genome.fa.s8527.2.7.7.80.10.50.1000.13.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: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9057482

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   

This is table  13  of  37  ( 4336 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)
3139224--3139255	15	2.1	15	100	0	64	25	0	18	56	1.42
3144149--3144328	20	8.8	21	67	4	116	18	17	23	39	1.92
3144146--3144328	41	4.5	41	92	0	312	19	18	23	39	1.92
3144317--3144369	22	2.4	22	87	0	88	18	16	28	35	1.93
3144467--3144505	6	6.7	6	97	2	71	30	51	17	0	1.46
3145109--3145309	20	9.9	20	78	5	206	39	23	21	15	1.92
3145115--3145330	41	5.3	41	88	1	326	37	24	20	17	1.93
3145110--3145330	122	1.8	122	95	0	406	38	23	20	16	1.93
3148371--3148405	8	4.4	8	85	0	52	85	0	8	5	0.73
3160245--3160353	34	3.1	35	79	11	125	34	20	7	37	1.80
3161625--3161661	13	2.7	14	88	12	51	64	5	0	29	1.15
3161793--3161833	20	2.0	20	86	9	57	39	2	17	41	1.62
3161894--3161953	25	2.4	27	76	21	67	51	5	8	35	1.54
3161892--3162018	29	4.5	29	69	24	92	51	4	7	35	1.52
3161891--3162077	54	3.4	50	82	14	187	51	3	8	35	1.50
3161936--3162057	7	17.4	7	70	20	51	53	3	7	36	1.45
3161919--3162073	51	2.9	53	83	10	142	51	3	8	36	1.50
3166816--3166858	12	3.4	12	87	6	59	46	2	0	51	1.13
3166919--3167121	2	99.0	2	69	20	100	51	2	6	39	1.42
3166913--3167165	28	8.9	27	74	19	164	51	1	7	38	1.42
3166888--3167187	6	47.5	6	74	16	101	54	1	7	37	1.38
3167026--3167179	13	11.8	13	71	17	97	53	0	9	37	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3167087--3167220	22	6.1	22	74	18	88	55	0	7	36	1.28
3166916--3167188	63	4.3	64	76	13	207	52	1	7	37	1.41
3167085--3167217	38	3.7	36	80	11	116	55	0	7	36	1.28
3167234--3167281	23	2.1	23	88	0	69	43	8	6	41	1.60
3170980--3171013	16	2.1	16	88	0	50	50	0	2	47	1.16
3171056--3171089	16	2.0	18	88	11	54	26	2	5	64	1.30
3171560--3171807	130	1.9	130	92	0	415	35	12	15	36	1.86
3172205--3172280	35	2.2	35	92	0	125	35	1	23	39	1.63
3174143--3174330	93	2.0	94	87	3	272	32	14	17	35	1.90
3176279--3176313	8	4.5	8	85	7	54	85	0	0	14	0.59
3176279--3176313	15	2.2	16	90	5	54	85	0	0	14	0.59
3177575--3177632	2	30.0	2	86	13	86	50	0	1	48	1.11
3185731--3185769	20	2.0	20	89	0	60	58	15	12	12	1.62
3214169--3214198	2	15.0	2	100	0	60	50	0	0	50	1.00
3214398--3214485	28	3.1	28	98	0	167	52	3	13	30	1.57
3214923--3214983	31	2.0	31	90	6	97	37	6	8	47	1.59
3219524--3219609	12	7.2	12	77	0	91	50	11	11	26	1.73
3219523--3219609	24	3.6	24	96	0	156	50	11	11	26	1.72
3220945--3221004	29	2.0	31	90	6	97	35	6	16	41	1.75
3221069--3221135	19	3.5	19	87	0	89	38	11	13	35	1.82
3222161--3222216	26	2.2	26	100	0	112	26	14	17	41	1.88
3225809--3226254	185	2.5	175	88	5	624	35	8	17	38	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3225809--3226254	93	4.9	93	87	7	646	35	8	17	38	1.80
3226058--3226232	82	2.1	83	91	1	280	36	9	17	37	1.82
3258065--3258138	23	3.3	22	74	10	62	56	2	1	39	1.22
3258916--3259035	44	2.8	44	85	9	167	45	7	10	36	1.68
3272107--3272196	7	12.9	7	73	9	58	23	0	32	44	1.54
3272117--3272214	21	4.7	21	75	15	78	23	1	30	44	1.60
3272096--3272168	35	2.1	35	85	10	96	28	0	27	43	1.55
3272104--3272196	42	2.2	42	84	3	116	24	0	31	44	1.54
3274277--3274313	17	2.2	17	95	0	65	24	16	29	29	1.96
3274298--3274373	11	6.6	11	77	8	80	26	23	25	25	2.00
3274307--3274374	23	2.9	24	88	2	93	27	25	23	23	2.00
3275094--3275145	24	2.1	26	85	7	72	19	11	13	55	1.68
3275992--3276271	57	4.9	57	91	0	416	32	30	20	16	1.95
3277372--3277510	20	7.0	20	95	0	226	26	27	8	37	1.86
