genome.fa.s9585.2.7.7.80.10.50.1000.19.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: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8285662

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   30   31   32   
          33   34   35   

This is table  19  of  35  ( 4106 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)
3899308--3899359	22	2.3	22	76	3	59	13	11	13	61	1.57
3910013--3910059	4	11.8	4	91	8	78	51	21	0	27	1.48
3910623--3910656	3	11.3	3	100	0	68	67	0	32	0	0.91
3911237--3911281	22	2.0	22	82	0	54	40	13	8	37	1.76
3912259--3912289	16	2.0	16	93	6	55	61	12	6	19	1.53
3912803--3912830	3	9.3	3	100	0	56	64	0	0	35	0.94
3916534--3916740	113	1.8	114	86	7	303	40	22	8	28	1.84
3919080--3919407	98	3.4	98	85	8	487	28	30	13	28	1.94
3919165--3919351	88	2.1	88	95	2	331	26	30	14	28	1.95
3919365--3919431	24	2.8	24	86	0	98	32	29	11	25	1.92
3920651--3920698	24	2.0	24	91	0	78	41	22	18	16	1.90
3920680--3920790	15	7.4	15	69	8	82	44	17	18	19	1.87
3920683--3920799	45	2.6	45	90	0	180	41	17	20	20	1.90
3922674--3922733	26	2.3	26	85	0	84	30	15	13	41	1.85
3922659--3922732	13	5.7	13	72	0	58	31	14	10	43	1.80
3924083--3924132	26	1.9	26	95	0	91	30	30	6	34	1.81
3927611--3927653	22	2.0	22	100	0	86	16	13	18	51	1.77
3932218--3932258	20	2.0	20	86	9	57	60	0	2	36	1.10
3940889--3941014	60	2.2	56	80	9	139	30	22	6	40	1.79
3942935--3943001	27	2.5	27	97	0	125	46	2	16	34	1.62
3947033--3947243	106	2.0	106	96	0	386	44	2	8	45	1.48
3952340--3952368	8	3.6	8	100	0	58	10	0	0	89	0.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3962108--3962222	51	2.3	51	82	0	140	52	7	25	14	1.69
3962119--3962258	51	2.6	53	78	10	131	52	7	24	15	1.68
3964433--3964477	23	2.0	23	86	0	63	26	28	24	20	1.99
3964458--3964753	149	2.0	149	96	0	547	34	19	16	29	1.94
3965573--3965607	18	1.9	18	88	11	54	22	17	5	54	1.64
3966183--3966227	21	2.1	21	87	0	63	15	24	28	31	1.96
3970124--3970205	5	15.2	5	78	14	83	8	20	52	18	1.71
3970117--3970205	22	4.0	22	98	0	169	10	21	50	17	1.75
3970233--3970279	10	4.8	10	86	7	62	25	29	27	17	1.97
3970225--3970299	29	2.5	30	85	12	102	28	28	26	17	1.98
3970206--3970298	19	4.8	19	76	17	75	29	29	25	16	1.96
3970206--3970299	9	9.8	9	76	11	62	28	28	25	17	1.97
3977467--3977548	5	15.2	5	78	14	83	8	20	52	18	1.71
3977460--3977548	22	4.0	22	98	0	169	10	21	50	17	1.75
3977549--3977641	9	9.7	9	77	11	78	30	27	25	16	1.96
3977568--3977642	29	2.5	31	89	8	120	29	26	26	17	1.97
3977549--3977641	19	4.8	19	76	17	75	30	27	25	16	1.96
3979138--3979182	23	2.0	23	86	0	63	26	28	24	20	1.99
3979163--3979458	149	2.0	149	97	0	556	34	19	16	28	1.94
3979788--3979825	18	2.1	18	85	9	51	39	23	0	36	1.55
3980270--3980304	18	1.9	18	88	11	54	22	17	5	54	1.64
3981638--3981680	2	21.5	2	100	0	86	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)
3982449--3982512	18	3.6	18	95	0	119	40	17	29	12	1.86
4001161--4001244	33	2.5	33	92	0	141	21	25	16	36	1.94
4001354--4001395	21	2.0	22	85	4	59	45	0	7	47	1.30
4009459--4009486	2	14.0	2	100	0	56	50	0	0	50	1.00
4011225--4011254	2	15.0	2	100	0	60	50	0	0	50	1.00
4011629--4011670	2	21.0	2	100	0	84	50	0	0	50	1.00
4028472--4028535	22	2.9	22	76	2	65	56	14	14	15	1.68
4030198--4030237	21	1.9	21	94	0	71	37	7	20	35	1.81
4035086--4035147	3	20.0	3	80	6	70	38	0	1	59	1.07
4035080--4035125	15	3.1	15	84	6	58	39	0	2	58	1.10
4037278--4037329	20	2.6	21	76	11	56	26	7	0	65	1.20
4044281--4044566	82	3.5	82	97	0	545	27	12	22	37	1.90
4047099--4047153	22	2.5	22	90	0	92	34	10	12	41	1.78
4047665--4048384	76	9.5	76	98	0	1341	22	21	20	35	1.96
