	11	53	41	2	0	56	1.13
5641697--5641740	15	2.9	15	86	10	54	40	0	0	59	0.98
5644095--5644142	15	3.2	15	76	8	53	43	2	0	54	1.12

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