genome.fa.s7923.2.7.7.80.10.50.1000.16.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: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8415618

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   

This is table  16  of  40  ( 4704 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)
3232428--3232490	14	4.4	14	77	18	58	49	0	0	50	1.00
3232449--3232496	16	3.0	16	82	14	55	41	0	0	58	0.98
3232633--3232678	19	2.4	19	85	7	58	45	0	2	52	1.13
3232639--3232700	30	2.2	27	83	13	72	46	1	3	48	1.28
3235689--3235813	29	4.3	29	77	15	125	57	1	0	40	1.14
3246802--3246866	29	2.2	29	97	0	121	21	33	12	32	1.90
3246930--3246984	25	2.2	26	93	3	94	47	10	10	30	1.73
3254737--3254825	43	2.0	44	89	2	135	41	10	8	39	1.70
3255131--3255227	51	1.9	51	87	4	142	13	29	34	22	1.92
3255645--3255669	13	1.9	13	100	0	50	8	16	4	72	1.24
3266560--3266646	21	4.1	21	83	0	84	44	18	35	1	1.57
3267032--3267145	43	2.7	43	81	2	122	35	27	16	21	1.95
3279176--3279214	20	2.0	20	89	0	60	20	15	33	30	1.94
3287693--3287741	19	2.6	19	87	9	66	32	18	24	24	1.97
3287757--3287844	45	1.9	46	90	2	142	28	19	25	27	1.99
3299451--3299541	45	2.0	45	100	0	182	34	15	32	17	1.91
3299841--3300001	1	161.0	1	74	0	115	85	1	3	8	0.78
3299838--3299982	18	8.1	18	84	9	145	84	0	4	10	0.75
3299841--3300010	16	10.1	16	78	13	130	85	2	3	8	0.80
3299841--3300010	17	10.2	16	82	10	166	85	2	3	8	0.80
3299975--3300005	11	2.8	11	95	0	53	87	12	0	0	0.55
3301339--3302006	53	12.6	53	93	3	1114	30	18	25	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3301339--3302012	107	6.3	106	93	3	1128	31	18	25	25	1.98
3302331--3302356	2	13.0	2	100	0	52	50	0	0	50	1.00
3305946--3306002	27	2.1	27	100	0	114	29	3	10	56	1.50
3306078--3306135	30	1.9	31	82	3	73	43	5	29	22	1.75
3306856--3306899	18	2.4	19	81	7	56	54	2	0	43	1.12
3308725--3308810	28	3.1	28	84	3	129	38	2	16	43	1.61
3308714--3308805	27	3.4	27	86	3	139	42	4	14	39	1.65
3310550--3310588	19	2.1	18	90	4	60	56	0	0	43	0.99
3310626--3310692	29	2.4	25	74	25	64	49	1	1	47	1.19
3310695--3310782	46	1.9	46	88	4	133	51	0	2	46	1.13
3310665--3310791	46	3.1	39	74	22	116	49	0	2	48	1.14
3310881--3310936	29	1.9	29	86	13	80	53	0	1	44	1.11
3310904--3310964	21	2.9	19	75	17	59	55	1	0	42	1.09
3311129--3311306	88	2.0	89	92	1	295	46	18	12	21	1.83
3314153--3314187	16	2.2	16	94	0	61	25	11	17	45	1.81
3315650--3315697	23	2.2	21	82	14	53	52	6	0	41	1.27
3315650--3315697	11	4.4	11	89	5	62	52	6	0	41	1.27
3317246--3317276	2	15.5	2	100	0	62	48	0	0	51	1.00
3318735--3318771	15	2.5	15	90	0	56	8	16	67	8	1.40
3319091--3319115	7	3.6	7	100	0	50	72	0	28	0	0.86
3320116--3320196	35	2.3	35	95	0	144	23	23	16	37	1.94
3320191--3320348	21	7.7	21	76	12	157	34	24	18	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3320182--3320348	41	4.1	41	96	0	289	34	24	17	23	1.96
3320182--3320327	20	7.2	20	74	13	145	32	25	18	23	1.97
3320491--3320541	22	2.3	22	96	0	93	19	45	15	19	1.86
3320916--3320981	20	3.3	20	74	18	57	18	13	25	42	1.87
3320927--3321018	39	2.3	40	90	1	141	13	15	25	46	1.81
3320927--3321018	20	4.7	20	82	2	105	13	15	25	46	1.81
3320947--3321021	20	3.8	20	87	1	116	12	14	22	50	1.76
3322932--3323014	20	4.4	20	68	17	70	36	20	21	21	1.96
3323014--3323055	19	2.2	19	86	0	57	11	14	30	42	1.81
3323023--3323059	19	1.9	19	94	0	65	5	13	29	51	1.63
3323024--3323103	33	2.4	33	85	0	97	10	18	23	47	1.79
3323047--3323164	33	3.3	33	78	12	101	13	21	23	41	1.88
3323095--3323163	20	3.5	20	93	0	120	14	21	26	37	1.92
3323650--3323753	21	5.0	21	74	3	84	22	35	17	25	1.95
