genome.fa.s8356.2.7.7.80.10.50.1000.19.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: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12862612

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   

This is table  19  of  56  ( 6656 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)
3855582--3855794	80	2.7	80	87	0	300	31	16	20	30	1.95
3856208--3856402	53	3.7	53	84	4	218	30	19	25	24	1.98
3869479--3869535	29	2.0	28	89	3	87	29	7	17	45	1.75
3871272--3871942	22	30.6	22	82	5	668	43	0	9	47	1.38
3871272--3871942	44	15.3	44	86	5	768	43	0	9	47	1.38
3871967--3872025	31	1.9	31	89	0	91	44	6	5	44	1.52
3872453--3872530	33	2.4	34	76	21	85	46	0	0	53	1.00
3872545--3872569	10	2.5	10	100	0	50	52	8	0	40	1.31
3872481--3872583	52	2.0	52	81	9	120	52	2	0	44	1.16
3873658--3873700	2	21.5	2	100	0	86	51	0	0	48	1.00
3873839--3873923	15	5.9	15	79	8	104	41	7	18	32	1.78
3873855--3873923	30	2.3	30	97	2	131	40	7	18	33	1.78
3873906--3873975	20	3.5	20	92	0	122	40	8	14	37	1.76
3874202--3874523	36	9.2	36	75	13	248	46	2	5	45	1.41
3874202--3874461	37	7.1	36	80	7	294	45	3	6	44	1.45
3874427--3874492	29	2.3	29	83	0	78	46	3	4	45	1.38
3874457--3874522	32	2.0	34	88	5	100	51	0	3	45	1.16
3874457--3874523	34	2.0	34	85	5	91	50	0	2	46	1.16
3874580--3874612	15	2.1	16	88	5	50	18	9	0	72	1.10
3875171--3875203	17	2.0	17	94	5	59	78	18	0	3	0.87
3877059--3877092	17	1.9	18	88	5	52	5	11	8	73	1.24
3881140--3882006	84	10.4	83	81	5	941	29	24	20	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3881237--3882006	249	3.1	249	86	3	1023	30	24	20	25	1.99
3881131--3882071	333	2.8	331	86	4	1200	30	24	20	24	1.99
3882659--3882945	37	7.8	36	78	9	278	45	3	5	44	1.45
3882659--3882947	147	2.0	148	88	6	435	45	3	5	44	1.44
3882911--3882976	29	2.3	29	83	0	78	46	3	4	45	1.38
3882659--3882975	109	2.8	111	79	9	263	46	3	5	45	1.43
3882940--3883015	34	2.2	36	88	4	111	50	0	2	47	1.15
3882872--3883008	66	2.1	64	81	7	161	48	1	4	45	1.31
3883664--3883697	18	1.9	18	94	5	61	79	17	0	2	0.86
3884889--3884993	29	3.6	29	80	13	108	54	1	0	42	1.18
3885006--3885049	22	2.0	23	86	4	63	54	0	0	45	0.99
3885010--3885066	21	2.6	22	81	10	64	52	0	0	47	1.00
3884946--3885066	54	2.3	51	77	19	133	50	0	0	47	1.12
3885255--3885369	42	2.7	42	95	0	203	45	19	18	17	1.86
3887379--3887406	14	2.0	14	100	0	56	42	0	0	57	0.99
3889054--3889103	19	2.4	21	77	16	68	16	18	28	38	1.91
3889065--3889103	19	2.1	19	95	0	69	15	17	25	41	1.89
3889725--3889786	5	12.0	5	86	6	61	0	25	38	35	1.56
3889871--3889914	22	2.0	22	100	0	88	40	27	13	18	1.88
3889907--3889953	19	2.5	19	100	0	94	40	19	21	19	1.92
3889942--3889980	20	2.0	20	100	0	78	48	20	20	10	1.78
3890388--3890661	20	13.6	20	76	8	196	38	24	17	19	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3890449--3890664	41	5.3	41	84	6	271	37	24	17	20	1.93
3891224--3891295	20	3.5	20	81	5	83	50	18	16	15	1.79
3891239--3891298	21	2.9	21	80	7	70	48	18	20	13	1.81
3891280--3891344	33	2.0	33	90	0	103	47	20	20	12	1.81
3891285--3891356	33	2.2	33	84	0	90	48	22	18	11	1.79
3891360--3891467	20	5.8	19	77	14	109	12	23	17	47	1.81
3893491--3893557	21	3.2	21	66	6	55	23	35	20	19	1.95
3893448--3893557	42	2.6	42	80	7	107	24	33	20	21	1.97
3895082--3895202	19	6.8	19	69	21	93	12	21	20	45	1.84
3895097--3895199	53	2.0	52	86	5	145	12	22	21	43	1.86
3895151--3895233	33	2.5	34	86	9	125	10	19	24	45	1.82
3895158--3895216	14	3.9	14	76	20	55	10	16	25	47	1.78
3895575--3895687	41	2.8	40	73	16	115	23	17	24	34	1.96
3895615--3895664	21	2.4	21	90	3	75	20	20	26	34	1.96