4048512--4048573	3	20.0	3	80	6	70	38	0	1	59	1.07
4048506--4048551	15	3.1	15	84	6	58	39	0	2	58	1.10
4066824--4067032	106	2.0	106	98	0	400	17	29	20	32	1.95
4076573--4076925	175	2.0	176	99	0	699	40	20	11	26	1.87
4082759--4082799	15	2.9	15	75	24	52	17	2	24	56	1.53
4092710--4092741	12	2.7	12	95	0	55	9	15	28	46	1.77
4103905--4103946	2	21.0	2	95	0	75	47	0	0	52	1.00
4106770--4106808	15	2.6	16	84	12	55	64	0	2	33	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4106770--4106809	7	5.4	7	82	11	53	65	0	2	32	1.06
4107803--4107871	14	4.3	15	70	17	50	31	0	4	63	1.14
4107798--4107873	34	2.2	34	82	13	93	31	0	3	64	1.12
4107831--4107909	34	2.4	34	81	12	92	37	1	1	59	1.14
4107821--4107909	34	2.7	32	77	10	90	38	1	2	58	1.18
4108049--4108102	17	3.2	17	72	0	54	31	0	3	64	1.11
4109684--4109777	21	4.5	21	92	5	145	18	34	27	20	1.95
4110300--4110396	33	2.9	34	85	3	133	55	4	3	37	1.35
4110298--4110403	34	3.2	33	82	8	133	54	4	2	37	1.36
4110796--4111552	128	5.9	128	96	0	1363	31	19	25	23	1.98
4111623--4111663	8	5.2	8	82	5	57	36	29	0	34	1.58
4127811--4127863	23	2.2	24	83	3	63	37	3	7	50	1.49
4127829--4127876	25	2.0	24	87	4	69	41	0	8	50	1.33
4131096--4131138	13	3.3	13	73	0	50	46	2	13	37	1.57
4139934--4139974	17	2.4	17	87	0	64	0	17	46	36	1.48
4139934--4139981	6	8.3	6	77	9	55	0	16	45	37	1.48
4139934--4139981	11	4.2	12	81	7	55	0	16	45	37	1.48
4168160--4168241	29	2.8	29	76	10	78	31	23	4	40	1.76
4168078--4168241	59	2.8	60	81	7	181	30	21	6	42	1.77
4168150--4168235	30	3.0	28	69	14	75	30	23	5	40	1.78
4178388--4178413	3	8.7	3	100	0	52	0	30	0	69	0.89
4188332--4188558	37	6.1	37	79	12	184	45	4	5	44	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4188523--4188584	26	2.4	26	89	5	90	41	1	6	50	1.38
4188487--4188628	63	2.2	63	85	9	180	44	1	6	47	1.37
4188626--4188692	6	11.5	6	81	9	52	22	2	1	73	1.06
4188626--4188692	13	5.2	13	74	15	59	22	2	1	73	1.06
4188626--4188680	9	6.0	10	76	21	50	23	0	1	74	0.91
4188626--4188662	16	2.4	15	86	8	56	24	0	0	75	0.80
4189780--4189805	12	2.2	12	100	0	52	7	26	0	65	1.20
4191481--4191526	19	2.4	19	96	0	83	10	13	10	65	1.48
4192233--4192329	48	2.0	48	100	0	194	26	28	22	21	1.99
4194895--4196271	84	16.4	84	83	3	1722	30	25	20	24	1.98
4194969--4196271	252	5.2	252	97	0	2382	30	25	19	24	1.98
4196995--4197221	37	6.1	37	79	12	184	45	4	5	44	1.47
4197185--4197247	26	2.4	26	84	5	83	44	1	4	49	1.33
4197192--4197253	28	2.3	27	82	2	79	50	1	3	45	1.27
4197289--4197355	6	11.5	6	81	9	52	22	2	1	73	1.06
4197289--4197355	13	5.2	13	74	15	59	22	2	1	73	1.06
4197289--4197343	9	6.0	10	76	21	50	23	0	1	74	0.91
4197289--4197325	16	2.4	15	86	8	56	24	0	0	75	0.80
4198637--4198676	20	2.0	20	85	0	53	15	17	0	67	1.23
4198804--4198828	12	2.1	12	100	0	50	40	0	0	60	0.97
4215069--4215133	23	2.8	24	86	4	89	21	20	20	38	1.94
4221780--4221836	20	2.9	20	84	2	71	54	1	12	31	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4223231--4223270	21	1.9	21	85	10	55	72	5	0	22	1.04
4225472--4225509	2	20.0	2	89	10	62	50	0	0	50	1.00
4227927--4227954	2	14.0	2	100	0	56	0	50	0	50	1.00
4229295--4229372	28	2.9	28	92	5	126	28	34	2	34	1.71
4229793--4229843	10	5.1	10	90	0	57	49	7	0	43	1.32
4229800--4229843	2	22.0	2	90	0	70	50	4	0	45	1.22
4249086--4249165	34	2.4	33	87	6	115	21	27	30	21	1.98
4249280--4249321	21	2.0	21	100	0	84	23	19	28	28	1.98
4250945--4251024	40	2.0	40	100	0	160	32	15	0	52	1.43
4251438--4251466	13	2.2	13	100	0	58	62	6	0	31	1.22

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   30   31   32   
          33   34   35