genome.fa.s4114.2.7.7.80.10.50.1000.3.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: VEPZ01004114.1 Hibiscus syriacus cultivar Beakdansim tig00009003_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1048340

Tables:   1   2   3   4   5   

This is table  3  of  5  ( 517 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)
562353--562950	268	2.2	270	88	2	857	35	23	15	25	1.94
563790--563823	17	2.0	17	100	0	68	29	0	0	70	0.87
563904--563965	16	3.6	15	72	27	52	12	6	4	75	1.15
563951--563998	17	2.8	17	77	3	51	20	4	0	75	0.97
566703--566824	41	3.0	41	90	0	199	40	18	18	23	1.91
569226--569274	20	2.5	20	96	0	89	46	12	6	34	1.66
571339--571446	4	27.5	4	67	12	55	66	4	3	25	1.27
571341--571415	27	3.0	25	78	16	93	66	5	4	24	1.30
571339--571418	22	3.4	22	80	14	88	66	5	3	25	1.29
571391--571463	30	2.4	30	81	4	83	65	4	2	27	1.24
574181--574223	23	1.9	22	90	4	68	72	4	0	23	1.04
577471--577496	13	2.0	13	100	0	52	38	7	23	30	1.83
590846--590977	34	3.9	34	97	0	246	14	30	0	55	1.40
592603--592715	32	3.6	32	92	1	174	34	15	19	30	1.93
598465--598516	26	2.0	26	84	0	68	28	21	17	32	1.96
598513--598728	85	2.6	83	78	8	249	33	19	14	31	1.92
602487--602763	138	2.0	138	99	0	545	43	19	12	23	1.86
604295--604333	18	2.2	18	100	0	78	33	17	15	33	1.92
610942--611042	28	3.5	29	85	10	136	38	11	9	39	1.75
611339--611383	22	2.0	23	95	4	83	51	31	17	0	1.46
613720--614149	221	1.9	221	88	0	646	36	27	12	23	1.91
614561--614659	33	3.2	28	72	25	74	52	3	0	44	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
615172--615242	21	3.6	20	73	14	60	23	4	2	69	1.20
615171--615232	21	3.0	20	83	9	70	24	4	3	67	1.25
615171--615232	11	5.9	10	83	9	70	24	4	3	67	1.25
619664--620109	222	2.0	222	90	0	694	35	26	14	23	1.94
621745--621774	14	2.1	14	93	0	51	63	0	0	36	0.95
621807--621858	22	2.4	21	84	9	68	46	1	0	51	1.12
621806--621859	23	2.3	23	87	6	74	48	1	0	50	1.11
627278--627345	35	2.0	35	91	2	111	41	2	10	45	1.53
627288--627469	47	4.0	47	72	16	159	40	3	13	42	1.63
627324--627357	12	2.8	12	95	0	59	41	5	8	44	1.60
627348--627407	23	2.6	23	91	0	102	40	3	15	41	1.63
627389--627451	16	4.2	16	82	15	89	34	6	19	39	1.77
627394--627447	28	1.9	28	96	0	99	37	7	16	38	1.77
627540--627623	19	4.6	17	76	12	71	30	0	2	66	1.04
627550--627618	33	2.2	28	85	14	84	31	0	1	66	1.00
627550--627621	26	2.7	27	85	10	94	31	0	1	66	1.00
635936--635981	20	2.3	21	82	10	53	34	21	15	28	1.94
636564--636624	23	2.7	23	94	0	113	44	4	11	39	1.62
636611--636637	13	2.1	13	100	0	54	44	7	7	40	1.60
636695--636748	26	2.1	25	83	10	65	33	1	0	64	1.04
636694--636787	12	8.6	11	72	17	63	31	1	2	64	1.12
639460--639500	4	10.2	4	84	10	57	70	2	0	26	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
639632--639661	9	3.2	9	95	4	51	86	0	0	13	0.57
640870--641026	23	6.8	22	73	11	102	64	0	3	32	1.09
640882--641020	30	4.6	29	70	22	92	64	0	2	32	1.08
640897--640957	17	3.8	16	79	18	56	62	0	1	36	1.05
640884--641111	52	4.3	53	73	14	143	59	0	3	36	1.19
640892--641105	72	3.0	69	78	14	193	59	0	3	36	1.20
641034--641105	21	3.6	21	68	19	55	52	0	4	43	1.20
640911--641239	48	6.5	52	68	23	170	55	2	2	39	1.28
640974--641231	2	141.5	2	64	25	110	53	3	1	41	1.28
642078--642143	21	3.0	21	71	20	55	36	22	19	21	1.95
642813--642862	20	2.5	20	84	15	68	32	28	12	28	1.92
643499--643563	31	2.1	31	94	0	112	41	30	3	24	1.70
657271--657313	21	2.1	21	91	8	72	9	27	0	62	1.25
