genome.fa.s54.2.7.7.80.10.50.1000.4.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

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: Scaffold54
Parameters: 2 7 7 80 10 50 1000
Length:  3629595

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  4  of  20  ( 2342 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)
492986--493016	10	3.1	10	95	0	53	51	6	0	41	1.27
493043--493096	27	2.0	27	100	0	108	29	3	22	44	1.70
496338--496366	2	15.0	2	92	7	51	48	0	0	51	1.00
498815--498890	39	2.0	38	94	2	134	32	5	25	36	1.78
504772--504800	2	14.5	2	100	0	58	0	48	0	51	1.00
507249--507443	5	38.6	5	64	21	52	57	1	2	38	1.19
507288--507407	32	3.6	33	78	7	102	55	0	1	41	1.15
507374--507421	20	2.4	20	86	6	62	54	2	0	43	1.12
507411--507453	18	2.5	17	85	7	68	67	0	2	30	1.03
509114--509147	14	2.4	14	95	0	59	52	0	0	47	1.00
509145--509234	24	4.0	24	78	16	86	40	0	0	60	0.97
509150--509224	18	4.4	18	71	15	54	37	0	0	62	0.95
509761--509801	16	2.6	16	84	0	55	48	9	2	39	1.49
509969--510104	27	5.2	26	73	16	77	59	0	0	38	1.08
510042--510099	16	3.9	15	71	24	50	63	1	0	34	1.04
510299--510343	8	5.8	8	76	23	51	62	0	0	37	0.96
510299--510351	21	2.3	24	84	15	69	62	0	0	37	0.96
510946--510989	22	2.0	22	82	4	54	38	2	0	59	1.10
521599--521631	17	2.0	17	94	5	59	66	0	3	30	1.06
523191--523242	22	2.4	22	87	6	70	57	0	0	42	0.98
531795--531836	14	3.1	14	79	6	50	69	2	0	28	1.01
531811--531844	17	2.0	18	88	11	54	73	0	0	26	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
531800--531856	27	2.1	27	83	6	71	68	0	0	31	0.90
532504--532544	5	8.4	5	79	15	50	36	0	0	63	0.95
532620--532673	14	3.7	14	77	22	58	40	1	1	55	1.21
535761--535824	27	2.4	26	80	19	78	51	0	1	46	1.10
536821--536849	14	2.0	15	93	6	51	62	3	0	34	1.12
537208--537269	32	1.9	33	83	9	83	51	0	3	45	1.17
537245--537291	22	2.1	22	84	7	60	42	2	0	55	1.12
541796--541825	3	10.0	3	92	0	51	33	63	0	3	1.11
543185--543228	13	3.5	13	81	15	56	56	0	0	43	0.99
543869--543902	13	2.6	13	90	0	50	44	0	0	55	0.99
544440--544476	15	2.5	15	86	0	56	62	0	2	35	1.10
544440--544518	24	3.1	23	75	18	68	59	0	1	39	1.06
544462--544527	31	2.1	31	81	15	75	57	1	1	39	1.17
544471--544512	18	2.3	19	88	8	61	57	0	0	42	0.99
544471--544538	19	3.8	17	79	16	57	55	1	0	42	1.08
544890--544946	19	3.2	19	74	18	59	57	0	0	42	0.98
544958--544994	19	1.9	19	88	0	56	45	0	0	54	1.00
544957--545001	5	9.6	5	79	11	51	42	0	0	57	0.98
547242--547278	2	18.5	2	100	0	74	0	48	0	51	1.00
547278--547310	2	16.5	2	100	0	66	48	0	0	51	1.00
547538--547582	18	2.5	18	85	0	54	15	2	8	73	1.18
547550--547585	18	2.0	18	100	0	72	11	5	11	72	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
547845--547899	19	2.9	19	78	7	60	56	14	5	23	1.59
557102--557137	2	18.0	2	100	0	72	50	0	0	50	1.00
557305--557332	2	14.0	2	100	0	56	50	0	0	50	1.00
557930--557979	24	2.1	24	88	7	75	68	0	2	30	1.01
557928--557979	12	4.5	11	76	21	52	67	0	1	30	1.02
558764--558839	32	2.3	32	78	14	84	59	0	0	40	0.98
558829--558871	15	2.7	17	86	10	56	58	4	0	37	1.19
558832--558873	20	2.0	21	86	4	59	61	7	0	30	1.22
560727--560760	2	17.0	2	100	0	68	50	0	0	50	1.00
561161--561262	51	2.0	51	92	0	168	18	20	26	34	1.96
561805--561877	24	3.1	23	71	15	60	46	1	6	45	1.38
561867--561910	17	2.5	17	81	7	52	38	0	0	61	0.96
563179--563220	3	14.0	3	100	0	84	66	0	0	33	0.92
563978--564056	19	4.1	19	70	14	72	50	0	0	49	1.00
