genome.fa.s190.2.7.7.80.10.50.1000.52.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: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  14308945

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   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   

This is table  52  of  62  ( 7381 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)
12227824--12227947	64	1.9	65	87	8	182	32	22	18	26	1.97
12227919--12227967	19	2.6	19	84	9	57	24	30	18	26	1.98
12231942--12232687	37	20.2	37	82	6	743	26	8	24	40	1.84
12231942--12232687	76	10.1	76	80	8	824	26	8	24	40	1.84
12232242--12232685	39	12.2	34	73	19	260	26	9	23	40	1.84
12232865--12232914	23	2.2	23	81	0	55	48	10	2	40	1.48
12232933--12233025	48	2.0	47	89	6	145	47	9	20	22	1.79
12235765--12235846	41	2.0	41	100	0	164	29	21	19	29	1.98
12244984--12245282	42	7.1	42	93	0	492	16	21	25	36	1.94
12247186--12247219	12	2.8	12	90	0	50	8	41	17	32	1.80
12249268--12249384	17	6.8	17	76	14	89	41	7	11	39	1.69
12257640--12257684	2	22.5	2	100	0	90	48	0	0	51	1.00
12258083--12258255	90	1.9	89	95	1	310	38	10	6	43	1.67
12260473--12260519	18	2.8	18	87	9	64	14	10	0	74	1.07
12265613--12265673	23	2.7	23	92	0	104	18	27	27	26	1.98
12267029--12267089	6	9.7	6	85	7	68	75	0	24	0	0.80
12267029--12267089	19	3.2	19	80	13	72	75	0	24	0	0.80
12267028--12267089	12	4.9	12	84	7	79	75	0	24	0	0.80
12267129--12267175	17	2.8	17	87	12	71	85	0	12	2	0.70
12270677--12270795	31	3.9	31	78	5	134	23	20	20	36	1.95
12271057--12271108	23	2.3	23	93	0	86	51	9	21	17	1.73
12272969--12273016	25	2.0	23	84	15	62	12	6	2	79	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12272991--12273045	17	3.1	18	85	10	69	12	10	0	76	1.02
12273009--12273055	17	2.8	17	96	3	87	19	10	0	70	1.16
12279401--12279425	2	12.5	2	100	0	50	52	0	48	0	1.00
12288545--12288606	32	1.9	32	100	0	124	20	9	35	33	1.86
12317905--12318007	24	4.3	24	75	10	77	48	16	12	22	1.79
12319416--12319504	38	2.4	37	83	5	124	47	0	1	51	1.08
12319576--12319650	29	2.5	30	93	2	125	16	38	13	32	1.87
12321074--12321121	18	2.7	18	96	0	87	14	20	45	18	1.85
12321060--12321104	23	2.0	23	90	0	72	13	22	46	17	1.83
12322298--12322520	108	2.1	108	95	0	401	34	9	12	43	1.75
12323479--12323545	32	2.1	32	83	5	82	28	23	11	35	1.91
12325639--12325707	30	2.2	30	82	15	86	33	5	18	42	1.75
12325648--12325707	29	2.0	30	90	6	95	31	6	18	43	1.76
12325779--12325848	29	2.4	30	85	4	90	22	38	18	20	1.93
12325777--12325841	21	3.0	21	84	6	69	23	36	20	20	1.95
12325883--12325996	20	5.7	20	89	2	165	17	28	22	31	1.97
12326353--12326422	34	2.1	32	86	5	95	31	15	28	24	1.96
12328570--12328629	29	2.0	30	90	6	95	33	8	16	41	1.78
12328699--12328774	21	3.6	21	78	5	82	23	34	19	22	1.97
12329207--12329276	34	2.1	32	86	5	95	31	15	30	22	1.95
12330350--12330415	34	1.9	34	100	0	132	36	16	6	40	1.73
12330361--12330431	34	2.1	34	81	5	81	43	14	4	38	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12330696--12330735	2	20.0	2	100	0	80	50	0	0	50	1.00
12331354--12331402	23	2.2	23	85	3	64	18	20	8	53	1.70
12333994--12334190	98	2.0	98	100	0	394	40	18	8	32	1.80
12334553--12334613	23	2.7	23	81	0	77	27	24	26	21	1.99
12337911--12337992	18	4.4	19	86	11	100	34	30	14	20	1.93
12337911--12337992	38	2.2	36	85	8	103	34	30	14	20	1.93
12337900--12338012	18	5.9	19	77	13	90	31	29	18	20	1.96
12343112--12343200	18	4.6	19	78	10	83	32	28	19	20	1.96
12343106--12343200	38	2.4	40	81	10	124	30	28	18	22	1.97
12343126--12343200	20	3.7	21	76	18	79	32	29	17	21	1.96
12343877--12343926	19	2.6	19	87	0	73	24	22	20	34	1.97
12343960--12344030	19	3.7	19	98	0	133	21	32	16	29	1.95
12352465--12352987	51	9.8	51	83	7	462	30	25	14	30	1.95
12352459--12352988	106	5.0	102	79	11	487	29	24	15	30	1.96
