genome.fa.s40.2.7.7.80.10.50.1000.3.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: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  3440810

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   

This is table  3  of  24  ( 2833 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)
333773--333805	16	2.1	16	100	0	66	24	27	12	36	1.91
334708--334761	20	2.7	20	82	5	74	50	9	0	40	1.35
337233--337283	19	2.5	22	81	12	63	56	0	3	39	1.18
339064--339098	18	2.0	17	94	5	61	68	0	2	28	1.04
345170--345215	20	2.3	20	84	0	56	32	4	52	10	1.56
346046--346071	13	2.0	13	100	0	52	53	0	15	30	1.42
349252--349300	22	2.2	22	92	0	80	22	0	36	40	1.54
353150--353336	56	3.4	55	66	19	129	50	3	4	42	1.38
353140--353431	109	2.7	109	84	3	354	47	4	3	44	1.41
356173--356208	3	12.0	3	100	0	72	33	0	0	66	0.92
358635--358738	18	5.4	18	72	15	66	55	0	0	44	0.99
358721--358777	20	2.8	20	76	12	62	43	0	1	54	1.10
358708--358785	41	1.9	41	81	5	95	47	0	1	51	1.09
359587--359678	9	10.6	8	74	22	55	42	0	0	57	0.98
359571--359664	45	2.1	46	88	6	138	41	0	0	58	0.98
359586--359680	25	4.0	24	72	14	81	43	0	0	56	0.99
359945--359974	12	2.6	12	94	5	53	56	0	0	43	0.99
359965--360041	17	4.6	17	70	20	56	49	1	0	49	1.09
360421--360450	2	15.0	2	100	0	60	50	0	50	0	1.00
362065--362156	1	92.0	1	100	0	184	0	100	0	0	0.00
366467--366493	12	2.2	12	100	0	54	0	66	25	7	1.17
372400--372741	166	2.1	166	84	3	447	32	11	13	42	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
372835--373293	152	3.0	151	73	8	399	27	13	18	40	1.88
383139--383649	27	18.7	27	88	3	706	23	33	14	28	1.94
383139--383649	245	2.1	246	90	2	814	23	33	14	28	1.94
383416--383755	54	6.1	55	83	6	166	26	32	14	25	1.94
383656--383876	32	7.3	31	89	4	233	33	27	18	20	1.96
387913--387985	32	2.2	33	80	4	85	24	16	27	31	1.96
387939--388618	32	22.5	31	83	7	626	21	18	28	31	1.97
387925--388671	182	4.1	182	86	3	924	22	18	28	30	1.97
387931--388618	150	4.5	150	80	8	682	21	18	28	31	1.97
388629--388971	27	12.6	27	86	4	431	30	15	31	22	1.95
388629--388965	82	4.1	81	84	5	414	31	15	30	22	1.95
389977--391400	713	2.0	713	98	0	2758	24	18	27	29	1.98
396236--396276	21	2.0	20	85	9	55	60	9	9	19	1.55
397716--398316	28	20.4	28	79	10	456	30	28	16	23	1.97
397739--397908	96	1.8	90	85	7	232	32	27	17	22	1.96
397716--398316	58	10.2	56	78	11	380	30	28	16	23	1.97
400177--400233	29	2.0	29	82	6	71	35	7	10	47	1.65
403395--403435	13	3.2	13	89	3	57	39	0	0	60	0.96
404413--404455	22	2.0	22	95	0	77	34	4	4	55	1.41
411494--411549	29	1.9	29	82	13	71	44	10	5	39	1.62
412638--412670	15	2.3	15	89	5	50	60	0	3	36	1.12
412625--412688	32	2.0	32	93	0	110	57	1	4	35	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
412625--412677	18	3.2	18	71	20	60	60	1	1	35	1.19
412900--412948	19	2.4	21	80	10	57	42	0	0	57	0.99
417414--417467	11	4.9	11	80	13	58	66	0	0	33	0.92
417411--417462	20	2.5	20	90	3	77	67	0	0	32	0.91
417428--417491	28	2.4	27	82	10	78	57	0	0	42	0.98
417449--417524	33	2.3	33	84	4	91	51	1	1	46	1.17
418380--418413	11	3.2	10	88	12	50	35	0	11	52	1.38
418946--419081	69	2.0	70	97	1	256	38	3	5	52	1.44
420668--420708	15	2.8	14	85	10	55	48	2	2	46	1.28
420734--420775	22	1.9	22	85	9	59	64	4	2	28	1.26
422836--422930	46	2.1	46	85	0	127	44	17	8	29	1.78
423300--423334	18	1.9	18	88	0	52	60	2	0	37	1.12
424066--424196	29	4.6	28	77	16	135	41	2	3	52	1.29
424086--424195	59	1.9	57	85	10	152	42	2	2	51	1.30
