genome.fa.s25.2.7.7.80.10.50.1000.40.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  40  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)
6857610--6857663	20	2.7	20	85	2	72	38	12	14	33	1.85
6857736--6857804	20	3.5	20	70	7	68	27	18	17	36	1.94
6857736--6857827	40	2.3	40	94	0	166	26	18	16	39	1.91
6857753--6857824	20	3.6	20	75	14	85	26	15	16	41	1.88
6859182--6859239	21	2.8	21	81	5	73	36	15	15	32	1.89
6859276--6859358	19	4.7	19	80	17	106	33	13	19	33	1.90
6859277--6859339	32	2.0	32	100	0	126	33	12	19	34	1.89
6859296--6859320	13	1.9	13	100	0	50	36	16	16	32	1.90
6861771--6861868	51	1.9	51	86	12	139	32	20	9	37	1.84
6861829--6862049	79	2.8	78	81	6	241	27	28	13	31	1.94
6861829--6862049	80	2.8	78	78	8	236	27	28	13	31	1.94
6861982--6862151	52	3.3	50	80	8	189	30	26	11	31	1.91
6862164--6862367	78	2.6	79	79	5	209	24	30	17	27	1.97
6873964--6874016	21	2.5	21	100	0	106	60	9	11	18	1.57
6874933--6875003	20	3.6	19	77	7	70	40	12	11	35	1.79
6878254--6878303	15	3.4	14	78	10	55	84	10	6	0	0.79
6878255--6878303	25	2.0	25	88	8	73	83	10	6	0	0.80
6879319--6879993	55	11.9	54	87	5	704	27	28	20	24	1.99
6879319--6879993	165	4.0	168	84	7	812	27	28	20	24	1.99
6879774--6879919	29	5.2	29	62	18	76	28	30	19	21	1.98
6880741--6880817	21	3.7	20	79	6	82	37	12	16	32	1.87
6880854--6880918	19	3.8	18	75	24	68	35	13	18	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6880855--6880930	32	2.4	32	95	0	134	35	14	18	31	1.91
6880874--6880931	13	4.0	13	76	23	62	37	15	17	29	1.90
6883349--6883465	51	2.4	51	86	12	156	30	23	11	34	1.91
6883404--6883628	79	2.9	78	82	5	258	26	27	15	30	1.96
6883560--6883729	52	3.3	52	80	2	182	30	26	12	31	1.93
6883560--6883706	51	2.8	53	84	2	156	29	25	12	32	1.92
6883717--6883788	28	2.6	28	82	4	83	22	33	19	25	1.97
6887110--6887151	7	6.0	7	88	0	66	28	16	26	28	1.97
6892243--6892299	13	3.9	13	76	24	60	36	14	15	33	1.88
6892242--6892326	32	2.7	32	94	0	143	35	12	15	36	1.86
6892240--6892318	13	4.9	17	70	27	57	36	12	13	36	1.83
6892371--6892395	13	1.9	13	100	0	50	32	16	16	36	1.90
6893279--6893327	21	2.4	20	83	6	62	22	18	16	42	1.88
6895675--6895738	32	2.0	33	90	3	103	40	15	14	29	1.86
6896414--6896530	54	2.2	54	92	3	191	35	19	0	44	1.57
6896529--6896560	16	2.1	16	94	5	57	6	43	0	50	1.27
6898413--6898449	13	2.8	13	87	0	56	32	16	16	35	1.91
6900673--6900724	21	2.5	21	87	0	77	42	19	11	26	1.85
6901858--6901934	21	3.7	21	89	3	111	35	12	16	35	1.88
6901970--6902037	19	3.9	19	78	21	85	35	11	14	38	1.83
6901991--6902015	13	1.9	13	100	0	50	36	16	16	32	1.90
6901972--6902034	32	2.0	32	96	0	117	34	12	15	36	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6902057--6902123	33	2.0	33	85	0	89	25	14	17	41	1.88
6904464--6904587	51	2.4	51	84	1	167	32	24	10	33	1.89
6904576--6904647	28	2.6	28	86	4	92	22	34	19	23	1.96
6904601--6904877	78	3.5	78	87	3	351	24	28	16	30	1.96
6917276--6917337	1	62.0	1	73	0	52	87	8	4	0	0.68
6917275--6917337	8	7.8	8	81	10	65	85	9	4	0	0.72
6917275--6917337	13	4.8	13	83	9	67	85	9	4	0	0.72
6917275--6917331	21	2.9	19	80	16	71	85	10	3	0	0.70
6918307--6918963	55	11.3	59	88	5	818	26	28	20	24	1.99
6919692--6919747	21	2.7	21	97	0	103	33	10	19	35	1.87
6922356--6922427	28	2.6	28	86	4	92	22	34	19	23	1.96
6922381--6922661	79	3.6	79	87	1	314	25	28	15	30	1.96
6922302--6922501	107	1.9	108	82	4	260	27	28	14	29	1.95
6924490--6924531	15	2.8	16	78	10	52	28	16	2	52	1.56
6925441--6925507	37	1.9	35	88	11	102	29	25	11	32	1.92
