genome.fa.s1279.2.7.7.80.10.50.1000.17.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   

This is table  17  of  29  ( 3433 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)
3985417--3985711	30	9.9	29	79	5	239	21	26	9	43	1.82
3985408--3985712	60	5.1	60	77	5	287	20	26	9	43	1.82
3985417--3985676	90	2.9	90	80	0	268	21	26	8	43	1.81
3985408--3985709	90	3.4	89	75	6	263	21	26	9	43	1.82
3986111--3986175	30	2.3	27	78	10	76	46	1	1	50	1.20
3986193--3986244	21	2.5	20	73	11	52	42	0	0	57	0.98
3986287--3986390	30	3.5	29	77	5	102	23	25	7	43	1.80
3986401--3987512	30	37.2	30	72	10	384	22	25	9	43	1.82
3986401--3987512	60	18.6	60	73	9	598	22	25	9	43	1.82
3986510--3987449	90	10.5	90	71	11	500	22	25	8	43	1.82
3988725--3989039	30	10.5	29	74	11	226	22	25	9	42	1.83
3988717--3989039	90	3.6	89	75	7	262	22	25	9	43	1.82
3988948--3989033	31	2.8	31	75	8	86	25	24	6	43	1.79
3989516--3989567	21	2.5	20	73	11	52	42	0	0	57	0.98
3989585--3989684	30	3.3	30	83	2	103	25	22	10	43	1.84
3989762--3989837	28	2.6	28	74	22	68	19	23	10	46	1.81
3989833--3990974	30	38.5	30	69	9	266	22	24	9	44	1.82
3990280--3990387	29	3.7	28	75	18	87	23	22	8	46	1.78
3990277--3990528	59	4.3	59	76	9	171	23	24	7	44	1.79
3990598--3990731	62	2.2	60	81	10	164	19	25	8	46	1.79
3992174--3992492	30	10.6	30	78	6	270	22	24	9	43	1.83
3992173--3992492	90	3.6	90	77	7	301	22	25	9	43	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3992888--3992954	30	2.3	27	80	10	80	46	1	1	50	1.19
3993066--3993140	30	2.5	30	77	0	78	25	21	8	45	1.79
3993282--3993365	30	2.8	30	83	0	105	21	23	10	44	1.84
3993366--3994532	30	39.2	29	70	12	414	21	24	8	44	1.80
3995754--3995858	29	3.6	28	81	14	101	24	24	10	40	1.87
3995723--3996036	30	10.7	29	76	8	244	22	25	9	42	1.84
3996431--3996497	30	2.3	27	80	10	80	46	1	1	50	1.19
3996817--3996900	30	2.8	30	83	0	105	21	23	10	44	1.84
3996684--3997083	186	2.1	187	88	5	574	22	25	9	43	1.82
3996901--3998058	30	39.0	30	70	8	465	22	24	8	44	1.81
3997907--3998059	59	2.5	60	81	7	184	21	26	9	43	1.82
3999257--3999548	59	4.9	60	77	9	226	21	25	9	43	1.83
3999236--3999548	30	10.6	30	76	9	234	21	24	9	43	1.83
3999936--4000002	30	2.3	27	80	10	80	46	1	1	50	1.19
4000114--4000188	30	2.5	30	77	0	78	25	21	8	45	1.79
4000421--4001536	30	37.8	29	70	13	356	22	24	8	44	1.80
4001032--4001329	29	10.3	31	70	14	104	21	25	8	44	1.79
4002727--4003036	29	10.6	30	72	14	177	21	24	10	43	1.83
4002756--4002861	28	3.7	29	80	14	121	24	23	10	41	1.85
4002756--4002861	30	3.7	29	81	12	121	24	23	10	41	1.85
4002727--4002945	57	3.8	57	78	13	193	22	23	10	43	1.83
4003425--4003479	27	1.9	30	89	10	89	40	1	1	56	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4003421--4003486	27	2.3	27	82	7	87	45	1	1	51	1.19
4003541--4003579	20	2.0	20	85	10	53	51	7	0	41	1.31
4003595--4003668	29	2.5	30	77	2	78	25	21	8	44	1.79
4003804--4003886	29	2.8	29	79	3	85	20	24	10	44	1.83
4003685--4004066	190	2.1	183	83	9	474	22	25	9	43	1.83
4004044--4004128	32	2.8	29	77	8	89	21	24	8	45	1.78
4004149--4004274	58	2.2	57	81	8	139	24	23	8	42	1.82
4004374--4004436	29	2.2	29	85	5	83	19	22	7	50	1.72
4004488--4004793	58	5.2	58	71	12	171	21	25	8	45	1.79
4003991--4005033	30	35.6	29	67	16	246	21	24	8	45	1.80
4004857--4005027	58	2.9	58	80	9	150	19	27	9	43	1.81
4006232--4006524	30	9.8	30	75	10	188	21	25	9	43	1.82
4006230--4006524	60	4.9	60	78	7	208	21	25	9	43	1.82
4006237--4006524	90	3.2	90	77	4	251	22	25	9	43	1.82
4007084--4007187	30	3.5	30	78	2	111	23	25	7	44	1.79
