oyster.v9_M.fa.s50.2.7.7.80.10.50.500.2.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.04

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: scaffold1423
Parameters: 2 7 7 80 10 50 500
Length:  1072665

Tables:   1   2   3   

This is table  2  of  3  ( 360 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)
342393--342433	16	2.6	16	96	0	73	92	4	2	0	0.44
343400--343446	16	2.9	17	87	6	62	12	36	23	27	1.91
344398--344429	15	2.1	16	94	5	57	31	6	6	56	1.49
344591--344670	42	1.9	42	86	0	115	27	17	16	38	1.91
344587--344673	21	4.2	21	79	1	86	26	16	14	42	1.87
349165--349203	16	2.4	16	95	0	69	15	33	20	30	1.94
352914--352956	16	2.8	16	96	3	79	41	4	20	32	1.73
355514--355541	14	2.0	14	100	0	56	28	0	14	57	1.38
355867--356035	84	2.0	84	100	0	338	32	18	27	21	1.97
361224--361262	18	2.2	18	90	0	60	0	20	43	35	1.52
361488--361698	104	2.0	104	93	1	361	31	14	27	26	1.95
361592--362565	166	5.9	166	89	1	1368	34	14	22	27	1.94
361592--362565	331	2.9	328	88	2	1373	34	14	22	27	1.94
366006--366099	30	3.1	30	72	11	84	42	21	7	28	1.80
368708--369703	46	21.8	45	77	7	811	44	24	10	20	1.83
368697--369703	92	11.0	90	78	8	903	44	24	10	20	1.82
368829--368953	45	2.7	46	82	11	150	46	20	9	23	1.80
372333--372380	22	2.2	22	84	0	60	22	27	18	31	1.97
372610--372642	2	16.5	2	100	0	66	0	48	0	51	1.00
375952--376004	20	2.7	19	83	16	56	33	16	7	41	1.77
376703--376798	28	3.4	28	80	5	122	32	26	13	28	1.94
377265--377829	43	13.1	43	98	0	1058	23	32	12	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
378849--379101	45	5.3	45	76	17	260	35	35	5	24	1.78
378860--379101	46	4.9	50	83	13	244	35	35	4	24	1.76
378862--379101	91	2.5	95	82	13	294	35	35	4	24	1.76
382221--382291	27	2.6	27	81	0	88	29	9	32	28	1.89
387093--387117	2	12.5	2	100	0	50	52	0	48	0	1.00
387115--387249	4	35.8	4	74	10	52	49	19	28	2	1.60
387093--387253	12	13.4	12	70	10	69	49	16	32	1	1.56
387133--387229	36	2.6	38	80	6	126	51	19	26	2	1.58
387110--387231	32	3.6	33	74	12	95	50	18	28	2	1.60
387213--387254	18	2.3	18	87	0	57	47	14	35	2	1.57
387187--387249	22	2.9	22	79	9	74	49	20	28	1	1.58
392181--392230	25	2.0	25	100	0	100	32	16	8	44	1.76
396412--396458	24	2.0	24	91	8	78	31	8	17	42	1.79
410790--410830	18	2.3	18	87	4	57	29	21	12	36	1.90
417991--418139	78	1.9	78	90	2	237	22	30	13	34	1.92
434324--434367	2	22.0	2	100	0	88	0	50	0	50	1.00
444834--445018	21	8.8	21	89	0	280	36	11	18	32	1.87
444834--445018	63	2.9	63	99	0	361	36	11	18	32	1.87
448789--448840	2	26.0	2	100	0	104	0	50	0	50	1.00
449226--449270	2	22.5	2	100	0	90	51	0	48	0	1.00
453902--453941	2	20.0	2	100	0	80	50	0	50	0	1.00
456454--456491	2	19.0	2	100	0	76	50	0	50	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
460418--460448	16	1.9	16	93	0	53	64	6	6	22	1.40
471984--472019	18	2.0	18	94	0	63	13	11	25	50	1.75
478988--479043	15	4.0	15	70	25	59	28	41	8	21	1.83
478995--479223	26	8.8	26	91	0	368	32	36	10	20	1.87
479158--479329	26	6.6	27	76	6	90	27	31	13	26	1.94
479204--479311	52	2.1	51	81	5	119	27	27	16	27	1.97
490536--490628	36	2.5	36	96	3	168	40	10	5	43	1.62
490536--490635	19	5.4	19	95	4	186	40	10	6	44	1.63
495151--495203	2	26.5	2	100	0	106	0	50	0	49	1.00
508169--508221	2	26.5	2	100	0	106	50	0	49	0	1.00
525466--526097	28	23.1	28	97	0	1098	35	10	11	42	1.76
526410--526556	24	6.0	24	88	4	204	34	11	14	40	1.82
529619--529669	24	2.1	24	92	0	84	39	35	15	9	1.81
537466--537491	1	26.0	1	100	0	52	0	0	100	0	0.00
