genome.fa.s9579.2.7.7.80.10.50.1000.20.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: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6215474

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  20  of  29  ( 3390 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)
3727928--3727968	8	5.2	8	82	5	57	34	0	29	36	1.58
3728049--3728903	128	6.7	128	94	1	1501	20	23	21	33	1.97
3729299--3729405	34	3.1	34	87	0	151	36	2	4	56	1.35
3729925--3729996	21	3.4	21	87	11	103	22	26	31	19	1.97
3730001--3730044	21	2.1	21	87	4	63	20	9	43	27	1.82
3731604--3731638	17	2.0	18	88	5	54	65	2	0	31	1.07
3733365--3733398	12	2.7	13	81	9	52	64	0	0	35	0.94
3737967--3738026	31	1.9	31	93	0	102	40	6	10	43	1.64
3740081--3740535	228	2.0	232	86	4	634	34	14	33	17	1.90
3754972--3755060	20	4.4	20	76	12	92	33	11	22	32	1.89
3757348--3757407	28	2.1	28	81	6	68	46	3	0	50	1.18
3758854--3758935	29	2.8	29	94	1	137	32	14	9	42	1.79
3763622--3763703	29	2.8	29	94	1	137	32	14	9	42	1.79
3767375--3767421	16	3.1	15	82	8	60	25	2	4	68	1.19
3769490--3769648	64	2.5	64	85	4	196	33	20	18	27	1.96
3770303--3770396	31	3.0	31	90	3	145	19	19	22	39	1.93
3773914--3774072	64	2.5	64	83	4	187	33	19	17	28	1.95
3774727--3774820	31	3.0	31	90	3	145	19	18	24	38	1.93
3778683--3778726	21	2.1	21	86	0	61	47	11	2	38	1.52
3778615--3778749	68	2.0	68	94	0	234	45	9	5	39	1.61
3779795--3779837	16	2.6	16	74	3	50	30	0	2	67	1.03
3790941--3790981	2	21.0	2	95	5	75	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3791257--3791321	2	32.5	2	100	0	130	50	0	0	49	1.00
3796166--3796253	35	2.5	35	96	0	158	47	20	1	30	1.57
3796393--3796459	34	2.0	34	83	13	86	50	1	0	47	1.10
3797619--3797693	35	2.1	35	82	0	96	36	0	18	45	1.50
3798050--3798117	2	34.0	2	100	0	136	50	0	50	0	1.00
3798209--3798277	28	2.5	28	97	0	129	43	15	23	17	1.87
3803371--3803415	11	4.3	11	83	11	67	48	0	0	51	1.00
3803379--3803420	20	2.1	20	100	0	84	45	0	0	54	0.99
3803379--3803438	20	3.0	20	87	7	68	45	3	0	51	1.17
3804023--3804105	32	2.6	32	88	7	98	21	16	16	44	1.86
3805754--3805805	22	2.4	22	87	9	72	15	5	1	76	1.05
3805768--3805841	9	8.6	8	74	22	53	9	6	1	82	0.90
3805774--3805820	10	4.5	10	77	17	51	6	6	2	85	0.82
3805757--3805839	21	3.7	22	79	10	80	10	7	1	80	0.95
3805772--3805841	19	3.9	18	75	16	65	8	7	1	82	0.89
3805954--3806037	9	9.6	9	71	20	54	16	4	2	76	1.07
3805964--3806102	20	6.7	19	69	20	73	14	8	2	74	1.18
3805968--3806105	15	9.1	15	68	19	65	13	9	2	73	1.19
3805949--3806037	26	3.4	26	86	9	119	16	5	2	75	1.10
3805949--3806090	51	2.7	53	78	15	132	14	8	2	74	1.16
3806673--3806722	18	2.8	18	84	3	66	26	30	8	36	1.85
3812581--3812768	60	3.1	60	77	6	175	31	21	6	39	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3812893--3813058	60	2.8	58	82	6	183	42	4	22	30	1.72
3812915--3813058	60	2.4	60	83	5	186	44	4	19	31	1.72
3813296--3813357	2	31.0	2	100	0	124	50	0	0	50	1.00
3813618--3813680	23	2.7	25	79	16	73	49	1	12	36	1.51
3822190--3822219	15	1.9	16	93	6	53	33	0	0	66	0.92
3836580--3836671	23	4.0	23	76	0	85	34	26	19	19	1.96
3836580--3836671	46	2.0	46	89	0	139	34	26	19	19	1.96
3838059--3838198	64	2.2	63	83	6	167	24	17	22	35	1.95
3838123--3838159	19	1.9	19	100	0	74	24	27	16	32	1.96
3838097--3838219	63	1.9	64	83	11	162	24	17	21	35	1.95
3841153--3841214	20	3.0	20	93	4	106	14	29	40	16	1.88
3841153--3841214	21	3.0	21	95	2	108	14	29	40	16	1.88
3843485--3843562	37	2.1	37	82	0	93	23	11	35	29	1.90
3843613--3843666	21	2.5	23	75	19	62	27	3	18	50	1.64
3845104--3845181	2	39.0	2	100	0	156	50	0	0	50	1.00
