genome.fa.s1.2.7.7.80.10.50.1000.30.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  30  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)
5217416--5217555	33	4.2	33	90	6	221	28	35	16	19	1.93
5217416--5217555	67	2.1	66	92	5	230	28	35	16	19	1.93
5217555--5218302	49	15.8	48	83	7	917	25	26	18	30	1.98
5217550--5218311	92	8.1	92	88	6	1078	25	26	17	30	1.98
5218212--5218371	52	3.0	53	81	7	187	25	25	15	33	1.95
5219177--5219243	33	2.0	33	88	0	98	34	11	13	40	1.81
5219197--5219221	13	1.9	13	100	0	50	36	16	16	32	1.90
5219286--5219310	13	1.9	13	100	0	50	32	16	16	36	1.90
5219319--5219439	52	2.3	52	97	0	224	34	18	18	28	1.94
5225098--5225393	165	1.8	161	84	4	405	56	5	9	29	1.53
5226371--5227144	60	12.9	59	81	6	382	40	12	23	23	1.88
5226519--5226629	30	3.7	30	71	7	100	36	11	24	27	1.90
5226731--5227138	30	13.7	29	67	13	175	41	12	23	21	1.88
5226579--5227400	60	13.7	60	82	2	711	40	13	23	22	1.90
5226940--5227167	30	7.6	30	72	9	178	40	14	25	20	1.89
5226610--5227222	30	20.5	30	64	14	156	41	13	23	22	1.89
5228775--5228815	19	2.2	19	91	4	66	7	19	0	73	1.07
5228775--5228831	9	6.4	9	77	18	50	7	17	0	75	1.02
5228799--5228832	16	2.1	16	89	10	52	2	14	0	82	0.79
5228753--5228824	23	3.1	22	75	18	67	8	16	1	73	1.14
5231227--5231606	158	2.4	156	80	5	408	37	11	21	29	1.89
5231227--5231604	79	4.8	78	80	5	352	37	11	21	29	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5234026--5234081	20	2.8	20	97	0	103	30	12	10	46	1.76
5234898--5235727	62	13.4	62	84	4	933	31	18	24	25	1.97
5234898--5236566	247	6.7	247	81	6	1568	31	18	24	25	1.97
5234898--5236566	185	8.9	184	80	7	1573	31	18	24	25	1.97
5235718--5235745	9	3.1	9	100	0	56	25	21	42	10	1.85
5235736--5236566	62	13.5	62	82	4	928	31	18	24	25	1.97
5244461--5244536	31	2.5	31	88	0	116	36	13	18	31	1.89
5244568--5244620	20	2.7	20	93	0	97	32	15	7	45	1.74
5249086--5249401	159	2.1	149	81	9	361	37	13	12	36	1.82
5249359--5249439	40	2.0	40	88	4	119	38	12	23	25	1.90
5249200--5249594	195	2.0	199	86	5	554	40	14	13	32	1.84
5250395--5250430	14	2.8	13	88	12	56	0	13	0	86	0.58
5251063--5251443	166	2.3	163	86	6	518	55	7	10	26	1.60
5251303--5251578	135	2.0	139	86	5	384	57	7	10	23	1.59
5262066--5262117	25	2.0	25	88	7	77	51	0	1	46	1.12
5263365--5263538	13	12.4	14	66	23	59	35	1	1	62	1.10
5263402--5263561	5	31.4	5	65	17	62	35	1	1	61	1.12
5263390--5263433	18	2.3	20	80	11	56	40	4	0	54	1.21
5263441--5263497	11	5.4	11	79	12	66	28	0	1	70	0.98
5263438--5263561	38	3.1	39	76	14	119	33	0	1	64	1.09
5263469--5263531	18	3.4	17	71	28	56	30	0	1	68	0.99
5263422--5263571	22	6.9	23	69	20	83	36	1	1	61	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5263399--5263522	29	4.4	27	74	14	101	33	0	1	64	1.09
5263362--5263531	12	13.5	12	68	19	80	34	1	1	63	1.10
5263445--5263539	39	2.5	38	89	5	138	31	0	2	66	1.04
5264389--5264455	17	3.9	16	75	12	62	41	0	0	58	0.98
5264865--5264917	24	2.1	26	86	6	74	41	1	0	56	1.10
5264971--5265031	17	3.5	17	72	16	54	40	1	1	55	1.19
5265706--5265770	24	2.9	24	76	17	68	35	0	3	61	1.12
5265742--5265801	11	5.6	10	75	16	50	31	3	0	65	1.09
5265746--5265802	21	2.5	21	83	11	60	31	3	0	64	1.10
5265837--5265885	17	2.8	18	82	14	59	28	0	2	69	1.00
5265850--5265885	18	2.1	17	90	10	56	30	0	0	69	0.89
5266290--5266325	2	18.0	2	88	0	54	47	2	2	47	1.31
5268233--5268282	19	2.6	19	82	14	59	62	10	0	28	1.27
5268208--5268282	32	2.3	33	80	15	86	60	9	1	29	1.36
5268829--5268880	23	2.3	23	100	0	104	44	3	32	19	1.69
