genome.fa.s1547.2.7.7.80.10.50.1000.17.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: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  10425128

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   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   

This is table  17  of  51  ( 6083 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)
3414318--3414760	109	4.2	103	81	8	394	33	24	18	23	1.97
3415239--3415314	36	2.1	37	87	7	111	39	15	14	30	1.88
3415786--3415867	11	7.3	11	70	20	53	34	3	2	59	1.28
3416037--3416070	16	2.1	16	88	0	50	32	5	0	61	1.20
3416051--3416101	21	2.4	22	80	3	59	27	3	1	66	1.20
3416285--3416338	27	2.1	27	83	13	69	33	9	0	57	1.31
3416777--3416817	16	2.6	16	88	3	57	82	0	14	2	0.76
3426257--3426305	17	2.9	17	77	17	57	57	2	0	40	1.10
3428673--3428702	2	15.0	2	100	0	60	50	0	0	50	1.00
3429383--3429474	45	2.0	45	91	0	148	39	5	16	39	1.71
3429524--3429737	60	3.6	59	74	5	187	28	17	7	45	1.77
3429526--3429749	120	1.9	120	83	3	290	28	19	7	44	1.78
3432917--3432951	6	5.8	6	93	0	52	31	17	11	40	1.85
3432908--3432951	12	3.6	12	84	3	52	31	18	11	38	1.86
3434874--3434952	36	2.2	36	88	0	113	34	11	37	16	1.85
3435121--3435151	12	2.6	12	94	0	53	22	48	19	9	1.78
3445807--3445839	16	2.0	17	88	5	50	24	12	9	54	1.66
3450523--3450575	13	3.9	13	85	7	61	15	39	22	22	1.91
3450503--3450555	18	3.2	18	75	25	71	15	47	20	16	1.83
3450537--3450582	15	3.2	15	90	6	69	15	34	26	23	1.94
3450550--3450582	7	4.4	8	85	14	52	15	33	27	24	1.95
3451888--3451923	18	2.0	18	88	0	54	52	0	16	30	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3453027--3453142	24	4.8	24	89	4	162	25	15	18	39	1.91
3453979--3454016	18	2.1	19	85	5	51	39	0	0	60	0.97
3458568--3458655	44	2.0	43	93	2	149	27	13	23	35	1.93
3459157--3459265	33	3.2	33	82	13	139	40	35	9	14	1.78
3467486--3467518	16	2.1	15	94	5	57	45	0	3	51	1.16
3470997--3471078	17	4.9	17	71	12	53	74	0	8	17	1.06
3471088--3471115	2	14.0	2	100	0	56	50	0	0	50	1.00
3471165--3471230	29	2.3	29	76	2	71	72	9	0	18	1.10
3471329--3471411	2	42.5	2	92	4	143	49	1	0	49	1.08
3471440--3471490	20	2.6	19	81	9	57	62	0	5	31	1.19
3472019--3472123	37	2.8	37	86	0	147	30	14	15	40	1.87
3472854--3474234	106	13.1	106	89	1	1979	23	18	24	34	1.96
3475034--3475132	22	4.5	22	94	0	171	21	13	27	38	1.90
3475720--3475760	21	2.0	21	85	9	57	2	14	9	73	1.19
3475730--3475803	21	3.4	21	73	14	69	4	13	9	72	1.23
3475727--3475815	44	2.0	45	86	6	126	4	13	10	71	1.27
3476991--3477039	23	2.1	23	100	0	98	34	16	16	32	1.91
3478760--3478804	17	2.6	18	86	6	58	77	0	6	15	0.96
3478813--3478837	2	12.5	2	100	0	50	52	0	0	48	1.00
3479654--3479755	37	2.8	37	87	3	134	33	12	14	39	1.84
3481838--3481898	2	31.0	2	93	3	106	52	0	0	47	1.00
3486672--3486712	2	20.5	2	94	0	73	51	2	0	46	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3486941--3486982	16	2.7	15	78	14	50	45	0	0	54	0.99
3487462--3487486	9	2.8	9	100	0	50	88	0	0	12	0.53
3487492--3487567	24	2.7	29	65	23	72	57	5	3	32	1.39
3487660--3487746	14	6.2	14	68	9	52	50	1	1	47	1.16
3487660--3487749	28	3.3	28	72	7	78	50	1	1	47	1.15
3487689--3487757	30	2.3	31	82	9	81	49	0	1	49	1.09
3487853--3488306	200	2.3	199	85	3	610	40	13	15	30	1.86
3488324--3488510	87	2.1	87	93	0	320	33	16	10	40	1.83
3488398--3488449	23	2.3	23	89	0	77	32	19	7	40	1.80
3488421--3488577	64	2.5	64	92	0	260	31	14	10	42	1.80
3488334--3488664	151	2.2	151	91	0	527	32	14	10	42	1.80
3488485--3488723	87	2.7	87	90	3	374	33	12	10	43	1.78
3488559--3488603	23	2.0	23	90	0	72	42	17	4	35	1.70
3488646--3488690	23	2.0	23	86	0	63	42	15	8	33	1.78
3494360--3494463	21	4.8	21	82	9	102	18	25	31	24	1.97
