genome.fa.s9643.2.7.7.80.10.50.1000.15.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: 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  15  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)
3088502--3088598	24	4.0	24	80	0	95	19	12	17	50	1.77
3092853--3092945	24	3.9	24	81	1	98	20	13	17	48	1.81
3095643--3095695	21	2.5	21	81	0	70	22	24	16	35	1.95
3095685--3095777	20	4.7	20	95	0	168	38	20	20	20	1.93
3095975--3096040	22	3.0	21	80	8	69	24	34	15	25	1.94
3096376--3096466	20	4.6	20	84	1	94	14	14	23	48	1.80
3098323--3098479	20	8.5	20	74	18	117	42	21	18	18	1.90
3098395--3098428	14	2.4	15	85	14	54	55	23	11	8	1.63
3098524--3098671	20	7.4	20	93	1	199	22	19	22	35	1.96
3098524--3098671	59	2.5	60	88	1	208	22	19	22	35	1.96
3100696--3100722	14	1.9	14	100	0	54	7	11	29	51	1.64
3100724--3100762	3	13.0	3	88	0	60	0	28	0	71	0.86
3100723--3100762	15	2.7	15	100	0	80	0	27	0	72	0.85
3100937--3100996	24	2.5	24	80	0	75	40	16	18	25	1.91
3101832--3101898	20	3.3	20	95	0	116	22	19	26	31	1.98
3101885--3101997	20	5.7	20	93	0	181	21	20	19	38	1.93
3101872--3101997	40	3.1	42	84	8	138	21	19	20	38	1.94
3102540--3102587	25	1.9	25	100	0	96	20	16	33	29	1.95
3105935--3106015	27	3.0	27	100	0	162	48	11	7	33	1.67
3113051--3113192	58	2.5	58	80	10	150	30	23	5	39	1.78
3115839--3115934	29	3.3	28	72	18	90	28	30	31	10	1.90
3115944--3116028	41	2.1	41	89	8	129	16	16	44	22	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3115944--3116028	40	2.1	42	89	8	131	16	16	44	22	1.86
3116221--3116259	21	1.9	21	89	5	62	20	23	23	33	1.97
3116583--3116658	24	3.4	23	78	12	95	28	1	14	55	1.48
3116671--3116695	8	3.1	8	100	0	50	28	0	12	60	1.32
3117414--3117443	14	2.1	14	100	0	60	50	6	0	43	1.28
3117428--3117470	21	2.0	21	90	0	68	46	4	2	46	1.36
3118347--3118571	47	4.9	47	86	9	320	43	0	11	45	1.39
3118570--3118604	17	2.0	18	94	5	63	57	0	5	37	1.23
3118783--3118836	12	4.7	12	84	8	60	53	0	3	42	1.18
3118775--3119128	23	14.8	23	71	18	124	46	1	7	43	1.41
3118858--3119037	26	7.3	26	77	12	182	46	2	7	43	1.45
3118882--3119128	97	2.5	97	82	6	270	46	1	7	44	1.40
3118989--3119065	3	26.3	3	75	5	59	54	2	3	38	1.33
3119246--3119530	26	11.6	26	78	14	216	46	2	8	43	1.45
3119335--3119368	8	4.2	8	85	14	52	41	0	8	50	1.34
3119323--3119455	21	6.8	20	74	22	95	47	1	7	43	1.40
3119388--3119468	3	27.3	3	72	12	51	53	1	6	39	1.34
3119413--3119477	17	3.8	17	76	17	64	53	0	7	38	1.30
3122075--3122164	29	3.0	30	81	12	96	45	10	2	42	1.50
3122538--3122601	27	2.3	28	76	15	71	46	15	1	35	1.56
3122679--3122716	9	4.2	9	83	10	51	65	2	0	31	1.06
3122763--3122793	15	2.1	15	93	0	53	6	32	6	54	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3123018--3123081	27	2.3	28	91	2	103	20	32	26	20	1.97
3123137--3123229	29	3.2	28	86	7	89	20	34	30	15	1.93
3123149--3123236	29	3.1	29	93	1	142	18	36	29	15	1.92
3126219--3126264	20	2.3	20	96	0	83	23	26	8	41	1.83
3126280--3126317	18	2.1	19	90	5	60	34	23	18	23	1.96
3127894--3127987	40	2.3	42	85	7	122	27	35	20	17	1.94
3128101--3128152	19	2.5	22	78	15	65	19	11	34	34	1.88
3128176--3128297	42	3.0	42	87	2	167	21	12	31	35	1.90
3128413--3128455	12	3.6	12	77	0	50	27	4	2	65	1.25
3132144--3132223	22	3.7	22	88	5	92	20	26	28	25	1.99
3132125--3132224	21	4.9	21	80	9	91	19	26	29	26	1.98
3135874--3135916	21	2.0	22	86	13	63	34	11	4	48	1.60
3139769--3139804	18	2.0	18	94	0	63	19	0	22	58	1.40
3142268--3142319	19	2.7	19	96	0	95	30	17	28	23	1.97
3146090--3146168	22	3.5	24	81	13	98	29	18	26	25	1.98