537926--538846	18	50.9	18	69	13	369	32	10	17	39	1.84
537895--538372	179	2.7	177	88	4	689	30	10	19	39	1.85
538283--538369	38	2.4	35	83	9	102	34	9	17	39	1.81
539009--539058	18	2.8	18	87	6	66	30	8	22	40	1.82
539073--539128	29	1.9	29	88	0	85	26	8	25	39	1.85
539650--539690	22	2.0	21	85	9	57	46	9	9	34	1.70
546021--546057	12	3.2	12	88	7	58	43	8	13	35	1.74
557381--557459	2	39.5	2	97	0	149	49	0	49	1	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
566262--566300	13	3.0	13	92	7	62	84	0	2	12	0.72
575287--575345	2	29.5	2	100	0	118	49	0	50	0	1.00
582004--582030	13	2.1	13	100	0	54	18	0	29	51	1.46
587994--588018	12	2.1	12	100	0	50	44	0	8	48	1.32
604266--604417	33	4.6	34	70	8	107	28	32	16	21	1.95
604378--604512	50	2.7	49	94	3	234	25	33	18	22	1.97
604472--604543	34	2.1	34	92	0	117	25	36	18	20	1.95
625528--625561	17	2.0	17	100	0	68	35	11	5	47	1.65
643701--643735	15	2.2	16	95	5	63	60	5	5	28	1.43
644802--644842	20	2.0	20	100	0	82	19	29	26	24	1.98
645337--645364	10	2.8	10	100	0	56	42	10	10	35	1.74
645825--645850	11	2.4	11	100	0	52	11	0	0	88	0.52
647066--647324	136	1.9	134	86	5	369	30	10	16	42	1.82
649773--649807	2	17.5	2	100	0	70	0	51	0	48	1.00
665602--665873	146	1.9	144	91	1	445	29	22	19	27	1.98
668527--668992	161	2.9	160	88	2	618	37	21	13	27	1.91
678323--678352	15	2.0	15	100	0	60	20	26	20	33	1.97
681789--682045	85	3.0	85	100	0	514	24	21	23	31	1.98
684948--685106	59	2.7	59	88	4	227	42	16	17	23	1.89
698957--698993	2	18.5	2	100	0	74	0	0	51	48	1.00
721545--721574	2	15.0	2	100	0	60	50	0	50	0	1.00
729399--730574	166	7.1	166	87	2	1647	25	25	16	33	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
731989--732016	12	2.3	12	100	0	56	32	25	42	0	1.55
737455--737479	13	1.9	13	100	0	50	48	0	52	0	1.00
739654--739860	69	3.1	66	80	8	229	49	13	17	19	1.79
739655--739859	66	3.0	66	79	7	225	49	13	18	19	1.79
740275--740301	12	2.2	12	100	0	54	22	7	25	44	1.79
744480--744506	12	2.2	12	100	0	54	33	25	40	0	1.56
747950--748248	136	2.2	138	90	2	460	38	19	20	20	1.93
751123--751172	4	12.8	4	82	4	66	0	42	26	32	1.56
751129--751175	12	3.9	12	91	0	76	0	40	25	34	1.56
755818--755862	18	2.5	18	85	0	54	17	11	40	31	1.85
756768--756802	4	8.8	4	87	0	52	0	42	25	31	1.55
756772--756809	12	3.2	12	96	0	67	0	36	26	36	1.57
756812--757503	146	4.7	146	90	2	1079	29	19	21	29	1.98
762800--762927	63	2.0	63	98	0	247	24	18	16	40	1.90
788982--789016	17	2.1	17	94	0	61	40	11	17	31	1.85
797714--798728	436	2.3	437	89	1	1500	29	16	16	37	1.90
799905--800021	56	2.1	56	96	0	216	45	15	17	21	1.85
802124--802211	45	2.0	42	82	6	104	56	6	11	25	1.58
821172--821906	384	1.9	384	83	2	949	35	15	17	31	1.91
823026--823062	1	37.0	1	88	0	56	0	94	2	2	0.36
823027--823062	16	2.2	16	95	0	63	0	94	2	2	0.37
823837--824775	437	2.1	436	80	3	1071	32	18	13	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
825196--825231	11	3.3	11	92	0	54	86	0	0	13	0.58
825715--826644	436	2.1	434	84	3	1190	30	18	14	36	1.91
829199--829283	43	2.0	43	100	0	170	42	14	12	30	1.83
829522--829583	21	2.8	24	76	20	71	24	27	19	29	1.98
829577--829625	21	2.3	21	85	0	62	36	28	18	16	1.92
832594--832634	11	3.7	11	93	0	73	29	9	36	24	1.87
832715--832753	11	3.6	11	82	3	53	28	23	10	38	1.87
832713--832753	21	1.9	22	95	5	75	29	24	9	36	1.87
833155--833182	2	14.0	2	100	0	56	0	50	0	50	1.00
834872--834914	11	3.9	11	93	0	77	30	9	32	27	1.88

Tables:   1   2   3