genome.fa.s9643.2.7.7.80.10.50.1000.16.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: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8859806

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   

This is table  16  of  41  ( 4862 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)
3269858--3269967	33	3.3	33	80	8	116	73	2	7	16	1.17
3269888--3269938	15	3.5	14	86	7	75	78	0	1	19	0.85
3269888--3269966	19	4.2	19	76	7	72	73	2	5	18	1.13
3271152--3271309	84	1.9	85	82	1	201	25	19	23	31	1.98
3271317--3271399	34	2.5	34	92	2	141	33	10	18	37	1.85
3271504--3271562	30	2.0	30	83	12	77	33	11	16	37	1.86
3271548--3271630	36	2.3	36	87	0	112	42	13	19	25	1.87
3271517--3271885	101	3.7	99	78	8	367	39	12	16	30	1.86
3271648--3271711	33	1.9	33	87	6	94	42	15	14	28	1.86
3271522--3271885	194	1.9	198	79	5	427	40	12	17	30	1.86
3271792--3271934	65	2.2	65	82	2	171	39	12	17	30	1.87
3271961--3272008	21	2.3	21	92	0	78	39	10	22	27	1.87
3271973--3272015	21	2.0	21	90	0	68	48	9	13	27	1.73
3271982--3272234	72	3.5	72	86	2	346	41	13	16	28	1.86
3277826--3277893	35	1.9	36	85	8	95	64	2	2	29	1.22
3279706--3279820	44	2.7	44	91	4	191	41	32	13	13	1.82
3282019--3282057	17	2.3	18	86	8	55	61	5	5	28	1.39
3282477--3282513	2	18.5	2	100	0	74	51	0	0	48	1.00
3284233--3284279	3	15.7	3	78	8	51	59	4	2	34	1.29
3284490--3284694	91	2.3	91	96	0	376	36	21	18	23	1.95
3284783--3285142	43	8.1	43	78	9	364	29	29	13	27	1.94
3284777--3285142	86	4.1	86	80	9	403	28	29	13	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3284863--3285206	141	2.4	141	90	0	555	29	28	13	29	1.94
3284949--3285053	55	1.9	55	88	0	156	27	29	13	29	1.94
3285277--3285389	35	3.2	35	83	5	156	35	14	23	26	1.93
3285289--3285390	36	2.9	35	86	2	159	35	14	25	24	1.94
3285364--3285485	21	6.4	20	69	22	93	37	12	25	24	1.90
3285328--3285449	57	2.1	57	90	3	192	37	13	24	24	1.91
3285385--3285527	36	4.0	36	88	1	209	35	14	24	25	1.93
3285293--3285485	93	2.1	92	89	2	289	37	13	24	24	1.92
3285842--3285927	33	2.6	33	85	5	104	34	11	23	30	1.90
3286031--3286164	33	4.2	32	85	7	166	30	26	14	29	1.95
3286031--3286164	64	2.1	64	84	5	173	30	26	14	29	1.95
3292036--3292073	17	2.3	17	90	4	60	63	2	5	28	1.30
3292493--3292525	2	16.5	2	100	0	66	51	0	0	48	1.00
3292648--3292701	25	2.2	23	78	18	63	38	7	1	51	1.41
3294313--3294353	3	13.7	3	85	10	57	63	0	2	34	1.08
3294314--3294365	9	6.4	8	82	12	54	61	0	1	36	1.07
3294313--3294365	15	3.5	15	87	7	65	62	0	1	35	1.06
3303641--3303673	2	17.5	2	87	12	52	48	0	0	51	1.00
3305275--3305308	10	3.8	9	85	14	52	73	0	0	26	0.83
3306360--3306414	23	2.4	24	79	14	62	40	1	0	58	1.09
3308756--3309021	76	3.5	76	80	5	279	33	23	24	18	1.97
3308756--3309019	115	2.3	115	82	5	322	34	23	24	18	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3308756--3309021	39	7.0	39	78	5	267	33	23	24	18	1.97
3310321--3310402	29	2.8	29	88	1	119	41	15	3	39	1.65
3311697--3311737	16	2.6	16	88	0	64	68	4	2	24	1.22
3311757--3311816	31	1.9	31	89	0	93	40	5	10	45	1.60
3312273--3312316	17	2.6	16	79	13	52	63	0	0	36	0.95
3312296--3312457	61	2.6	62	91	6	258	59	1	0	38	1.13
3313141--3313176	15	2.5	15	86	4	56	61	0	11	27	1.30
3313441--3313468	9	3.1	9	100	0	56	89	0	0	10	0.49
3314374--3314403	2	15.0	2	100	0	60	50	0	0	50	1.00
3314386--3314445	25	2.3	26	80	11	70	53	3	1	41	1.27
3314437--3314590	29	6.1	26	73	19	121	42	8	3	44	1.53
3314437--3314567	52	2.5	53	80	13	148	43	8	3	44	1.52
3314462--3314566	25	4.2	25	71	20	87	42	9	2	44	1.51
3314475--3314593	22	5.0	22	72	20	89	42	9	2	46	1.49
