genome.fa.s9634.2.7.7.80.10.50.1000.42.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

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   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   

This is table  42  of  78  ( 9351 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)
8313270--8313301	3	10.7	3	100	0	64	34	0	0	65	0.93
8314383--8314412	3	10.0	3	92	0	51	33	3	0	63	1.11
8321419--8321447	12	2.5	12	94	5	51	75	0	6	17	1.01
8326661--8326812	73	2.1	73	91	0	241	39	17	21	22	1.92
8330256--8330294	20	2.0	20	84	0	51	28	15	15	41	1.87
8330408--8330447	20	2.0	21	90	5	64	35	20	20	25	1.96
8331696--8331743	19	2.5	20	86	3	62	45	6	14	33	1.70
8332879--8333156	148	1.9	149	91	2	461	37	8	14	39	1.77
8336250--8336289	21	2.0	20	90	5	62	15	7	2	75	1.14
8336677--8336706	3	10.0	3	100	0	60	66	0	0	33	0.92
8337032--8337257	119	1.9	119	84	0	299	26	17	26	30	1.97
8337157--8337416	140	1.9	139	87	4	389	27	16	26	28	1.97
8337672--8337782	30	3.5	30	68	20	91	40	11	16	31	1.84
8337567--8337825	66	3.9	66	81	3	288	38	11	16	32	1.85
8337702--8338009	99	3.0	100	79	6	311	37	11	16	34	1.84
8338053--8338186	36	3.7	36	71	5	99	36	11	18	32	1.88
8338714--8338745	16	2.0	16	93	0	55	37	18	3	40	1.67
8340829--8340889	16	3.8	16	81	16	65	3	9	6	80	1.00
8340768--8340888	15	7.5	15	71	14	66	3	14	4	76	1.08
8352472--8352534	20	3.2	20	88	2	92	65	0	14	20	1.27
8360788--8360979	68	2.9	65	88	8	282	42	6	6	43	1.57
8364302--8364562	13	19.2	15	75	24	237	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8364303--8364567	5	50.0	5	94	4	370	39	0	0	60	0.97
8365477--8365504	2	14.0	2	100	0	56	0	50	0	50	1.00
8366029--8366131	30	3.4	29	86	5	134	15	10	10	63	1.53
8371601--8371635	16	2.3	15	95	5	61	51	28	0	20	1.47
8371949--8372036	36	2.3	36	83	14	99	32	25	9	32	1.87
8372048--8372095	21	2.3	21	92	0	87	39	20	10	29	1.86
8372379--8372451	29	2.5	29	90	0	119	24	17	12	45	1.83
8372491--8372526	18	2.0	18	94	0	63	36	16	11	36	1.84
8380387--8380429	2	21.5	2	90	0	59	6	0	41	51	1.29
8380427--8380483	4	14.2	4	88	0	87	26	3	22	47	1.67
8383008--8383078	20	3.5	20	92	0	106	30	11	29	28	1.91
8383206--8383758	108	5.1	108	90	0	865	32	16	19	31	1.94
8383206--8383758	54	10.2	54	88	2	781	32	16	19	31	1.94
8388129--8388247	63	1.9	63	84	6	161	42	15	6	36	1.73
8388219--8388278	31	1.9	31	89	0	93	45	15	3	36	1.62
8405556--8405616	21	2.9	22	87	7	99	24	9	27	37	1.87
8409847--8409948	41	2.5	41	91	1	168	25	14	17	42	1.88
8413754--8413865	26	4.3	26	97	0	206	40	10	17	31	1.84
8414704--8414745	14	3.2	14	77	19	54	59	4	9	26	1.48
8425756--8425794	2	19.5	2	100	0	78	51	0	0	48	1.00
8427468--8427629	80	2.0	80	98	0	315	30	13	21	34	1.92
8431290--8431357	20	3.4	20	79	4	75	29	33	8	27	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8431401--8431440	20	2.0	20	95	0	71	37	25	20	17	1.94
8431571--8431613	22	2.0	22	85	0	59	23	34	16	25	1.95
8431908--8431949	20	2.1	20	86	0	57	14	19	21	45	1.85
8432328--8432367	14	2.9	14	80	0	53	30	0	17	52	1.45
8432718--8432804	39	2.2	39	95	0	156	17	13	20	48	1.81
8433116--8433152	18	2.1	18	89	0	56	51	10	5	32	1.60
8433745--8433797	19	2.8	19	94	0	97	33	9	20	35	1.85
8433785--8433831	21	2.2	21	81	7	60	40	17	21	21	1.91
8433839--8433892	20	2.7	19	77	8	63	31	14	27	25	1.95
8434715--8434790	31	2.4	31	78	6	82	27	30	26	15	1.96
8434667--8434790	63	2.0	63	82	9	155	26	27	27	18	1.98
8435659--8435689	7	4.4	7	100	0	62	25	29	29	16	1.96
8435679--8435738	17	3.4	17	80	8	75	13	23	45	18	1.84
8435686--8435735	19	2.5	19	90	9	73	8	22	50	20	1.74
8435709--8435736	14	2.0	14	100	0	56	7	21	50	21	1.72