3845563--3845587	2	12.5	2	100	0	50	48	0	0	52	1.00
3845963--3846007	24	1.9	24	86	13	67	66	2	2	28	1.15
3846088--3846113	3	8.7	3	100	0	52	69	30	0	0	0.89
3850882--3854046	855	3.6	880	79	7	3190	34	15	23	26	1.95
3855281--3856026	252	3.0	251	89	1	1102	34	13	26	25	1.94
3859709--3859738	2	15.0	2	100	0	60	50	0	0	50	1.00
3861873--3861912	18	2.2	18	95	0	71	32	40	17	10	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3863835--3863864	14	2.1	14	93	0	51	60	0	3	36	1.14
3865585--3866728	313	3.7	311	90	4	1677	21	18	16	43	1.88
3871521--3871592	27	2.7	28	76	8	78	58	4	2	34	1.32
3874025--3874079	28	2.0	28	81	0	65	40	18	14	27	1.89
3877758--3877819	2	31.0	2	96	0	115	50	1	0	48	1.10
3877924--3877962	19	2.1	19	85	0	51	64	5	2	28	1.28
3879190--3879666	139	3.5	135	85	3	598	25	18	15	40	1.90
3879190--3879650	137	3.4	137	88	2	606	26	18	15	39	1.90
3879631--3879814	83	2.2	82	88	3	262	27	15	19	38	1.91
3879715--3880116	121	3.3	122	86	3	596	25	17	16	40	1.90
3879566--3879944	204	1.9	205	91	1	627	25	16	17	40	1.91
3880021--3880225	102	2.0	102	94	1	358	26	21	13	37	1.91
3884331--3884465	71	1.9	72	90	1	218	35	16	19	28	1.93
3888385--3888472	46	1.9	46	88	4	133	29	20	10	39	1.85
3889791--3889823	2	16.5	2	100	0	66	51	0	0	48	1.00
3894958--3895027	23	3.0	23	87	0	86	27	28	22	21	1.99
3895044--3895364	103	3.1	103	97	0	597	36	23	13	26	1.92
3899285--3899354	23	3.0	23	85	6	70	27	27	22	22	1.99
3899375--3899691	103	3.1	103	97	0	580	36	24	12	26	1.91
3900869--3900908	21	1.9	21	84	0	53	20	17	30	32	1.95
3907499--3907579	22	3.4	23	76	17	69	51	2	2	43	1.28
3909410--3909556	74	2.0	74	90	0	231	37	25	15	21	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3927478--3927541	31	2.1	31	100	0	128	46	6	18	28	1.73
3928809--3928846	2	19.0	2	100	0	76	50	0	0	50	1.00
3940899--3941227	161	2.0	161	98	0	631	41	16	18	24	1.90
3941813--3942194	40	9.3	40	90	4	584	21	18	23	36	1.95
3941813--3942194	82	4.7	81	90	3	588	21	18	23	36	1.95
3941813--3942194	122	3.1	122	93	1	629	21	18	23	36	1.95
3942907--3943113	21	10.0	21	72	14	162	35	23	20	20	1.96
3942910--3943088	42	4.3	42	92	4	301	36	24	19	20	1.95
3942910--3943113	42	4.9	41	89	5	270	35	24	20	20	1.96
3946729--3946771	21	2.0	21	82	8	52	44	34	0	20	1.52
3947095--3947131	2	18.5	2	100	0	74	48	0	0	51	1.00
3958903--3958935	15	2.1	16	88	5	50	42	0	0	57	0.98
3966848--3966887	21	1.9	21	84	0	53	70	2	0	27	1.01
3966832--3966898	5	13.2	5	87	4	64	61	1	1	35	1.15
3969294--3969327	2	17.0	2	100	0	68	50	0	0	50	1.00
3984129--3984166	20	1.9	20	84	10	51	68	5	15	10	1.36
3990862--3990965	33	2.9	36	83	12	135	16	9	33	40	1.81
3997972--3998040	23	3.0	23	84	0	102	30	26	26	17	1.97
4002962--4003030	23	3.0	23	80	0	93	31	24	26	17	1.97
4006331--4006360	15	2.0	15	93	0	51	43	10	26	20	1.83
4009095--4009188	22	4.4	22	76	8	104	39	24	17	19	1.92
4009117--4009207	41	2.2	41	90	5	139	40	24	18	16	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4010105--4010133	12	2.3	13	94	5	51	68	0	0	31	0.89
4011978--4012281	152	2.0	152	98	0	590	25	14	25	34	1.94
4012130--4012610	170	2.8	170	98	0	917	24	16	25	33	1.96
4012426--4012525	44	2.2	44	84	7	121	26	16	23	35	1.95
4013477--4013503	10	2.7	10	100	0	54	0	11	7	81	0.87
4020201--4020280	39	2.1	39	88	4	117	21	21	27	30	1.98
4022899--4022941	17	2.5	18	85	11	63	81	4	4	9	0.97
4023718--4023746	12	2.3	13	94	5	51	68	0	0	31	0.89
4033379--4033446	23	3.0	23	84	0	91	19	26	25	29	1.98
4043015--4043054	21	1.9	21	89	0	62	25	40	25	10	1.86

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