6925957--6925995	13	3.0	13	96	0	69	33	15	20	30	1.94
6925938--6925977	20	2.0	20	85	9	55	25	15	20	40	1.90
6926111--6926137	9	3.0	9	100	0	54	44	11	22	22	1.84
6927282--6927326	23	2.0	23	82	8	56	37	22	8	31	1.85
6927723--6927777	21	2.7	21	82	2	67	40	14	12	32	1.84
6927840--6927887	20	2.5	19	86	3	60	43	16	10	29	1.81
6931113--6931151	20	2.1	20	86	13	57	69	5	0	25	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6931198--6931271	34	2.1	34	83	14	89	62	6	0	31	1.21
6931327--6931382	18	3.1	18	84	2	67	76	0	19	3	0.93
6931560--6931601	23	2.0	20	86	13	57	26	0	2	71	0.98
6931623--6931652	12	2.4	13	94	5	53	36	3	0	60	1.14
6932151--6932206	16	3.5	16	71	9	51	48	19	10	21	1.79
6932273--6932334	24	2.5	25	81	5	72	53	20	3	22	1.60
6932375--6932417	16	2.6	17	85	10	63	51	27	6	13	1.67
6933618--6933648	16	1.9	16	93	0	53	61	19	0	19	1.35
6934129--6934201	29	2.6	27	79	14	69	61	0	1	36	1.05
6934141--6934196	23	2.5	23	78	16	73	66	0	0	33	0.92
6935660--6935728	29	2.4	29	85	2	86	56	2	4	36	1.34
6935899--6935924	6	4.3	6	100	0	52	84	0	0	15	0.62
6936281--6936312	15	2.1	15	94	0	55	62	0	0	37	0.95
6936211--6936300	24	3.8	24	69	8	76	51	0	0	48	1.00
6936284--6936348	21	3.0	21	78	13	62	63	0	0	36	0.95
6936279--6936350	36	2.1	36	83	16	93	61	0	0	38	0.96
6936289--6936334	15	3.1	15	84	12	60	65	0	0	34	0.93
6936289--6936336	14	3.4	14	83	13	62	64	0	0	35	0.94
6936280--6936351	23	3.1	21	69	15	54	61	0	0	38	0.96
6936261--6936397	51	2.8	47	70	10	114	54	0	0	45	1.05
6936858--6936893	17	2.1	18	90	10	58	36	0	8	55	1.30
6936948--6937011	20	3.1	20	73	20	60	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6936959--6937010	11	4.9	11	77	22	58	48	0	0	51	1.00
6936958--6937021	20	3.1	20	76	8	65	51	0	0	48	1.00
6937229--6937261	17	2.0	17	88	5	50	45	0	0	54	0.99
6941220--6941276	16	3.3	16	82	9	60	24	0	1	73	0.92
6941910--6941963	21	2.6	21	80	16	67	25	25	7	40	1.82
6945479--6945521	18	2.4	19	80	11	54	25	18	4	51	1.66
6950193--6950332	52	2.7	52	90	0	226	44	12	12	30	1.80
6955612--6955675	20	3.2	20	86	0	92	46	12	0	40	1.42
6955623--6955679	4	14.2	4	81	0	51	47	8	0	43	1.34
6955623--6955679	6	9.5	6	76	0	51	47	8	0	43	1.34
6955926--6955974	23	2.1	23	81	7	55	24	2	6	67	1.24
6956295--6956363	2	35.0	2	80	2	68	50	7	0	42	1.30
6957513--6957558	19	2.4	20	86	13	62	47	0	0	52	1.00
6957521--6957585	26	2.7	25	76	19	68	44	0	0	55	0.99
6957911--6957943	15	2.1	16	88	5	50	69	0	12	18	1.18
6959561--6959668	17	6.1	17	65	16	58	40	12	6	39	1.69
6963380--6963435	17	3.4	17	73	14	53	39	16	5	39	1.71
6963412--6963445	17	2.0	17	94	0	59	47	11	2	38	1.55
6965903--6965993	20	4.6	20	71	15	64	36	12	19	31	1.89
6974730--6974791	33	1.9	32	87	9	90	43	16	12	27	1.84
6976079--6976119	15	2.6	16	84	7	57	31	4	7	56	1.48
6978166--6978207	17	2.5	17	92	0	66	59	2	2	35	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6978816--6978851	15	2.4	15	100	0	72	52	0	0	47	1.00
6978881--6978945	32	2.2	30	84	13	82	60	1	0	38	1.07
6978894--6978946	16	3.3	16	83	0	79	56	1	0	41	1.10
6980484--6980518	17	2.0	18	94	5	63	34	2	0	62	1.10
6982122--6982202	9	8.4	9	70	16	56	48	1	1	49	1.17
6982194--6982273	15	5.7	15	75	19	66	55	1	1	42	1.16
6982203--6982258	24	2.5	23	85	8	71	53	1	1	42	1.21
6982177--6982258	39	2.1	38	84	6	103	53	1	1	43	1.16
6982230--6982282	15	3.5	15	84	2	52	54	0	3	41	1.18
6982295--6982336	19	2.2	20	86	4	59	69	0	0	30	0.89

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