genome.fa.s1547.2.7.7.80.10.50.1000.50.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: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  10425128

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   

This is table  50  of  51  ( 6083 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)
9863361--9863399	18	2.2	18	90	0	60	38	35	7	17	1.79
9875575--9875608	18	1.9	17	88	5	50	44	0	14	41	1.45
9878577--9878672	26	3.5	26	71	25	90	56	9	13	20	1.65
9878573--9878681	56	2.0	56	89	7	172	55	11	13	20	1.68
9883687--9883763	23	3.3	23	68	22	63	54	0	3	41	1.19
9883684--9883759	22	3.4	22	72	15	57	53	0	3	42	1.19
9883684--9883720	15	2.4	15	90	4	56	54	0	2	43	1.14
9886842--9886871	2	15.0	2	100	0	60	50	0	0	50	1.00
9887243--9887277	16	2.1	17	89	5	54	65	17	0	17	1.27
9890242--9890303	22	2.7	23	76	18	76	40	3	0	56	1.15
9890229--9890309	23	3.5	23	78	18	80	41	2	1	54	1.21
9899270--9899369	48	2.1	48	100	0	200	26	18	29	27	1.98
9902621--9902647	13	2.1	13	100	0	54	37	14	14	33	1.88
9905398--9905435	20	1.9	20	88	0	58	23	34	31	10	1.89
9905915--9906218	149	2.0	149	99	0	599	28	16	19	35	1.94
9906197--9906241	23	2.0	23	81	0	54	22	24	26	26	2.00
9908258--9908293	2	18.0	2	100	0	72	0	50	0	50	1.00
9908412--9908450	2	19.5	2	100	0	78	51	0	48	0	1.00
9933674--9933724	20	2.5	20	100	0	102	19	23	11	45	1.83
9934393--9934483	2	45.5	2	100	0	182	49	0	0	50	1.00
9943460--9943509	23	2.1	24	85	3	66	58	6	6	30	1.46
9956998--9957057	32	1.9	31	83	10	77	48	1	3	46	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9957020--9957070	26	2.0	26	84	7	68	52	1	3	41	1.31
9959219--9959243	2	12.5	2	100	0	50	52	0	0	48	1.00
9979060--9979111	18	2.9	18	91	0	86	17	34	15	32	1.91
9983474--9983514	20	1.9	20	85	14	55	65	7	4	21	1.37
9991943--9991998	23	2.4	23	94	5	96	17	17	5	58	1.56
9993303--9993329	3	9.0	3	100	0	54	66	0	0	33	0.92
9997587--9997664	39	2.0	39	100	0	156	43	10	5	41	1.61
10000162--10000261	21	4.8	21	88	2	139	27	27	23	23	2.00
10020073--10020135	29	2.2	29	82	5	74	28	14	11	46	1.78
10031602--10031649	21	2.3	21	88	0	69	43	4	2	50	1.33
10033014--10033197	60	3.1	60	77	4	167	30	22	5	41	1.76
10033915--10034183	50	5.6	50	71	11	200	17	33	28	20	1.95
10033930--10034224	141	2.1	141	96	0	545	17	31	30	20	1.95
10038643--10038975	111	3.0	111	96	0	612	45	10	7	36	1.68
10039107--10039142	10	3.5	11	88	11	51	41	0	25	33	1.55
10045733--10045903	81	2.1	81	84	4	220	24	21	19	34	1.96
10050581--10050613	16	2.0	17	88	5	50	24	6	12	57	1.57
10051218--10051242	12	2.1	12	100	0	50	60	8	0	32	1.26
10059451--10059486	2	18.0	2	100	0	72	50	0	0	50	1.00
10060504--10060532	2	14.5	2	100	0	58	0	48	0	51	1.00
10064614--10064687	21	3.5	21	73	14	62	24	0	27	48	1.51
10064629--10064695	21	3.2	21	74	4	64	20	1	28	49	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10064974--10065010	17	2.2	17	95	0	65	24	16	29	29	1.96
10064995--10065059	11	5.6	11	72	22	53	26	26	23	24	2.00
10064989--10065060	23	3.1	23	83	2	99	25	26	23	25	2.00
10066805--10066869	2	32.5	2	100	0	130	49	0	0	50	1.00
10068264--10068344	34	2.4	34	97	0	153	22	14	11	51	1.73
10068264--10068359	34	2.8	34	90	3	120	23	13	16	45	1.83
10073858--10073930	31	2.4	31	81	6	87	38	12	6	42	1.69
10082830--10082882	21	2.5	21	87	0	79	20	24	18	35	1.95
10082872--10082944	20	3.7	20	96	0	128	38	20	20	20	1.94
10082931--10083017	20	4.3	20	92	0	147	29	27	19	22	1.98
10082872--10083002	40	3.3	40	85	6	133	34	23	20	21	1.97
10083853--10083912	24	2.5	24	77	0	75	28	18	15	38	1.91
10086338--10086391	14	3.5	14	73	22	54	44	20	24	11	1.83
10086318--10086413	33	2.8	33	92	3	147	42	20	23	12	1.86