4007305--4007912	30	20.4	30	69	12	174	22	25	8	43	1.81
4007305--4008463	60	19.8	60	68	14	276	22	24	9	43	1.82
4007327--4007706	90	4.2	88	75	10	297	23	24	8	43	1.82
4007810--4007885	29	2.6	29	95	0	134	19	25	9	46	1.79
4007752--4007912	88	1.8	88	82	5	209	21	25	8	44	1.81
4008030--4008463	30	14.5	29	71	14	231	21	24	9	44	1.82
4009629--4009947	30	10.7	30	77	6	254	21	25	10	42	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4010407--4010451	18	2.6	17	79	6	54	40	0	0	60	0.97
4010495--4010573	30	2.7	29	76	5	77	25	20	7	46	1.76
4010651--4010717	30	2.3	28	78	9	71	17	22	11	47	1.80
4010659--4010718	30	2.0	30	86	0	84	21	21	11	45	1.84
4010656--4010745	28	3.1	29	78	6	76	21	24	12	42	1.87
4010721--4010795	30	2.5	30	82	0	87	25	24	6	44	1.78
4010580--4010993	193	2.2	191	90	1	641	22	25	9	42	1.83
4010915--4010987	29	2.5	29	77	6	76	30	21	4	43	1.71
4010806--4012503	30	57.0	30	71	7	702	22	24	9	43	1.82
4012776--4013811	525	2.0	513	96	3	1898	38	14	14	32	1.86
4014185--4014533	30	11.7	30	79	7	298	21	24	9	43	1.82
4014171--4014533	90	4.1	88	79	9	337	21	24	9	44	1.82
4014931--4014995	30	2.3	27	78	10	76	46	1	1	50	1.20
4015080--4015154	30	2.5	30	80	0	87	24	20	13	42	1.87
4015105--4015179	30	2.5	30	82	0	87	25	25	8	41	1.82
4015231--4015687	30	15.2	30	68	14	86	23	24	9	42	1.83
4015219--4016296	60	18.2	58	68	13	260	22	24	9	43	1.82
4015327--4016497	30	39.3	30	69	11	396	22	24	9	43	1.82
4016093--4016371	151	1.9	149	80	6	330	19	24	10	45	1.82
4017216--4017363	80	1.9	80	81	2	181	12	29	9	49	1.71
4017699--4018017	30	10.7	30	78	7	265	21	25	9	44	1.82
4018415--4018479	30	2.3	27	78	10	76	46	1	1	50	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4018496--4018547	21	2.5	20	73	11	52	42	0	0	57	0.98
4018565--4018639	30	2.5	30	80	0	87	24	20	13	42	1.87
4018590--4018664	30	2.5	30	82	0	87	25	25	8	41	1.82
4018755--4018838	28	2.9	29	78	5	80	21	22	13	42	1.87
4018704--4019977	30	43.2	30	69	9	289	22	24	9	43	1.82
4020724--4020756	13	2.5	13	100	0	66	6	18	12	63	1.48
4021205--4021500	30	9.9	30	74	12	187	21	24	9	44	1.81
4021205--4021502	60	5.0	59	78	8	209	21	24	9	44	1.81
4021240--4021464	91	2.5	90	80	8	244	22	24	8	44	1.80
4021976--4022027	21	2.5	20	73	11	52	42	0	0	57	0.98
4022070--4022170	30	3.4	30	82	5	116	22	25	7	43	1.80
4022070--4022183	30	3.8	29	81	4	102	21	25	9	43	1.82
4022184--4023328	30	39.0	29	69	13	429	22	25	8	42	1.82
4023037--4023326	121	2.4	120	78	6	282	20	26	9	43	1.82
4024540--4024815	30	9.6	29	72	16	164	21	23	10	44	1.83
4025356--4025421	30	2.2	30	83	0	78	24	27	12	36	1.91
4025494--4026427	30	31.6	29	72	10	522	22	24	9	43	1.83
4025633--4025848	117	1.8	118	85	3	301	22	26	10	39	1.87
4025899--4026115	118	1.8	118	83	6	287	26	23	7	42	1.80
4025599--4026383	208	3.8	206	77	8	605	23	24	8	43	1.82
4026766--4026904	30	4.6	30	77	0	125	21	25	11	41	1.87
4027012--4028133	30	37.6	30	71	9	566	22	24	8	44	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4028867--4028936	13	4.9	14	70	17	54	7	28	14	50	1.69
4029339--4029504	30	5.6	29	82	9	158	20	25	9	44	1.82
4029915--4029963	19	2.6	18	77	6	53	34	2	2	61	1.19
4029976--4030022	15	2.9	16	78	12	51	42	0	0	57	0.98
4029994--4030043	21	2.3	21	79	3	55	46	0	0	54	1.00
4030008--4030044	10	3.3	12	82	17	53	54	0	0	45	1.00
4030059--4030443	30	12.6	30	71	12	194	21	25	8	44	1.80
4030059--4030270	65	3.4	61	79	11	175	20	25	7	46	1.77
4030245--4030403	58	2.7	57	77	10	142	20	25	9	44	1.81
4032125--4032159	12	2.8	12	91	4	52	45	0	14	40	1.45

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29