oyster.v9_M.fa.s56.2.7.7.80.10.50.500.2.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: scaffold241
Parameters: 2 7 7 80 10 50 500
Length:  1040028

Tables:   1   2   3   

This is table  2  of  3  ( 317 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)
440634--440760	47	2.7	47	90	2	182	33	17	25	24	1.96
445451--445496	2	23.0	2	100	0	92	50	0	50	0	1.00
465675--465706	16	2.0	16	93	0	55	43	15	12	28	1.83
483538--483590	2	26.5	2	100	0	106	0	49	0	50	1.00
497614--497798	102	1.8	102	100	0	370	34	16	14	35	1.88
506385--506502	29	3.9	31	87	6	172	20	32	10	37	1.86
506385--506501	60	2.0	58	89	3	180	20	31	10	37	1.86
507643--507731	31	2.9	31	88	3	128	22	32	10	34	1.88
513484--513566	27	3.1	27	98	0	157	34	45	15	3	1.64
513492--513650	27	5.9	26	80	7	122	36	39	18	5	1.73
513484--513596	54	2.1	54	85	3	147	34	43	17	4	1.69
513553--513665	27	4.2	27	77	1	93	39	36	18	5	1.74
514464--514645	89	2.0	90	88	1	267	33	7	14	44	1.73
522835--522866	16	2.0	16	100	0	64	18	12	18	50	1.78
524736--524765	16	1.9	15	93	6	51	13	26	10	50	1.73
532126--532157	9	3.6	9	91	0	55	12	34	0	53	1.39
532122--532157	18	2.0	18	100	0	72	16	33	0	50	1.46
533205--533310	2	53.0	2	94	0	185	50	2	47	0	1.16
533208--533324	16	7.3	16	90	0	72	51	3	44	0	1.24
533322--533366	4	12.2	4	77	17	53	48	26	24	0	1.51
533322--533371	18	2.8	18	87	0	64	50	28	22	0	1.49
533327--533366	14	2.9	14	100	0	80	50	27	22	0	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
533276--533366	8	12.1	8	75	13	59	50	17	30	1	1.53
535178--535811	18	33.6	18	74	13	337	9	0	47	41	1.39
535135--535811	75	9.2	73	73	12	216	10	0	47	41	1.40
535312--535409	3	32.7	3	80	0	61	7	0	39	53	1.29
535558--535613	27	2.1	27	86	0	76	10	0	50	39	1.37
535609--535652	3	14.7	3	90	0	61	4	0	36	59	1.18
535572--535654	27	2.9	29	85	7	116	9	0	42	48	1.36
535576--535664	30	3.1	28	79	10	99	10	0	42	47	1.37
535657--535748	3	30.7	3	73	16	75	5	0	60	33	1.19
547267--547541	138	2.0	136	95	1	496	30	9	8	52	1.63
552102--552137	18	1.9	19	88	5	56	55	5	13	25	1.60
554228--554364	2	71.5	2	90	8	223	0	51	0	48	1.05
555404--555492	28	3.2	28	62	25	71	40	13	12	33	1.82
555392--555500	55	2.0	55	100	0	218	38	13	12	34	1.83
557065--557297	26	9.0	26	94	0	385	33	30	19	15	1.93
558740--558779	2	20.0	2	100	0	80	50	0	50	0	1.00
560169--560250	30	2.7	29	79	7	74	52	8	4	34	1.53
565588--565727	70	2.0	70	97	0	262	17	14	32	35	1.90
570712--571005	43	6.8	43	94	0	516	32	14	16	35	1.90
571628--571896	21	12.7	21	80	3	270	33	17	13	36	1.89
571628--571896	43	6.3	43	84	2	346	33	17	13	36	1.89
571936--572046	54	2.1	54	100	0	222	42	3	10	43	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
572355--572397	16	2.9	15	82	6	52	27	25	11	34	1.91
575987--576030	2	22.0	2	100	0	88	50	0	50	0	1.00
579552--579614	2	31.5	2	96	0	117	1	49	0	49	1.10
588547--588584	2	19.0	2	100	0	76	0	50	0	50	1.00
589477--589510	15	2.3	15	94	0	59	50	0	0	50	1.00
591431--591474	16	2.8	16	89	0	61	27	20	22	29	1.99
591437--591975	4	134.2	4	74	5	228	32	30	14	23	1.94
591498--591979	20	22.8	20	74	11	340	32	31	13	22	1.93
591756--591827	37	2.0	36	86	2	99	31	31	13	22	1.93
591945--591999	24	2.3	24	80	0	65	34	30	12	21	1.91
601558--601595	2	19.0	2	100	0	76	0	50	0	50	1.00
603135--603181	16	2.9	16	84	6	60	34	12	25	27	1.92
611745--611790	2	23.0	2	100	0	92	50	0	50	0	1.00
615234--615261	1	28.0	1	100	0	56	0	100	0	0	0.00
