genome.fa.s9605.2.7.7.80.10.50.1000.15.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: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9158330

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  15  of  35  ( 4090 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)
3253873--3253900	2	14.0	2	100	0	56	50	0	0	50	1.00
3263962--3264967	257	3.9	257	84	2	1275	32	15	17	34	1.91
3264860--3264954	42	2.3	41	85	1	127	23	24	22	30	1.99
3265418--3265664	134	1.8	134	82	0	314	29	18	19	33	1.95
3267790--3267826	19	1.9	19	94	0	65	54	0	2	43	1.14
3269080--3270012	237	3.7	244	81	5	816	33	15	17	33	1.91
3269263--3270065	262	3.1	255	84	3	1000	32	16	17	33	1.93
3269958--3270052	42	2.3	41	83	1	118	24	23	22	30	1.99
3270512--3270757	134	1.8	134	83	0	321	26	19	21	33	1.96
3274141--3274208	27	2.5	27	82	0	73	26	14	7	51	1.68
3277309--3277375	27	2.5	27	97	2	127	58	5	13	22	1.57
3279508--3279534	5	5.4	5	100	0	54	81	18	0	0	0.69
3280903--3280934	15	2.1	15	100	0	64	21	0	37	40	1.54
3284051--3284112	26	2.4	26	100	0	124	45	4	8	41	1.55
3284077--3284351	37	7.9	37	77	15	236	44	3	7	44	1.50
3284077--3284225	39	3.9	39	85	6	218	45	4	8	40	1.56
3284077--3284228	75	2.0	76	92	1	252	45	4	8	41	1.55
3284189--3284317	28	4.4	28	71	22	113	42	3	6	47	1.46
3284189--3284282	26	3.5	26	85	8	109	42	3	6	47	1.45
3284152--3284367	65	3.4	64	76	11	228	44	2	6	45	1.43
3284206--3284294	26	3.4	25	83	9	106	41	2	6	49	1.41
3284353--3284423	7	10.0	7	73	13	56	38	0	1	60	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3284353--3284404	23	2.2	24	93	3	88	38	0	0	61	0.96
3284471--3284508	13	3.0	13	80	3	51	36	28	15	18	1.92
3285624--3285658	12	2.8	13	87	12	56	20	0	0	80	0.72
3285623--3285656	18	1.9	17	94	5	59	20	0	0	79	0.73
3302070--3302342	123	2.2	123	86	2	361	41	20	13	25	1.88
3302917--3303248	37	9.1	37	82	12	375	45	1	7	45	1.42
3302980--3303114	11	11.1	11	66	22	58	45	1	7	45	1.40
3303083--3303187	30	3.2	30	76	19	111	44	0	8	45	1.40
3302917--3303226	106	2.9	108	87	9	447	45	1	7	44	1.43
3303244--3303296	22	2.5	22	87	3	72	35	1	3	58	1.27
3305142--3305193	28	1.9	27	88	7	79	44	0	3	51	1.19
3305176--3305236	7	8.3	7	76	15	52	39	1	1	57	1.18
3304918--3305181	37	7.1	37	84	8	347	43	1	7	46	1.43
3305190--3305236	22	2.1	22	84	7	60	38	2	2	57	1.23
3305233--3305271	16	2.3	18	83	16	57	12	10	0	76	1.01
3306847--3307180	37	9.1	37	83	12	422	44	1	7	45	1.43
3306944--3306968	12	2.1	12	100	0	50	40	8	8	44	1.63
3307013--3307117	30	3.2	30	76	19	111	44	0	8	45	1.40
3306847--3307157	106	2.9	107	88	9	463	45	1	8	44	1.44
3307176--3307228	22	2.5	22	84	3	63	33	1	3	60	1.26
3307221--3307254	15	2.4	14	85	5	50	11	5	0	82	0.83
3307221--3307254	14	2.4	14	86	13	52	11	5	0	82	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3308847--3309112	37	7.1	37	83	8	335	43	1	8	45	1.43
3308988--3309047	11	5.1	11	70	21	50	46	0	8	45	1.33
3310914--3310984	11	6.1	11	72	18	63	46	1	8	43	1.42
3310914--3311021	48	2.2	48	91	3	182	45	1	8	44	1.44
3310776--3310973	37	5.4	37	84	7	285	45	2	7	44	1.45
3310962--3311031	37	1.9	36	94	2	122	44	2	7	45	1.46
3311010--3311065	28	1.9	30	89	7	89	44	0	3	51	1.18
3312720--3312985	37	7.1	37	86	7	360	45	2	6	45	1.44
3312858--3312917	11	5.1	11	70	21	50	46	0	8	45	1.33
3312720--3313002	75	3.8	73	80	10	306	45	2	6	45	1.42
3313007--3313049	22	1.9	23	90	4	70	30	2	0	67	1.03
3313037--3313075	16	2.3	18	83	16	57	12	10	0	76	1.01
3314990--3315034	23	2.0	23	86	0	63	37	0	8	53	1.32
3316074--3316112	17	2.3	17	95	0	69	30	10	12	46	1.75
3317307--3317554	132	1.9	132	87	1	363	33	11	19	34	1.88
