genome.fa.s9001.2.7.7.80.10.50.1000.19.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: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4740655

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   

This is table  19  of  24  ( 2777 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)
3844733--3844787	14	3.6	14	73	21	56	45	20	23	10	1.82
3844628--3844885	52	4.9	55	82	14	252	46	17	22	14	1.84
3844892--3845007	53	2.2	53	98	1	225	13	24	18	43	1.86
3844910--3845007	19	5.4	19	84	13	143	14	22	17	45	1.84
3845093--3845129	14	2.6	14	91	0	65	45	21	0	32	1.52
3846461--3846517	14	3.7	14	77	20	60	45	22	21	10	1.82
3846442--3846534	33	2.8	33	95	0	168	47	21	20	10	1.80
3846405--3846539	19	7.6	19	76	16	128	45	23	19	11	1.82
3846535--3846663	19	7.3	19	75	17	125	8	17	28	45	1.77
3846535--3846626	33	2.8	33	93	3	150	7	18	28	45	1.76
3846711--3847179	93	5.1	93	98	0	913	46	19	12	22	1.83
3848886--3848974	14	5.6	14	71	23	70	43	23	23	8	1.82
3848878--3848992	33	3.5	33	96	0	212	46	20	22	10	1.81
3848900--3848997	19	5.7	19	70	22	81	43	22	22	11	1.84
3849009--3849065	14	3.7	14	75	20	60	8	24	22	43	1.81
3848993--3849073	33	2.5	33	95	0	144	8	22	22	46	1.78
3849050--3849125	21	3.7	21	83	3	109	11	25	17	46	1.82
3849049--3849126	41	1.9	41	97	0	147	12	25	16	44	1.83
3849205--3849275	33	2.2	33	89	5	108	49	18	21	11	1.78
3849457--3849511	22	2.5	22	81	0	74	20	16	40	23	1.91
3849657--3849871	60	3.6	60	84	0	295	19	19	26	35	1.95
3849658--3849871	20	10.6	20	83	5	261	19	19	26	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3849858--3849940	21	4.0	21	73	6	78	25	16	24	33	1.96
3849838--3849936	42	2.4	43	77	11	100	21	18	23	37	1.94
3851369--3851416	21	2.2	23	85	7	64	56	0	10	33	1.34
3857711--3857843	56	2.4	56	90	0	203	30	15	19	34	1.93
3857716--3857809	28	3.4	28	66	21	79	29	17	20	32	1.95
3862775--3862809	18	1.9	18	94	0	61	25	17	0	57	1.40
3866319--3866354	18	2.0	18	94	0	63	25	16	0	58	1.38
3866882--3866914	2	17.0	2	93	6	59	0	51	0	48	1.00
3867486--3867511	2	13.0	2	100	0	52	50	0	0	50	1.00
3869677--3869751	35	2.1	35	90	0	114	33	29	26	10	1.90
3869828--3869911	24	3.5	24	85	3	125	35	20	16	27	1.94
3876238--3876268	2	15.5	2	100	0	62	48	0	0	51	1.00
3888981--3889029	18	2.7	18	78	9	55	30	2	0	67	1.02
3889452--3889510	25	2.4	24	80	8	57	37	20	22	20	1.95
3889480--3889555	24	3.2	25	78	12	79	39	19	19	21	1.93
3889673--3889751	24	3.3	24	73	7	61	41	17	22	17	1.90
3897229--3897274	18	2.6	18	80	10	51	21	8	4	65	1.38
3903599--3903644	16	2.9	16	96	0	83	36	19	13	30	1.90
3904072--3904117	16	2.9	16	96	0	83	36	19	13	30	1.90
3903406--3904355	473	2.0	473	99	0	1864	40	19	12	27	1.88
3905684--3905722	20	2.0	19	90	5	60	15	33	23	28	1.95
3905766--3905817	18	2.6	21	82	8	65	26	13	25	34	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3905851--3905877	12	2.2	12	100	0	54	25	29	7	37	1.83
3917957--3918005	14	3.4	14	81	10	62	36	14	14	34	1.86
3920367--3920402	4	8.8	4	93	6	63	22	0	0	77	0.76
3924531--3924582	20	2.6	20	87	0	86	46	5	13	34	1.67
3924781--3924850	31	2.2	29	77	20	70	47	0	4	48	1.21
3925012--3925069	23	2.7	22	71	12	59	55	0	1	43	1.10
3925102--3925145	22	2.0	22	90	0	70	50	0	2	47	1.13
3925115--3925183	24	3.0	22	80	16	70	49	1	2	46	1.25
3925380--3925474	42	2.3	42	88	0	136	49	15	16	17	1.80
3927523--3927567	18	2.5	18	85	0	63	22	28	13	35	1.92
3927653--3927780	16	7.4	16	67	23	66	55	8	2	33	1.43
3927683--3927783	18	5.6	19	71	19	83	56	7	0	34	1.35
3928529--3928811	72	4.0	72	84	1	372	40	12	21	25	1.88
3928518--3929344	143	5.9	142	78	8	746	38	11	21	28	1.88