10086351--10086417	20	3.7	19	72	22	72	46	19	22	11	1.82
10088607--10088693	20	4.3	20	92	0	147	42	22	18	16	1.89
10088726--10088772	20	2.3	20	85	0	58	23	19	23	34	1.97
10090686--10090806	20	6.5	19	70	13	81	44	23	17	14	1.85
10090684--10090806	53	2.2	56	87	8	171	45	23	17	13	1.84
10090720--10090807	39	2.3	39	82	4	106	44	22	18	14	1.86
10091143--10091207	22	3.0	22	81	2	78	21	13	36	27	1.92
10091404--10091476	20	3.7	20	92	0	119	21	20	19	38	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10091473--10091518	21	2.2	21	92	0	74	39	17	26	17	1.91
10093022--10093065	20	2.2	20	87	0	61	43	22	9	25	1.82
10093029--10093077	20	2.5	20	83	3	55	51	16	10	22	1.74
10093576--10093619	21	2.1	21	95	0	79	38	4	6	50	1.50
10097322--10097349	5	5.6	5	100	0	56	82	0	0	17	0.68
10108712--10108974	131	2.0	131	97	0	499	26	9	17	46	1.78
10111368--10111418	2	26.0	2	96	4	95	49	0	0	50	1.00
10123301--10123410	54	2.0	55	98	1	213	31	11	21	34	1.90
10126236--10126311	39	1.9	39	91	0	125	59	3	5	31	1.38
10126236--10126295	20	3.0	21	69	14	63	61	3	3	31	1.28
10129926--10129958	11	3.0	11	95	0	57	51	0	3	45	1.16
10130711--10130774	31	2.1	31	84	0	83	48	6	4	40	1.49
10131485--10131514	2	14.5	2	93	6	51	46	0	3	50	1.18
10133262--10133288	13	2.1	13	100	0	54	7	51	0	40	1.30
10138663--10138717	20	2.6	22	75	13	62	47	3	1	47	1.30
10145101--10145139	2	20.0	2	94	5	71	48	0	0	51	1.00
10145817--10146014	100	2.0	98	96	3	362	31	18	19	30	1.96
10148808--10148852	24	2.0	23	86	8	65	31	2	4	62	1.27
10149439--10149471	16	2.1	16	100	0	66	42	12	12	33	1.79
10150359--10150386	2	14.0	2	100	0	56	50	0	0	50	1.00
10155610--10155719	55	2.0	55	96	3	204	35	10	9	45	1.69
10156738--10156808	36	2.0	36	100	0	142	36	15	14	33	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10157203--10157231	2	15.0	2	92	7	51	51	0	0	48	1.00
10157680--10157705	6	4.3	6	100	0	52	15	0	34	50	1.45
10159468--10159506	3	13.0	3	100	0	78	66	0	0	33	0.92
10159742--10160189	222	2.0	221	96	1	835	44	8	11	35	1.70
10161233--10161262	15	2.0	15	100	0	60	26	33	20	20	1.97
10174324--10174401	4	19.5	4	83	0	75	47	28	3	20	1.67
10174324--10174401	16	4.9	16	80	0	84	47	28	3	20	1.67
10174326--10174396	20	3.5	20	84	0	88	47	28	4	19	1.68
10184474--10184510	14	2.5	15	83	16	51	45	8	0	45	1.32
10185128--10185203	36	2.1	36	85	7	100	47	1	3	47	1.29
10198375--10198425	2	25.5	2	100	0	102	50	0	0	49	1.00
10201916--10201981	32	2.1	32	83	8	82	22	10	24	42	1.85
10205206--10205230	12	2.1	12	100	0	50	36	16	16	32	1.90
10206483--10206535	27	2.0	27	82	14	65	67	1	3	26	1.17
10215555--10215591	17	2.1	18	85	14	51	8	40	8	43	1.64
10217299--10217415	34	3.7	33	83	15	142	41	0	0	58	1.04
10217508--10217585	14	5.6	14	73	8	61	46	28	0	25	1.53
10222135--10222188	27	2.0	28	96	3	101	38	11	7	42	1.68
10222283--10222323	12	3.5	12	83	12	50	51	0	0	48	1.00
10222326--10222363	16	2.4	16	91	4	60	63	0	5	31	1.17
10222357--10222417	21	2.9	20	73	7	59	60	3	4	31	1.34
10222431--10222477	21	2.3	22	82	14	64	34	4	0	61	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10222488--10222513	7	3.7	7	100	0	52	73	0	0	26	0.84
10227817--10227887	34	2.1	34	100	0	142	46	0	11	42	1.39
10227830--10227896	19	3.7	19	67	18	54	46	0	10	43	1.38
10228167--10228199	3	11.0	3	100	0	66	66	0	0	33	0.92
10229072--10229118	17	2.8	17	90	0	76	74	0	21	4	0.99
10229367--10229523	59	2.6	57	78	8	154	32	21	7	39	1.80
10232914--10233057	78	1.9	77	86	4	209	45	4	2	47	1.36
10242750--10242822	36	2.1	35	97	2	137	27	13	15	43	1.84
10243711--10243778	35	1.9	35	93	0	118	14	8	14	61	1.55
10245136--10245169	10	3.4	10	100	0	68	17	0	0	82	0.67

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