genome.fa.s1.2.7.7.80.10.50.1000.3.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  3  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)
308381--308816	165	2.6	165	86	2	581	50	6	11	32	1.63
309769--309802	16	2.1	16	88	0	50	26	0	2	70	1.01
309780--309861	43	2.0	42	83	11	107	29	6	0	64	1.17
310689--310804	31	3.8	31	75	6	112	25	20	11	43	1.85
310711--310823	59	1.9	59	94	0	199	26	21	10	41	1.85
310790--310843	20	2.7	20	94	5	92	31	14	11	42	1.81
324630--324709	1	80.0	1	74	0	52	85	13	1	0	0.67
324628--324709	11	7.1	11	82	9	101	84	14	1	0	0.69
325958--326295	28	12.0	28	87	3	432	28	29	17	24	1.97
326273--326337	34	1.9	33	82	14	80	30	26	12	30	1.92
326402--326652	48	5.3	48	90	1	373	20	27	15	35	1.93
327444--327520	20	3.8	20	77	11	84	33	12	11	41	1.80
331400--331472	20	3.7	20	98	0	137	31	17	10	39	1.85
336031--336086	27	2.1	27	96	0	103	25	25	10	39	1.87
339296--339352	20	2.8	20	87	7	80	29	21	10	38	1.87
341996--342085	29	3.0	28	80	9	83	46	2	6	44	1.42
343332--343374	16	2.6	16	81	3	50	58	11	11	18	1.63
348978--349503	50	10.6	49	73	5	254	27	21	15	34	1.94
348955--349503	100	5.5	99	70	9	300	27	21	15	35	1.94
349027--349244	99	2.2	100	76	3	226	28	22	15	32	1.95
349541--350149	50	12.3	50	72	7	348	28	23	14	34	1.93
349391--349634	131	1.9	131	81	3	303	25	25	17	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
349862--350196	100	3.4	98	77	6	291	28	22	13	34	1.92
349873--350196	150	2.2	150	79	4	341	28	22	13	35	1.92
352754--352787	17	2.0	17	88	0	50	67	17	5	8	1.37
365121--365171	11	4.6	11	86	13	70	0	11	0	88	0.52
365121--365171	6	9.2	6	82	18	58	0	11	0	88	0.52
365124--365182	26	2.2	27	87	3	84	3	10	0	86	0.68
365121--365182	16	3.6	16	86	8	79	3	11	0	85	0.71
365124--365171	1	48.0	1	78	0	51	0	10	0	89	0.48
367211--367268	30	1.9	30	100	0	116	34	6	32	25	1.83
369911--370250	154	2.2	153	82	4	405	42	19	13	25	1.87
370520--370578	8	7.8	8	79	7	61	71	3	3	22	1.16
370522--370579	7	7.9	7	83	11	71	70	3	3	22	1.17
370529--370652	15	7.5	15	71	19	77	68	7	2	21	1.26
370522--370615	7	12.7	7	73	18	57	70	7	3	19	1.25
370567--370642	9	8.3	9	76	13	57	68	10	1	19	1.26
370607--370670	28	2.3	28	81	7	78	65	9	0	25	1.22
370715--370816	20	5.4	20	75	13	108	44	8	25	21	1.81
370703--370816	37	3.1	37	94	0	192	42	7	26	22	1.81
373409--374231	157	5.3	154	81	5	777	23	18	19	38	1.93
373409--374289	309	2.8	311	79	6	955	23	18	19	38	1.93
376974--377009	18	2.1	18	89	5	56	33	25	16	25	1.96
377682--380920	42	77.5	42	69	8	1083	19	27	17	35	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
377769--378131	169	2.2	168	81	4	426	19	27	18	34	1.95
378694--378755	31	2.0	31	87	6	90	20	32	19	27	1.97
378503--378956	242	1.9	243	83	1	597	19	28	18	34	1.95
378727--379156	127	3.4	127	77	6	368	18	26	17	37	1.93
379284--379636	169	2.1	169	82	2	433	19	28	17	34	1.94
380248--380482	127	1.9	127	78	1	265	20	27	16	36	1.93
380501--384247	127	29.5	126	72	8	1648	19	27	16	36	1.93
380271--380932	85	7.8	84	73	6	336	20	27	16	35	1.94
380931--384219	42	78.1	42	71	8	988	19	27	16	36	1.93
380755--381096	186	1.8	187	84	4	476	20	29	15	34	1.93
380931--381617	85	8.1	86	72	8	245	20	26	15	36	1.93
381100--381613	85	6.1	84	75	8	380	21	26	15	37	1.93
381041--381401	170	2.1	169	80	6	408	20	26	16	36	1.93
381954--382838	211	4.2	211	75	5	585	19	27	16	36	1.93
381619--384219	169	15.4	169	74	5	1167	19	27	17	36	1.93