3494360--3494463	23	4.7	23	89	2	108	18	25	31	24	1.97
3501337--3501393	30	1.9	30	82	10	73	15	19	10	54	1.70
3502036--3502066	16	1.9	16	93	0	53	45	16	3	35	1.63
3503032--3503097	30	2.2	30	97	0	123	27	16	21	34	1.95
3505464--3505701	76	3.1	76	84	4	293	31	14	13	41	1.84
3505539--3505669	36	3.5	37	67	12	97	31	11	15	41	1.82
3505713--3506158	39	11.5	39	93	0	660	28	18	17	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3507445--3507740	89	3.3	89	77	1	315	31	18	19	31	1.95
3515836--3515861	2	13.0	2	100	0	52	50	0	0	50	1.00
3517195--3517255	31	2.0	31	96	0	113	44	0	4	50	1.23
3517277--3517400	22	5.6	22	82	12	141	48	3	0	48	1.17
3517277--3517399	43	2.8	43	82	11	144	48	3	0	47	1.17
3517386--3517425	12	3.6	12	77	16	50	52	0	2	45	1.14
3520524--3520681	21	7.8	20	71	7	77	37	25	17	19	1.93
3520687--3520841	20	7.7	20	82	4	204	33	25	19	21	1.97
3520648--3520842	40	4.9	39	81	4	203	35	25	18	19	1.95
3520648--3520841	60	3.2	60	81	2	237	35	25	19	19	1.95
3521224--3521294	33	2.2	33	92	0	115	11	22	18	47	1.80
3521374--3521483	21	5.8	20	74	17	108	45	18	24	11	1.83
3521367--3521483	41	3.1	38	81	14	145	46	17	25	11	1.81
3521434--3521490	14	3.7	14	75	20	60	43	22	24	8	1.81
3521426--3521494	33	2.1	33	100	0	138	46	20	24	8	1.79
3521426--3521506	33	2.5	33	93	4	128	45	22	22	9	1.81
3521524--3521613	14	5.7	14	67	23	54	11	23	22	43	1.85
3521507--3521621	33	3.5	33	92	0	203	11	22	20	46	1.82
3521502--3521599	19	5.7	18	67	22	68	12	22	21	43	1.85
3523320--3523695	93	4.1	93	98	0	727	21	12	19	46	1.83
3523743--3523871	19	7.3	19	75	17	125	45	28	17	8	1.77
3523779--3523871	33	2.8	32	91	4	150	46	27	18	7	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3523743--3523871	52	2.5	52	74	14	140	45	28	17	8	1.77
3523867--3524001	19	7.6	19	75	16	128	11	19	23	45	1.82
3523889--3523945	14	3.7	14	77	20	60	10	21	22	45	1.82
3523872--3523964	33	2.8	33	95	0	168	10	20	21	47	1.80
3525926--3525961	14	2.6	14	95	0	63	33	0	22	44	1.53
3526068--3526165	19	5.4	19	82	13	134	45	17	21	15	1.84
3526068--3526183	53	2.2	53	96	1	216	43	18	23	14	1.86
3526212--3526390	19	10.4	19	71	23	164	13	21	18	46	1.83
3526190--3526390	52	3.9	52	75	15	213	13	21	18	46	1.83
3526250--3526337	14	5.6	14	69	23	59	11	22	19	46	1.81
3526231--3526423	67	2.9	67	92	2	300	12	21	19	46	1.83
3526231--3526404	33	5.2	33	91	4	296	12	21	18	46	1.83
3526231--3526412	100	1.8	99	91	3	303	13	21	18	46	1.83
3527233--3527462	20	11.5	20	85	1	237	19	18	24	36	1.94
3527449--3527527	21	3.8	21	77	5	88	24	17	21	36	1.94
3532828--3532908	41	2.0	39	81	9	92	40	4	1	53	1.31
3533328--3533367	21	1.9	21	89	0	62	37	5	12	45	1.64
3535153--3535187	10	3.6	10	92	3	54	28	0	0	71	0.86
3535543--3535594	24	2.2	23	82	3	59	32	7	11	48	1.68
3535716--3535778	2	32.0	2	96	3	119	50	0	0	49	1.00
3535825--3535879	29	1.9	30	85	7	78	50	0	5	43	1.25
3536680--3537048	20	18.5	20	84	4	440	34	25	19	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3537716--3537761	24	2.0	23	87	12	67	26	15	21	36	1.93
3540113--3540350	19	14.6	15	75	20	107	47	18	19	14	1.82
3540170--3540374	19	11.8	19	77	18	189	46	17	19	16	1.84
3540191--3540374	101	1.8	102	92	3	318	45	17	20	16	1.85
3540191--3540358	51	3.3	51	90	6	279	46	17	20	15	1.84
3540365--3540459	18	5.6	18	76	21	107	14	24	17	43	1.87
3540426--3540456	16	2.0	16	93	6	55	12	25	12	48	1.77
3540559--3540595	14	2.6	14	91	0	65	45	21	0	32	1.52
3540714--3541056	174	2.0	169	97	2	641	34	19	11	34	1.88
3542711--3542767	14	3.7	14	77	20	60	45	22	21	10	1.82

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   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51