627923--627957	12	2.8	12	91	4	52	42	2	14	40	1.60
640313--640345	2	16.5	2	100	0	66	0	48	0	51	1.00
640343--640375	3	11.0	3	93	0	57	0	30	3	66	1.06
643811--643849	17	2.3	17	95	0	69	15	23	33	28	1.95
648456--648480	2	12.5	2	100	0	50	0	52	0	48	1.00
653369--653435	21	3.2	21	79	8	91	14	20	22	41	1.89
653344--653458	42	2.7	42	87	2	169	18	21	19	40	1.91
653385--653468	21	4.0	21	81	6	107	19	25	15	40	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
654489--654605	21	5.5	22	77	8	118	17	23	18	40	1.91
654485--654589	42	2.5	42	93	0	183	17	22	20	40	1.92
654471--654605	42	3.2	42	87	0	171	17	24	17	40	1.91
658583--658642	29	2.1	28	82	14	70	25	8	1	65	1.30
659614--659786	86	2.0	87	95	1	312	36	16	9	38	1.80
662792--663615	413	2.0	410	96	0	1531	34	12	15	36	1.86
668225--668262	2	19.0	2	88	0	58	0	52	2	44	1.14
669955--669994	2	20.0	2	100	0	80	50	0	50	0	1.00
676136--676263	23	5.6	23	83	3	141	19	14	15	50	1.79
679718--679875	29	5.1	29	86	13	226	37	12	31	18	1.88
679679--679875	67	3.1	63	85	12	269	37	12	31	18	1.88
679804--679891	38	2.3	38	88	5	133	38	10	31	19	1.85
682499--682629	31	4.2	31	100	0	262	25	23	25	25	2.00
682770--682800	16	1.9	16	93	0	53	29	22	19	29	1.98
683242--683285	24	1.9	23	90	9	72	38	11	9	40	1.73
683272--683340	15	4.9	15	69	16	58	42	13	7	37	1.71
687747--687782	18	2.0	18	100	0	72	33	11	16	38	1.84
691448--691525	39	2.0	39	94	0	138	21	25	15	37	1.93
694589--694624	2	18.0	2	100	0	72	0	50	0	50	1.00
703744--703792	2	24.5	2	100	0	98	0	51	0	48	1.00
708828--708880	26	2.0	26	100	0	106	45	3	11	39	1.58
710566--710600	17	2.1	16	89	5	52	20	37	17	25	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
710657--710691	17	2.1	16	89	5	52	25	17	37	20	1.94
716695--716720	2	13.0	2	100	0	52	50	0	50	0	1.00
725345--725393	17	3.0	17	72	27	52	40	38	8	12	1.72
743754--743788	4	8.8	4	100	0	70	77	0	22	0	0.78
744799--744862	31	2.1	31	96	0	119	42	12	4	40	1.64
744792--744856	31	2.2	28	84	12	94	40	10	6	43	1.65
750380--750408	14	2.1	14	100	0	58	0	6	6	86	0.72
758298--758350	2	26.5	2	100	0	106	49	0	50	0	1.00
760991--761238	121	2.0	121	99	0	487	43	12	16	26	1.84
765552--765611	4	15.0	4	85	0	66	0	35	25	40	1.56
765557--765618	12	5.2	12	92	0	106	0	37	25	37	1.57
765553--765618	16	4.1	16	88	0	96	0	36	25	37	1.57
765561--765618	4	14.5	4	85	0	62	0	37	25	36	1.57
765642--765971	166	2.0	166	89	2	511	29	17	15	37	1.91
771107--771210	30	3.5	30	90	0	163	25	25	25	25	2.00
779708--779742	17	2.1	17	94	0	61	25	5	17	51	1.67
779637--779830	84	2.3	84	92	2	327	32	12	15	39	1.85
779792--779826	17	2.1	17	100	0	70	22	5	17	54	1.64
783256--783287	15	2.1	15	94	0	55	15	40	0	43	1.47
787689--787769	33	2.5	33	93	0	135	28	18	23	29	1.98
789347--789376	15	2.0	15	100	0	60	60	6	13	20	1.55
799271--799307	2	18.5	2	100	0	74	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)
800795--800834	2	20.0	2	94	0	71	0	0	52	47	1.00
804172--804238	30	2.3	30	92	2	109	10	0	71	17	1.13
812169--812202	16	2.1	16	94	0	59	32	11	20	35	1.89
814493--814525	2	17.0	2	93	6	59	0	51	0	48	1.00
814491--814522	15	2.1	15	100	0	64	0	53	0	46	1.00
817815--817843	13	2.2	13	100	0	58	48	6	6	37	1.57
819527--819593	2	33.5	2	100	0	134	0	49	0	50	1.00
826609--826933	177	1.8	178	89	2	519	30	14	17	37	1.90
830298--831044	177	4.2	176	89	1	937	23	17	25	33	1.96
830511--830550	19	2.1	19	90	0	62	22	2	37	37	1.68

Tables:   1   2   3