383168--384247	212	5.1	208	75	6	622	17	27	18	36	1.93
384677--384933	44	6.0	44	74	5	193	13	30	16	39	1.87
384684--384973	86	3.4	84	78	6	296	14	29	16	40	1.88
384728--384948	42	5.2	42	72	8	151	14	30	15	39	1.87
385556--385593	7	5.0	8	87	12	62	76	0	0	23	0.79
385554--385593	15	2.7	15	92	0	71	77	0	0	22	0.77
385554--385663	8	14.3	7	70	19	60	73	5	0	20	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
385554--385667	22	4.8	23	75	10	81	73	5	0	20	1.07
385571--385656	17	4.8	19	71	18	60	72	6	1	19	1.15
385551--385661	15	7.1	15	74	18	61	72	5	0	20	1.09
385580--385656	9	8.4	9	72	16	52	72	7	1	18	1.15
385588--385686	10	10.5	10	71	15	54	69	9	1	20	1.21
385716--385775	17	3.4	17	78	13	75	46	6	26	20	1.75
385728--385792	20	3.4	20	81	12	91	46	9	26	18	1.79
385716--385792	37	2.1	37	97	0	145	44	7	27	20	1.79
386418--386490	22	3.2	22	71	7	65	61	15	15	8	1.55
388310--389315	154	6.5	154	80	5	879	22	18	20	38	1.93
388310--389315	312	3.2	307	79	7	982	22	18	20	38	1.93
399296--399414	51	2.3	51	100	0	238	37	16	14	31	1.89
403883--403939	16	3.6	16	69	9	53	22	3	19	54	1.59
405354--405454	43	2.4	41	80	12	123	22	24	7	44	1.79
405459--406388	61	15.3	61	80	6	834	26	25	19	28	1.98
405459--406388	242	3.8	238	80	6	910	26	25	19	28	1.98
405459--406384	181	5.1	181	80	6	799	26	25	19	28	1.98
409914--410037	42	2.9	42	83	9	162	24	25	10	40	1.86
418095--419279	62	19.4	61	77	7	925	27	24	17	30	1.97
419261--419394	41	3.2	40	80	9	137	23	24	13	38	1.91
422485--423198	158	4.5	156	84	4	871	28	25	13	32	1.93
422458--423198	314	2.4	316	86	4	980	29	25	13	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
422485--423198	79	9.1	78	82	5	787	28	25	13	32	1.93
428623--428761	69	2.0	69	94	0	242	49	10	17	21	1.77
430964--431073	55	2.0	55	83	3	141	37	20	12	29	1.90
432254--432279	1	26.0	1	100	0	52	100	0	0	0	0.00
432286--432368	40	2.1	40	100	0	166	60	18	14	7	1.56
432677--432719	17	2.5	17	80	0	59	16	16	27	39	1.90
433386--433773	214	1.8	214	88	1	598	30	22	13	34	1.92
444178--444216	2	20.5	2	84	10	55	51	0	2	46	1.14
445111--445175	23	2.8	23	80	2	67	27	10	15	46	1.79
452062--452101	15	2.5	16	88	8	55	57	0	0	42	0.98
452062--452104	16	2.6	17	85	10	63	55	0	0	44	0.99
452120--452189	17	4.1	17	70	12	63	67	1	0	31	1.00
452470--452526	7	7.7	7	86	9	78	0	19	0	80	0.71
452480--452528	4	13.0	4	79	12	59	0	20	0	79	0.73
452471--452526	22	2.5	21	85	8	58	0	19	0	80	0.71
452470--452528	8	7.8	8	82	3	61	0	20	0	79	0.73
452470--452526	29	1.9	30	96	3	107	0	19	0	80	0.71
452984--453047	20	3.3	19	85	10	85	6	12	0	81	0.87
452987--453044	4	14.8	4	77	10	57	6	13	0	79	0.93
453159--453279	57	2.1	59	81	6	140	49	5	9	35	1.58
453999--454039	4	10.5	4	84	5	57	0	26	2	70	0.99
454440--454464	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
456021--456071	6	8.3	6	83	12	68	78	0	0	21	0.75
456021--456069	14	3.4	14	83	11	55	79	0	0	20	0.73
456021--456072	20	2.8	20	85	8	74	76	0	0	23	0.78
458263--458290	2	14.0	2	100	0	56	50	0	0	50	1.00
462551--462595	19	2.3	20	84	3	56	48	2	0	48	1.13
474755--474801	20	2.3	21	85	3	60	31	0	6	61	1.21
475683--475721	19	2.0	20	90	5	62	23	2	5	69	1.21
478402--478445	16	2.7	17	83	16	58	72	0	0	27	0.85
479080--479111	7	4.7	7	96	3	57	43	0	0	56	0.99
479295--479370	27	2.9	28	75	15	72	52	1	1	44	1.17

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