3928751--3928881	57	2.3	56	80	3	145	40	13	20	25	1.89
3928679--3929222	142	4.0	130	79	11	416	37	11	22	28	1.89
3928808--3929256	34	12.5	38	67	12	236	37	10	22	28	1.88
3928808--3929256	72	6.3	72	88	1	625	37	10	22	28	1.88
3928808--3929292	142	3.4	142	85	4	638	37	10	22	29	1.88
3928808--3929300	214	2.3	216	84	4	640	37	10	22	29	1.87
3928808--3929344	72	7.5	72	85	3	622	37	10	21	30	1.87
3929238--3929346	36	3.0	36	71	4	94	38	10	16	34	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3931435--3931476	19	2.2	19	91	8	68	80	2	16	0	0.81
3935643--3935667	10	2.5	10	100	0	50	32	20	16	32	1.94
3935801--3935880	29	2.7	30	90	3	126	40	10	17	32	1.83
3939704--3939733	14	2.1	14	100	0	60	63	6	0	30	1.20
3941631--3941702	14	5.1	14	68	11	58	27	0	29	43	1.56
3941650--3941741	21	4.4	21	72	21	68	23	0	28	47	1.52
3941623--3941695	35	2.1	35	89	5	112	28	0	27	43	1.55
3941635--3941702	28	2.4	27	78	7	82	26	0	29	44	1.55
3942016--3942052	17	2.2	17	95	0	65	24	16	29	29	1.96
3942037--3942101	11	5.6	11	72	22	53	26	26	23	24	2.00
3942031--3942102	23	3.1	23	83	2	99	25	26	23	25	2.00
3943982--3944032	13	3.6	14	77	15	52	25	9	0	64	1.24
3948258--3948300	20	2.2	20	86	0	59	20	18	6	53	1.67
3949873--3949927	20	2.6	21	80	8	58	60	3	12	23	1.49
3952359--3952538	60	3.0	60	87	3	254	38	22	16	22	1.93
3957528--3957554	2	13.5	2	100	0	54	51	0	0	48	1.00
3958425--3958478	28	1.9	28	85	7	74	14	16	22	46	1.84
3958700--3958745	20	2.4	19	81	3	56	43	2	4	50	1.34
3960051--3960105	21	2.7	21	78	10	60	30	14	21	32	1.93
3963648--3963737	34	2.6	35	87	5	139	35	7	13	43	1.73
3963648--3963736	17	5.2	17	81	6	99	35	7	13	42	1.73
3966247--3966297	22	2.3	22	100	0	102	11	7	35	45	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3969487--3969539	22	2.4	22	93	0	88	22	24	26	26	2.00
3972309--3972399	42	2.2	42	95	0	164	24	15	27	32	1.95
3973850--3973909	29	2.2	28	85	11	88	41	5	10	43	1.60
3976128--3976157	14	2.1	14	93	0	51	36	6	33	23	1.81
3979266--3979309	22	2.0	22	91	4	72	25	22	9	43	1.82
3983146--3983207	22	2.8	21	79	18	72	25	3	0	70	1.02
3993974--3994019	3	15.0	3	90	4	74	36	0	0	63	0.95
3998889--3998961	22	3.4	22	73	16	62	19	15	9	56	1.66
4001507--4001585	8	9.4	8	74	19	63	81	2	13	2	0.91
4001523--4001583	14	4.4	14	77	10	63	83	3	11	1	0.83
4001533--4001593	11	5.4	11	77	13	52	81	3	13	1	0.88
4001522--4001577	26	2.2	26	93	6	96	83	3	10	1	0.83
4001507--4001593	34	2.6	34	81	7	97	79	2	16	2	0.94
4001530--4001586	26	2.1	27	87	3	80	85	3	8	1	0.77
4001522--4001586	27	2.7	24	88	11	89	84	3	10	1	0.80
4006197--4006295	22	4.5	22	96	0	180	33	12	13	41	1.81
4006803--4007129	166	2.0	164	93	1	555	35	14	12	37	1.84
4007136--4007617	76	6.3	76	97	0	885	23	19	22	35	1.96
4007748--4007796	3	16.0	3	82	4	62	40	0	0	59	0.98
4007749--4007793	9	4.9	9	89	5	72	42	0	0	57	0.98
4013341--4013403	19	3.6	18	75	16	69	42	0	1	55	1.09
4017535--4017559	6	4.2	6	100	0	50	36	32	0	32	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4017556--4017615	6	10.0	6	100	0	120	33	50	16	0	1.46
4020032--4020093	2	31.0	2	100	0	124	50	0	0	50	1.00
4021220--4021249	13	2.2	14	94	5	53	66	0	16	16	1.25
4021596--4021751	63	2.5	63	78	12	167	35	18	18	26	1.94
4022375--4022434	23	2.6	23	84	5	77	18	28	30	23	1.98
4022872--4022898	2	13.5	2	100	0	54	51	0	0	48	1.00
4031005--4031185	37	4.8	38	80	4	181	46	7	2	43	1.45
4031010--4031175	75	2.2	74	79	3	181	46	7	3	42	1.46
4032578--4032648	29	2.4	31	80	4	92	32	11	5	50	1.61
4032771--4032829	29	2.1	28	90	3	91	47	8	11	32	1.70

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