3895673--3895725	20	2.7	20	91	5	81	13	18	24	43	1.86
3897748--3897791	20	2.2	20	83	0	52	75	4	0	20	0.98
3899549--3899623	38	2.0	37	84	5	98	48	4	1	46	1.29
3905625--3905661	12	3.1	12	96	0	65	51	27	8	13	1.69
3913482--3913851	191	1.9	190	93	1	643	37	10	13	39	1.78
3925151--3925235	37	2.2	41	81	12	99	35	12	4	47	1.63
3932008--3932238	38	6.0	38	80	6	266	24	16	16	41	1.89
3932008--3932239	80	3.0	77	83	5	288	25	16	16	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3934338--3934524	38	4.9	38	86	3	252	24	17	18	40	1.91
3934338--3934566	76	3.0	76	82	6	264	23	18	18	39	1.92
3934489--3934845	45	8.0	45	77	6	262	21	17	21	40	1.92
3934532--3934835	135	2.3	135	84	1	385	21	17	21	39	1.92
3934532--3934835	90	3.4	89	78	4	306	21	17	21	39	1.92
3935392--3936118	134	5.5	132	84	6	800	29	20	18	30	1.97
3935392--3936118	259	2.7	262	85	7	909	29	20	18	30	1.97
3938323--3938359	14	2.7	14	84	16	51	27	0	2	70	1.01
3939931--3940038	38	3.0	35	83	13	132	44	4	5	45	1.47
3939897--3940020	38	3.4	38	83	9	143	43	3	7	45	1.47
3939897--3940038	71	2.0	71	82	8	173	44	3	6	45	1.46
3939985--3940041	17	3.4	17	75	20	57	47	5	3	43	1.43
3940016--3940071	24	2.3	25	87	3	78	48	3	3	44	1.37
3939966--3940092	57	2.2	57	87	5	175	46	3	4	44	1.42
3940182--3940238	19	3.3	19	65	34	56	43	3	0	52	1.18
3940137--3940236	32	3.3	30	84	14	125	39	3	3	55	1.31
3940166--3940239	32	2.3	32	100	0	148	40	2	0	56	1.13
3940736--3940885	78	1.9	78	86	2	212	42	27	17	13	1.86
3941582--3941619	17	2.2	17	90	0	58	26	5	0	68	1.11
3941589--3941640	22	2.4	22	83	6	61	19	5	0	75	1.01
3941605--3941640	11	3.4	11	88	3	56	16	5	0	77	0.94
3941604--3941652	22	2.3	21	83	13	64	14	6	2	77	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3947275--3947311	19	1.9	19	88	0	56	40	8	16	35	1.78
3956037--3956068	14	2.2	15	94	5	57	56	18	9	15	1.66
3957109--3957360	36	7.1	35	77	13	234	44	4	9	42	1.57
3957155--3957183	14	2.1	14	100	0	58	41	6	6	44	1.58
3957220--3957287	32	2.2	31	84	7	84	42	4	10	42	1.58
3957384--3957459	28	2.6	28	83	8	82	38	2	3	55	1.33
3957461--3957500	20	2.1	19	85	4	53	12	10	0	77	0.99
3958962--3958998	17	2.2	17	90	4	58	27	5	0	67	1.12
3959000--3959054	6	9.7	6	94	2	80	14	10	1	72	1.19
3959949--3959974	2	13.0	2	100	0	52	50	0	0	50	1.00
3959996--3960027	2	16.5	2	93	6	57	53	0	0	46	1.00
3961204--3961241	18	2.2	17	86	9	51	39	5	0	55	1.23
3962033--3962066	16	2.1	17	88	5	52	29	0	2	67	1.05
3963537--3963648	60	1.9	60	85	9	158	33	24	4	38	1.75
3963845--3963979	60	2.2	60	82	0	171	41	4	20	33	1.73
3965912--3965937	3	8.7	3	100	0	52	69	0	30	0	0.89
3967109--3967139	11	2.7	12	90	10	55	32	0	0	67	0.91
3977318--3977344	10	2.7	10	100	0	54	51	0	37	11	1.37
3979969--3979995	2	13.5	2	100	0	54	48	0	51	0	1.00
3984341--3984365	3	8.3	3	100	0	50	32	0	0	68	0.90
3985972--3986010	20	2.0	20	85	10	53	43	0	0	56	0.99
4001626--4001662	18	2.1	18	100	0	74	37	10	5	45	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4008285--4008547	44	6.0	44	85	0	337	30	18	16	34	1.93
4008656--4008769	36	3.2	36	87	5	167	28	13	10	48	1.75
4009014--4009051	3	13.0	3	83	5	51	28	2	0	68	1.03
4009008--4009048	12	3.3	12	82	3	55	24	4	0	70	1.06
4012285--4012382	21	4.7	21	88	0	151	25	22	17	34	1.95
4012489--4012526	20	1.9	20	88	0	58	31	21	23	23	1.98
4015035--4015090	24	2.3	24	100	0	112	28	17	16	37	1.91
4020223--4020293	27	2.6	27	84	4	90	22	18	43	15	1.87
4021991--4022044	8	6.3	9	75	12	60	64	1	1	31	1.14
4021993--4022042	17	3.1	16	91	2	73	62	2	2	34	1.18

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