genome.fa.s25.2.7.7.80.10.50.1000.55.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  55  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)
9344257--9344577	33	9.9	33	90	4	485	19	19	33	28	1.96
9344259--9344582	98	3.3	98	95	1	555	20	18	33	27	1.96
9344588--9344955	31	12.0	31	75	14	216	31	14	31	22	1.94
9344586--9344890	88	3.3	88	79	7	315	31	14	32	22	1.93
9345877--9345916	21	1.9	21	85	10	55	2	12	2	82	0.87
9346169--9346220	11	4.5	11	86	13	52	0	0	13	86	0.57
9346156--9346220	12	5.4	12	84	14	73	0	1	13	84	0.69
9346165--9346222	7	8.4	7	81	11	75	0	0	15	84	0.62
9346156--9346220	24	2.7	23	86	9	85	0	1	13	84	0.69
9346157--9346222	20	3.4	20	78	18	77	0	1	15	83	0.72
9350755--9350805	25	2.0	25	100	0	102	33	11	27	27	1.92
9353093--9353221	52	2.5	52	94	0	222	29	17	16	37	1.91
9353230--9353254	13	1.9	13	100	0	50	36	16	16	32	1.90
9353297--9353361	33	2.0	32	87	3	94	40	13	10	35	1.80
9360220--9360258	16	2.5	16	88	12	55	58	5	17	17	1.56
9363381--9363603	113	2.0	115	81	8	269	40	12	9	37	1.75
9365957--9366051	20	4.8	20	88	7	131	27	15	13	43	1.85
9365957--9366051	40	2.4	40	94	0	163	27	15	13	43	1.85
9368343--9368508	51	3.2	52	77	3	149	28	24	12	35	1.91
9368467--9368670	76	2.6	78	83	6	261	26	25	13	33	1.94
9368603--9368773	51	3.4	50	81	1	216	30	25	12	32	1.92
9368753--9368828	28	2.7	29	85	4	111	23	32	19	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9368816--9368929	51	2.2	51	84	0	147	30	24	9	35	1.88
9371157--9371181	4	6.2	4	100	0	50	24	0	0	76	0.80
9381442--9381528	1	87.0	1	73	0	66	86	9	4	0	0.71
9381442--9381526	9	9.8	9	77	16	81	85	9	4	0	0.72
9381443--9381528	24	3.5	24	87	7	102	86	9	4	0	0.71
9381442--9381527	33	2.5	36	79	9	74	86	9	4	0	0.71
9381442--9381528	36	2.4	36	84	7	106	86	9	4	0	0.71
9382489--9382877	100	4.0	100	89	4	571	23	29	17	29	1.97
9382804--9383488	55	12.3	55	89	1	938	27	24	21	26	1.99
9382804--9383710	222	4.1	221	84	6	1001	26	25	20	27	1.99
9383510--9383718	61	3.5	61	83	10	258	24	26	19	29	1.98
9383687--9383830	45	3.5	39	79	17	150	19	27	16	36	1.93
9383708--9383829	45	2.8	43	84	10	167	18	27	13	40	1.88
9383708--9383847	42	3.2	41	81	13	165	16	26	13	43	1.85
9383764--9383877	42	2.7	42	85	8	124	20	22	16	40	1.91
9384566--9384612	20	2.4	19	96	0	67	25	17	14	42	1.87
9384648--9384761	20	5.7	20	91	4	176	27	14	14	43	1.84
9387455--9387499	21	2.1	21	84	8	56	53	4	20	22	1.63
9389303--9389333	15	2.1	15	93	0	53	48	16	22	12	1.80
9391401--9391426	13	2.0	13	100	0	52	30	15	15	38	1.88
9391547--9391592	21	2.2	20	81	11	58	32	19	4	43	1.71
9393938--9393963	13	2.0	13	100	0	52	38	15	15	30	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9396905--9397084	51	3.5	50	81	6	193	28	24	12	35	1.91
9397020--9397317	79	3.8	79	86	4	390	27	24	15	32	1.95
9397020--9397326	155	2.0	154	83	3	384	27	24	15	32	1.95
9397253--9397370	50	2.3	52	84	4	152	31	26	12	29	1.93
9397389--9397501	51	2.2	51	85	0	154	29	29	9	31	1.89
9397174--9397539	129	2.8	129	79	5	407	29	25	12	32	1.92
9397196--9397637	130	3.4	129	77	7	412	29	24	11	33	1.90
9399298--9399441	43	3.4	43	98	0	272	41	0	18	40	1.50
9403174--9403239	28	2.4	27	78	14	71	50	4	6	39	1.48
9403845--9403881	18	2.1	18	94	0	65	43	5	16	35	1.71
9404152--9404208	16	3.6	16	83	11	64	43	29	19	7	1.77
9404773--9404831	16	3.7	16	76	0	64	33	38	20	6	1.79
9404764--9404830	32	2.1	32	88	0	98	35	34	20	8	1.84
9404910--9404951	15	2.9	14	86	10	57	54	4	9	30	1.53
9408610--9408652	21	2.0	21	86	0	59	30	20	20	27	1.98
