genome.fa.s1.2.7.7.80.10.50.1000.31.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  31  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)
5344909--5344949	21	2.0	21	85	9	57	46	0	4	48	1.23
5345007--5345035	9	3.3	9	95	4	51	41	0	0	58	0.98
5345183--5345219	19	1.9	19	88	0	56	43	10	0	45	1.39
5345905--5346008	44	2.3	47	82	11	126	50	0	0	49	1.00
5345943--5345988	20	2.4	20	82	7	60	50	0	0	50	1.00
5346786--5346829	18	2.4	19	81	7	56	56	0	0	43	0.99
5347587--5347627	16	2.6	16	78	17	50	46	7	0	46	1.30
5348971--5349005	18	1.9	18	88	0	52	74	0	5	20	1.02
5349618--5349682	16	4.1	16	80	5	60	32	0	4	63	1.15
5349627--5349683	22	2.6	22	72	2	53	33	0	1	64	1.04
5349627--5349685	16	3.7	16	77	8	66	32	0	1	66	1.02
5350451--5350496	23	2.0	23	86	0	65	45	2	8	43	1.47
5352139--5352171	2	16.5	2	100	0	66	48	0	0	51	1.00
5352559--5352612	25	2.2	25	87	12	76	48	1	0	50	1.11
5353620--5353652	7	4.9	7	96	3	59	45	30	24	0	1.53
5356398--5356453	18	3.1	18	86	0	85	19	32	23	25	1.98
5360160--5360256	30	3.2	31	67	14	85	57	5	0	37	1.21
5360152--5360267	59	2.0	59	92	0	196	57	6	0	36	1.23
5360977--5361019	17	2.5	17	88	7	61	27	2	0	69	1.00
5361805--5361844	20	2.0	20	90	0	62	45	0	2	52	1.14
5364961--5365007	19	2.4	19	89	10	69	51	0	0	48	1.00
5366063--5366152	45	2.0	45	97	0	171	42	10	13	34	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5366261--5366298	20	1.9	20	94	0	67	34	18	7	39	1.80
5371027--5371059	17	2.0	17	88	5	50	36	0	6	57	1.23
5371283--5371345	25	2.5	25	100	0	126	44	0	7	47	1.32
5371530--5371593	18	3.4	18	77	12	58	43	0	1	54	1.09
5373740--5373847	22	4.8	22	69	18	78	33	1	3	61	1.25
5374231--5374262	17	1.9	16	93	6	55	31	15	0	53	1.43
5374273--5374322	22	2.3	22	82	6	57	36	12	2	50	1.51
5374343--5374408	28	2.2	30	81	7	82	34	10	3	51	1.52
5374728--5374787	21	2.8	22	76	14	63	33	15	3	48	1.61
5375065--5375103	17	2.2	18	86	4	53	28	5	7	58	1.47
5375225--5375287	22	2.8	24	76	11	71	36	0	1	61	1.05
5375318--5375368	23	2.2	23	82	0	66	70	0	1	27	0.98
5377747--5377771	13	1.9	13	100	0	50	48	12	8	32	1.69
5377857--5377896	9	4.7	9	79	20	50	55	0	0	45	0.99
5377866--5377894	15	1.9	15	100	0	58	58	0	0	41	0.98
5378565--5378605	2	20.5	2	100	0	82	51	0	0	48	1.00
5379894--5380120	113	2.0	113	94	0	400	21	14	20	43	1.88
5400459--5400506	25	2.0	25	88	12	73	33	12	10	43	1.77
5400692--5400754	24	2.7	24	76	11	67	49	7	3	39	1.48
5400767--5400857	21	4.3	20	77	12	76	34	4	7	53	1.49
5400869--5401002	21	6.4	21	71	13	87	32	6	9	51	1.61
5401463--5401528	24	2.9	22	82	10	78	48	6	3	42	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5402046--5402096	20	2.5	20	77	3	57	33	11	7	47	1.69
5402105--5402158	21	2.8	18	83	13	63	35	5	9	50	1.58
5402272--5402310	20	2.0	20	85	10	53	30	2	10	56	1.46
5404906--5404975	28	2.5	28	88	4	97	27	30	17	25	1.97
5404770--5404948	82	2.2	80	80	6	193	27	24	11	36	1.90
5405568--5405593	13	2.0	13	100	0	52	30	15	15	38	1.88
5406513--5406558	21	2.2	20	82	14	58	26	17	15	41	1.88
5414181--5414231	2	25.5	2	100	0	102	49	0	0	50	1.00
5418081--5418147	33	2.0	33	85	5	91	35	20	11	31	1.89
5418395--5418434	6	6.7	6	97	0	71	0	20	12	67	1.22
5422591--5422809	50	4.4	50	87	0	312	30	18	18	31	1.95
5425262--5425302	21	2.0	21	100	0	82	41	19	24	14	1.89
5427175--5427327	77	2.0	77	100	0	306	30	12	27	30	1.93
5427324--5427582	50	5.2	50	90	1	367	30	18	20	31	1.96
5430822--5430868	24	2.0	23	84	12	60	25	10	0	63	1.26
5432134--5432172	20	2.1	18	85	9	51	41	7	0	51	1.31
