oyster.v9_M.fa.s27.2.7.7.80.10.50.500.3.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  3  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)
664537--664579	22	2.0	22	100	0	86	32	25	4	37	1.77
668078--668153	2	38.0	2	100	0	152	0	50	0	50	1.00
674287--674427	21	6.7	21	71	6	106	39	17	25	17	1.91
674303--674407	42	2.5	42	90	3	158	39	20	23	17	1.92
674303--674419	42	2.8	42	88	2	146	39	19	23	17	1.92
675426--675559	21	6.4	21	77	6	101	41	17	23	17	1.90
675436--675535	42	2.4	42	93	0	164	43	20	22	15	1.88
678247--678295	21	2.3	22	89	3	73	38	6	8	46	1.58
698900--699298	63	6.3	63	91	1	557	25	21	13	40	1.90
701882--701920	19	2.1	19	100	0	78	64	10	15	10	1.50
703779--703966	21	8.8	21	73	11	112	34	20	16	28	1.94
703771--703902	63	2.1	63	81	5	151	32	20	16	30	1.95
704967--704996	2	15.0	2	100	0	60	50	0	50	0	1.00
705442--705467	11	2.4	11	100	0	52	30	7	19	42	1.79
708646--708778	21	6.3	21	83	6	171	24	19	23	33	1.97
708654--708784	63	2.1	63	89	2	201	22	19	22	36	1.95
713066--713193	14	8.5	14	70	13	76	41	1	25	32	1.65
713073--713136	23	2.8	23	90	0	101	42	0	21	35	1.54
713073--713161	8	11.8	8	65	23	50	41	0	25	32	1.56
713138--713202	32	2.0	32	90	0	103	40	3	27	29	1.71
714109--714155	23	2.1	22	92	4	76	40	0	25	34	1.56
714419--714505	4	21.8	4	100	0	174	25	25	0	49	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
716092--716130	20	1.9	20	100	0	78	2	41	25	30	1.69
716092--716126	4	8.8	4	90	0	52	2	42	25	28	1.69
716138--716678	148	3.7	146	85	5	686	30	19	21	28	1.98
721020--721111	42	2.2	42	80	3	114	25	8	25	41	1.83
721046--721183	63	2.2	63	96	0	249	24	7	23	44	1.80
721142--721275	42	3.4	41	66	24	99	27	5	25	41	1.76
721196--721338	21	7.1	21	84	6	156	23	4	25	46	1.72
721224--721361	21	7.2	18	77	11	107	20	5	27	47	1.71
721287--721361	36	2.1	35	95	2	132	16	5	28	50	1.66
722282--722515	21	11.1	21	78	7	244	43	26	7	22	1.79
722282--722473	41	4.6	42	80	6	228	42	27	7	22	1.80
722282--722466	62	2.9	62	87	4	255	43	27	7	22	1.80
722272--722386	20	5.8	19	84	5	63	43	26	7	21	1.80
722290--722518	107	2.2	108	84	5	299	43	27	7	22	1.79
724252--724640	195	2.0	194	100	0	769	39	12	11	35	1.81
733269--733314	16	3.0	15	84	12	58	30	13	28	28	1.94
736987--737021	17	2.0	18	88	5	54	28	14	25	31	1.95
737062--737104	15	2.6	17	82	14	63	34	11	18	34	1.87
737374--737404	16	1.9	16	100	0	62	45	12	19	22	1.84
747293--747361	2	34.5	2	100	0	138	0	49	0	50	1.00
757725--757756	15	2.1	15	94	0	55	21	31	0	46	1.52
758663--758705	20	2.0	22	91	8	72	32	13	23	30	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
766830--766943	46	2.4	47	79	4	124	21	20	21	35	1.96
767752--767801	2	25.0	2	100	0	100	0	50	0	50	1.00
783622--784219	115	5.3	112	76	9	493	37	17	26	18	1.92
783622--784225	38	16.1	38	77	6	505	37	17	26	18	1.93
786892--786922	16	1.9	16	93	0	53	51	12	3	32	1.56
789714--790619	38	23.5	38	79	8	875	37	16	26	19	1.93
791511--791541	16	1.9	16	93	0	53	51	12	3	32	1.56
796168--796221	8	7.4	8	76	19	64	40	25	33	0	1.56
796168--796214	12	3.9	12	91	0	67	40	25	34	0	1.56
796168--796209	4	10.5	4	84	0	57	42	26	30	0	1.55
798994--799020	14	1.9	14	100	0	54	37	14	3	44	1.63
825419--825518	21	4.8	21	79	11	98	42	7	8	43	1.61
825430--825560	42	3.0	42	74	12	122	39	6	8	45	1.61
825562--825619	21	2.8	21	94	0	98	36	8	8	46	1.65
831476--831519	16	2.8	16	92	0	70	31	6	18	43	1.76
