oyster.v9_M.fa.s25.2.7.7.80.10.50.500.2.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: scaffold393
Parameters: 2 7 7 80 10 50 500
Length:  1263635

Tables:   1   2   3   4   

This is table  2  of  4  ( 399 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)
300594--300631	17	2.2	17	90	0	58	52	0	15	31	1.43
301176--301371	21	9.1	21	69	14	114	36	12	16	34	1.86
301407--301545	42	3.3	42	70	0	125	35	15	13	35	1.87
301407--301564	21	7.6	21	72	0	84	33	17	14	34	1.90
304297--304393	23	4.2	23	97	0	185	28	19	12	39	1.88
313526--313571	3	15.3	3	83	0	56	58	32	4	4	1.37
320626--320676	12	4.5	11	74	16	50	0	1	19	78	0.85
320626--320678	22	2.4	22	81	6	63	0	1	20	77	0.87
322012--322047	18	2.0	18	88	0	54	30	11	25	33	1.90
323628--323660	16	2.1	16	100	0	66	18	18	33	30	1.94
325315--325760	166	2.7	165	87	3	585	34	14	24	26	1.94
328369--328403	16	2.2	16	89	0	52	48	0	31	20	1.50
338269--338310	2	21.0	2	100	0	84	50	0	0	50	1.00
356289--356359	26	2.7	26	86	0	88	39	9	11	39	1.74
357018--357202	26	7.0	26	86	3	244	41	13	15	29	1.86
357018--357581	52	10.9	52	74	11	365	39	13	15	31	1.86
357285--357581	26	11.3	26	80	5	265	37	12	15	33	1.86
357344--357581	103	2.3	103	83	3	287	38	13	15	31	1.87
357507--357564	17	3.7	16	71	17	50	37	12	15	34	1.85
357496--357569	30	2.6	30	81	8	93	40	13	13	32	1.84
357596--357628	17	1.9	17	93	0	57	33	9	21	36	1.85
370053--370099	22	2.1	22	84	0	58	44	19	10	25	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
376451--376480	10	3.0	10	95	0	51	60	33	6	0	1.23
378270--378363	32	2.9	32	85	6	136	27	26	17	28	1.97
379855--379893	19	2.1	19	85	4	53	35	35	2	25	1.70
401013--401095	24	3.4	24	90	3	121	32	30	13	24	1.93
405055--405467	209	2.0	204	94	1	718	28	23	16	30	1.96
417200--417264	32	2.0	32	85	5	87	26	40	7	26	1.83
417216--417674	44	10.3	44	88	6	638	26	39	6	27	1.81
417229--417342	54	2.1	54	91	0	192	25	39	8	26	1.85
421428--422334	23	39.6	23	89	1	1331	13	24	22	39	1.90
427382--427464	41	2.0	41	95	0	148	37	10	26	25	1.89
433620--433663	2	22.0	2	100	0	88	0	50	0	50	1.00
441308--441358	26	2.0	26	100	0	102	41	15	7	35	1.76
441515--441985	37	12.6	37	93	2	754	21	14	21	42	1.88
441515--441985	55	8.4	56	93	3	749	21	14	21	42	1.88
441515--441985	92	5.1	93	94	2	795	21	14	21	42	1.88
441579--441982	19	22.0	16	75	21	110	21	14	21	42	1.88
442523--442644	18	6.5	19	85	8	139	21	9	24	44	1.82
442523--442647	19	6.7	19	86	7	159	20	10	24	44	1.82
442523--442647	37	3.4	37	87	6	173	20	10	24	44	1.82
445308--445377	4	17.5	4	93	0	122	0	45	25	28	1.54
445401--446360	166	5.8	166	89	1	1363	29	16	15	38	1.89
445401--446360	331	2.9	331	88	1	1404	29	16	15	38	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
448663--448693	14	2.2	14	100	0	62	41	25	12	19	1.87
448677--448776	36	2.8	36	96	0	191	28	18	27	27	1.98
449430--449532	25	4.1	25	88	0	143	16	23	17	42	1.88
449593--449822	25	9.1	25	81	9	270	19	19	21	40	1.92
449593--449822	50	4.5	50	88	2	325	19	19	21	40	1.92
449593--449822	75	3.0	74	87	3	298	19	19	21	40	1.92
452339--452527	40	4.7	40	99	0	369	26	32	12	28	1.92
462810--462870	2	30.5	2	93	0	104	1	47	1	49	1.21
467774--467961	20	9.4	20	70	6	103	25	20	15	38	1.92
467792--467936	40	3.6	40	77	7	125	26	21	16	35	1.94
467971--468044	20	3.7	20	74	0	67	24	25	9	40	1.85
474516--475569	39	26.0	39	83	8	1268	44	7	29	17	1.77
474516--475569	126	8.7	121	87	5	1297	44	7	29	17	1.77
478205--478389	31	6.0	31	96	0	334	37	19	10	32	1.85
