genome.fa.s1279.2.7.7.80.10.50.1000.14.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

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   

This is table  14  of  29  ( 3433 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)
3283328--3283379	18	2.9	18	91	0	77	21	48	17	13	1.81
3283344--3283368	13	1.9	13	100	0	50	16	48	24	12	1.79
3285949--3285987	12	3.2	12	79	13	53	28	12	23	35	1.91
3285933--3286027	48	2.0	48	89	4	147	25	13	21	40	1.90
3285933--3286027	24	4.0	24	83	5	129	25	13	21	40	1.90
3286143--3286233	43	2.1	43	97	0	173	16	10	37	35	1.84
3288383--3288423	13	3.2	13	78	0	55	14	41	19	24	1.89
3288374--3288423	26	1.9	26	91	0	82	18	42	18	22	1.90
3288400--3288448	18	2.7	18	90	0	71	18	44	18	18	1.87
3291004--3291042	12	3.2	12	79	13	53	28	12	23	35	1.91
3290988--3291082	48	2.0	48	91	4	156	26	13	20	40	1.89
3290988--3291082	24	4.0	24	86	5	138	26	13	20	40	1.89
3291198--3291288	43	2.1	43	97	0	173	16	10	37	35	1.84
3297877--3298083	85	2.4	87	79	4	215	36	20	14	28	1.92
3300033--3300200	90	1.9	90	92	0	282	45	6	13	35	1.69
3300949--3301297	131	2.7	130	85	2	468	40	17	10	31	1.84
3302118--3302313	107	1.8	109	83	4	263	48	15	11	23	1.78
3303293--3303333	3	13.7	3	94	0	73	65	2	0	31	1.05
3304454--3304492	19	2.1	19	85	9	53	10	12	0	76	1.01
3332575--3332645	20	3.5	20	72	11	72	49	2	5	42	1.41
3332640--3332674	3	11.7	3	93	0	61	28	0	2	68	1.04
3336750--3336812	3	21.0	3	96	0	117	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3338325--3338423	35	2.8	36	84	4	119	32	15	14	38	1.87
3338879--3339644	109	7.4	103	80	8	715	22	20	24	32	1.98
3339359--3339639	102	2.8	99	83	6	342	20	21	24	32	1.98
3340052--3340237	36	5.3	36	71	12	127	40	13	18	27	1.88
3340052--3340435	101	3.8	101	89	3	580	37	12	20	29	1.90
3340289--3340408	63	1.9	63	84	3	161	35	14	20	29	1.92
3340360--3340414	15	3.2	17	69	19	51	38	12	27	21	1.90
3340352--3340453	36	2.9	35	94	2	170	37	13	24	24	1.92
3341294--3341344	22	2.3	22	96	0	93	25	11	27	35	1.91
3341960--3342016	15	3.7	15	76	17	55	0	12	7	80	0.89
3341952--3342019	20	3.4	20	84	13	79	1	10	7	80	0.95
3341987--3342026	21	2.0	21	85	5	55	0	17	5	77	0.94
3346147--3346191	2	22.5	2	100	0	90	51	0	0	48	1.00
3349598--3349639	21	2.0	21	85	0	57	7	0	23	69	1.13
3353926--3354082	64	2.5	64	79	6	147	35	18	21	24	1.95
3355270--3355309	2	20.0	2	100	0	80	50	0	0	50	1.00
3360068--3360101	14	2.4	14	90	0	50	32	2	29	35	1.73
3360076--3360109	14	2.4	14	100	0	68	29	5	32	32	1.81
3360334--3360366	2	16.5	2	93	0	57	48	3	0	48	1.17
3360712--3360755	23	1.9	23	86	9	63	20	27	25	27	1.99
3360710--3360761	23	2.3	23	76	6	61	23	25	25	26	2.00
3361562--3362106	273	2.0	273	94	1	950	30	20	19	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3369610--3369649	17	2.4	17	100	0	80	35	0	12	52	1.39
3371531--3371600	27	2.6	26	82	10	79	25	1	12	60	1.41
3375674--3375743	12	5.8	12	80	6	79	51	18	15	14	1.77
3375674--3375766	24	3.9	24	85	0	105	48	18	15	18	1.81
3375672--3375763	48	1.9	48	88	0	139	48	17	15	18	1.81
3375672--3375776	48	2.2	48	84	3	131	47	17	16	19	1.83
3376922--3376956	18	1.9	18	88	0	52	28	17	0	54	1.43
3378266--3378341	13	5.3	13	77	17	71	19	22	42	15	1.89
3378266--3378359	31	3.1	30	86	4	120	19	21	43	15	1.88
3378246--3378305	8	7.5	8	77	21	56	21	26	36	15	1.93
3378318--3378363	18	2.6	18	100	0	92	13	17	52	17	1.75
3380483--3380552	12	5.8	12	76	6	70	51	17	15	15	1.77
3380481--3380589	48	2.3	47	83	3	128	47	16	16	19	1.83
3380481--3380589	24	4.5	25	76	6	100	47	16	16	19	1.83
3381730--3381765	18	2.0	18	88	0	54	30	16	0	52	1.44
