oyster.v9_M.fa.s27.2.7.7.80.10.50.500.2.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: scaffold142
Parameters: 2 7 7 80 10 50 500
Length:  1252394

Tables:   1   2   3   4   

This is table  2  of  4  ( 420 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)
365949--366015	7	9.6	7	83	0	89	26	22	14	35	1.93
365949--366015	21	3.2	21	86	0	98	26	22	14	35	1.93
366484--366523	2	20.0	2	94	0	71	0	52	0	47	1.00
369084--369145	21	3.0	21	79	9	72	1	6	27	64	1.27
377554--377597	20	2.2	20	91	0	70	38	25	36	0	1.56
377551--377604	8	7.4	8	74	19	55	40	25	33	0	1.56
381371--381408	17	2.2	18	86	13	53	0	0	34	65	0.93
381370--381417	26	1.9	24	87	8	69	0	0	31	68	0.90
386946--386991	11	3.8	12	80	11	58	34	2	0	63	1.07
390363--390483	59	2.0	60	93	4	208	33	11	21	33	1.89
393159--393283	2	62.5	2	96	0	196	0	47	0	48	1.02
400256--400322	7	9.6	7	83	0	89	35	14	22	26	1.93
402712--402762	2	25.5	2	95	0	93	50	0	49	0	1.00
402968--403010	2	22.0	2	88	4	61	2	44	0	53	1.13
403505--403567	7	9.0	7	82	0	81	25	23	14	36	1.93
403505--403567	21	3.0	21	88	0	90	25	23	14	36	1.93
407999--408070	32	2.3	31	95	4	135	25	31	16	26	1.96
408000--408090	32	2.8	32	90	5	121	28	28	18	24	1.98
410418--410502	36	2.5	33	86	7	118	27	17	30	24	1.97
410486--410519	17	2.0	17	88	0	50	35	11	35	17	1.87
412694--412727	17	2.0	17	100	0	68	23	5	23	47	1.73
412776--412810	17	2.1	17	88	0	52	22	5	17	54	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
412659--412861	84	2.4	84	86	1	273	34	14	14	35	1.87
413405--413456	19	2.7	19	90	0	86	9	40	7	42	1.66
421472--421548	2	38.5	2	100	0	154	0	50	0	49	1.00
425134--425491	167	2.1	171	86	5	496	32	14	25	28	1.95
428724--428767	12	3.8	12	90	6	72	36	0	6	56	1.26
432314--432363	25	2.0	25	92	0	82	32	18	18	32	1.94
434657--434927	86	3.2	86	98	0	515	29	18	19	32	1.95
434876--434985	58	1.9	57	96	3	204	32	16	20	30	1.94
434932--435149	88	2.5	88	91	2	354	29	17	20	32	1.95
434706--435149	230	1.9	228	94	2	775	29	17	20	32	1.96
435323--435448	31	4.1	31	91	0	198	28	37	16	17	1.92
435755--435808	2	27.0	2	100	0	108	50	0	50	0	1.00
440320--440352	10	3.3	10	84	16	50	42	6	9	42	1.61
458301--458391	2	45.5	2	82	4	103	1	41	6	50	1.35
462608--462761	21	7.5	20	71	5	92	56	7	9	27	1.56
463210--463242	4	8.2	4	100	0	66	75	0	24	0	0.80
463240--463307	4	17.0	4	100	0	136	50	0	25	25	1.50
466611--466694	2	42.0	2	90	0	132	0	45	3	51	1.18
480544--480571	2	14.0	2	100	0	56	50	0	50	0	1.00
497420--497471	4	13.2	4	95	4	97	25	0	25	50	1.50
503208--503287	21	3.8	21	86	4	99	26	7	25	41	1.81
503530--503584	21	2.6	21	91	0	83	27	14	20	38	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
503699--503754	21	2.7	21	88	5	78	44	16	14	25	1.84
503911--504010	42	2.4	42	81	0	128	29	18	16	37	1.92
503911--504071	21	7.7	21	73	2	108	32	17	14	36	1.90
504140--504268	21	6.1	21	68	3	71	40	17	15	27	1.89
504188--504268	42	1.9	42	87	0	117	45	16	16	22	1.85
504365--504420	21	2.7	21	85	0	67	28	17	14	39	1.89
507022--507054	17	1.9	17	100	0	66	24	21	24	30	1.99
507963--508040	17	4.6	17	83	10	72	21	2	1	74	1.01
507985--508036	26	2.0	26	85	14	72	17	1	0	80	0.80
524483--524568	4	21.5	4	92	0	145	26	20	0	52	1.47
531265--531290	11	2.4	11	100	0	52	42	19	7	30	1.79
532084--532132	2	24.5	2	100	0	98	0	51	0	48	1.00
532259--532317	2	29.5	2	85	0	73	1	44	3	50	1.28
539777--539910	21	6.4	21	76	3	117	38	18	23	19	1.93