485817--485849	14	2.4	14	100	0	66	33	15	36	15	1.88
486836--486860	12	2.1	12	100	0	50	44	16	24	16	1.86
494302--494361	17	3.6	17	93	2	95	3	36	8	51	1.49
494281--494327	2	23.5	2	87	8	69	0	44	2	53	1.12
497088--497138	16	3.1	16	80	5	57	47	19	15	17	1.83
497092--497137	9	5.3	9	74	10	51	50	19	17	13	1.78
497270--497324	18	3.1	17	84	7	65	38	12	16	32	1.86
497446--497490	18	2.5	18	88	0	63	37	15	17	28	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
497200--497810	176	3.5	176	88	2	920	35	11	14	39	1.81
497627--497667	18	2.3	18	91	0	64	43	12	14	29	1.82
497847--497895	18	2.8	18	90	3	73	32	14	12	40	1.83
497852--497905	17	3.1	18	86	5	76	25	14	11	48	1.77
498038--498070	16	2.1	16	94	0	57	21	12	18	48	1.80
504472--504655	35	5.8	34	67	21	89	35	17	17	29	1.93
504549--504661	31	3.5	32	78	16	101	36	16	19	27	1.93
511134--511257	35	3.9	34	65	24	88	35	18	16	29	1.93
511211--511323	31	3.5	32	78	16	101	36	17	19	26	1.94
513037--513150	37	3.1	37	96	0	210	21	25	19	34	1.96
513274--513373	53	1.9	52	91	2	164	30	18	17	35	1.93
528444--528528	22	3.9	22	90	0	134	31	25	12	29	1.93
528955--528995	12	3.5	12	84	15	59	0	34	24	41	1.55
528954--528988	16	2.3	15	90	5	52	0	34	22	42	1.54
529165--530861	166	10.2	165	89	3	2526	32	16	25	25	1.96
535572--535634	23	2.7	24	83	9	69	25	15	17	41	1.89
535686--535741	23	2.4	23	79	5	60	16	21	19	42	1.89
536037--536106	23	3.1	23	75	4	61	21	15	20	42	1.88
548061--548207	37	4.0	37	88	0	213	13	18	25	42	1.87
548079--548140	21	3.2	21	65	21	62	9	19	30	40	1.84
548752--548792	2	20.5	2	94	0	73	0	48	0	51	1.00
553582--553686	35	2.9	37	83	5	119	20	9	26	43	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
555116--555639	47	11.5	47	91	4	785	20	21	18	38	1.93
555116--555604	180	2.7	181	89	5	728	20	21	18	39	1.93
555054--555639	226	2.6	227	88	6	819	21	21	18	38	1.93
556932--556989	2	29.0	2	96	0	107	0	48	0	51	1.00
557326--558391	440	2.4	434	89	3	1577	35	16	14	33	1.90
558901--558961	14	4.4	14	83	2	79	47	19	9	22	1.79
558942--558997	18	3.1	18	80	10	78	53	17	8	19	1.70
562456--562480	1	25.0	1	100	0	50	0	0	100	0	0.00
562737--562977	34	7.1	34	91	0	376	22	15	28	33	1.95
562774--562834	18	3.6	18	70	18	58	22	18	27	31	1.97
562737--562977	101	2.4	102	91	1	403	22	15	28	33	1.95
573223--573434	62	3.4	62	99	0	415	38	21	16	23	1.92
573422--573496	37	2.0	37	89	0	114	44	24	10	21	1.84
576642--576697	2	28.0	2	100	0	112	50	0	50	0	1.00
578673--578857	26	7.1	26	92	0	298	42	10	15	31	1.81
585160--585192	2	16.5	2	100	0	66	0	0	48	51	1.00
585786--585810	1	25.0	1	100	0	50	0	0	0	100	0.00
592246--592506	128	2.0	128	97	0	488	32	17	9	40	1.82
596865--596894	1	30.0	1	100	0	60	100	0	0	0	0.00
603626--603682	29	2.0	29	100	0	114	7	28	12	52	1.64
610437--610522	2	43.5	2	90	6	140	1	51	1	46	1.16
614336--614377	14	3.0	14	96	0	75	54	14	7	23	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
618191--618217	2	13.5	2	100	0	54	0	51	0	48	1.00
630926--631010	2	42.5	2	92	0	143	1	47	0	51	1.08
634050--634074	13	1.9	13	100	0	50	84	0	0	16	0.63
636176--636216	21	2.0	21	85	0	55	51	21	9	17	1.74
644577--644686	55	2.1	52	88	8	159	25	10	13	50	1.72
645374--645410	2	18.5	2	94	0	65	54	0	45	0	1.00
646231--646470	29	8.3	29	86	5	335	9	21	17	51	1.73
658973--659077	13	8.1	13	89	0	156	28	8	12	50	1.69
658973--659077	26	4.0	26	92	0	174	28	8	12	50	1.69
665618--665674	27	2.1	27	93	0	96	38	12	10	38	1.77

Tables:   1   2   3   4