3320608--3320657	23	2.2	23	92	3	84	20	36	20	24	1.95
3333334--3333367	17	2.0	17	100	0	68	17	35	29	17	1.93
3335772--3335838	35	1.9	35	87	0	98	40	14	25	19	1.90
3339192--3339311	35	3.3	36	89	5	181	43	20	5	31	1.73
3339243--3339303	21	3.2	21	65	29	64	42	21	4	31	1.74
3339194--3339338	35	4.1	36	83	11	142	41	19	6	33	1.76
3343381--3343414	16	2.1	16	94	0	59	32	26	8	32	1.87
3343825--3343937	35	3.2	36	91	5	176	43	18	4	33	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3346473--3346510	2	19.0	2	100	0	76	50	0	0	50	1.00
3352331--3352381	26	1.9	27	84	11	70	49	0	0	50	1.00
3355339--3355384	24	2.0	23	83	8	58	21	13	8	56	1.63
3356234--3356267	17	1.9	18	88	5	52	29	0	5	64	1.17
3356245--3356326	37	2.2	39	86	4	114	28	1	3	67	1.15
3356302--3356506	104	2.0	104	97	0	383	28	4	10	56	1.53
3356367--3356577	115	1.8	115	81	11	263	28	4	10	56	1.52
3356465--3356525	21	2.8	22	80	12	63	29	0	4	65	1.13
3357508--3357581	22	3.4	22	90	0	112	32	20	12	35	1.89
3357566--3357713	70	2.1	70	85	0	206	23	17	14	44	1.85
3357819--3357856	12	3.2	12	81	3	51	47	0	0	52	1.00
3357801--3357858	23	2.4	23	82	5	71	51	1	0	46	1.11
3357818--3357879	19	3.1	21	81	9	67	50	0	0	50	1.00
3357842--3357881	19	2.1	19	95	0	71	50	0	0	50	1.00
3358184--3358233	19	2.6	20	78	9	59	58	0	0	42	0.98
3358851--3358895	17	2.6	18	76	23	51	75	8	0	15	1.03
3363495--3363541	19	2.6	17	75	18	51	51	2	0	46	1.13
3373903--3373944	21	2.0	21	81	9	50	42	2	4	50	1.36
3375913--3375974	23	2.7	23	89	0	88	14	24	27	33	1.94
3378538--3378634	30	3.2	30	95	2	169	45	8	19	26	1.78
3384263--3384444	85	2.1	85	83	4	231	32	16	20	29	1.95
3384645--3384752	44	2.4	45	86	8	143	42	4	3	49	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3384727--3384806	26	3.0	26	81	15	85	46	5	0	48	1.24
3384764--3384818	2	27.5	2	100	0	110	49	0	0	50	1.00
3384727--3384780	28	2.0	25	89	10	81	44	7	0	48	1.31
3384808--3384850	22	2.0	22	90	9	70	41	6	4	46	1.51
3384930--3384959	15	2.1	15	93	6	53	36	13	6	43	1.70
3390754--3391202	229	2.0	227	94	2	785	44	8	7	39	1.62
3391268--3391313	20	2.3	19	89	10	74	54	10	17	17	1.70
3391434--3391480	20	2.4	19	79	10	58	55	8	17	19	1.67
3391625--3391677	24	2.2	24	86	6	72	54	13	5	26	1.60
3393798--3393863	33	2.0	33	87	0	96	28	1	45	24	1.62
3395653--3395696	19	2.4	19	92	3	72	31	2	9	56	1.43
3395779--3397655	199	9.4	200	97	0	3464	37	15	15	31	1.88
3397650--3398223	184	3.1	184	98	0	1103	34	14	16	34	1.90
3399348--3399410	23	2.7	23	90	0	90	36	6	19	38	1.77
3399348--3399420	23	3.2	23	86	3	85	35	5	19	39	1.75
3399563--3399629	30	2.2	30	82	10	75	52	4	0	43	1.21
3399775--3399835	21	2.7	23	82	7	72	36	6	19	37	1.78
3399797--3399845	23	2.1	23	88	7	73	36	2	18	42	1.62
3399781--3399850	21	3.2	21	78	11	61	34	5	20	40	1.76
3399990--3400055	29	2.2	29	84	7	80	53	3	0	43	1.16
3399250--3400263	426	2.4	427	97	1	1939	40	8	13	38	1.74
3400138--3400183	22	2.1	22	87	0	65	41	8	10	39	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3400201--3400265	23	2.8	23	85	0	85	35	7	16	40	1.78
3400468--3400504	18	2.1	18	89	0	56	32	5	10	51	1.60
3400460--3400506	24	2.0	24	86	0	67	34	4	14	46	1.64
3428895--3428927	16	2.0	17	88	5	50	51	0	0	48	1.00
3430380--3430421	3	14.0	3	89	0	66	61	2	0	35	1.09
3430596--3431265	76	8.8	76	96	0	1241	36	20	19	22	1.95
3431942--3431996	22	2.5	22	90	0	92	38	14	12	34	1.84
3434569--3434886	115	2.8	115	93	0	523	33	20	14	31	1.93
3434787--3434971	93	2.0	92	88	5	275	36	19	14	29	1.91
3439854--3439895	22	2.0	21	85	4	57	57	9	14	19	1.64

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