oyster.v9_M.fa.s28.2.7.7.80.10.50.500.2.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: scaffold301
Parameters: 2 7 7 80 10 50 500
Length:  1229110

Tables:   1   2   3   4   

This is table  2  of  4  ( 385 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)
376423--376448	2	13.0	2	100	0	52	50	0	0	50	1.00
388407--388475	2	35.0	2	83	2	86	44	0	1	52	1.10
402514--402559	2	23.0	2	100	0	92	0	0	50	50	1.00
406395--406451	2	28.5	2	100	0	114	0	49	0	50	1.00
416765--416836	34	2.2	33	89	2	108	25	5	19	50	1.69
417960--418008	2	24.5	2	100	0	98	0	51	0	48	1.00
419397--419443	2	23.5	2	100	0	94	0	48	0	51	1.00
425481--425532	2	26.0	2	96	0	95	0	48	0	51	1.00
427392--427423	4	8.0	4	92	0	55	0	28	25	46	1.53
443615--443684	2	35.0	2	100	0	140	0	50	0	50	1.00
447778--447810	17	1.9	17	93	0	57	81	18	0	0	0.68
449546--449713	84	2.0	83	98	1	327	32	27	19	20	1.97
450948--450993	2	23.0	2	100	0	92	0	50	0	50	1.00
454312--454614	164	1.9	163	83	4	396	36	15	21	26	1.93
455902--456125	78	2.9	77	87	3	317	25	20	12	41	1.87
457961--458006	16	3.0	15	90	6	58	30	17	26	26	1.97
457972--458006	16	2.2	16	100	0	70	28	22	22	25	1.99
458428--458452	12	2.1	12	100	0	50	36	24	0	40	1.55
458526--458914	163	2.4	159	81	6	480	33	13	17	35	1.89
459433--459462	8	3.8	8	90	0	51	0	33	26	40	1.57
459657--460529	165	5.2	165	92	4	1407	32	15	26	25	1.96
463465--463528	30	2.2	30	82	2	76	40	15	9	34	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
463478--463537	30	2.0	30	96	0	111	43	15	6	35	1.72
465710--465760	25	2.0	25	88	7	77	33	3	15	47	1.64
468130--468504	187	2.0	187	98	0	732	26	14	22	36	1.93
472031--472118	32	2.9	29	74	9	77	36	15	19	28	1.93
475458--475665	103	2.0	103	96	0	380	29	14	17	38	1.89
476643--476986	184	1.9	184	84	6	473	32	13	15	38	1.87
477434--477472	11	3.5	11	82	0	51	20	25	10	43	1.83
481061--481162	21	4.9	21	85	2	125	16	18	31	33	1.94
482716--482744	2	14.5	2	100	0	58	0	48	0	51	1.00
483849--483888	2	20.0	2	100	0	80	0	50	0	50	1.00
484308--484429	21	5.8	20	75	11	102	14	16	31	37	1.89
484317--484399	42	2.0	42	92	4	141	15	13	32	38	1.86
487368--487406	20	1.9	20	89	0	60	41	2	12	43	1.56
487491--487551	20	3.0	20	76	4	61	37	3	11	47	1.56
487501--487568	20	3.4	20	80	8	75	32	2	11	52	1.53
490224--490303	41	1.9	42	87	2	117	30	7	8	53	1.59
495339--495742	172	2.3	172	96	0	745	29	18	15	36	1.92
498143--498170	2	14.0	2	100	0	56	50	0	50	0	1.00
499150--499186	2	18.5	2	100	0	74	0	51	0	48	1.00
506917--506985	24	2.9	24	91	0	102	4	40	23	31	1.74
506917--506976	4	15.0	4	82	0	66	5	41	23	30	1.75
516335--516373	14	2.7	14	80	4	51	30	25	0	43	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
521577--521644	17	4.0	17	92	7	120	51	7	0	41	1.30
539112--539188	14	5.5	14	90	3	79	46	1	49	2	1.23
539135--539190	2	28.0	2	100	0	112	50	0	50	0	1.00
541052--541084	17	1.9	17	100	0	66	24	21	24	30	1.99
541916--541972	2	28.5	2	100	0	114	0	50	0	49	1.00
542176--542220	22	2.1	21	83	4	54	17	28	6	46	1.73
542471--542539	2	34.5	2	97	0	129	0	50	0	49	1.00
543664--543714	2	25.5	2	100	0	102	0	50	0	49	1.00
550617--550692	2	38.0	2	100	0	152	0	50	0	50	1.00
552574--552618	2	22.5	2	100	0	90	48	0	51	0	1.00
553355--553422	2	34.0	2	93	0	118	52	0	47	0	1.00
565770--565794	3	8.3	3	100	0	50	32	68	0	0	0.90
567500--567548	2	24.5	2	100	0	98	0	48	0	51	1.00
574082--574534	167	2.7	169	87	1	651	33	19	17	29	1.95
