genome.fa.s25.2.7.7.80.10.50.1000.37.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  37  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)
6392215--6392279	33	2.0	32	85	11	87	36	15	16	30	1.90
6397071--6397110	21	2.0	21	90	5	64	50	10	15	25	1.74
6402649--6402737	39	2.3	40	77	14	98	58	1	3	37	1.22
6404568--6404659	47	2.0	47	100	0	184	28	28	23	19	1.98
6411450--6411518	23	3.3	23	69	26	80	52	0	0	47	1.00
6411435--6411526	39	2.4	39	98	0	175	52	0	0	47	1.00
6411435--6411546	39	2.9	39	90	5	147	52	0	0	45	1.13
6411452--6411553	16	5.7	18	67	27	65	52	0	0	45	1.13
6411839--6411876	16	2.4	16	86	0	58	28	10	13	47	1.76
6415844--6415920	20	3.8	20	73	0	82	46	10	10	32	1.72
6415843--6415920	40	2.0	39	87	2	111	46	11	10	32	1.74
6416246--6416292	16	2.9	16	87	0	67	36	14	10	38	1.81
6416725--6416772	18	2.8	17	77	22	55	29	0	0	70	0.87
6416724--6416774	19	2.7	19	85	8	61	31	0	0	68	0.90
6416769--6416833	33	1.9	34	84	3	87	24	1	9	64	1.31
6421200--6421237	18	2.1	18	100	0	76	57	10	15	15	1.64
6421902--6421947	20	2.2	21	88	3	67	39	8	19	32	1.82
6421902--6421975	21	3.6	20	81	3	76	39	9	17	33	1.82
6422041--6422158	51	2.3	52	86	1	166	29	14	13	42	1.84
6425923--6425951	14	2.1	14	100	0	58	13	0	44	41	1.44
6426492--6426529	20	1.9	20	100	0	76	39	10	13	36	1.79
6427405--6427619	49	4.2	49	81	7	234	34	18	24	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6427405--6427625	102	2.2	101	85	2	300	33	18	24	23	1.96
6427542--6427794	87	3.0	85	86	4	332	27	20	26	25	1.99
6427539--6427802	39	6.1	43	76	13	229	28	20	26	25	1.99
6427717--6427848	49	2.8	49	82	6	132	28	15	26	29	1.96
6427935--6428184	33	7.8	32	79	12	264	38	12	29	19	1.89
6428019--6428071	27	2.0	27	88	7	81	32	15	30	22	1.94
6428127--6428199	33	2.2	33	85	0	92	35	13	31	19	1.91
6428061--6428199	66	2.1	68	82	2	165	37	12	30	19	1.89
6428193--6428426	31	7.6	30	80	5	252	30	12	29	26	1.93
6428203--6428426	30	7.2	30	74	5	169	31	12	29	26	1.93
6428196--6428419	92	2.4	92	87	1	304	30	12	29	27	1.93
6428239--6428426	61	3.0	61	85	6	254	29	13	30	26	1.94
6429676--6429719	19	2.2	20	84	4	63	2	4	13	79	0.98
6430218--6430765	79	6.9	77	78	4	472	29	25	10	34	1.89
6430219--6430765	236	2.3	234	80	6	584	29	25	10	34	1.89
6430218--6430762	158	3.5	157	79	5	546	29	25	10	34	1.89
6443597--6443725	48	2.7	49	87	2	179	35	23	6	34	1.82
6445346--6445510	90	1.8	90	92	0	276	25	13	17	43	1.85
6447647--6447702	25	2.3	23	78	6	58	53	0	5	41	1.24
6449724--6449758	3	11.7	3	93	0	61	34	2	0	62	1.10
6450573--6450611	2	19.5	2	100	0	78	51	0	48	0	1.00
6456387--6456411	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6458449--6458486	19	2.1	19	85	5	51	44	0	10	44	1.38
6462426--6462450	13	1.9	13	100	0	50	36	16	16	32	1.90
6462406--6462472	33	2.0	33	88	0	98	32	11	14	40	1.83
6462513--6462537	13	1.9	13	100	0	50	32	16	16	36	1.90
6462546--6462674	52	2.5	52	96	0	231	34	18	17	29	1.94
6463831--6463874	22	2.0	22	100	0	88	27	13	27	31	1.94
6468396--6468479	26	3.3	27	76	17	72	72	2	20	4	1.14
6468406--6468468	15	4.4	14	72	22	51	74	1	19	4	1.08
6468949--6469225	39	6.9	39	72	11	170	19	10	16	54	1.69
6469596--6469769	93	1.8	96	91	6	293	41	9	13	35	1.78
6469924--6469976	26	2.0	26	100	0	106	26	15	20	37	1.92
6469950--6470755	338	2.4	336	90	2	1288	41	9	17	31	1.82
6471216--6471334	36	3.4	35	80	9	134	26	8	21	44	1.80
6471628--6471761	50	2.7	50	89	0	196	32	11	23	32	1.90
6471819--6471903	34	2.5	34	78	14	95	32	8	14	44	1.74
6471919--6471944	7	3.7	7	100	0	52	26	0	26	46	1.53