845388--845419	16	2.0	16	100	0	64	87	12	0	0	0.54
846514--846549	18	2.0	18	88	0	54	33	19	36	11	1.87
850590--850620	9	3.3	9	95	4	53	0	22	32	45	1.53
850973--851254	156	1.8	154	82	3	359	33	13	22	30	1.93
852637--852674	18	2.1	18	100	0	76	55	21	5	18	1.62
853184--853230	2	23.5	2	100	0	94	0	48	0	51	1.00
858818--858853	18	2.0	18	94	0	63	52	16	8	22	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
863091--863136	2	23.0	2	100	0	92	0	50	0	50	1.00
871600--871882	21	13.5	21	82	0	314	31	18	12	37	1.88
871596--871882	84	3.4	84	90	0	421	32	18	12	36	1.88
871596--871838	42	5.8	42	94	0	405	32	18	13	36	1.89
873486--873550	21	3.1	21	90	0	103	35	13	18	32	1.90
873580--873609	11	2.7	11	100	0	60	30	10	33	26	1.89
873679--873728	11	4.7	10	82	7	55	28	24	10	38	1.87
873678--873729	22	2.4	22	87	12	81	26	23	9	40	1.85
873678--873782	22	4.8	22	66	9	54	24	23	11	40	1.88
874045--874123	2	39.5	2	92	0	131	2	46	0	50	1.14
874342--874565	112	2.0	112	94	0	394	30	19	19	29	1.97
875140--875168	6	4.8	6	100	0	58	34	48	0	17	1.47
886549--886597	24	2.0	24	100	0	98	24	20	30	24	1.98
888066--888126	2	30.5	2	100	0	122	50	0	49	0	1.00
893779--893950	74	2.3	75	80	6	183	28	12	12	46	1.78
900609--900633	1	25.0	1	100	0	50	0	0	100	0	0.00
911042--911085	2	22.0	2	100	0	88	50	0	50	0	1.00
911427--911467	2	20.5	2	94	0	73	0	51	0	48	1.00
913386--913419	10	3.3	10	84	8	50	47	26	0	26	1.53
913379--913419	21	2.0	21	100	0	82	48	29	0	21	1.50
913379--913413	11	3.3	11	84	8	54	48	31	0	20	1.50
914804--914845	21	2.0	21	86	9	59	54	16	7	21	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
916163--916220	2	29.0	2	96	0	107	0	50	0	48	1.01
916784--916820	1	37.0	1	94	0	65	0	97	0	2	0.18
917577--917902	159	2.0	164	88	5	493	30	14	15	38	1.88
927317--927349	16	2.1	16	94	0	57	0	0	21	78	0.75
930170--930221	26	2.0	26	92	0	86	38	9	13	38	1.77
934088--934131	2	22.0	2	100	0	88	50	50	0	0	1.00
944739--944773	2	17.5	2	87	0	52	45	0	51	2	1.16
947183--947213	2	15.5	2	93	0	53	45	51	0	3	1.17
948057--948171	2	57.5	2	100	0	230	50	0	49	0	1.00
952205--952239	17	2.1	17	100	0	70	28	22	17	31	1.96
966273--966307	15	2.2	16	95	5	63	60	17	0	22	1.37
966329--966417	21	4.2	21	89	2	126	38	11	14	35	1.82
968200--968226	2	13.5	2	100	0	54	48	0	51	0	1.00
970131--970179	2	24.5	2	100	0	98	0	48	0	51	1.00
977403--977454	21	2.5	21	96	0	95	59	13	1	25	1.44
984395--984426	13	2.5	13	94	0	55	21	28	31	18	1.97
996524--996583	27	2.2	27	91	5	95	31	23	25	20	1.98
1002363--1002444	21	3.9	20	75	9	65	64	9	20	4	1.42
1002386--1002439	9	5.0	12	71	28	50	68	9	14	7	1.38
1004912--1004981	22	3.5	22	62	28	55	25	18	20	35	1.95
1004906--1004983	38	2.1	38	100	0	156	23	17	21	37	1.94
1008661--1008718	2	29.0	2	100	0	116	50	0	50	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1013681--1013722	2	21.0	2	100	0	84	0	50	0	50	1.00
1016894--1016936	7	6.7	7	80	20	58	58	9	0	32	1.30
1016901--1016937	12	3.1	12	100	0	74	59	8	0	32	1.27
1020465--1020498	17	2.0	17	100	0	68	41	17	11	29	1.85
1039657--1039694	2	19.0	2	100	0	76	0	50	0	50	1.00
1042900--1042934	2	17.5	2	100	0	70	0	51	0	48	1.00
1043129--1043161	2	16.5	2	100	0	66	0	51	0	48	1.00
1043543--1043608	2	33.0	2	100	0	132	50	0	50	0	1.00
1043656--1043691	15	2.4	15	90	9	56	8	0	88	2	0.59
1044807--1044857	2	25.5	2	91	0	84	0	47	0	52	1.00

Tables:   1   2   3   4