424956--425003	18	2.7	18	78	18	55	62	2	2	33	1.18
424956--425007	23	2.3	22	78	18	54	61	1	1	34	1.18
424994--425028	18	2.1	18	89	10	56	54	5	0	40	1.24
425640--425671	2	16.0	2	93	0	55	53	0	0	46	1.00
426813--426846	2	17.0	2	100	0	68	50	0	0	50	1.00
427265--427322	25	2.5	23	83	13	66	46	3	0	50	1.18
428476--428539	31	2.0	31	87	6	92	50	3	0	46	1.17
429035--429060	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
429125--429188	25	2.6	24	81	18	71	35	0	0	64	0.94
429614--429694	3	27.0	3	89	0	117	34	4	0	60	1.18
430173--430254	40	2.0	40	92	0	137	19	21	30	28	1.98
430317--430401	29	2.9	29	80	16	95	45	1	0	52	1.08
431125--431160	2	18.0	2	100	0	72	50	0	0	50	1.00
437952--438548	73	8.4	73	71	9	326	55	9	2	32	1.45
437878--438525	144	4.6	141	76	11	419	55	9	2	32	1.44
438391--438526	72	1.9	73	82	1	175	59	6	1	32	1.32
438497--438586	41	2.2	39	86	5	126	56	11	1	31	1.41
438425--438662	113	2.1	113	80	4	266	55	8	4	32	1.49
438538--438977	72	6.1	71	78	10	371	54	9	4	32	1.51
438723--438835	32	3.3	32	68	21	93	55	8	1	33	1.41
438538--438977	217	2.0	214	81	7	498	54	9	4	32	1.51
438551--438977	144	3.0	144	81	8	453	54	9	3	32	1.50
438736--439210	264	1.8	263	84	7	635	55	10	1	32	1.44
439020--439286	141	1.9	138	84	6	362	55	9	1	33	1.41
439449--439498	26	2.0	26	92	4	84	54	6	2	38	1.37
441364--441414	27	1.9	27	92	4	86	27	19	33	19	1.96
443352--443385	11	3.1	11	100	0	68	35	17	11	35	1.87
443618--443693	20	3.8	19	75	6	80	40	13	13	32	1.83
444306--445465	28	40.6	28	81	7	1171	21	18	32	27	1.97
444287--445463	143	8.2	140	85	4	1351	21	18	31	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
446697--446738	9	4.7	9	82	5	50	0	2	11	85	0.68
446711--446737	14	1.9	14	100	0	54	0	0	11	88	0.50
458387--458437	27	1.9	27	92	4	86	27	19	33	19	1.96
460730--460801	20	3.6	19	75	7	72	41	11	13	33	1.80
462999--463035	18	2.0	19	89	5	58	51	0	0	48	1.00
464454--464486	14	2.5	14	90	9	52	18	6	0	75	1.00
467035--467073	11	3.6	11	86	6	53	82	2	15	0	0.79
467731--467789	17	3.8	16	74	12	52	77	0	18	3	0.90
468145--468169	2	12.5	2	100	0	50	48	0	0	52	1.00
474206--474252	16	3.1	16	79	17	55	70	10	14	4	1.31
474197--474274	37	2.1	36	81	11	88	70	10	14	5	1.31
475567--476246	28	24.6	27	87	4	876	24	32	13	28	1.93
476266--476937	32	22.4	28	88	5	544	30	31	18	20	1.96
476347--476994	32	21.2	31	86	6	624	29	31	18	20	1.96
476319--476994	96	7.4	95	83	8	743	29	31	18	20	1.96
477526--477573	10	4.6	10	87	7	69	87	4	8	0	0.66
478233--478282	24	2.1	23	85	10	66	72	0	24	4	1.02
478245--478296	17	3.1	16	75	8	50	75	0	19	5	1.01
483950--484205	50	5.1	50	86	0	350	28	17	19	33	1.95
486321--486358	18	2.1	18	100	0	76	65	0	5	28	1.14
486328--486374	18	2.5	18	86	6	58	65	2	10	21	1.33
493335--493400	27	2.4	27	89	2	96	43	3	1	51	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
494282--494322	21	2.0	21	85	0	55	19	9	17	53	1.70
495944--496015	22	3.2	22	70	20	60	44	0	0	55	0.99
496461--496490	6	5.2	6	92	8	53	66	0	0	33	0.92
496461--496490	11	2.6	11	94	5	51	66	0	0	33	0.92
496609--496634	12	2.2	12	100	0	52	42	15	7	34	1.75
501091--501115	13	1.9	13	100	0	50	36	16	16	32	1.90
501071--501137	33	2.0	33	85	0	89	34	11	13	40	1.81
501178--501202	13	1.9	13	100	0	50	32	16	16	36	1.90
501211--501339	52	2.5	52	96	0	231	34	18	17	29	1.94
516103--516138	17	2.1	17	94	0	63	86	0	13	0	0.58

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