6472172--6472231	22	2.8	22	81	16	72	75	6	8	10	1.20
6484133--6484467	51	6.4	51	72	12	232	30	11	26	30	1.92
6484285--6484360	27	2.8	28	87	2	100	19	21	35	23	1.96
6486819--6486844	13	2.0	13	100	0	52	38	15	15	30	1.88
6486798--6486864	33	2.0	33	88	0	98	43	16	14	25	1.86
6486884--6486951	19	3.9	18	76	23	83	38	14	11	35	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6486906--6486930	13	1.9	13	100	0	50	32	16	16	36	1.90
6486887--6486949	32	2.0	32	96	0	117	36	15	12	34	1.86
6486987--6487064	21	3.7	21	89	3	113	34	17	12	34	1.88
6494557--6494589	16	2.0	17	88	5	50	81	12	0	6	0.85
6496022--6496321	114	2.7	113	87	3	417	30	30	16	22	1.96
6496024--6496321	29	10.5	29	81	8	301	30	30	16	21	1.96
6496250--6496331	28	2.8	29	83	14	107	34	26	18	20	1.96
6496343--6496571	43	5.1	43	71	18	169	24	24	18	31	1.98
6496349--6496462	39	2.8	41	84	5	151	26	24	20	28	1.99
6496430--6496564	49	2.7	50	83	3	164	22	26	19	31	1.98
6496429--6496692	101	2.6	99	78	7	266	22	27	17	32	1.96
6497487--6497513	13	2.1	13	100	0	54	29	14	14	40	1.86
6497467--6497532	33	2.0	33	85	5	89	28	18	12	40	1.86
6500938--6500970	17	1.9	17	93	0	57	27	12	0	60	1.32
6500929--6500985	18	3.2	18	82	5	71	22	10	1	64	1.34
6503946--6504010	28	2.3	28	83	0	76	52	3	12	32	1.54
6511947--6511987	2	20.5	2	100	0	82	51	0	0	48	1.00
6513143--6513171	2	14.5	2	100	0	58	48	0	0	51	1.00
6513967--6514013	22	2.1	22	96	0	85	44	8	21	25	1.80
6516852--6516889	20	1.9	20	88	0	58	81	0	15	2	0.80
6517254--6517301	19	2.4	21	76	20	57	50	0	6	43	1.27
6517265--6517299	18	1.9	17	88	11	52	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6517326--6517364	14	2.8	14	80	0	51	71	0	2	25	0.98
6521120--6521449	167	2.0	167	96	0	615	30	20	19	29	1.97
6521814--6521870	20	2.8	20	89	2	78	28	8	12	50	1.69
6524109--6524330	97	2.3	98	84	9	301	30	21	10	37	1.88
6527976--6528022	20	2.3	20	88	0	76	34	14	12	38	1.85
6531650--6531686	18	2.1	18	100	0	74	40	32	10	16	1.83
6536160--6536360	79	2.6	78	84	4	235	29	16	28	25	1.97
6536157--6536357	78	2.6	78	83	2	233	29	16	29	24	1.97
6536312--6536388	28	2.8	28	85	0	91	23	20	33	22	1.97
6536372--6536710	52	6.4	52	67	17	162	31	12	25	29	1.93
6536529--6536598	27	2.6	27	86	2	86	24	21	30	24	1.99
6536233--6536652	107	3.9	105	72	11	332	30	15	27	27	1.96
6536587--6536715	51	2.4	51	78	12	134	34	10	24	31	1.88
6539054--6539092	13	3.0	13	100	0	78	38	15	15	30	1.88
6539132--6539195	19	3.7	18	76	23	75	35	14	12	37	1.83
6539154--6539178	13	1.9	13	100	0	50	32	16	16	36	1.90
6539135--6539195	32	1.9	32	96	0	113	36	14	13	36	1.85
6539995--6541119	55	20.4	55	89	4	1557	21	20	29	28	1.98
6540097--6540181	27	3.1	27	61	15	66	23	18	29	28	1.98
6540319--6540404	26	3.2	26	66	26	70	18	18	33	29	1.95
6540480--6540569	26	3.3	26	67	19	76	20	17	33	28	1.95
6540924--6541064	27	5.1	27	61	16	74	22	19	29	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6548742--6548786	7	6.9	7	78	12	51	84	4	0	11	0.76
6548745--6548786	6	6.8	6	82	12	50	85	4	0	9	0.72
6548742--6548786	13	3.5	13	84	3	65	84	4	0	11	0.76
6548744--6548786	19	2.3	19	88	11	70	86	4	0	9	0.71
6548742--6548793	26	2.0	27	88	3	79	82	7	0	9	0.84
6548758--6548801	18	2.3	18	84	7	52	81	11	2	4	0.92
6550134--6550205	28	2.6	28	80	6	85	23	27	22	26	1.99
6550398--6550563	32	5.2	31	84	5	206	28	30	20	21	1.98
6550382--6550563	96	1.9	95	89	1	283	30	29	20	19	1.97
6556743--6556789	20	2.3	21	85	3	60	38	10	17	34	1.84

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