genome.fa.s1.2.7.7.80.10.50.1000.32.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  32  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)
5508475--5508548	21	3.6	21	80	7	80	40	14	17	27	1.89
5511752--5511794	21	2.0	21	100	0	86	13	9	13	62	1.53
5513671--5513699	14	2.0	15	93	6	51	75	0	3	20	0.94
5516322--5516372	25	2.0	25	84	0	66	50	0	1	47	1.12
5516652--5516715	16	4.0	16	73	15	51	59	9	0	31	1.29
5519435--5519464	2	15.0	2	100	0	60	50	0	0	50	1.00
5520801--5520830	12	2.5	12	94	0	51	33	26	16	23	1.96
5521689--5521714	2	13.0	2	100	0	52	50	0	0	50	1.00
5529596--5529647	27	1.9	27	96	0	95	30	25	15	28	1.96
5531012--5531564	158	3.6	151	77	8	508	24	19	19	36	1.95
5532183--5532218	15	2.4	15	90	0	63	63	11	5	19	1.46
5535120--5535167	12	3.9	12	78	10	53	75	0	25	0	0.81
5535117--5535171	15	3.3	17	76	16	53	76	0	23	0	0.79
5537327--5537455	36	3.6	35	76	5	125	21	23	12	42	1.87
5537420--5537745	48	6.6	48	78	9	307	18	21	18	42	1.89
5537423--5537745	49	6.6	47	76	9	268	18	21	17	42	1.89
5537420--5537755	104	3.4	97	80	8	347	18	20	17	42	1.89
5537754--5538171	44	9.4	44	68	10	190	21	23	15	39	1.91
5537884--5538171	88	3.3	88	74	6	251	21	22	15	39	1.91
5537754--5538085	132	2.5	130	76	10	339	21	23	15	39	1.91
5538123--5538320	100	2.0	101	91	1	326	22	24	11	41	1.87
5538380--5538709	84	3.9	84	80	2	331	13	26	19	40	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5538409--5538694	42	6.8	42	84	1	349	14	25	19	40	1.89
5539459--5539645	82	2.3	82	90	1	306	34	12	24	28	1.92
5540069--5540115	24	2.0	24	82	0	58	68	8	17	6	1.37
5541116--5541167	19	2.7	20	90	3	79	40	15	17	26	1.89
5548758--5548797	18	2.2	19	86	4	55	42	10	17	30	1.82
5549055--5549095	20	2.0	21	90	4	66	36	12	12	39	1.80
5549153--5549200	20	2.5	20	86	3	62	43	18	14	22	1.87
5550128--5550154	13	2.1	13	100	0	54	29	14	14	40	1.86
5550109--5550170	33	1.9	32	87	9	90	27	14	16	41	1.87
5550139--5550195	19	2.9	19	84	5	78	31	12	17	38	1.87
5550135--5550195	20	3.1	19	79	6	77	32	11	18	37	1.86
5550224--5550286	33	1.9	32	87	12	92	33	12	19	34	1.89
5551884--5551917	3	11.3	3	87	0	50	38	0	32	29	1.58
5559026--5559096	22	3.2	23	71	15	69	71	8	11	8	1.30
5559025--5559121	45	2.2	44	82	12	110	71	10	11	7	1.32
5560386--5560626	27	8.8	27	80	5	243	24	29	14	31	1.95
5560386--5560626	55	4.4	55	80	6	249	24	29	14	31	1.95
5560381--5560599	110	2.0	110	86	3	307	24	30	14	31	1.94
5560630--5562923	32	74.4	32	73	13	973	31	29	17	20	1.96
5561221--5561264	19	2.3	19	84	4	52	31	27	20	20	1.97
5560605--5563077	245	10.3	241	81	8	1975	31	29	17	21	1.96
5561791--5561918	28	4.5	28	78	9	105	31	34	14	19	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5561913--5561956	19	2.3	19	84	4	52	31	27	20	20	1.97
5560660--5563077	692	3.5	682	87	5	2947	31	29	17	21	1.96
5563980--5564033	20	2.8	19	79	15	67	35	11	14	38	1.82
5564049--5564099	20	2.5	20	87	0	66	35	9	13	41	1.78
5564052--5564130	20	4.0	20	78	6	61	32	13	10	43	1.78
5564101--5564145	20	2.2	20	88	0	63	28	22	8	40	1.84
5570701--5570743	20	2.0	22	86	8	63	34	4	20	39	1.74
5575479--5575552	20	3.7	21	76	7	64	35	14	16	33	1.89
5575581--5575656	21	3.7	21	80	3	91	34	15	13	36	1.87
5575580--5575675	41	2.3	42	89	3	149	36	16	10	36	1.83
5578116--5578210	36	2.9	34	81	9	108	29	23	13	33	1.93
5578647--5578690	20	2.2	20	88	4	63	38	18	13	29	1.89
5578785--5578809	13	1.9	13	100	0	50	36	16	16	32	1.90
5581468--5581713	93	2.6	93	83	8	282	31	13	29	25	1.94
5583911--5583988	20	3.9	19	80	6	84	41	14	11	33	1.81
