genome.fa.s25.2.7.7.80.10.50.1000.31.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   53   54   55   56   

This is table  31  of  56  ( 6609 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)
5200309--5200344	17	2.1	17	100	0	72	30	16	5	47	1.70
5202786--5202851	33	2.0	33	100	0	132	33	9	24	33	1.87
5203843--5203897	25	2.2	25	90	3	83	67	5	1	25	1.22
5203851--5203909	25	2.3	25	82	5	64	67	1	1	28	1.10
5208673--5208710	12	3.0	12	88	11	58	23	0	5	71	1.07
5211665--5211698	14	2.3	15	90	5	52	26	5	0	67	1.13
5212205--5212280	23	3.2	23	82	16	84	38	0	2	59	1.12
5212557--5212607	26	2.0	26	88	3	77	33	0	5	60	1.21
5212624--5212681	24	2.4	24	100	0	116	32	6	13	46	1.70
5212722--5213841	72	15.5	73	80	5	1075	33	2	10	53	1.49
5212799--5213841	73	14.5	69	74	13	380	32	2	10	54	1.48
5212721--5213841	145	7.8	143	80	5	1037	33	2	10	53	1.49
5213441--5213550	33	3.2	33	65	26	82	30	1	10	56	1.44
5215236--5215271	16	2.3	15	90	4	54	58	0	2	38	1.13
5230253--5230337	42	2.0	42	93	0	143	27	15	28	29	1.96
5232219--5232321	31	3.3	31	76	8	111	48	15	15	20	1.81
5232207--5232336	62	2.1	62	88	4	201	50	16	13	20	1.78
5232219--5232335	31	3.8	31	74	8	103	49	15	15	19	1.79
5243380--5243407	2	14.0	2	100	0	56	50	0	0	50	1.00
5244754--5244786	2	16.5	2	100	0	66	48	0	0	51	1.00
5245247--5245606	121	3.0	118	92	5	609	45	16	16	21	1.85
5249752--5249781	2	15.0	2	92	0	51	46	0	3	50	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5253481--5253510	10	3.0	10	100	0	60	20	30	10	40	1.85
5255142--5255203	33	1.9	32	86	3	88	45	1	0	53	1.10
5255250--5255303	15	3.4	16	78	16	67	59	0	3	37	1.15
5255355--5255396	6	7.5	6	79	15	54	33	2	0	64	1.07
5255343--5255396	12	5.0	11	78	17	60	37	1	0	61	1.07
5255346--5255396	21	2.4	22	90	3	77	37	1	0	60	1.08
5255355--5255399	15	2.8	16	86	13	65	33	2	0	64	1.06
5255379--5255479	23	4.5	22	71	14	73	39	1	0	58	1.09
5257598--5258277	228	3.0	226	81	2	714	20	24	26	28	1.99
5258716--5258746	16	2.0	15	93	6	53	45	0	0	54	0.99
5260322--5260362	17	2.5	16	84	4	55	63	0	0	36	0.95
5262032--5262077	22	2.1	22	100	0	92	52	0	4	43	1.21
5262552--5262592	20	2.1	20	86	4	57	31	0	2	65	1.05
5262552--5262603	19	2.7	19	82	8	61	34	0	1	63	1.06
5262593--5262653	27	2.3	27	80	5	70	62	6	0	31	1.21
5265745--5265781	2	18.5	2	88	0	56	51	5	0	43	1.24
5267109--5267151	21	2.0	21	100	0	86	9	27	9	53	1.63
5269132--5269262	64	2.0	64	98	0	253	34	4	20	40	1.73
5273106--5273140	2	17.5	2	100	0	70	48	0	51	0	1.00
5277539--5277591	16	3.2	16	86	5	70	33	0	3	62	1.13
5277795--5277872	15	4.8	16	72	21	56	58	0	1	39	1.06
5277997--5278030	17	1.9	18	88	5	52	29	5	2	61	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5277991--5278385	195	2.0	193	90	0	610	43	4	6	45	1.49
5278310--5278366	26	2.3	24	77	16	62	63	5	5	26	1.37
5278033--5278439	193	2.1	195	82	4	475	45	3	6	43	1.48
5279981--5280030	16	3.1	15	78	18	55	34	0	0	66	0.92
5280560--5280586	2	13.5	2	100	0	54	51	0	0	48	1.00
5285178--5285215	3	12.7	3	100	0	76	68	0	31	0	0.90
5285948--5285982	2	17.5	2	93	0	61	48	2	0	48	1.16
5286769--5286848	16	5.1	16	76	10	76	40	2	3	53	1.32
5286771--5286848	15	4.9	16	73	18	58	38	2	3	55	1.32
5289098--5289391	147	2.0	147	91	2	475	46	5	9	37	1.61
5290189--5290473	119	2.4	119	79	8	287	50	3	1	43	1.29
5291049--5291099	18	2.8	19	76	8	61	70	0	1	27	0.98
5292595--5292623	2	14.5	2	100	0	58	48	0	0	51	1.00
5293060--5293099	18	2.2	18	86	4	53	52	2	0	45	1.14
5295620--5295715	16	6.0	16	72	11	81	39	21	18	19	1.92