563981--564056	21	3.9	20	67	23	63	51	0	0	48	1.00
564486--564524	21	1.9	21	84	5	53	53	2	0	43	1.14
565012--565051	2	21.0	2	90	10	66	50	0	0	50	1.00
565185--565253	31	2.3	31	82	7	79	46	1	2	49	1.25
565265--565302	20	2.0	18	90	10	58	31	2	0	65	1.06
569229--569261	11	3.1	11	86	8	50	21	0	15	63	1.30
570455--570492	13	2.8	13	88	11	51	47	0	0	52	1.00
578128--578162	19	1.9	19	88	11	56	62	0	20	17	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
579154--579185	13	2.3	15	89	10	50	50	3	0	46	1.17
580870--580910	2	20.5	2	100	0	82	51	0	0	48	1.00
582434--582475	2	20.0	2	90	9	66	47	2	2	47	1.28
583386--583415	2	15.0	2	100	0	60	50	0	0	50	1.00
584154--584205	25	2.1	25	81	0	59	30	5	3	59	1.39
584638--584673	2	18.0	2	100	0	72	50	0	0	50	1.00
585755--585794	2	20.0	2	100	0	80	50	0	0	50	1.00
591584--591629	22	2.2	20	85	14	58	47	0	2	50	1.13
591602--591639	18	2.0	19	85	10	51	42	2	5	50	1.39
591765--591949	34	5.5	34	88	0	264	25	7	26	40	1.82
592254--592316	19	3.3	19	90	0	90	28	17	19	34	1.94
596382--596566	34	5.5	34	88	0	264	25	7	26	40	1.82
597798--597840	22	2.0	22	95	0	77	53	16	4	25	1.62
598796--598837	2	21.0	2	100	0	84	50	0	0	50	1.00
599000--599030	2	15.5	2	93	0	53	48	3	0	48	1.17
599402--599439	18	2.1	18	100	0	76	44	18	5	31	1.72
600644--600680	2	19.0	2	88	5	58	48	2	0	48	1.15
600906--600934	14	2.1	14	100	0	58	68	0	0	31	0.89
602708--602740	17	1.9	17	88	11	50	0	18	0	81	0.68
603410--603475	24	2.7	26	86	11	86	68	0	0	31	0.90
606078--606113	3	12.0	3	87	0	54	66	5	0	27	1.13
606078--606110	12	2.8	12	100	0	66	66	6	0	27	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
606811--606848	20	1.9	20	88	0	58	13	28	0	57	1.36
608107--608268	60	2.6	61	77	8	166	28	1	7	62	1.33
609016--609074	26	2.3	25	80	8	82	50	0	1	47	1.11
609209--609241	14	2.3	15	94	5	59	60	0	0	39	0.97
609274--609338	33	2.0	33	84	6	87	53	0	1	44	1.09
609292--609368	27	2.7	28	80	9	77	57	0	1	41	1.07
609903--609929	14	1.9	14	100	0	54	51	0	0	48	1.00
612324--612372	26	1.9	26	91	4	82	51	0	0	48	1.00
614509--614583	17	4.2	17	71	18	55	40	4	4	52	1.39
617732--617863	66	2.0	66	93	0	228	39	13	7	39	1.73
617935--617980	18	2.7	18	83	6	51	69	2	0	28	1.00
619171--619300	66	2.0	67	95	1	235	37	13	7	41	1.73
620229--620276	24	2.0	24	95	0	87	52	6	12	29	1.63
620356--620395	16	2.4	16	87	8	53	35	0	0	65	0.93
620559--620592	2	17.0	2	93	0	59	47	0	0	52	1.00
624616--624646	13	2.4	13	100	0	62	32	9	22	35	1.87
631397--631448	22	2.3	23	74	12	54	50	1	0	48	1.12
632606--632657	20	2.6	20	71	17	54	53	1	1	42	1.23
640051--640079	14	2.1	14	100	0	58	13	20	17	48	1.81
642994--643027	2	17.0	2	93	0	59	52	0	47	0	1.00
645421--645479	29	2.0	29	100	0	118	23	32	13	30	1.93
650922--650947	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
651547--651644	44	2.2	43	80	10	110	31	5	3	60	1.34
651575--651657	44	1.9	43	85	2	112	33	4	3	57	1.37
653856--653898	19	2.3	19	88	8	61	67	2	0	30	1.03
653856--653898	9	4.6	9	82	5	50	67	2	0	30	1.03
655210--655262	16	3.3	15	84	5	61	28	0	13	58	1.35
656301--656345	16	2.8	16	86	0	54	28	15	11	44	1.81
656334--656394	16	3.8	17	77	16	67	26	9	14	49	1.75
656317--656395	32	2.5	31	80	17	99	27	11	13	46	1.78
656334--656430	32	3.0	32	76	11	90	30	9	12	47	1.73
658909--658957	21	2.3	21	85	0	62	44	2	4	48	1.33

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20