5583911--5583988	40	2.0	39	84	2	102	41	14	11	33	1.81
5584605--5585919	28	45.8	28	87	5	1277	23	17	31	28	1.97
5584528--5585940	57	24.5	57	85	6	1393	23	17	31	28	1.97
5584528--5585919	85	16.1	85	85	6	1357	23	17	31	28	1.97
5585146--5585403	96	2.8	96	80	8	282	21	17	31	30	1.96
5585648--5585938	109	2.6	110	89	2	404	27	14	32	26	1.95
5586986--5587015	13	2.3	13	94	0	51	3	3	0	93	0.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5592041--5592287	94	2.6	94	83	5	311	31	14	29	24	1.94
5594491--5594565	20	3.8	20	77	7	80	40	12	13	34	1.81
5594488--5594565	40	2.0	39	84	2	102	39	12	12	34	1.82
5596641--5596684	21	2.1	21	83	8	54	25	31	4	38	1.76
5598324--5598370	21	2.3	21	76	23	55	42	4	19	34	1.70
5598491--5598529	13	3.0	13	96	0	69	35	15	17	30	1.91
5598515--5598593	20	3.7	20	75	15	68	45	15	13	25	1.83
5600610--5600640	15	2.1	15	93	0	53	12	22	16	48	1.80
5601957--5601982	13	2.0	13	100	0	52	38	15	15	30	1.88
5602442--5602508	37	1.9	35	88	11	102	32	11	25	29	1.92
5605684--5605708	13	1.9	13	100	0	50	36	16	16	32	1.90
5607618--5607643	13	2.0	13	100	0	52	38	15	15	30	1.88
5608103--5608169	37	1.9	35	88	11	102	32	11	25	29	1.92
5609295--5609339	21	2.1	21	84	8	56	22	20	4	53	1.63
5611558--5611583	13	2.0	13	100	0	52	30	15	15	38	1.88
5613014--5613073	21	2.9	21	78	14	70	20	26	1	51	1.56
5618528--5618555	13	2.2	13	100	0	56	39	17	14	28	1.89
5618510--5618575	33	2.0	33	88	5	98	40	13	15	30	1.85
5626786--5626855	25	2.8	25	74	8	88	58	2	5	32	1.36
5627616--5627669	11	4.8	11	77	8	56	35	0	0	64	0.94
5627615--5627671	14	4.5	14	73	20	54	35	0	0	64	0.93
5628071--5628114	22	2.0	22	86	8	63	40	0	2	56	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5628064--5628121	23	2.5	23	77	11	64	36	1	1	60	1.17
5629263--5629293	14	2.1	15	94	5	55	45	0	0	54	0.99
5631133--5631166	12	2.9	12	91	4	52	38	0	0	61	0.96
5631147--5631251	17	6.4	17	65	28	50	33	0	2	62	1.16
5632097--5632129	3	11.0	3	100	0	66	33	0	0	66	0.92
5633469--5633550	17	5.0	16	73	17	71	37	0	0	62	0.96
5633501--5633554	22	2.5	22	93	0	90	31	0	0	68	0.90
5633501--5633555	11	5.0	11	77	16	60	32	0	0	67	0.91
5633501--5633564	22	3.0	22	88	4	78	34	0	0	65	0.93
5638477--5638516	16	2.4	17	83	4	55	50	0	35	15	1.44
5644725--5644764	18	2.2	18	86	0	53	60	0	0	40	0.97
5645097--5645130	2	17.0	2	100	0	68	50	0	0	50	1.00
5645645--5645699	2	28.0	2	96	3	103	50	0	49	0	1.00
5646327--5646375	24	2.0	24	88	0	71	44	12	0	42	1.41
5646565--5646645	31	2.6	31	79	13	78	39	4	2	53	1.36
5649019--5649197	3	59.7	3	90	0	214	24	0	70	5	1.06
5650571--5650596	6	4.3	6	100	0	52	38	0	0	61	0.96
5651643--5651676	2	17.0	2	100	0	68	50	0	50	0	1.00
5654142--5654176	15	2.2	16	90	5	54	68	0	0	31	0.90
5655608--5655672	16	4.0	17	70	21	50	38	1	4	55	1.30
5661999--5662051	27	2.0	27	85	14	74	47	0	3	49	1.19
5662005--5662062	25	2.3	23	77	16	62	48	0	3	48	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5662212--5662243	2	16.0	2	100	0	64	50	0	50	0	1.00
5663972--5664020	3	16.3	3	100	0	98	67	0	0	32	0.91
5664729--5664787	31	1.9	31	86	6	84	40	3	0	55	1.16
5665838--5665879	15	2.8	15	85	0	57	61	0	2	35	1.09
5679332--5679390	16	3.7	16	88	0	82	50	8	5	35	1.55
5679333--5679407	32	2.3	32	81	2	78	53	8	4	34	1.49
5679365--5679411	16	2.9	16	93	3	76	59	6	0	34	1.23
5679420--5679460	15	2.7	15	85	7	57	58	7	0	34	1.26
5680001--5680066	32	2.0	33	85	2	89	53	4	0	42	1.21
5680010--5680066	16	3.6	15	75	17	53	50	3	0	45	1.18

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