539787--539890	42	2.5	42	93	0	172	37	21	23	18	1.94
539945--539971	14	1.9	14	100	0	54	37	0	11	51	1.37
550480--550519	2	20.0	2	100	0	80	0	0	50	50	1.00
566919--566970	20	2.6	20	87	9	79	5	34	19	40	1.75
570523--570649	24	5.5	22	75	13	87	21	0	44	33	1.52
570558--570666	18	6.3	18	71	21	81	21	0	45	33	1.52
570566--570693	46	2.7	47	90	4	206	21	0	45	32	1.58
570600--570656	28	2.0	28	83	12	73	21	0	47	31	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
570581--570666	18	5.2	18	72	23	82	19	0	47	32	1.50
570726--570771	24	2.0	23	91	4	74	23	2	41	32	1.67
570753--570794	18	2.3	18	95	0	75	21	0	47	30	1.51
570712--570892	99	1.8	98	91	1	299	20	1	44	34	1.59
570852--570911	18	3.4	18	90	4	95	21	3	43	31	1.69
571956--572001	2	23.0	2	100	0	92	50	0	50	0	1.00
580907--580946	2	20.5	2	94	5	73	0	50	0	50	1.00
582627--582680	2	27.0	2	100	0	108	0	50	0	50	1.00
585854--585964	21	5.3	20	85	2	123	35	13	13	37	1.84
586265--586317	21	2.5	21	87	0	70	32	9	20	37	1.85
586422--586464	21	2.1	21	86	4	61	25	13	18	41	1.88
588315--588358	2	22.0	2	100	0	88	0	50	0	50	1.00
588632--588684	21	2.5	21	87	0	70	37	20	9	32	1.85
588925--589137	42	5.1	42	76	6	198	35	14	15	35	1.87
588985--589137	21	7.3	21	92	0	216	34	14	15	35	1.88
590959--590997	2	19.5	2	89	0	60	0	43	0	56	0.99
591495--591555	2	30.5	2	100	0	122	50	0	49	0	1.00
595543--595720	53	3.1	59	81	14	217	22	17	16	43	1.87
595603--595714	53	2.1	53	100	0	224	25	16	17	41	1.89
598859--598894	16	2.1	18	90	10	58	33	27	2	36	1.72
601903--602034	63	2.1	63	95	0	237	19	18	13	47	1.82
603006--603063	2	29.0	2	100	0	116	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
603351--603400	2	25.0	2	100	0	100	0	50	0	50	1.00
604023--604047	1	25.0	1	100	0	50	0	100	0	0	0.00
605629--605684	2	28.0	2	100	0	112	0	50	0	50	1.00
616266--616323	21	2.7	22	84	5	66	36	20	12	31	1.89
616602--616690	42	2.1	42	95	0	160	38	22	5	33	1.78
616597--616690	21	4.5	22	86	7	133	38	22	6	32	1.79
617654--619370	331	5.2	332	85	4	2263	25	24	15	33	1.95
617654--619370	165	10.3	166	85	4	2206	25	24	15	33	1.95
619568--619609	4	10.8	4	82	5	50	42	26	30	0	1.55
621815--622087	46	6.0	46	90	3	376	34	6	16	42	1.74
621815--622087	94	3.0	92	87	4	385	34	6	16	42	1.74
622013--622090	42	2.0	37	82	12	93	33	7	12	46	1.71
627981--628728	47	16.0	47	86	1	1000	43	15	4	36	1.68
630199--630240	4	10.8	4	84	5	50	0	40	26	33	1.56
630199--630243	12	3.8	12	85	2	56	0	37	26	35	1.57
630198--630240	16	2.8	16	92	3	70	0	39	25	34	1.56
633956--634002	2	23.5	2	100	0	94	0	51	0	48	1.00
640553--641424	41	21.5	41	88	3	1239	40	20	14	24	1.90
640553--641422	363	2.4	366	88	3	1290	40	20	14	24	1.90
649165--649480	41	7.6	41	84	6	406	38	21	16	23	1.92
649165--649478	83	3.8	83	95	1	542	39	21	16	22	1.92
649165--649480	124	2.5	123	84	6	431	38	21	16	23	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
653885--653954	37	1.9	36	94	2	122	38	10	18	32	1.84
656211--656968	36	21.1	36	89	1	1026	19	37	15	26	1.92
657957--658162	21	9.9	20	87	8	288	26	6	8	58	1.52
657957--658162	83	2.5	83	91	4	317	26	6	8	58	1.52
657957--658162	62	3.3	62	92	2	306	26	6	8	58	1.52
658310--658638	21	15.8	20	89	4	478	58	8	7	25	1.53
658310--658639	62	5.3	62	90	5	488	58	8	7	25	1.53
659279--659303	13	1.9	13	100	0	50	40	8	4	48	1.51
663972--664035	2	32.0	2	100	0	128	0	50	0	50	1.00
664472--664515	2	22.0	2	100	0	88	0	50	0	50	1.00

Tables:   1   2   3   4