3146070--3146144	22	3.5	22	83	16	95	29	16	29	25	1.96
3146069--3146167	46	2.4	39	80	14	101	31	17	27	24	1.97
3147458--3147519	23	2.8	22	92	4	106	30	11	25	32	1.91
3147726--3147786	23	2.7	23	82	2	79	19	26	26	27	1.99
3152919--3152967	23	2.1	23	88	3	71	38	18	18	24	1.93
3152932--3152984	23	2.3	23	83	6	63	37	16	16	28	1.91
3153899--3153954	20	2.8	20	94	0	94	32	8	21	37	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3155978--3156007	2	15.0	2	100	0	60	50	0	0	50	1.00
3157538--3157740	43	4.7	43	83	2	239	31	20	24	24	1.98
3157581--3157740	85	1.9	85	89	0	248	31	19	25	23	1.98
3164044--3164109	28	2.4	28	94	2	116	31	6	7	54	1.53
3165229--3165285	22	2.7	22	81	13	66	47	3	12	36	1.58
3173870--3173988	44	2.7	44	97	0	220	28	4	23	43	1.72
3174138--3174215	31	2.5	31	100	0	156	28	7	7	56	1.55
3176237--3176327	39	2.3	39	88	0	128	31	20	27	19	1.97
3178791--3178824	12	2.8	12	86	0	50	20	14	44	20	1.87
3178954--3178989	17	2.2	17	90	5	56	47	0	0	52	1.00
3179032--3179067	15	2.4	15	90	0	54	41	2	0	55	1.14
3179289--3179342	16	3.2	16	77	15	56	38	0	0	61	0.96
3187940--3187979	18	2.2	18	86	8	55	10	10	22	57	1.61
3188682--3188736	16	3.4	16	89	0	92	10	12	20	56	1.66
3190868--3191318	134	3.4	133	85	4	606	27	16	26	29	1.97
3201894--3201928	16	2.1	16	94	5	61	65	0	0	34	0.93
3208380--3208419	20	2.0	20	85	0	53	47	7	2	42	1.45
3208869--3208897	15	1.9	15	100	0	58	34	0	10	55	1.34
3208855--3208939	26	3.4	25	75	16	77	37	0	10	51	1.37
3208891--3208922	16	2.0	16	93	0	55	37	0	15	46	1.46
3208853--3208993	59	2.3	63	84	7	175	39	1	9	49	1.43
3208974--3209048	24	3.3	22	83	10	80	52	4	4	40	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3208972--3209044	13	5.7	13	79	8	51	50	4	4	41	1.40
3209095--3209137	22	2.0	22	90	0	68	41	6	6	44	1.58
3209075--3209117	16	2.7	16	88	0	68	39	6	11	41	1.68
3209460--3209554	21	4.3	21	73	13	75	43	2	6	48	1.40
3209547--3209617	24	2.9	25	87	8	110	50	4	5	39	1.45
3209540--3209624	24	3.5	24	80	15	104	50	3	7	38	1.47
3209659--3209703	22	2.0	23	86	4	65	42	2	6	48	1.41
3209727--3209772	17	2.8	16	83	9	58	45	2	0	52	1.13
3212151--3212228	36	2.2	35	86	9	104	50	7	0	42	1.31
3212259--3212322	33	1.9	34	96	3	121	48	9	0	42	1.35
3212330--3212384	23	2.4	23	96	3	103	54	16	0	29	1.42
3212695--3212734	17	2.4	17	83	4	55	40	17	7	35	1.78
3213052--3213114	18	3.5	18	77	0	81	36	23	1	38	1.65
3216394--3216431	18	2.1	18	85	9	51	52	2	0	44	1.14
3218099--3218134	5	7.2	5	100	0	72	41	19	0	38	1.52
3222703--3223007	149	2.0	149	97	0	574	27	15	20	36	1.93
3225329--3225366	18	2.2	18	90	4	60	57	0	28	13	1.36
3228076--3228120	22	2.0	23	86	4	65	22	24	24	28	1.99
3231381--3231433	23	2.3	23	80	0	61	28	24	26	20	1.99
3234965--3235065	43	2.3	44	79	5	116	27	20	17	33	1.96
3238374--3238442	23	3.0	23	71	12	61	31	24	24	18	1.98
3239945--3240081	64	2.2	63	80	6	143	24	24	18	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3244742--3244775	16	2.2	16	94	5	61	58	14	8	17	1.61
3246542--3246594	24	2.2	24	89	0	79	20	39	18	20	1.92
3252903--3252935	2	16.5	2	100	0	66	0	48	0	51	1.00
3258659--3258701	18	2.4	18	100	0	86	30	23	13	32	1.93
3259417--3259466	24	2.1	24	84	0	64	32	18	20	30	1.96
3261617--3262148	93	5.7	93	87	0	715	33	16	26	23	1.96
3261617--3262148	279	1.9	279	88	2	800	33	16	26	23	1.96
3262083--3262214	66	2.0	66	82	2	158	31	15	27	25	1.96
3264333--3264362	15	2.0	15	100	0	60	13	46	13	26	1.80
3268588--3268778	96	2.0	96	89	2	294	36	12	5	46	1.65

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