3318798--3318841	15	3.1	15	83	9	56	22	50	20	6	1.72
3320287--3320333	20	2.3	20	85	3	58	29	2	38	29	1.69
3320298--3320341	20	2.2	20	100	0	88	22	0	34	43	1.54
3325037--3325335	58	5.2	57	81	8	252	38	8	8	44	1.66
3325038--3325336	116	2.6	114	82	6	325	38	8	8	44	1.66
3327160--3327193	16	2.1	16	89	10	52	32	44	2	20	1.67
3328171--3328201	16	1.9	16	93	0	53	38	0	32	29	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3328786--3329018	84	2.8	84	89	1	342	36	20	15	27	1.93
3328798--3329025	126	1.8	126	87	0	339	36	20	17	26	1.94
3328786--3329025	42	5.7	42	82	1	257	35	20	16	27	1.94
3329040--3329217	36	4.9	36	90	0	257	22	17	20	38	1.93
3329278--3329375	42	2.3	41	79	5	106	32	23	18	25	1.97
3334555--3334731	90	2.0	89	94	1	309	36	11	6	44	1.68
3335063--3335142	37	2.2	37	95	0	142	38	8	15	37	1.78
3341406--3341492	22	4.1	20	73	14	75	49	3	4	42	1.40
3341718--3341766	18	2.7	18	90	0	71	40	16	20	22	1.91
3342614--3342644	16	1.9	16	93	0	53	38	0	32	29	1.57
3343345--3343496	45	3.4	44	80	8	148	34	7	17	40	1.77
3343640--3344046	58	7.0	57	81	5	417	34	8	13	44	1.73
3343640--3344046	116	3.5	114	82	4	460	34	8	13	44	1.73
3344046--3344274	98	2.4	98	81	8	254	38	7	9	44	1.65
3344194--3344292	39	2.5	39	85	3	119	38	8	12	41	1.72
3344194--3344314	39	3.1	38	76	10	118	36	8	10	44	1.69
3344101--3344449	137	2.6	136	79	6	377	38	8	10	42	1.70
3344339--3344653	39	8.4	39	72	11	194	39	7	9	43	1.67
3344339--3344561	77	2.9	78	82	5	240	37	7	10	44	1.67
3345326--3345369	20	2.2	20	96	4	81	40	9	18	31	1.81
3352897--3352943	11	4.3	11	91	5	69	80	0	19	0	0.70
3352897--3352940	16	2.9	15	86	6	54	79	0	20	0	0.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3355454--3355504	25	2.0	25	96	0	93	33	13	19	33	1.91
3355614--3355768	67	2.3	67	83	1	195	27	19	14	38	1.91
3355609--3355761	66	2.3	66	82	1	189	26	18	15	39	1.90
3357021--3357045	5	5.0	5	100	0	50	20	0	0	80	0.72
3362670--3362761	46	2.0	46	93	0	157	40	7	21	30	1.81
3375345--3375393	20	2.5	20	93	0	80	24	30	20	24	1.98
3375430--3375495	31	2.1	31	97	0	123	27	3	24	45	1.68
3379971--3380026	20	2.8	20	94	0	94	25	23	19	32	1.98
3381194--3381255	3	20.7	3	96	0	115	32	1	0	66	1.02
3381385--3381658	43	6.2	45	71	9	154	25	17	7	50	1.71
3381446--3381612	89	1.9	90	80	6	196	25	16	5	52	1.65
3381537--3381646	44	2.5	43	77	2	112	24	18	5	51	1.66
3383774--3383815	22	2.0	22	85	4	59	57	19	7	16	1.62
3385513--3385548	16	2.2	16	100	0	72	41	19	11	27	1.85
3397733--3397785	25	2.2	24	82	3	61	64	1	30	3	1.22
3401434--3401844	81	5.1	81	83	3	468	34	10	20	33	1.88
3405538--3405620	33	2.5	33	98	0	157	28	6	26	38	1.80
3413205--3413271	31	2.2	31	97	0	125	38	17	22	20	1.93
3414320--3414383	24	2.7	24	77	0	56	50	18	7	23	1.73
3418976--3419044	24	2.9	24	77	0	66	49	21	10	18	1.77
3427225--3427735	105	4.9	105	89	1	740	40	16	19	23	1.91
3431276--3431321	19	2.4	19	96	0	83	23	30	21	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3436420--3436473	26	2.1	26	100	0	108	48	3	14	33	1.62
3437206--3437646	81	5.5	81	88	1	627	34	12	19	33	1.89
3437208--3437646	242	1.8	243	89	1	702	34	12	19	33	1.89
3438643--3439035	55	7.1	55	87	1	520	36	18	11	33	1.87
3445016--3445394	55	6.9	55	87	4	480	35	17	12	35	1.87
3445776--3445829	19	2.6	21	88	8	76	31	16	14	37	1.89
3449133--3449171	21	1.9	21	84	5	53	28	10	20	41	1.85
3450334--3450414	42	2.0	41	87	7	119	58	4	16	20	1.57
3454757--3454788	16	1.9	17	93	6	57	50	0	0	50	1.00
3455412--3455533	20	6.1	20	83	0	118	38	20	13	27	1.91

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