genome.fa.s9585.2.7.7.80.10.50.1000.17.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: 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  17  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)
3405515--3405642	66	1.9	66	82	0	157	39	16	14	28	1.88
3405710--3405800	32	2.8	32	88	5	121	31	20	15	31	1.94
3406809--3406853	21	2.1	22	83	4	56	6	13	8	71	1.31
3406819--3406857	15	2.6	15	84	8	53	5	10	7	76	1.13
3406825--3406872	22	2.1	22	84	3	60	6	10	8	75	1.20
3408870--3409088	63	3.5	62	89	2	305	42	15	18	22	1.88
3408944--3409052	35	3.3	34	66	31	92	40	15	20	23	1.91
3409070--3409108	12	3.6	12	74	25	50	46	15	20	17	1.84
3409070--3409108	20	2.0	20	100	0	78	46	15	20	17	1.84
3411132--3411192	32	1.9	32	90	6	97	57	9	14	18	1.64
3412053--3412135	6	13.8	6	72	9	53	34	22	2	39	1.68
3412053--3412137	18	4.7	18	76	0	89	35	22	3	38	1.71
3412053--3412137	36	2.4	36	97	0	161	35	22	3	38	1.71
3412373--3412425	12	4.5	12	78	4	54	28	22	15	33	1.94
3412499--3412673	38	4.6	38	94	0	287	24	26	24	24	2.00
3412521--3412665	21	7.5	21	65	25	86	25	25	25	23	2.00
3412542--3412606	17	3.6	17	74	22	69	23	30	26	20	1.98
3412825--3412918	33	2.8	33	98	0	179	27	14	13	43	1.84
3413811--3413864	9	6.0	9	84	0	72	46	20	9	24	1.79
3414066--3414141	30	2.5	30	77	10	84	34	22	9	34	1.86
3415164--3415214	17	2.9	17	75	13	50	45	5	9	39	1.62
3416265--3416297	15	2.2	15	89	10	50	78	3	3	15	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3416677--3416784	29	3.6	30	75	18	84	55	7	17	19	1.65
3416725--3416781	30	1.9	30	89	7	89	54	5	21	19	1.63
3416712--3416788	30	2.6	30	78	13	79	55	5	19	19	1.61
3417890--3417930	17	2.4	17	91	0	64	9	29	34	26	1.88
3418849--3418912	24	2.7	24	85	0	83	21	12	17	48	1.80
3423479--3423543	24	2.7	24	78	0	67	20	15	18	46	1.84
3423648--3423685	6	6.3	6	93	0	67	15	18	18	47	1.83
3432295--3432337	16	2.7	15	79	10	50	39	4	0	55	1.20
3443333--3443897	281	2.0	282	98	0	1105	25	18	22	33	1.96
3450729--3450855	66	1.9	66	95	0	227	28	14	11	45	1.79
3451880--3451933	29	1.9	27	88	7	81	24	20	14	40	1.90
3465025--3465050	13	2.0	13	100	0	52	61	0	15	23	1.33
3478586--3478623	12	2.8	13	88	11	51	36	7	0	55	1.29
3478886--3478946	23	2.7	23	84	0	86	24	26	26	22	2.00
3488008--3488045	12	2.8	13	88	11	51	36	7	0	55	1.29
3488304--3488364	23	2.7	23	84	0	86	24	26	26	22	2.00
3491415--3491450	12	3.0	12	83	0	54	50	16	25	8	1.73
3492704--3492742	18	2.1	19	85	4	53	28	0	10	61	1.28
3492990--3493037	2	24.0	2	100	0	96	50	0	0	50	1.00
3499388--3499415	2	14.0	2	100	0	56	50	0	0	50	1.00
3499697--3499811	15	7.7	14	75	16	83	78	1	18	1	0.93
3499695--3499812	20	5.9	20	74	15	93	77	1	18	1	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3500450--3500513	27	2.3	28	91	2	103	43	29	4	21	1.73
3500987--3501051	34	1.9	35	90	6	107	27	18	10	43	1.83
3501168--3501273	36	3.0	36	69	6	90	36	16	11	35	1.84
3501287--3501734	72	6.5	66	70	17	263	27	20	13	39	1.90
3501402--3501594	36	5.4	36	82	4	178	25	19	14	40	1.90
3501402--3501550	73	2.1	72	83	1	181	23	20	15	40	1.90
3501419--3501562	73	2.0	73	83	1	182	25	19	13	40	1.89
3501364--3501757	207	1.9	207	88	1	592	26	19	14	39	1.90
3501609--3501896	36	7.9	36	86	1	360	24	20	15	39	1.91
3501685--3501749	21	3.4	20	65	30	52	26	27	10	35	1.90
3501402--3501911	109	4.8	108	79	7	506	25	20	14	39	1.90
3501918--3502110	52	3.7	51	80	7	208	28	11	16	43	1.83
3502218--3502308	42	2.2	42	82	4	103	24	21	19	34	1.97
3502235--3502316	42	2.0	42	87	0	119	23	21	20	34	1.97
3502444--3502519	20	3.7	20	77	6	80	26	19	22	31	1.98