9415150--9415715	155	3.7	153	82	4	620	51	7	9	31	1.62
9415667--9415716	26	2.0	24	81	14	57	56	0	6	38	1.24
9419233--9419359	35	3.7	33	73	15	105	30	17	12	39	1.87
9419233--9419361	33	3.8	32	76	11	114	31	17	12	38	1.87
9420126--9420243	52	2.3	52	86	0	155	34	21	11	32	1.90
9424993--9425035	22	2.0	22	86	9	61	46	6	9	37	1.63
9425134--9425198	33	2.0	33	84	6	87	35	13	13	36	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9431300--9431401	46	2.2	46	98	0	195	33	17	15	33	1.92
9431523--9431579	21	2.8	20	76	7	60	40	28	0	31	1.57
9434475--9434537	34	1.9	33	90	9	103	36	12	20	30	1.90
9436058--9436124	37	1.9	35	88	11	102	29	25	11	32	1.92
9436561--9436603	22	2.0	22	100	0	86	34	13	23	27	1.93
9436654--9436754	10	9.7	10	69	16	71	38	8	26	25	1.85
9436660--9436739	22	3.7	22	78	6	92	38	8	25	27	1.85
9436656--9436754	42	2.4	42	94	0	171	38	8	27	26	1.84
9436682--9436754	20	3.5	20	77	14	85	39	8	26	26	1.84
9436890--9436930	21	2.0	21	85	9	57	36	12	14	36	1.84
9437754--9437805	19	2.6	19	84	6	68	80	1	11	5	0.96
9439729--9439754	13	2.0	13	100	0	52	30	15	15	38	1.88
9440453--9440496	21	2.1	21	83	8	54	25	31	4	38	1.76
9442302--9442326	13	1.9	13	100	0	50	36	16	16	32	1.90
9445548--9445578	15	2.1	15	93	0	53	12	22	16	48	1.80
9447380--9447424	21	2.1	21	84	8	56	22	20	4	53	1.63
9449651--9449676	13	2.0	13	100	0	52	30	15	15	38	1.88
9450084--9450242	82	2.0	82	96	1	293	30	10	11	47	1.74
9461617--9461675	23	2.5	23	73	13	57	57	0	3	38	1.15
9464317--9464351	13	2.7	13	90	0	52	34	22	11	31	1.90
9464341--9464424	39	2.2	39	88	0	132	29	16	14	39	1.88
9464439--9464463	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9468362--9468416	22	2.5	22	96	0	101	61	9	9	20	1.52
9469328--9469402	20	3.8	20	80	3	80	40	12	13	34	1.81
9469325--9469402	40	2.0	39	87	2	111	39	12	12	34	1.82
9476252--9476550	146	2.1	145	94	1	519	24	13	22	39	1.90
9476561--9476600	13	3.1	13	88	0	62	40	20	10	30	1.85
9482644--9482698	20	2.7	20	83	16	69	43	16	14	25	1.86
9484436--9484714	79	3.6	79	82	8	338	27	19	10	41	1.84
9484918--9484967	24	2.2	24	85	7	68	16	4	16	64	1.44
9485734--9485764	11	2.7	12	90	10	55	64	6	9	19	1.45
9487583--9487631	8	6.1	8	86	9	73	26	0	0	73	0.83
9487586--9487631	17	2.9	16	87	9	67	28	0	0	71	0.86
9487586--9487634	15	3.1	15	83	11	62	32	0	0	67	0.91
9488563--9488614	24	2.1	25	82	3	61	61	1	0	36	1.07
9499662--9499866	79	2.6	79	88	0	302	24	17	32	25	1.97
9507452--9507491	17	2.3	18	86	4	55	70	5	5	20	1.26
9507452--9507493	18	2.4	17	88	4	57	69	4	7	19	1.31
9510014--9510080	31	2.1	32	88	2	100	55	5	0	38	1.25
9514445--9514496	17	3.2	16	77	17	54	42	0	0	57	0.98
9514445--9514488	16	2.6	17	82	13	56	40	0	0	59	0.98
9514470--9514516	24	2.0	24	87	8	69	44	2	0	53	1.12
9515079--9515109	6	5.2	6	96	0	53	67	19	0	12	1.22
9516284--9516324	18	2.5	15	79	20	55	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9516290--9516324	18	2.0	18	94	5	63	65	0	0	34	0.93
9516311--9516359	24	2.0	24	84	7	64	42	2	0	55	1.11
9516318--9516380	24	2.6	23	73	9	54	38	1	0	60	1.07
9518147--9518179	2	16.5	2	93	0	57	48	3	0	48	1.17
9518937--9518976	3	13.3	3	94	0	71	32	0	2	65	1.06
9520948--9520983	18	2.0	18	94	0	63	52	0	2	44	1.15
9523504--9523541	19	2.0	20	89	5	60	36	7	0	55	1.29
9525936--9525986	20	2.5	20	83	3	66	43	11	13	31	1.80
9526546--9526575	15	2.1	15	93	6	53	50	36	6	6	1.55
9529791--9529842	22	2.3	23	80	9	63	3	15	3	76	1.07

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