12354338--12354408	21	3.2	22	79	16	76	9	19	0	70	1.15
12354320--12354408	19	4.2	23	77	18	72	10	20	0	69	1.16
12354324--12354407	44	1.9	43	81	15	102	10	20	0	69	1.18
12363998--12364105	46	2.3	48	90	4	166	41	19	8	30	1.81
12378200--12378254	22	2.5	22	79	8	58	20	0	16	63	1.31
12388817--12388927	19	5.8	19	82	17	124	79	0	0	19	0.79
12388816--12388919	33	3.2	33	89	10	160	78	0	0	21	0.74
12388817--12388933	14	8.6	13	81	13	114	78	0	0	20	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12388824--12388941	33	3.6	31	79	15	123	77	0	1	20	0.85
12389186--12389237	21	2.4	22	80	6	61	69	0	3	26	1.06
12390361--12390418	22	2.7	21	82	17	75	0	22	0	77	0.77
12390376--12390418	10	3.9	11	85	14	54	0	23	0	76	0.78
12391259--12391311	18	2.9	18	85	0	79	28	32	18	20	1.97
12400263--12400301	16	2.5	15	84	12	51	66	2	12	17	1.35
12403627--12403815	5	38.0	5	72	14	99	74	2	5	17	1.12
12403627--12403715	23	3.9	23	85	10	112	77	0	2	20	0.87
12403627--12403815	28	6.7	27	70	21	104	74	2	5	17	1.12
12404080--12404122	20	2.2	20	100	0	86	51	4	25	18	1.66
12406710--12406740	15	2.1	15	100	0	62	22	25	12	38	1.90
12412535--12412583	24	2.2	21	82	10	53	34	10	2	53	1.47
12413624--12413679	28	2.0	28	89	0	85	30	14	10	44	1.79
12422440--12422485	2	23.0	2	100	0	92	50	0	0	50	1.00
12424195--12424251	24	2.4	24	87	0	87	38	21	19	21	1.93
12424643--12424791	21	7.1	21	93	3	228	27	21	23	27	1.99
12430564--12430630	22	3.0	22	82	0	80	28	16	23	31	1.96
12434387--12434451	22	3.0	22	100	0	130	23	21	27	27	1.99
12435809--12435922	23	5.0	23	89	0	165	28	21	19	30	1.98
12449297--12449339	20	2.2	20	86	0	59	34	20	13	30	1.92
12449405--12449463	23	2.6	23	83	0	82	35	22	16	25	1.95
12452683--12452726	22	2.0	22	95	0	79	43	2	4	50	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12452767--12453545	196	4.0	193	82	5	873	47	10	4	37	1.59
12452767--12453548	198	4.0	197	83	4	911	47	10	4	37	1.59
12452798--12453563	395	1.9	393	83	4	999	46	10	4	37	1.59
12457200--12458056	81	10.7	81	80	7	675	25	19	19	34	1.96
12457253--12457594	165	2.1	164	84	1	443	26	18	21	33	1.96
12457277--12458067	243	3.3	239	78	8	752	26	19	19	34	1.96
12458072--12458159	36	2.4	37	88	1	133	23	18	17	40	1.90
12473415--12473463	22	2.2	22	82	7	64	20	18	26	34	1.95
12474462--12474636	29	6.1	29	70	21	93	35	1	16	46	1.57
12474661--12474692	10	2.8	12	86	13	50	25	28	18	28	1.98
12480608--12480676	29	2.4	29	92	4	113	30	0	18	50	1.47
12480693--12480795	29	3.5	29	74	11	93	43	2	11	41	1.56
12482381--12482419	19	2.1	19	95	0	69	28	23	10	38	1.87
12488124--12488183	22	2.7	23	84	2	77	13	26	25	35	1.93
12488123--12488189	23	3.0	22	82	2	80	16	23	25	34	1.95
12490120--12490196	3	25.7	3	100	0	154	32	0	0	67	0.91
12494723--12494774	27	1.9	27	84	7	70	26	5	5	61	1.42
12495640--12495670	16	1.9	16	100	0	62	51	19	9	19	1.74
12497408--12497486	41	2.0	40	87	9	117	36	10	8	44	1.70
12497757--12497873	44	2.6	45	93	5	202	39	23	17	20	1.92
12497786--12497858	24	3.2	24	66	15	73	39	24	17	17	1.91
12497794--12497867	24	3.2	24	64	14	66	43	24	14	17	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12499665--12499706	18	2.3	18	87	0	57	28	19	38	14	1.90
12503024--12503088	21	3.0	21	80	10	62	36	15	24	23	1.93
12503202--12503242	21	2.0	21	85	9	57	36	19	0	43	1.51
12503886--12503920	18	1.9	18	94	0	61	28	31	17	22	1.96
12504655--12504708	24	2.2	24	86	0	81	27	29	7	35	1.84
12507197--12507286	31	2.9	30	75	14	85	33	12	20	34	1.89
12521444--12521510	31	2.1	33	91	5	111	32	16	19	31	1.94
12524043--12524102	18	3.1	19	79	13	68	43	0	0	56	0.99
12527018--12527091	13	5.7	13	91	0	121	25	18	20	35	1.96
12527161--12527205	13	3.5	13	84	0	63	28	24	13	33	1.93

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   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62