3383082--3383142	13	4.3	13	77	18	68	16	21	45	16	1.85
3383091--3383125	18	1.9	18	100	0	70	14	22	45	17	1.84
3383082--3383160	31	2.5	31	89	0	122	16	20	45	17	1.85
3383119--3383164	18	2.6	18	92	0	83	13	17	50	19	1.78
3388964--3389056	48	1.9	48	97	0	177	41	5	15	37	1.69
3396785--3396822	2	19.0	2	100	0	76	50	0	0	50	1.00
3401470--3401499	14	2.1	14	93	0	51	16	23	3	56	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3402551--3402597	18	2.6	18	78	18	53	72	0	12	14	1.13
3402853--3402917	25	2.7	23	73	15	51	63	0	3	33	1.10
3402853--3402903	27	2.0	27	84	7	70	58	0	3	37	1.16
3402863--3402909	16	2.9	17	81	9	53	61	0	4	34	1.15
3404143--3404231	36	2.4	36	88	7	135	30	7	17	43	1.78
3404143--3404231	38	2.4	37	88	7	137	30	7	17	43	1.78
3404404--3404783	101	3.8	101	77	11	426	40	13	18	27	1.88
3404591--3404783	102	1.9	101	82	5	246	40	12	19	26	1.88
3404404--3404806	194	2.1	194	96	0	745	40	13	19	26	1.88
3404931--3405192	106	2.5	106	90	0	398	25	17	22	35	1.95
3406399--3406448	25	1.9	27	84	8	68	58	0	4	38	1.17
3412054--3412313	44	5.9	44	86	3	344	26	21	11	40	1.87
3412055--3412313	131	2.0	132	89	1	403	26	20	11	40	1.87
3412051--3412313	87	3.0	87	89	2	366	26	20	12	40	1.88
3419984--3420022	17	2.4	17	91	4	62	87	2	10	0	0.65
3419984--3420028	15	2.9	16	84	12	58	86	2	11	0	0.65
3426420--3426685	44	6.0	44	88	1	363	25	22	11	40	1.87
3433752--3433794	20	2.2	20	95	0	77	58	4	16	20	1.56
3435870--3435938	35	2.0	35	97	2	131	28	33	2	34	1.72
3438069--3438151	23	3.8	22	84	4	96	19	25	31	24	1.98
3441959--3441998	21	1.9	21	85	10	55	35	7	2	55	1.42
3446472--3446530	29	2.0	30	83	6	75	42	3	20	33	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3449235--3449393	61	2.6	60	88	3	221	24	15	28	31	1.96
3451867--3451914	9	5.1	9	82	9	60	12	27	31	29	1.93
3451874--3451912	19	2.0	20	95	5	71	15	25	30	28	1.96
3451911--3451957	5	9.8	5	81	9	62	23	57	17	2	1.50
3451912--3451957	19	2.4	19	89	7	58	23	58	15	2	1.48
3451914--3451958	14	3.2	14	90	0	72	22	57	17	2	1.50
3459163--3459242	10	8.2	10	68	9	58	17	22	25	35	1.95
3459169--3459246	19	4.1	19	88	1	102	19	23	25	32	1.98
3459245--3459277	5	6.8	5	86	6	50	24	57	18	0	1.40
3459248--3459278	14	2.2	14	94	0	53	22	58	19	0	1.40
3461536--3461573	14	2.7	14	100	0	76	23	5	28	42	1.76
3462864--3463337	54	8.8	54	86	3	578	37	16	14	31	1.89
3465235--3465360	47	2.8	45	81	8	139	30	21	7	41	1.80
3469278--3469366	18	5.0	17	77	16	83	8	17	1	71	1.17
3469282--3469329	16	3.3	15	75	24	57	8	18	0	72	1.08
3469281--3469338	17	3.4	17	72	23	59	8	17	0	74	1.06
3469278--3469353	18	4.4	17	80	15	84	9	18	1	71	1.20
3482824--3482949	47	2.8	44	84	5	153	29	23	7	38	1.83
3488351--3488410	26	2.3	26	100	0	120	43	18	16	21	1.88
3505309--3505381	16	4.7	15	81	8	83	78	0	10	10	0.98
3505316--3505357	8	5.2	8	83	11	59	78	0	11	9	0.96
3505301--3505380	34	2.4	33	78	16	92	78	0	11	10	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3505299--3505380	23	3.7	20	76	19	65	79	0	10	9	0.94
3506889--3507051	87	1.9	88	80	3	195	31	15	19	33	1.94
3506977--3507129	43	3.6	43	81	1	155	28	17	19	34	1.95
3507023--3507129	42	2.5	43	83	3	126	26	15	21	36	1.94
3506981--3507508	207	2.5	209	81	6	577	29	18	18	33	1.95
3506914--3507392	249	1.9	250	79	5	536	30	17	18	33	1.94
3507442--3507552	43	2.6	43	80	5	127	28	16	19	35	1.94
3507108--3507562	214	2.2	207	81	5	513	29	18	18	33	1.95
3509892--3509948	21	2.7	22	78	8	64	26	31	12	29	1.92
3514887--3514916	10	3.0	10	90	0	51	56	20	23	0	1.42

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