genome.fa.s2.2.7.7.80.10.50.1000.34.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  34  of  38  ( 4457 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)
5220929--5221376	156	2.9	153	76	6	436	39	19	15	25	1.91
5221901--5221929	5	5.8	5	100	0	58	79	0	0	20	0.74
5222233--5222579	166	2.1	165	79	6	371	50	9	12	28	1.70
5227588--5227716	52	2.5	52	90	0	213	27	17	19	34	1.95
5227725--5227749	13	1.9	13	100	0	50	36	16	16	32	1.90
5227794--5227877	13	5.5	13	71	28	60	35	17	13	33	1.89
5227802--5227864	19	3.7	18	76	24	73	36	17	12	33	1.88
5227794--5227879	32	2.7	32	98	0	163	36	18	12	32	1.89
5228380--5228406	13	2.1	13	100	0	54	40	14	14	29	1.86
5228458--5228507	19	2.6	19	96	0	91	38	18	12	32	1.87
5228496--5228520	13	1.9	13	100	0	50	32	16	16	36	1.90
5229316--5229637	88	3.6	88	76	7	285	31	22	10	34	1.89
5229306--5229671	177	2.1	177	80	5	409	30	24	10	33	1.90
5235037--5235097	19	3.6	18	72	25	60	39	18	9	32	1.83
5235054--5235110	13	3.9	13	76	24	60	33	17	14	35	1.90
5235022--5235112	32	2.8	32	91	0	146	37	16	12	34	1.86
5248280--5248304	13	1.9	13	100	0	50	36	16	16	32	1.90
5248368--5248392	13	1.9	13	100	0	50	32	16	16	36	1.90
5248401--5248529	52	2.5	52	94	0	222	34	17	17	29	1.94
5255732--5255784	20	2.6	21	84	3	72	28	13	11	47	1.77
5261218--5261263	13	3.4	14	79	8	60	86	4	8	0	0.68
5261232--5261269	19	2.0	20	90	10	62	81	5	13	0	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5262330--5262452	64	1.9	64	85	3	167	33	19	14	32	1.92
5262284--5263202	72	13.0	68	72	16	293	25	22	14	37	1.92
5262224--5263270	139	7.5	136	75	12	524	25	22	15	36	1.93
5262798--5263364	73	7.9	73	80	6	602	24	22	14	38	1.92
5262562--5263406	145	5.9	142	79	9	726	24	22	15	37	1.92
5263939--5263994	20	2.7	21	83	5	69	37	12	14	35	1.84
5268003--5268053	20	2.6	20	87	3	68	27	13	15	43	1.85
5269695--5269750	3	18.7	3	88	0	85	39	0	32	28	1.57
5275738--5275765	13	2.2	13	100	0	56	28	14	17	39	1.89
5275718--5275783	33	2.0	33	85	5	89	30	13	13	42	1.83
5278488--5278554	33	2.0	33	88	0	98	34	11	13	40	1.81
5278508--5278532	13	1.9	13	100	0	50	36	16	16	32	1.90
5278597--5278621	13	1.9	13	100	0	50	32	16	16	36	1.90
5278630--5278750	52	2.3	52	97	0	224	34	18	18	28	1.94
5285966--5285999	15	2.3	15	89	0	50	85	5	8	0	0.75
5287028--5287266	32	7.7	32	84	6	251	23	28	17	30	1.97
5287028--5287234	62	3.3	62	91	2	310	24	27	17	30	1.97
5287205--5287596	34	12.1	32	79	13	376	20	34	12	32	1.90
5287211--5287564	160	2.2	155	85	9	455	21	34	12	31	1.91
5287472--5287562	27	3.1	27	78	19	110	21	35	14	28	1.93
5287304--5287596	96	3.1	95	83	8	389	20	34	12	32	1.90
5287601--5287665	33	1.9	34	93	3	114	27	35	18	18	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5287670--5288334	49	13.8	49	87	4	935	24	26	17	31	1.97
5287670--5288333	98	6.9	98	97	1	1199	24	26	17	31	1.97
5288108--5288333	92	2.5	92	98	0	434	25	24	18	31	1.98
5288115--5288368	43	5.7	41	80	10	195	24	25	18	31	1.97
5288292--5288676	171	2.3	168	91	4	611	24	24	14	36	1.93
5289475--5289541	33	2.0	33	88	0	98	34	11	13	40	1.81
5289495--5289519	13	1.9	13	100	0	50	36	16	16	32	1.90
5289584--5289608	13	1.9	13	100	0	50	32	16	16	36	1.90
5289617--5289737	52	2.3	52	97	0	224	34	18	18	28	1.94
5298715--5298979	30	8.7	29	78	9	185	24	28	13	33	1.94
5298705--5298928	62	3.6	61	83	8	231	23	25	12	37	1.90
5298703--5298916	93	2.3	93	92	1	356	24	26	12	36	1.90
5298954--5299501	27	17.9	32	76	12	366	20	33	13	31	1.92
5298981--5299365	61	6.0	67	77	11	312	20	33	12	33	1.91
5298954--5299501	95	5.9	92	78	12	538	20	33	13	31	1.92