5432988--5433033	24	2.0	23	86	4	65	23	4	4	67	1.27
5433026--5433052	12	2.2	12	100	0	54	7	0	7	85	0.75
5440400--5440802	91	4.5	89	86	5	540	30	16	15	38	1.89
5440400--5440802	183	2.2	177	85	5	547	30	16	15	38	1.89
5440808--5441335	88	5.9	88	80	7	485	30	15	13	40	1.86
5440810--5441353	179	3.0	177	80	3	615	30	14	13	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5441654--5441703	15	3.3	15	82	0	73	12	20	18	50	1.78
5442742--5442819	31	2.5	32	87	2	113	26	17	11	43	1.84
5442775--5442907	71	1.9	71	93	3	232	33	15	12	39	1.84
5442806--5442862	20	2.8	20	84	5	71	33	14	12	40	1.83
5446329--5446375	23	2.0	23	95	0	85	27	19	21	31	1.97
5450710--5450762	20	2.7	20	85	14	74	33	18	18	28	1.95
5451277--5451373	34	2.9	33	83	6	131	37	14	15	32	1.88
5455175--5455217	21	2.0	21	100	0	86	13	23	13	48	1.79
5456494--5457010	62	8.4	62	77	2	418	33	17	23	26	1.96
5456528--5456958	123	3.5	124	80	4	383	33	17	23	26	1.96
5456543--5456980	185	2.4	186	82	2	497	33	17	23	26	1.96
5456888--5457165	154	1.8	153	85	3	389	32	18	21	26	1.97
5457043--5457766	62	11.5	61	78	9	589	32	17	24	25	1.97
5457771--5458055	62	4.5	65	80	5	282	32	17	24	25	1.96
5457683--5457864	100	1.8	98	83	4	240	30	19	24	25	1.98
5457552--5457996	225	2.0	220	80	7	497	32	18	24	25	1.97
5458100--5458280	62	2.9	62	85	1	238	30	18	23	27	1.98
5457483--5458282	291	2.8	285	80	7	895	33	17	23	25	1.96
5458287--5458482	63	3.1	63	83	7	200	35	17	25	21	1.95
5458321--5458631	63	4.9	63	77	5	270	31	17	24	26	1.97
5459161--5459194	18	1.9	18	88	5	52	44	14	0	41	1.45
5459766--5459868	23	4.6	21	76	11	75	6	10	9	72	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5459787--5459868	23	3.6	23	75	15	80	7	10	9	71	1.30
5466823--5466865	21	2.0	21	90	0	68	11	25	13	48	1.77
5467084--5467125	22	1.9	21	85	9	57	50	7	23	19	1.72
5467321--5467345	12	2.1	12	100	0	50	16	0	0	84	0.63
5469086--5469126	21	2.0	20	85	9	55	53	0	24	21	1.46
5472870--5472896	13	2.1	13	100	0	54	40	7	22	29	1.81
5481349--5481436	26	3.3	26	95	1	149	42	30	1	26	1.63
5482872--5482902	16	1.9	16	93	0	53	22	0	0	77	0.77
5482892--5482925	15	2.1	17	89	10	54	44	0	0	55	0.99
5483208--5483243	18	1.9	18	88	5	54	25	2	2	69	1.15
5483204--5483251	18	2.6	18	80	9	53	31	2	2	64	1.16
5483240--5483286	25	2.0	24	83	8	60	53	0	0	46	1.00
5483246--5483297	25	2.1	25	82	10	63	48	1	1	48	1.24
5483324--5483359	14	2.5	15	91	8	58	69	0	2	27	1.02
5483483--5483516	18	1.9	18	88	5	52	50	0	0	50	1.00
5483865--5483901	2	18.5	2	100	0	74	0	48	0	51	1.00
5488392--5488460	25	2.7	26	86	6	95	63	0	7	28	1.21
5488454--5488496	19	2.2	19	83	4	50	62	6	2	27	1.33
5489188--5489222	2	18.0	2	94	5	63	51	0	0	48	1.00
5494955--5494988	11	3.0	11	91	8	59	44	0	0	55	0.99
5495009--5495112	13	7.8	13	68	23	65	51	3	0	43	1.26
5495013--5495112	9	10.6	9	70	20	62	52	4	1	43	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5495054--5495110	28	2.0	28	89	6	87	56	5	0	38	1.22
5495973--5496026	23	2.5	21	80	16	58	46	3	1	48	1.30
5495975--5496027	22	2.3	23	84	9	65	47	3	1	47	1.31
5497787--5497825	20	1.9	20	84	5	51	38	0	7	53	1.30
5497874--5497915	22	1.9	22	90	9	68	61	0	0	38	0.96
5498331--5498370	20	2.0	20	95	0	71	50	7	0	42	1.30
5501387--5501484	29	3.3	29	65	18	74	54	7	0	38	1.28
5501364--5501485	61	2.0	61	96	0	226	55	6	0	37	1.26
5504358--5504405	23	2.1	23	84	7	62	35	4	4	56	1.38
5508476--5508527	20	2.5	20	87	3	68	42	13	19	25	1.87

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