3277669--3277745	20	3.9	20	89	1	111	23	24	10	41	1.85
3286193--3286222	2	15.0	2	100	0	60	50	0	0	50	1.00
3292902--3292931	3	10.0	3	100	0	60	66	0	0	33	0.92
3297085--3297207	61	2.0	60	82	4	149	34	16	17	32	1.92
3300031--3300488	223	2.1	223	89	2	706	46	13	13	25	1.80
3300031--3300488	112	4.1	112	92	2	708	46	13	13	25	1.80
3300364--3300853	182	2.7	181	89	3	743	42	13	16	28	1.85
3300544--3301147	295	2.1	294	92	0	1001	42	13	16	26	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3300724--3300965	112	2.2	113	89	0	360	44	14	15	25	1.84
3300248--3301286	477	2.2	475	92	1	1706	43	13	15	27	1.84
3300836--3301287	182	2.5	182	93	0	778	43	13	15	26	1.84
3301671--3301723	23	2.2	24	83	6	72	41	15	7	35	1.75
3303546--3303603	20	2.6	22	89	10	84	25	22	20	31	1.98
3303610--3303713	45	2.3	45	80	4	113	28	20	17	33	1.95
3305581--3305618	20	1.9	20	94	0	67	31	34	15	18	1.92
3305638--3305727	45	2.0	46	93	2	155	27	26	18	26	1.98
3307321--3307503	43	4.3	42	83	3	224	38	15	25	21	1.92
3307347--3307503	85	1.8	85	88	0	242	38	15	25	20	1.92
3307300--3307503	43	4.8	42	82	1	219	40	16	23	20	1.91
3307716--3307838	44	2.8	44	87	1	167	26	26	17	29	1.98
3307742--3307972	44	5.2	44	78	8	166	29	22	18	29	1.97
3307802--3307961	43	3.7	42	75	9	117	35	21	16	26	1.95
3309663--3309694	17	1.9	17	93	6	57	75	3	0	21	0.95
3310153--3310301	5	29.8	5	98	0	280	60	1	0	38	1.05
3310518--3310591	20	3.7	20	85	7	114	28	29	14	27	1.95
3310635--3310686	20	2.6	20	93	0	95	36	26	15	21	1.93
3313305--3313340	18	2.0	18	94	0	63	55	22	2	19	1.56
3313793--3313842	25	2.0	25	88	0	73	26	8	20	46	1.78
3314221--3314271	24	2.1	23	82	10	66	33	3	15	47	1.64
3314473--3314548	35	2.2	35	85	4	109	36	25	13	25	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3314540--3314626	39	2.2	39	97	0	165	47	20	14	17	1.83
3314885--3314942	20	2.9	20	94	0	98	20	20	20	37	1.94
3314957--3314994	20	1.9	20	88	0	58	15	13	26	44	1.83
3315053--3315193	61	2.2	63	83	8	171	50	17	1	31	1.54
3316569--3316668	42	2.4	42	80	6	112	22	17	35	26	1.95
3317683--3317725	21	2.0	22	82	13	54	48	2	4	44	1.36
3318884--3318915	13	2.5	13	94	0	55	78	12	6	3	1.06
3319286--3319350	20	3.2	20	93	0	112	18	16	24	40	1.91
3319295--3319492	20	9.8	21	76	11	110	27	15	25	31	1.96
3321372--3321443	30	2.4	30	82	11	78	59	4	4	31	1.35
3327735--3327818	45	1.9	43	82	4	105	48	21	25	4	1.69
3344686--3344742	28	2.0	28	100	0	114	35	10	24	29	1.89
3349454--3349505	20	2.5	20	81	12	61	40	0	1	57	1.10
3351032--3351081	22	2.3	22	82	6	66	52	4	4	40	1.39
3352475--3352538	31	2.1	31	91	2	103	39	6	23	31	1.79
3353415--3353459	12	3.8	12	87	0	54	22	15	17	44	1.86
3354707--3354792	29	3.0	29	66	19	70	34	15	6	43	1.73
3356037--3356078	20	2.1	19	86	13	57	38	2	23	35	1.68
3356224--3356276	20	2.7	20	90	0	79	26	22	22	28	1.99
3356309--3356378	20	3.5	20	80	7	88	37	15	18	28	1.92
3365574--3365684	58	1.9	56	96	3	204	27	15	14	42	1.86
3369694--3369821	3	41.7	3	87	4	184	35	0	0	62	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3371059--3371094	19	1.9	19	94	5	65	22	0	5	72	1.05
3371144--3371175	15	2.1	15	94	0	55	56	3	0	40	1.15
3382470--3382543	4	19.2	4	81	10	68	85	0	14	0	0.61
3382466--3382543	8	9.0	9	84	9	83	84	0	15	0	0.62
3382478--3382541	1	64.0	1	74	0	56	87	0	12	0	0.54
3382469--3382541	13	6.0	13	84	10	93	86	0	13	0	0.58
3383480--3384195	52	13.8	52	97	0	1314	22	14	24	37	1.92
3384796--3384835	21	1.9	21	85	10	55	45	10	10	35	1.71
3384841--3385377	113	4.8	113	95	0	921	38	14	20	27	1.91
3385317--3385415	40	2.5	40	100	0	198	48	9	24	18	1.76

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