3502443--3502585	42	3.4	41	80	5	153	27	20	20	30	1.98
3503572--3504295	136	5.3	135	81	5	728	35	17	20	25	1.95
3503572--3504295	272	2.6	271	81	6	836	35	17	20	25	1.95
3507327--3507384	27	2.1	27	90	0	89	22	13	17	46	1.83
3509936--3509982	21	2.2	22	77	11	53	38	8	2	51	1.45
3512842--3512891	18	2.8	18	96	0	91	16	50	22	12	1.77
3514081--3514149	23	3.0	22	83	8	93	31	26	24	17	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3518080--3518165	24	3.6	24	73	3	66	26	15	13	44	1.84
3522354--3522441	24	3.7	24	81	0	104	25	14	18	42	1.88
3522347--3522451	24	4.4	24	75	7	61	27	13	18	40	1.87
3523020--3523061	21	2.0	21	85	4	57	23	33	23	19	1.97
3523817--3523860	23	1.9	23	85	0	61	34	22	22	20	1.97
3528040--3528091	26	2.0	26	84	0	68	28	13	13	44	1.82
3528269--3528332	11	5.5	12	77	7	69	53	9	12	25	1.68
3528681--3528716	15	2.3	16	90	4	56	19	8	0	72	1.10
3528796--3528860	22	3.0	22	100	0	130	36	16	4	41	1.70
3528841--3528893	26	2.1	26	86	6	74	41	11	1	45	1.51
3534300--3534393	3	30.0	3	75	12	73	34	5	2	58	1.32
3534296--3534382	16	5.2	17	77	9	81	34	6	1	57	1.33
3534300--3534393	10	10.0	9	74	12	73	34	5	2	58	1.32
3534397--3534424	2	14.0	2	100	0	56	50	0	0	50	1.00
3536010--3536052	5	8.6	5	100	0	86	0	81	0	18	0.69
3543466--3543512	23	2.1	23	84	7	62	51	0	0	48	1.00
3543466--3543528	23	2.8	22	77	13	58	47	0	3	49	1.17
3546533--3546705	94	1.8	94	95	2	312	31	25	17	26	1.97
3547557--3547623	20	3.7	18	75	19	59	31	17	25	25	1.97
3547555--3547624	35	2.0	35	86	5	97	30	17	27	25	1.97
3550040--3550098	27	2.3	27	91	5	95	37	11	20	30	1.89
3550049--3550107	27	2.2	27	84	0	73	38	16	16	27	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3551276--3551384	24	4.5	24	82	2	121	18	11	17	52	1.74
3551290--3551370	12	6.8	12	76	5	74	18	13	18	49	1.79
3552342--3552421	21	3.8	21	78	6	99	25	15	21	38	1.92
3552332--3552428	42	2.3	42	85	0	131	23	17	23	35	1.96
3552690--3552736	23	2.0	23	83	0	58	40	4	17	38	1.69
3557736--3557818	14	6.4	13	68	18	57	43	0	3	53	1.18
3557716--3557878	35	4.7	35	67	15	108	39	1	1	57	1.17
3557687--3557826	65	2.2	65	88	6	212	42	0	2	55	1.17
3557709--3557838	64	2.1	61	85	9	174	43	1	2	53	1.23
3558371--3558428	30	1.9	30	92	0	98	36	22	29	12	1.90
3559384--3559443	31	1.9	31	89	0	93	41	10	6	41	1.65
3560400--3560490	3	31.3	3	81	6	107	38	2	0	59	1.10
3561975--3562017	14	3.1	14	79	0	50	39	2	0	58	1.11
3570096--3570255	54	3.0	54	85	0	232	36	15	23	25	1.93
3571297--3572142	116	7.3	116	93	1	1428	30	21	20	27	1.98
3571493--3571551	21	2.8	21	72	15	59	35	25	22	16	1.95
3571609--3571671	21	3.0	21	68	17	58	34	23	22	19	1.96
3571841--3571897	19	2.8	21	76	13	64	36	24	19	19	1.94
3571297--3572142	347	2.4	347	94	0	1460	30	21	20	27	1.98
3572072--3572130	21	2.8	21	72	15	59	35	25	22	16	1.95
3572396--3572448	3	18.3	3	92	7	92	33	0	0	66	0.92
3572396--3572446	20	2.5	20	93	0	93	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3572396--3572448	17	3.1	18	91	8	92	33	0	0	66	0.92
3573863--3574108	128	1.9	128	81	6	275	35	5	8	50	1.57
3574981--3575038	30	1.9	31	82	3	73	48	6	10	34	1.64
3575554--3575617	24	2.7	24	97	0	119	21	57	0	20	1.40
3591200--3591238	15	2.6	14	84	11	51	12	10	2	74	1.17
3594188--3594225	2	19.5	2	94	5	69	52	0	0	47	1.00
3595751--3596044	83	3.6	82	83	5	333	32	24	19	24	1.98
3595788--3596033	80	3.0	79	85	4	294	32	24	19	23	1.97
3595753--3596332	310	1.9	309	85	3	799	31	23	20	24	1.98
3596048--3596364	82	3.8	83	90	2	462	31	21	20	26	1.98

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