8435732--8435783	19	2.7	19	93	3	86	23	30	28	17	1.97
8435742--8435783	9	4.4	10	79	11	52	23	28	28	19	1.98
8442031--8442106	31	2.4	31	78	6	82	27	30	26	15	1.96
8441983--8442106	63	2.0	63	84	9	164	26	28	27	17	1.98
8442988--8443042	17	3.2	17	97	0	101	14	23	43	18	1.87
8447563--8447610	20	2.2	22	89	10	73	41	8	0	50	1.33
8448550--8448612	7	9.0	7	82	0	72	19	1	34	44	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8450968--8451018	2	26.0	2	92	4	86	47	0	0	52	1.00
8456171--8456203	13	2.5	13	90	9	50	42	0	12	45	1.41
8456453--8456508	17	3.0	19	72	12	62	67	3	0	28	1.07
8457260--8457374	60	1.9	60	87	0	167	34	21	11	32	1.89
8461854--8462604	182	4.1	181	87	2	1026	41	14	16	27	1.87
8463177--8463237	2	30.5	2	100	0	122	50	0	0	49	1.00
8463255--8463327	24	3.0	24	81	0	83	39	20	15	24	1.91
8463289--8463345	24	2.4	24	79	2	62	49	19	8	22	1.76
8464026--8464213	29	6.6	29	85	2	245	47	15	5	30	1.69
8464026--8464213	86	2.2	85	86	3	261	47	15	5	30	1.69
8464026--8464211	57	3.2	57	92	0	300	48	14	5	31	1.68
8470364--8470464	35	2.9	35	93	0	166	31	28	30	8	1.88
8470526--8470634	2	54.5	2	100	0	218	50	0	0	49	1.00
8470671--8470723	24	2.2	24	86	0	70	41	22	9	26	1.84
8470685--8470741	24	2.4	24	79	2	62	49	19	8	22	1.76
8471433--8471620	29	6.6	29	83	3	247	49	15	5	28	1.68
8471433--8471619	57	3.3	57	92	2	313	49	15	5	28	1.68
8471439--8471611	56	3.1	56	92	1	283	50	14	5	29	1.64
8474919--8474964	21	2.2	21	84	7	58	43	13	32	10	1.78
8474928--8474971	21	2.1	21	100	0	88	38	9	38	13	1.77
8475005--8475104	33	3.0	33	94	0	182	29	0	46	25	1.53
8475289--8475326	18	2.1	18	95	0	67	57	0	34	7	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8476881--8476929	19	2.6	19	96	0	89	32	2	10	55	1.45
8477193--8478150	199	4.8	199	81	6	1116	37	15	16	31	1.89
8477606--8477639	15	2.3	15	89	0	50	38	38	14	8	1.78
8477191--8478156	401	2.4	383	81	10	1107	37	15	15	31	1.89
8478811--8478836	2	13.0	2	100	0	52	50	0	0	50	1.00
8479650--8479708	3	19.7	3	89	0	91	37	0	30	32	1.58
8480817--8480871	13	4.2	13	92	0	92	25	21	18	34	1.96
8480844--8481008	85	1.9	85	80	9	194	30	21	17	30	1.96
8481028--8481060	2	16.5	2	100	0	66	48	0	0	51	1.00
8486637--8486692	24	2.3	24	84	6	69	28	7	16	48	1.72
8486984--8487022	20	2.0	20	84	0	51	41	7	15	35	1.76
8486748--8487277	199	2.7	200	89	1	769	38	13	16	32	1.87
8488765--8489241	200	2.4	197	86	6	640	39	13	15	32	1.86
8489288--8489450	87	1.9	87	93	0	281	31	14	12	41	1.82
8489372--8489416	23	2.0	23	86	0	63	37	20	8	33	1.83
8491402--8491438	18	2.1	18	100	0	74	32	10	27	29	1.90
8504521--8504570	12	4.4	11	80	9	55	84	0	12	4	0.76
8504491--8504563	8	8.2	8	75	15	56	79	2	13	4	0.99
8504491--8504563	17	4.1	17	73	18	67	79	2	13	4	0.99
8506968--8507378	209	1.9	211	88	5	616	35	16	10	37	1.83
8507640--8507680	21	2.0	21	85	0	55	7	31	0	60	1.24
8508181--8508227	20	2.3	20	92	0	76	34	19	10	36	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
8508263--8508311	20	2.5	19	75	21	55	30	14	14	40	1.85
8509540--8509659	9	14.9	8	76	16	83	23	4	0	71	1.08
8509582--8509659	3	26.7	3	82	12	92	26	2	0	70	1.00
8509671--8509719	25	1.9	26	84	12	66	38	4	0	57	1.18
8509896--8509924	11	2.6	11	100	0	58	17	0	0	82	0.66
8510765--8510794	13	2.3	13	94	0	51	26	43	16	13	1.85
8514194--8514389	95	2.1	94	86	1	275	33	18	17	30	1.94
8515816--8516435	251	2.5	252	88	1	893	32	23	18	25	1.97
8517964--8518006	15	2.7	15	82	7	50	25	2	0	72	0.97
8517984--8518037	3	18.7	3	88	11	78	27	1	0	70	0.98

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   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78