oyster.v9_M.fa.s4.2.7.7.80.10.50.500.2.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: scaffold1024
Parameters: 2 7 7 80 10 50 500
Length:  1774716

Tables:   1   2   3   4   5   

This is table  2  of  5  ( 509 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)
463069--463168	27	3.7	27	81	5	121	37	13	14	36	1.84
464602--464661	4	15.0	4	77	19	63	0	26	21	51	1.48
464604--464662	20	3.0	20	92	0	100	0	28	20	50	1.48
464692--465486	166	4.8	166	88	1	1117	28	16	15	39	1.89
469663--469692	15	2.0	15	100	0	60	40	0	0	60	0.97
473418--473448	2	15.5	2	100	0	62	51	0	48	0	1.00
480542--480594	25	2.1	25	85	0	70	35	15	7	41	1.75
480949--481444	163	3.1	160	86	5	655	30	14	18	36	1.91
487485--488184	166	4.2	166	89	2	1025	33	15	25	26	1.95
487514--488184	331	2.0	334	89	3	1032	32	15	25	26	1.95
493174--493213	16	2.6	16	84	4	55	5	27	30	37	1.78
494475--494512	17	2.4	16	86	8	51	21	28	15	34	1.94
502665--502775	53	2.0	54	84	6	143	38	17	11	32	1.86
503030--503079	23	2.2	23	88	0	73	70	16	0	12	1.15
503066--503094	1	29.0	1	100	0	58	100	0	0	0	0.00
509782--509838	2	28.5	2	100	0	114	0	50	0	49	1.00
509848--509887	14	2.9	14	84	0	53	50	45	5	0	1.23
510125--510155	16	1.9	16	93	0	53	22	25	19	32	1.97
510318--510352	17	2.1	17	100	0	70	37	11	11	40	1.77
515890--515925	12	3.0	12	91	0	63	0	0	11	88	0.50
515890--515924	6	6.0	6	90	3	54	0	0	11	88	0.51
516630--516664	18	1.9	18	94	0	61	57	11	0	31	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
523205--523244	11	3.6	11	83	10	55	40	15	2	42	1.60
523586--523648	30	2.1	30	87	0	90	38	4	26	30	1.77
556433--556799	177	2.1	176	86	4	506	23	16	26	33	1.96
557718--557777	15	4.3	15	67	26	51	36	10	8	45	1.68
558257--558290	16	2.1	16	94	0	59	38	14	20	26	1.91
560345--560464	46	2.6	46	96	1	215	41	10	15	32	1.81
563731--563783	2	26.5	2	100	0	106	50	0	49	0	1.00
567455--567494	21	1.9	20	95	5	71	27	15	17	40	1.89
570260--570285	12	2.2	12	100	0	52	0	38	26	34	1.57
570435--570775	166	2.0	167	88	1	495	37	18	15	28	1.92
572157--572564	165	2.5	165	80	4	439	37	15	17	29	1.91
573302--573343	2	21.0	2	100	0	84	0	50	0	50	1.00
573301--573349	10	4.5	11	87	12	66	2	51	0	46	1.12
574506--574539	11	3.1	11	88	12	52	52	8	26	11	1.67
576671--576701	15	2.0	16	93	6	55	45	19	3	32	1.66
576942--576987	24	1.9	24	86	0	65	34	8	15	41	1.78
577225--577541	65	4.9	65	88	1	431	37	31	9	21	1.86
577887--577920	16	2.1	16	100	0	68	5	17	20	55	1.62
577892--577933	16	2.6	16	88	3	57	9	23	16	50	1.75
579430--579466	16	2.3	16	90	0	56	35	29	13	21	1.92
582140--582205	2	33.5	2	96	3	125	50	0	50	0	1.00
583654--583730	37	1.9	39	85	12	104	25	12	29	31	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
583801--583964	67	2.4	67	84	2	204	35	15	17	31	1.91
587631--587672	18	2.3	18	91	0	66	40	11	14	33	1.82
588211--588252	18	2.3	18	83	0	57	35	14	11	38	1.83
589938--590689	2	355.5	2	71	10	390	42	7	43	6	1.58
589934--589997	31	2.1	31	93	0	110	43	12	35	7	1.71
589985--590660	13	56.8	13	67	25	117	41	8	44	6	1.60
589979--590637	19	35.6	19	77	15	463	41	8	44	6	1.60
589999--590672	25	29.4	24	71	23	235	41	8	44	6	1.59
591000--591146	75	2.0	75	100	0	294	30	13	17	38	1.89
592374--592415	21	2.0	22	85	4	59	26	16	23	33	1.96
598051--598150	2	50.5	2	97	2	193	0	50	0	50	1.00
600020--600063	2	22.0	2	100	0	88	0	50	0	50	1.00
601482--601538	2	28.5	2	92	0	96	49	3	47	0	1.18
604209--604358	79	1.9	80	91	1	248	25	15	12	47	1.79