5268829--5268888	23	2.6	23	92	5	86	48	5	30	16	1.67
5275210--5275244	2	17.5	2	100	0	70	0	48	0	51	1.00
5275494--5275545	20	2.6	20	80	14	63	76	0	7	15	0.99
5277751--5277798	24	2.0	24	91	0	78	43	10	14	31	1.79
5280494--5280598	20	5.6	18	68	26	74	47	1	0	50	1.12
5280986--5281031	19	2.3	20	82	17	69	45	0	4	50	1.21
5281039--5281080	15	2.8	15	79	10	50	57	2	0	40	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5281463--5281500	20	1.9	20	89	10	60	55	0	0	44	0.99
5281614--5281666	19	2.8	18	81	10	61	56	3	0	39	1.17
5284107--5284163	2	28.0	2	92	3	96	49	1	1	47	1.22
5286253--5286292	17	2.4	17	91	8	64	70	0	0	30	0.88
5287504--5287563	23	2.8	20	78	9	57	25	10	20	45	1.81
5292836--5293614	28	26.5	28	81	9	758	21	17	30	29	1.97
5292831--5293614	170	4.4	173	83	8	899	21	17	30	29	1.97
5294820--5294892	17	3.8	19	79	20	80	1	4	10	83	0.84
5294850--5294895	1	46.0	1	82	0	56	0	0	8	91	0.43
5294853--5294896	15	3.0	15	87	12	65	0	0	11	88	0.51
5294820--5294895	18	4.1	17	80	17	80	1	3	10	84	0.82
5294841--5294892	26	2.0	27	92	3	88	0	1	11	86	0.65
5294828--5294896	11	5.7	11	78	13	66	1	2	11	84	0.81
5297549--5297622	28	2.6	28	87	4	96	24	17	32	25	1.97
5297333--5297955	236	2.6	237	78	5	600	33	13	26	27	1.93
5297680--5297826	80	1.9	80	91	1	242	31	12	25	29	1.93
5297784--5297858	27	2.7	27	89	2	105	24	20	32	24	1.98
5297842--5297972	51	2.6	50	84	4	163	33	10	24	31	1.89
5301751--5301907	20	7.8	20	70	23	98	26	16	15	42	1.88
5301818--5301887	33	2.1	33	97	0	131	25	20	14	40	1.90
5301840--5301868	13	2.2	13	100	0	58	27	13	17	41	1.87
5304189--5304303	51	2.3	51	95	0	203	31	24	12	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5304239--5304545	79	3.9	79	80	4	368	28	25	13	32	1.94
5304110--5304382	130	2.1	128	81	6	320	28	24	13	33	1.93
5304239--5304534	157	1.9	158	83	4	393	29	24	13	32	1.93
5307497--5307535	19	2.1	19	85	0	51	69	7	10	12	1.37
5315138--5315180	15	2.8	15	89	3	59	48	4	0	46	1.22
5315744--5315776	15	2.1	16	88	5	50	48	0	0	51	1.00
5319452--5319528	33	2.3	34	86	10	113	38	16	15	28	1.90
5319604--5319630	13	2.1	13	100	0	54	29	14	14	40	1.86
5322139--5322361	51	4.3	51	81	4	241	29	26	11	32	1.91
5322178--5322361	53	3.5	51	80	11	205	28	26	11	33	1.91
5322295--5322550	79	3.2	79	80	3	239	26	28	15	29	1.96
5328309--5328522	118	1.8	116	82	7	270	52	2	1	43	1.24
5328346--5328622	110	2.4	112	85	8	357	52	2	1	43	1.23
5328562--5328634	23	3.2	22	69	18	60	57	2	0	39	1.13
5328927--5329264	124	2.7	126	84	11	439	41	4	2	52	1.34
5329495--5329528	18	1.9	18	88	5	52	58	2	5	32	1.37
5329744--5329824	11	7.4	11	82	0	108	37	0	0	62	0.95
5329743--5329824	22	3.7	22	100	0	164	36	0	0	63	0.95
5333809--5334254	90	5.0	90	81	5	526	34	16	6	42	1.75
5333829--5334254	86	4.8	85	80	9	397	35	16	7	41	1.75
5333814--5334254	177	2.5	177	86	3	598	34	16	6	42	1.75
5334193--5334311	57	2.1	58	82	1	141	34	17	8	39	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5335142--5335200	23	2.7	22	75	10	59	57	1	1	38	1.19
5335028--5335293	116	2.2	120	87	9	377	53	1	2	42	1.24
5335650--5335711	22	2.8	22	78	9	72	32	1	4	61	1.27
5335871--5335935	24	2.7	25	76	4	62	40	0	0	60	0.97
5335894--5335958	24	2.8	23	80	13	71	43	0	0	56	0.99
5335879--5336008	70	1.9	69	83	9	169	44	0	0	55	0.99
5336068--5336123	28	2.0	28	86	10	78	55	3	0	41	1.17
5336390--5336429	20	2.0	20	90	0	62	40	0	2	57	1.12
5338830--5338858	2	14.5	2	100	0	58	48	0	0	51	1.00
5343389--5343413	2	12.5	2	100	0	50	48	0	0	52	1.00

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