659981--660025	19	2.4	19	84	0	54	31	8	6	53	1.58
660341--660380	14	2.9	14	92	3	64	27	35	2	35	1.71
661013--661061	16	2.9	16	84	6	53	16	20	2	61	1.44
664478--664517	14	2.9	14	92	3	64	27	35	2	35	1.71
669459--669517	23	2.5	22	84	10	82	62	10	1	25	1.36
674588--674641	12	4.3	13	75	13	51	40	0	5	53	1.24
676098--676204	49	2.2	47	78	16	121	42	8	19	29	1.81
679099--679165	17	3.8	18	75	14	59	23	5	2	67	1.27
679132--679171	18	2.2	19	95	4	73	20	0	5	75	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
679141--679179	18	2.2	18	86	4	53	23	0	10	66	1.22
686108--686180	13	5.8	12	78	18	51	82	0	13	4	0.81
686108--686180	7	10.3	7	75	8	67	82	0	13	4	0.81
686120--686178	13	4.3	13	79	10	64	84	0	10	5	0.76
686125--686184	18	3.1	20	76	13	72	85	0	8	6	0.76
686111--686180	28	2.4	29	80	4	88	82	0	12	4	0.80
686125--686184	22	2.8	21	87	12	70	85	0	8	6	0.76
686125--686179	15	3.8	15	77	18	62	85	0	9	5	0.74
689652--689693	20	2.2	20	87	8	61	40	4	4	50	1.45
689636--689697	32	2.0	31	84	9	81	38	4	6	50	1.50
693692--693731	20	2.1	19	90	4	62	35	22	0	42	1.54
697143--697270	66	1.9	66	93	0	220	39	4	3	52	1.41
702913--702999	39	2.2	40	78	10	99	47	1	16	35	1.54
703004--703042	17	2.4	17	87	12	55	71	0	0	28	0.86
703004--703046	18	2.3	18	84	11	52	69	0	0	30	0.88
704224--704272	20	2.5	20	96	0	89	42	8	28	20	1.80
705064--705120	27	2.1	27	93	0	96	29	12	43	14	1.81
705146--705198	23	2.3	23	100	0	106	18	22	16	41	1.90
706693--706757	25	2.6	25	87	9	96	43	21	10	24	1.84
708865--709000	65	2.1	64	86	4	184	27	21	18	32	1.97
708865--709020	65	2.4	64	82	5	172	28	20	18	32	1.96
714770--714873	44	2.4	44	81	0	127	30	21	19	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
718616--718665	20	2.5	20	83	6	66	32	18	16	34	1.92
728506--728585	42	1.9	42	86	0	115	26	18	20	35	1.95
728199--728822	238	2.6	238	88	1	941	32	16	17	33	1.92
728622--729032	211	2.0	210	89	3	641	33	13	17	36	1.89
732901--732938	19	2.0	20	85	15	53	5	34	0	60	1.19
733907--733970	21	3.0	21	88	4	101	23	26	23	26	2.00
734466--734502	11	3.4	11	92	0	65	29	18	27	24	1.98
734494--734539	22	2.1	22	95	0	83	19	23	32	23	1.97
734571--734619	13	3.8	13	82	12	66	22	18	28	30	1.97
734935--734983	25	2.0	23	81	14	55	32	2	18	46	1.60
739798--739835	19	2.0	20	85	15	53	7	31	0	60	1.25
740808--740870	21	3.0	21	81	9	74	25	23	23	26	2.00
740807--740873	22	3.1	22	86	2	82	25	22	22	29	1.99
741366--741402	11	3.4	11	88	0	56	29	16	27	27	1.97
741394--741437	22	2.0	22	95	0	79	20	18	34	27	1.96
741471--741507	13	2.8	13	100	0	74	24	16	29	29	1.96
742570--742617	16	2.9	16	93	3	78	14	14	0	70	1.16
743187--743256	30	2.3	31	80	5	79	34	17	8	40	1.80
743307--743688	182	2.1	178	89	5	572	41	3	8	46	1.53
745376--745408	17	1.9	17	93	0	57	6	12	9	72	1.26
746026--746071	20	2.4	18	83	13	65	10	13	6	69	1.35
749471--750155	165	4.2	164	88	3	813	29	25	21	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
749669--750164	250	2.0	246	94	2	868	29	26	21	22	1.99
750751--751010	37	7.3	35	75	12	215	43	3	6	47	1.44
750751--751010	36	7.3	35	77	11	242	43	3	6	47	1.44
751070--751209	70	2.0	73	86	9	200	49	2	5	42	1.39
750931--751195	36	7.6	33	66	24	109	47	3	3	45	1.39
751205--751287	12	7.4	11	71	17	55	19	3	2	74	1.07
751205--751271	36	1.9	33	82	14	82	20	4	2	71	1.17
752655--752679	12	2.1	12	100	0	50	40	0	0	60	0.97
754244--754294	20	2.5	21	78	18	54	15	11	11	60	1.58
754258--754296	20	2.0	20	89	0	60	17	12	15	53	1.72

Tables:   1   2   3   4   5