genome.fa.s8016.2.7.7.80.10.50.1000.18.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: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  5469637

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   

This is table  18  of  25  ( 2971 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)
3936325--3936367	12	3.7	12	84	3	61	34	0	37	27	1.57
3940966--3941020	12	4.7	12	84	2	67	38	0	34	27	1.57
3978830--3978866	19	1.9	19	88	0	56	45	10	16	27	1.80
3978870--3978921	23	2.3	22	90	6	77	44	19	1	34	1.62
3978880--3978942	23	2.7	23	90	0	90	38	19	6	36	1.77
3979333--3979413	38	2.1	38	90	4	128	17	14	19	48	1.82
3979663--3979699	18	2.1	18	89	0	56	51	10	5	32	1.60
3979943--3979993	25	2.0	25	92	0	84	39	19	7	33	1.81
3980253--3980322	21	3.2	22	80	10	72	40	21	5	32	1.77
3980669--3980737	22	3.2	22	81	8	79	40	21	4	33	1.73
3982783--3984120	196	6.9	198	94	3	2313	30	16	15	36	1.90
3982783--3984120	391	3.4	394	94	3	2348	30	16	15	36	1.90
3984239--3984283	17	2.7	17	93	3	74	57	11	2	28	1.45
3986044--3986109	33	2.0	33	87	0	96	24	45	1	28	1.62
3988404--3988441	20	1.9	20	100	0	76	18	15	13	52	1.74
3989553--3989643	2	45.5	2	79	0	83	48	1	50	0	1.08
3989553--3989635	14	5.6	14	91	2	103	48	1	50	0	1.08
3989553--3989639	16	5.6	16	89	5	115	48	1	50	0	1.08
3990828--3990935	37	2.9	37	97	0	198	41	13	10	34	1.79
3991361--3991404	18	2.5	18	85	3	54	29	2	0	68	1.02
3999153--3999196	21	2.1	21	86	0	61	9	36	15	38	1.80
3999782--3999861	31	2.6	31	91	0	124	31	2	35	31	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4001213--4001243	3	10.3	3	92	0	53	29	0	0	70	0.87
4001213--4001257	9	4.8	10	84	15	53	26	2	0	71	0.98
4001871--4002108	5	47.6	5	93	6	412	60	0	0	39	0.97
4020302--4020391	20	4.4	20	79	9	85	31	22	13	33	1.92
4020547--4020583	16	2.4	16	86	8	51	29	5	0	64	1.15
4020397--4021166	379	2.0	384	95	2	1390	29	17	12	39	1.87
4021944--4021968	12	2.1	12	100	0	50	72	0	28	0	0.86
4021960--4021995	14	2.5	15	86	9	56	55	22	16	5	1.62
4022297--4022321	12	2.1	12	100	0	50	72	0	28	0	0.86
4021678--4022384	353	2.0	353	96	0	1288	37	14	20	27	1.92
4024111--4024177	20	3.3	20	87	4	82	20	17	20	40	1.92
4024146--4024244	33	2.9	34	77	3	119	13	19	22	45	1.84
4024100--4024244	34	4.1	34	71	11	112	15	18	21	44	1.87
4024216--4024267	20	2.6	20	90	0	77	17	15	25	42	1.88
4026167--4026255	20	4.5	20	80	1	72	44	21	15	17	1.86
4026591--4026656	22	3.0	22	89	8	107	21	12	39	27	1.88
4026853--4026905	20	2.7	20	96	0	97	18	20	22	37	1.94
4026902--4026947	21	2.2	21	92	0	74	39	17	26	17	1.91
4027230--4027259	14	2.1	14	100	0	60	40	0	6	53	1.27
4027239--4027329	42	2.1	44	81	4	114	32	1	12	53	1.45
4027445--4027483	10	4.1	10	87	6	55	30	0	0	69	0.89
4027637--4027698	22	2.9	21	69	19	56	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4027638--4027695	30	1.9	30	82	6	73	43	0	0	56	0.99
4027704--4027749	19	2.4	19	89	7	67	47	2	0	50	1.13
4027675--4027776	35	2.9	34	76	18	84	48	1	1	48	1.24
4030645--4030733	20	4.4	20	77	2	70	21	10	17	50	1.75
4042877--4042995	35	3.3	36	89	8	172	33	5	17	43	1.71
4047642--4047705	21	3.4	20	66	29	59	31	4	18	45	1.70
4047634--4047755	35	3.4	36	87	6	176	32	4	18	43	1.72
4056499--4056539	8	5.2	8	88	5	66	36	0	26	36	1.57
4056499--4056539	15	2.6	16	84	7	66	36	0	26	36	1.57
4056607--4056851	126	1.9	128	97	1	467	22	24	20	32	1.98
4057231--4057329	31	3.1	30	79	15	110	36	3	5	55	1.37
4059136--4059210	16	4.8	16	74	12	75	62	0	0	37	0.95
4059136--4059210	30	2.6	28	85	10	98	62	0	0	37	0.95
4059137--4059233	16	6.1	16	70	13	65	64	2	0	32	1.05