573972--574551	167	3.5	168	81	3	638	32	19	18	30	1.96
575733--575767	1	35.0	1	88	0	52	94	5	0	0	0.32
575730--575767	15	2.5	15	100	0	76	92	7	0	0	0.40
577554--577606	20	2.5	21	78	9	63	45	1	11	41	1.51
608122--608184	2	31.5	2	100	0	126	49	0	50	0	1.00
620327--620628	43	7.0	43	93	1	498	38	17	27	17	1.91
622738--622792	25	2.2	24	84	9	74	29	23	32	14	1.94
625912--625958	2	23.5	2	100	0	94	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
644997--645090	47	2.0	47	97	2	172	43	8	6	40	1.61
649515--649649	66	2.0	66	100	0	270	18	16	16	48	1.81
662458--662717	130	2.0	130	99	0	511	21	21	16	41	1.90
676446--676487	2	21.0	2	100	0	84	0	50	0	50	1.00
677359--677385	4	6.8	4	100	0	54	22	0	0	77	0.76
686056--686090	1	35.0	1	100	0	70	0	100	0	0	0.00
692698--692780	21	4.0	21	82	0	103	40	14	18	26	1.88
692701--692780	42	1.9	42	92	0	133	38	15	18	27	1.91
692931--692987	21	2.7	21	77	0	69	35	14	15	35	1.88
693020--693067	21	2.3	21	78	7	53	37	22	4	35	1.74
702825--702899	38	2.0	38	86	0	105	37	2	16	44	1.61
704322--704370	22	2.2	21	79	10	53	8	14	28	48	1.72
704339--704380	11	3.8	11	83	0	57	9	9	26	54	1.63
704333--704375	22	2.0	22	95	0	77	9	11	30	48	1.71
709085--709111	14	1.9	14	100	0	54	44	0	33	22	1.53
709963--709993	13	2.4	13	94	0	53	48	0	9	41	1.36
714197--714227	12	2.7	11	95	5	53	35	25	38	0	1.56
716433--716485	10	5.0	11	90	9	92	15	9	37	37	1.79
716433--716485	21	2.5	21	100	0	106	15	9	37	37	1.79
726988--727045	21	2.8	21	86	0	80	39	13	18	27	1.89
726989--727068	42	1.9	42	84	5	108	38	16	18	26	1.92
737561--737642	4	20.5	4	84	0	92	0	43	2	53	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
737561--737643	24	3.4	24	81	6	103	0	44	2	53	1.13
747538--747595	28	2.1	28	100	0	116	37	10	6	44	1.65
748679--748712	16	2.1	16	88	0	50	55	5	8	29	1.54
755144--755200	26	2.2	26	87	0	78	36	12	14	36	1.83
756165--756192	1	28.0	1	100	0	56	100	0	0	0	0.00
761288--761333	2	23.0	2	90	0	74	0	52	2	45	1.13
762599--762639	2	20.5	2	100	0	82	0	48	0	51	1.00
764350--764816	69	6.8	70	91	1	637	20	21	22	35	1.96
766265--766304	6	6.3	6	88	11	62	15	32	15	37	1.88
766264--766305	13	3.2	13	87	12	68	14	30	14	40	1.85
766404--766449	6	7.2	6	90	9	65	15	30	15	39	1.88
766403--766449	13	3.6	13	91	8	78	14	29	14	40	1.87
766403--766449	7	7.1	7	86	13	73	14	29	14	40	1.87
767132--767162	2	16.0	2	93	6	55	0	51	0	48	1.00
767331--767375	2	22.5	2	100	0	90	0	51	0	48	1.00
768774--768817	21	2.1	21	100	0	88	38	20	13	27	1.90
769403--769444	13	3.4	13	83	12	61	52	7	11	28	1.64
774340--774379	2	20.0	2	100	0	80	0	50	0	50	1.00
775443--775495	2	27.0	2	96	3	99	49	0	50	0	1.00
776479--776515	19	1.9	20	84	10	51	35	13	5	45	1.66
777252--777289	19	2.0	19	89	0	58	28	23	10	36	1.88
779286--779317	15	2.0	17	88	11	50	34	0	9	56	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
782573--782620	2	24.0	2	100	0	96	50	0	50	0	1.00
782771--782806	2	18.0	2	100	0	72	50	0	50	0	1.00
785156--785286	4	32.8	4	98	0	226	24	28	0	47	1.52
786317--786376	2	30.0	2	93	0	102	51	1	46	0	1.10
786394--786419	2	13.0	2	100	0	52	50	0	50	0	1.00
794887--795099	30	7.1	30	96	0	399	17	18	23	39	1.91
796504--796568	29	2.3	29	86	2	87	32	15	10	41	1.81
798674--798715	18	2.3	18	91	0	66	47	14	16	21	1.82
800860--800913	27	2.0	27	100	0	108	44	7	29	18	1.77
801203--801235	16	2.1	16	100	0	66	12	30	24	33	1.91

Tables:   1   2   3   4