5299480--5299604	29	4.3	30	84	7	168	32	34	17	16	1.92
5299480--5299604	57	2.2	59	88	5	184	32	34	17	16	1.92
5299631--5300150	87	6.0	87	88	0	743	27	25	17	28	1.98
5299626--5300149	175	3.0	172	87	1	751	28	25	17	29	1.98
5299801--5300337	223	2.4	224	79	10	671	27	25	18	29	1.98
5299627--5300150	262	2.0	262	91	0	850	28	25	17	28	1.98
5300063--5300430	49	7.8	48	78	9	308	25	26	17	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5299675--5300238	262	2.2	256	83	6	686	28	25	18	27	1.98
5300116--5300286	87	2.0	88	94	1	299	26	27	19	26	1.99
5299719--5300334	136	4.6	135	74	11	566	27	25	18	28	1.98
5300204--5300476	52	5.5	50	76	11	197	23	24	17	34	1.96
5300199--5300476	99	2.8	100	78	7	232	23	25	17	33	1.96
5301167--5301227	19	3.5	19	72	25	71	36	13	16	34	1.87
5301184--5301208	13	1.9	13	100	0	50	36	16	16	32	1.90
5301167--5301234	32	2.1	32	97	0	127	35	13	16	35	1.87
5301279--5301306	13	2.2	13	100	0	56	28	14	17	39	1.89
5301259--5301324	33	2.0	33	88	5	98	31	13	15	39	1.86
5304570--5304595	13	2.0	13	100	0	52	30	15	15	38	1.88
5304550--5304614	33	2.0	33	87	6	96	27	13	16	41	1.87
5305970--5306013	23	1.9	24	86	9	65	40	22	6	29	1.80
5306560--5306817	128	2.0	128	99	0	507	37	13	13	35	1.84
5310796--5310867	29	2.5	29	93	4	119	27	16	18	37	1.92
5310877--5310939	33	1.9	33	96	0	117	31	20	12	34	1.90
5310853--5310961	20	5.8	19	72	20	79	32	18	11	37	1.87
5313245--5313423	51	3.5	51	78	3	182	29	24	13	32	1.93
5313501--5313564	28	2.3	27	81	10	76	21	31	15	31	1.95
5313552--5313726	51	3.4	49	76	12	167	30	24	10	35	1.88
5313652--5313871	79	2.8	79	78	6	207	25	25	14	34	1.94
5326276--5326331	20	2.9	18	80	12	58	83	3	12	0	0.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5327336--5327549	55	3.9	55	90	2	313	28	27	21	22	1.99
5327336--5327549	111	1.9	110	88	2	322	28	27	21	22	1.99
5327362--5327759	211	1.9	205	87	4	573	26	27	21	24	1.99
5327591--5327883	61	4.9	60	81	9	305	26	26	19	26	1.99
5327570--5327823	116	2.2	117	85	4	327	27	27	21	23	1.99
5327859--5327966	42	2.5	42	86	8	139	22	25	14	37	1.93
5330431--5330612	51	3.6	51	75	0	168	27	26	13	32	1.93
5330597--5330668	28	2.6	28	84	0	90	26	31	15	26	1.95
5330550--5330826	110	2.6	107	81	4	331	28	24	12	33	1.93
5330706--5330779	28	2.6	28	82	6	96	21	29	21	27	1.99
5330762--5330933	51	3.4	50	79	4	184	27	22	13	36	1.92
5330905--5331093	79	2.4	78	80	7	204	26	23	15	34	1.94
5336045--5336144	43	2.4	42	91	1	155	33	13	18	36	1.89
5336131--5336186	20	2.8	20	83	0	76	30	17	12	39	1.87
5336212--5336267	19	2.9	19	75	2	58	39	8	16	35	1.80
5349535--5349595	28	2.2	28	85	5	90	39	0	3	57	1.15
5350847--5350963	39	3.1	38	80	2	128	39	5	13	41	1.67
5351003--5351581	233	2.5	233	76	4	576	41	8	15	34	1.77
5354716--5354740	13	1.9	13	100	0	50	36	16	16	32	1.90
5354788--5354871	13	5.5	13	68	28	51	35	19	13	32	1.90
5354796--5354858	19	3.7	18	74	24	64	36	19	12	31	1.89
5354788--5354873	32	2.7	32	94	0	154	37	18	12	31	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5355162--5355332	92	1.9	92	83	4	229	40	9	19	29	1.84
5358975--5359022	22	2.2	22	100	0	96	58	4	8	29	1.46
5362064--5362671	73	8.5	73	75	9	446	53	13	1	30	1.49
5363085--5363116	5	6.6	5	92	7	57	0	18	0	81	0.70
5363765--5363795	9	3.4	9	100	0	62	64	0	9	25	1.24
5364148--5364214	18	3.5	18	78	15	64	56	0	0	43	0.99
5364506--5364570	17	3.8	18	72	24	61	56	0	0	43	0.99
5364535--5364596	24	2.5	26	79	12	76	59	3	1	35	1.23
5369034--5369135	54	1.9	53	84	6	134	55	8	6	28	1.56
5368863--5369153	145	2.0	145	97	0	546	53	8	7	30	1.57

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