4059166--4059238	34	2.2	32	80	7	83	67	2	0	30	1.05
4082513--4082618	56	1.9	56	86	0	149	35	10	7	46	1.67
4084542--4084597	27	2.1	26	90	6	85	37	3	5	53	1.41
4085525--4085594	2	35.0	2	100	0	140	50	0	0	50	1.00
4098318--4098356	2	20.0	2	94	5	71	48	0	0	51	1.00
4098447--4098504	29	2.1	28	81	9	66	46	13	15	24	1.82
4098645--4098689	20	2.2	20	96	0	81	35	13	24	26	1.92
4098673--4099017	172	2.0	173	97	1	649	31	19	18	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4104946--4104999	21	2.6	21	75	13	58	29	0	22	48	1.51
4104955--4105013	27	2.1	28	87	3	84	28	0	20	50	1.48
4104955--4105013	7	8.6	7	77	7	50	28	0	20	50	1.48
4109954--4109999	2	23.0	2	100	0	92	50	0	0	50	1.00
4119839--4119907	23	3.0	23	72	8	77	15	23	26	34	1.95
4120062--4120100	20	2.0	20	90	10	62	43	0	12	43	1.42
4122677--4122752	35	2.2	35	85	4	100	46	7	9	36	1.65
4122705--4122752	18	2.8	17	84	6	60	50	6	8	35	1.58
4122722--4122770	18	2.8	17	84	6	53	40	12	14	32	1.83
4129695--4129729	2	17.5	2	100	0	70	48	0	0	51	1.00
4130888--4130952	30	2.2	30	82	0	76	36	23	26	13	1.92
4132193--4132251	25	2.2	26	76	8	66	33	5	5	55	1.43
4132395--4132439	23	2.0	23	90	0	72	51	20	8	20	1.73
4132868--4132907	19	2.1	19	95	0	71	32	25	10	32	1.89
4136984--4137041	10	5.6	10	80	8	62	67	3	6	22	1.30
4136984--4137041	21	2.8	20	76	7	62	67	3	6	22	1.30
4137506--4137557	18	2.9	18	80	2	61	38	0	0	61	0.96
4137605--4137663	21	2.8	21	82	7	66	22	3	3	71	1.16
4137605--4137663	10	5.7	10	80	7	64	22	3	3	71	1.16
4140426--4140452	6	4.5	6	100	0	54	55	0	0	44	0.99
4140537--4140609	38	2.0	36	86	10	103	75	5	4	15	1.14
4144220--4144286	23	3.0	23	84	2	82	46	20	13	19	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4144309--4144412	28	3.7	28	69	14	81	59	17	5	17	1.56
4148228--4148284	17	3.4	17	76	14	55	40	0	1	57	1.09
4148496--4148559	21	3.1	21	75	4	76	17	18	26	37	1.93
4148548--4148663	22	5.5	22	77	12	68	21	15	22	40	1.91
4148569--4148616	19	2.5	19	90	6	71	20	16	16	45	1.85
4148739--4148790	6	8.7	6	100	0	104	32	50	17	0	1.47
4149282--4149321	6	7.2	6	86	8	50	0	15	50	35	1.44
4149416--4149548	22	6.4	21	74	17	77	36	22	18	23	1.95
4149459--4149506	19	2.5	19	100	0	96	41	18	20	18	1.90
4149516--4149592	21	3.7	21	78	3	102	33	27	18	20	1.96
4149519--4149596	41	1.9	41	100	0	156	34	25	19	20	1.96
4152746--4152780	18	1.9	18	88	0	52	25	17	0	57	1.40
4154074--4154128	8	6.5	8	81	12	58	23	25	34	16	1.95
4155186--4155226	15	2.7	15	88	0	55	68	12	2	17	1.31
4155216--4155293	5	15.6	5	75	0	57	67	7	1	23	1.23
4155176--4155281	55	1.9	55	84	0	140	66	10	0	21	1.27
4155175--4155292	55	2.1	55	80	0	137	66	10	2	20	1.32
4158385--4158409	7	3.6	7	100	0	50	32	0	24	44	1.54
4158712--4158834	31	4.0	31	80	8	126	23	15	18	42	1.89
4158712--4158832	62	2.0	61	85	9	165	23	14	19	42	1.88
4162146--4162208	20	2.9	21	81	9	65	15	22	36	25	1.94
4168874--4169076	110	1.8	110	88	2	309	34	18	18	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4173307--4173414	54	2.0	54	100	0	216	35	14	18	31	1.91
4182232--4182402	85	2.0	85	100	0	342	34	12	5	46	1.66
4186261--4186311	26	2.0	26	92	0	84	35	15	9	39	1.81
4187146--4187182	11	3.5	11	79	20	51	10	40	0	48	1.38
4187147--4187189	21	2.0	21	95	0	77	9	39	2	48	1.48
4187927--4187968	20	2.1	20	95	0	75	35	16	14	33	1.89
4188611--4188671	2	30.5	2	100	0	122	50	0	0	49	1.00
4189633--4189667	18	1.9	18	94	0	61	74	0	0	25	0.82
4189706--4189730	12	2.1	12	100	0	50	68	8	0	24	1.16
4190429--4190466	20	1.9	20	100	0	76	36	10	28	23	1.88

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