5295619--5295704	32	2.7	32	82	7	95	40	22	18	18	1.91
5295747--5295788	21	2.0	22	85	4	59	52	0	4	42	1.22
5296595--5296643	22	2.3	22	85	3	64	44	12	6	36	1.67
5296940--5296980	2	20.5	2	100	0	82	51	0	0	48	1.00
5297190--5297239	23	2.2	22	79	6	55	56	0	0	44	0.99
5297314--5297349	16	2.2	16	90	9	56	44	0	8	47	1.33
5297943--5297970	3	9.3	3	100	0	56	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5298894--5298939	23	2.0	23	82	0	56	32	4	4	58	1.37
5299367--5299405	3	13.0	3	100	0	78	66	0	0	33	0.92
5309111--5309354	119	2.0	120	96	0	445	38	18	12	30	1.88
5311242--5311297	20	2.8	18	78	19	58	44	0	0	55	0.99
5311238--5311274	18	2.1	17	90	5	56	40	0	0	59	0.97
5311242--5311318	21	3.7	20	81	11	84	42	0	2	54	1.14
5311253--5311318	23	3.0	23	86	4	82	42	0	3	54	1.15
5315491--5315528	2	19.0	2	100	0	76	50	0	50	0	1.00
5322166--5322215	18	3.0	16	74	25	50	64	2	0	34	1.05
5329345--5329369	12	2.1	12	100	0	50	44	0	0	56	0.99
5329372--5329413	16	2.8	16	82	7	52	61	2	0	35	1.09
5337079--5337127	22	2.2	22	92	0	80	22	20	6	51	1.69
5340700--5340752	26	2.0	26	85	7	72	30	30	0	39	1.57
5350669--5350707	11	3.6	11	93	3	62	87	7	5	0	0.68
5350802--5350843	21	2.0	21	86	4	59	78	0	4	16	0.91
5351629--5351998	28	13.4	28	78	10	339	31	27	16	24	1.96
5351629--5351998	86	4.4	86	77	10	342	31	27	16	24	1.96
5351796--5351945	76	2.0	76	81	5	178	32	26	14	27	1.95
5351766--5351973	104	2.0	106	84	5	280	32	26	14	25	1.95
5353384--5353411	14	2.0	14	100	0	56	28	42	7	21	1.79
5354754--5354823	27	2.6	27	93	0	113	24	34	20	21	1.97
5358304--5358826	262	2.0	265	91	1	845	30	21	22	25	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5360929--5361005	26	2.9	27	71	19	72	37	11	18	32	1.87
5360926--5361013	14	6.6	14	69	10	58	35	11	17	36	1.85
5361024--5361615	28	21.1	27	78	9	483	31	27	15	25	1.96
5362078--5362107	11	2.6	12	94	5	53	90	3	0	6	0.56
5362618--5362675	20	2.9	20	81	0	80	32	12	12	43	1.79
5362665--5362741	32	2.4	32	89	2	120	27	15	10	46	1.78
5368520--5368603	39	2.2	38	79	14	91	66	4	0	28	1.12
5368799--5368833	2	17.5	2	93	0	61	54	0	0	45	0.99
5369300--5369386	40	2.2	40	100	0	174	47	2	2	48	1.27
5369295--5369390	15	7.1	14	66	25	55	47	2	2	47	1.25
5369538--5369592	16	3.4	16	76	14	58	58	0	0	41	0.98
5369807--5369996	4	47.5	4	88	0	200	49	9	1	40	1.42
5369807--5369996	28	6.7	28	85	2	227	49	9	1	40	1.42
5371030--5371350	167	1.9	168	92	0	536	34	14	10	40	1.80
5370745--5371648	449	2.0	451	87	1	1294	36	13	10	39	1.79
5371202--5371930	285	2.6	283	88	1	1079	35	13	11	39	1.82
5371480--5372296	451	1.8	445	86	2	1186	37	12	10	39	1.78
5376123--5376185	26	2.4	26	84	7	74	68	3	0	28	1.05
5378633--5378661	2	14.5	2	100	0	58	48	0	0	51	1.00
5381930--5381959	2	15.0	2	92	0	51	53	0	46	0	1.00
5381901--5381959	12	5.1	12	72	15	52	50	3	44	1	1.28
5382331--5382365	18	1.9	18	88	0	52	48	0	2	48	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5383439--5383468	5	5.8	5	96	4	51	83	0	0	16	0.65
5384283--5384312	2	15.0	2	100	0	60	50	0	0	50	1.00
5384836--5384876	21	2.0	21	85	0	55	65	7	2	24	1.30
5387305--5387362	28	2.3	23	73	26	64	58	3	0	37	1.15
5388448--5388482	17	1.9	18	88	11	54	40	5	11	42	1.65
5393162--5393219	28	2.1	28	83	6	73	12	8	5	74	1.21
5402613--5402659	19	2.2	22	85	14	64	63	0	0	36	0.94
5406908--5406979	35	2.1	35	83	0	90	45	5	15	33	1.69
5408508--5408585	38	2.1	38	100	0	156	28	24	21	25	1.99
5414705--5414729	13	1.9	13	100	0	50	36	16	16	32	1.90

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   53   54   55   56