3323650--3323768	42	2.8	42	75	9	127	23	35	16	24	1.95
3325075--3325305	65	3.5	63	86	9	241	29	3	17	49	1.63
3325147--3325258	27	3.7	27	69	22	89	28	1	17	51	1.56
3325357--3325410	20	2.7	20	82	5	65	44	25	18	11	1.83
3325453--3325663	20	10.9	20	83	6	263	26	18	22	33	1.97
3325409--3325663	134	1.9	133	86	0	357	25	18	21	33	1.96
3325453--3325655	74	2.6	76	87	4	275	25	18	23	33	1.97
3325634--3325916	140	2.0	140	99	0	557	43	15	13	27	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3325974--3326008	18	1.9	18	94	0	61	17	2	25	54	1.57
3328257--3328310	24	2.2	24	93	0	90	40	20	18	20	1.91
3329131--3329214	20	4.2	20	80	8	98	25	17	27	29	1.98
3334697--3334786	44	2.0	44	91	0	144	37	16	18	26	1.92
3344188--3344228	21	1.9	22	85	5	57	43	21	14	19	1.87
3344911--3345435	260	2.0	260	95	0	960	35	17	20	26	1.95
3351018--3351103	42	2.0	42	90	0	136	30	19	19	30	1.97
3351142--3351166	13	1.9	13	100	0	50	32	16	20	32	1.94
3351162--3351225	20	3.0	21	70	17	69	26	17	25	31	1.97
3351027--3351288	135	1.9	135	90	1	418	31	17	22	29	1.96
3351154--3351480	42	8.0	42	67	13	196	29	18	22	29	1.97
3351154--3351217	20	3.1	20	70	16	58	25	20	25	29	1.99
3351284--3351347	20	3.0	21	70	17	60	25	18	23	32	1.97
3351277--3351339	20	3.0	20	70	17	65	23	23	22	30	1.99
3351155--3351562	122	3.3	122	93	0	672	30	18	22	29	1.97
3351441--3351653	80	2.7	80	94	0	363	30	16	21	30	1.95
3351607--3351693	42	2.1	41	85	4	113	26	16	22	34	1.95
3352063--3352380	53	5.9	53	85	3	406	30	21	25	22	1.99
3352063--3352380	108	3.0	106	84	5	408	30	21	25	22	1.99
3359753--3359787	2	17.5	2	100	0	70	0	48	0	51	1.00
3360483--3360527	22	2.0	22	95	0	81	55	0	0	44	0.99
3360617--3360659	22	1.9	23	95	4	79	32	13	20	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3369745--3369784	14	2.9	14	85	7	55	35	0	0	65	0.93
3373003--3373072	22	2.9	25	71	18	76	25	24	17	32	1.96
3376316--3376350	3	11.7	3	88	11	54	34	0	0	65	0.93
3376318--3376354	12	3.2	12	82	17	51	32	0	0	67	0.91
3377698--3377758	29	2.1	29	82	11	72	13	14	14	57	1.66
3377733--3377796	30	2.1	30	82	5	76	9	14	18	57	1.63
3377883--3377925	22	2.0	21	90	4	68	27	0	11	60	1.31
3378699--3378749	4	11.5	4	88	12	57	68	0	9	21	1.18
3378806--3378843	9	4.2	9	87	9	51	89	0	10	0	0.49
3378809--3378835	10	2.7	10	100	0	54	92	0	7	0	0.38
3385395--3385451	19	3.0	19	82	5	71	36	10	12	40	1.77
3392233--3392275	18	2.4	18	96	0	77	11	11	25	51	1.72
3392377--3392481	54	1.9	54	84	0	138	29	17	16	37	1.91
3396334--3396372	18	2.1	19	85	4	53	23	5	5	66	1.32
3396448--3396490	21	2.2	20	84	15	56	41	2	0	55	1.12
3398523--3398586	27	2.3	27	86	13	85	35	1	4	57	1.29
3398624--3398690	18	3.8	18	76	2	64	23	7	0	68	1.15
3400416--3400449	10	3.4	10	87	0	50	20	5	0	73	1.04
3409840--3409933	48	1.9	49	84	2	127	45	14	24	14	1.83
3410686--3411460	105	7.4	105	96	0	1424	32	25	18	23	1.97
3413203--3413250	3	15.3	3	87	8	53	35	0	2	62	1.07
3413301--3413367	18	3.8	18	76	2	64	23	7	0	68	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3418069--3418123	24	2.2	26	80	9	60	38	12	34	14	1.84
3424269--3424339	6	11.8	6	89	0	70	18	11	32	38	1.86
3424305--3424350	12	3.8	12	88	0	56	26	0	23	50	1.50
3424305--3424350	18	2.6	18	85	0	65	26	0	23	50	1.50
3424340--3424366	2	13.5	2	100	0	54	48	0	0	51	1.00
3431750--3431801	3	18.0	3	88	7	81	32	0	1	65	1.04
3432259--3432314	26	2.2	26	96	0	103	16	32	28	23	1.96
3433408--3433455	2	24.0	2	95	0	87	52	0	0	47	1.00
3434383--3434439	30	2.0	28	86	6	78	36	5	1	56	1.32
3436126--3436173	14	3.4	14	82	5	60	10	12	14	62	1.54

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