607701--607726	1	26.0	1	100	0	52	100	0	0	0	0.00
610918--611253	174	1.9	171	93	1	573	30	21	18	29	1.97
615187--615373	35	5.5	34	77	10	123	24	28	23	23	2.00
615219--615369	35	4.4	35	82	8	159	25	28	22	23	1.99
616335--616372	17	2.2	16	90	9	58	2	0	10	86	0.66
616331--616372	16	2.6	16	88	7	59	4	0	9	85	0.72
617184--617517	141	2.4	141	86	0	461	43	14	17	24	1.86
617136--617610	47	10.1	47	74	7	286	44	14	16	23	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
617184--617570	141	2.7	140	79	6	431	43	14	17	24	1.87
620089--620344	28	9.1	28	80	5	275	31	13	16	37	1.88
620155--620196	14	2.9	16	73	26	56	30	14	16	38	1.89
620552--620599	25	1.9	25	82	0	60	18	20	20	39	1.92
620989--621053	2	34.5	2	82	11	75	55	0	44	0	0.99
620989--621043	20	2.8	20	100	0	110	54	0	45	0	0.99
620986--621059	10	7.4	10	73	22	66	58	0	41	0	0.98
629626--629651	3	8.7	3	100	0	52	69	0	0	30	0.89
633976--634309	161	2.1	161	93	1	562	38	21	11	28	1.89
641456--643519	28	73.8	28	79	4	1998	24	14	21	39	1.91
646162--646197	19	1.9	19	88	5	56	55	13	16	13	1.69
646250--646977	168	4.4	167	86	4	907	30	20	17	31	1.96
646250--647066	334	2.5	332	83	5	866	31	19	17	31	1.95
647724--647879	29	5.4	29	93	0	249	36	16	14	33	1.88
647885--648488	29	21.0	29	83	8	709	38	17	11	31	1.87
647812--648098	73	3.9	73	79	8	359	38	18	12	30	1.88
647972--648046	15	5.1	15	71	26	61	36	20	18	25	1.95
647943--648075	44	3.0	44	95	0	230	37	19	13	29	1.90
647841--648133	146	2.0	146	91	0	478	39	17	12	30	1.87
648176--648206	15	2.1	15	100	0	62	35	19	25	19	1.95
654958--654982	2	12.5	2	100	0	50	48	0	0	52	1.00
663339--663373	18	1.9	18	88	11	54	51	22	11	14	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
672140--672178	17	2.3	17	95	0	69	28	23	17	30	1.97
683300--683334	18	1.9	18	100	0	70	34	11	11	42	1.77
683545--683573	14	2.1	14	100	0	58	58	0	0	41	0.98
685949--685986	18	2.1	18	95	0	67	26	21	15	36	1.93
709079--709144	2	33.0	2	100	0	132	0	50	0	50	1.00
709446--709544	49	2.0	48	96	1	180	26	28	12	32	1.92
714555--714619	2	32.5	2	100	0	130	50	0	49	0	1.00
718311--719081	140	5.5	140	82	6	802	38	14	14	33	1.86
718705--719379	142	4.8	141	75	6	478	39	14	13	32	1.85
718249--719529	28	45.6	28	74	7	718	37	14	14	32	1.87
726748--726796	16	3.1	16	100	0	98	42	24	26	6	1.78
727176--727237	31	2.0	31	96	0	115	22	24	25	27	2.00
727245--727294	16	3.1	16	94	0	91	6	22	26	46	1.74
727615--727676	2	31.0	2	100	0	124	0	50	0	50	1.00
736468--736651	22	9.0	21	60	12	69	36	15	17	29	1.91
736458--736912	41	11.1	41	94	0	802	35	17	18	28	1.93
743025--743155	47	2.8	47	98	0	253	38	21	8	32	1.83
767380--767407	1	28.0	1	100	0	56	0	0	0	100	0.00
769257--769302	2	23.0	2	100	0	92	50	0	50	0	1.00
776030--776067	16	2.2	17	86	9	51	65	10	5	18	1.41
785618--785669	1	52.0	1	100	0	104	100	0	0	0	0.00
797821--797855	1	35.0	1	88	0	52	5	0	0	94	0.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
797814--797855	15	2.9	15	93	6	70	9	0	0	90	0.45
798107--798131	2	12.5	2	100	0	50	52	0	0	48	1.00
799138--799216	19	3.9	19	65	18	52	35	18	12	32	1.89
808420--808593	38	4.4	38	75	16	131	41	17	12	27	1.86
808487--808592	19	5.6	19	80	8	117	42	19	10	27	1.84
808401--808551	82	1.9	81	87	4	223	41	17	14	25	1.88
808848--809257	48	8.2	48	84	9	525	25	11	24	39	1.88
809449--809492	2	22.0	2	100	0	88	0	50	0	50	1.00
810725--811362	46	13.8	46	82	5	705	25	18	18	37	1.94
815343--815382	12	3.3	12	100	0	80	60	0	17	22	1.37

Tables:   1   2   3   4   5