genome.fa.s190.2.7.7.80.10.50.1000.42.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: 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  42  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)
9931480--9931510	15	2.1	15	93	0	53	45	0	0	54	0.99
9932318--9932474	64	2.5	62	82	7	179	34	18	22	24	1.96
9933687--9933730	2	22.0	2	100	0	88	50	0	0	50	1.00
9939191--9939251	23	2.6	22	77	10	68	16	22	27	32	1.96
9944538--9944591	28	1.9	28	81	7	65	37	1	18	42	1.61
9947746--9947907	64	2.5	64	78	5	175	33	17	22	26	1.96
9949011--9949043	2	16.5	2	100	0	66	51	0	0	48	1.00
9953150--9953244	31	3.0	31	75	3	100	33	16	15	33	1.91
9953170--9953272	32	3.3	32	73	11	81	32	20	14	33	1.93
9953574--9953626	10	6.1	10	68	31	50	62	18	11	7	1.52
9953574--9953626	26	2.0	26	86	13	74	62	18	11	7	1.52
9953577--9953627	16	3.1	17	94	5	88	62	19	11	5	1.49
9955544--9955580	13	2.9	13	92	4	58	29	2	24	43	1.68
9956037--9956187	18	8.0	18	67	19	76	46	5	2	45	1.41
9956017--9956102	11	7.5	11	69	19	59	50	4	0	45	1.22
9956078--9956230	13	11.1	13	68	15	76	47	5	4	43	1.46
9956042--9956226	98	1.9	98	95	0	334	46	5	3	43	1.46
9956113--9956190	18	4.2	18	79	12	79	48	5	2	43	1.38
9957062--9957382	159	2.0	160	99	0	635	28	14	28	28	1.96
9960079--9960127	22	2.2	22	96	0	89	38	16	26	18	1.91
9961089--9961238	79	1.9	79	88	2	230	46	2	6	44	1.41
9961402--9961460	7	8.4	7	84	0	64	22	0	33	44	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9961680--9961734	20	2.9	19	84	7	76	25	29	0	45	1.54
9961844--9961927	2	42.5	2	83	7	109	53	2	1	42	1.21
9962364--9962426	2	31.5	2	87	6	92	44	1	1	52	1.20
9962535--9962579	20	2.3	20	96	3	83	44	0	33	22	1.53
9962496--9962589	46	2.0	45	88	8	136	43	0	27	28	1.55
9962946--9962986	22	2.0	20	85	9	55	41	7	0	51	1.30
9963104--9963130	13	2.1	13	100	0	54	44	0	0	55	0.99
9963253--9963315	16	3.9	16	93	0	99	41	12	23	22	1.88
9963249--9963315	32	2.1	32	94	0	116	41	13	23	20	1.88
9963419--9963448	11	2.7	11	94	0	51	10	23	30	36	1.87
9974119--9974172	27	1.9	29	81	7	67	53	9	3	33	1.50
9974276--9974338	32	2.0	32	84	12	85	28	33	22	15	1.95
9974541--9974603	32	2.0	32	84	12	85	28	33	22	15	1.95
9974141--9974675	265	2.0	268	97	2	1015	33	20	17	28	1.95
9975196--9975236	21	2.0	21	85	0	55	43	4	12	39	1.63
9979416--9979453	19	2.0	19	89	0	58	34	18	28	18	1.95
9979487--9979569	23	3.3	23	72	16	58	12	16	43	27	1.84
9979511--9979573	28	2.2	28	94	0	108	9	15	47	26	1.76
9986055--9986119	30	2.2	31	86	5	89	44	0	3	52	1.16
9987959--9988027	23	3.0	23	78	0	84	30	26	23	20	1.98
9989493--9989536	13	3.4	13	83	0	52	27	18	15	38	1.91
9989519--9989672	84	1.8	84	82	8	197	31	18	18	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9994123--9994172	19	2.6	19	93	0	91	20	20	30	30	1.97
9997891--9997954	23	2.8	23	78	4	76	39	25	18	17	1.92
10004684--10004713	13	2.3	13	94	0	51	16	23	0	60	1.36
10011519--10011579	22	2.8	21	75	5	59	54	1	1	42	1.20
10011851--10011892	18	2.4	18	88	7	61	42	0	0	57	0.99
10012259--10012306	20	2.4	20	92	0	78	47	4	6	41	1.48
10016652--10016684	16	2.1	16	100	0	66	27	18	18	36	1.94
10017972--10018035	21	3.0	21	86	4	92	28	23	25	23	2.00
10018308--10018336	14	2.0	15	93	6	51	13	13	13	58	1.63
10026483--10026539	22	2.6	22	77	17	57	49	3	0	47	1.18
10026852--10026896	22	2.0	23	91	4	74	51	4	0	44	1.21
10026858--10026901	22	2.0	22	86	8	63	52	4	0	43	1.22
10026925--10026971	24	1.9	25	82	4	60	46	0	4	48	1.21
10030579--10030637	26	2.2	27	88	8	86	55	0	0	44	0.99
10030579--10030639	22	2.7	22	82	10	61	55	0	0	44	0.99
10033685--10033774	45	2.0	44	89	2	135	46	7	3	42	1.49
10036144--10036199	15	3.6	15	74	9	58	46	10	8	33	1.70
10036639--10036695	21	2.7	21	94	0	96	26	24	28	21	1.99
10036891--10036945	13	4.2	13	75	13	58	49	12	3	34	1.59
10036931--10037029	33	3.0	33	94	1	164	45	15	7	32	1.73
10037024--10037065	21	2.0	21	95	0	75	47	7	14	30	1.71
10039368--10039413	12	3.6	12	81	16	56	17	19	17	45	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10039367--10039406	15	2.9	14	85	14	57	20	17	15	47	1.83
10043773--10043881	54	2.0	54	98	0	209	38	14	21	25	1.91
10044247--10044347	51	2.0	51	92	0	166	33	20	10	34	1.88
10051886--10051944	13	4.2	13	76	19	64	20	44	18	16	1.87
10053014--10053052	18	2.2	18	90	0	60	51	0	17	30	1.46
10054157--10054272	24	4.8	24	88	4	162	25	15	18	39	1.91
10059028--10059209	102	1.8	97	87	0	229	29	29	17	24	1.97
10068590--10068621	16	2.1	15	94	5	55	0	15	0	84	0.63
10069488--10069567	31	2.6	31	93	0	133	38	17	28	15	1.90
10069954--10070008	21	2.9	18	72	15	56	25	7	14	52	1.67
10074716--10074759	16	2.8	15	80	10	52	75	0	9	15	1.05
10074750--10074816	23	3.0	23	76	10	77	74	2	8	13	1.17
10074693--10074893	13	15.9	13	65	21	72	71	0	4	22	1.12
10074865--10074915	2	25.5	2	84	7	59	56	0	1	41	1.10
10074726--10074894	51	3.4	49	78	14	143	71	1	5	21	1.13
10074814--10074923	32	3.7	32	80	13	119	66	0	1	31	1.02
10074973--10075031	23	2.6	23	78	10	59	67	3	8	20	1.31
10076116--10076198	37	2.3	36	86	10	109	33	9	14	42	1.78
10076113--10076198	34	2.4	34	84	9	111	32	9	16	41	1.80
10076333--10076380	15	3.1	15	78	6	51	45	14	20	18	1.85
10076371--10076557	102	1.8	102	83	4	252	40	13	18	27	1.88
10076705--10076966	106	2.5	105	89	2	407	24	18	24	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10077635--10077724	32	2.8	32	93	0	153	37	20	12	30	1.89
10078662--10078799	69	2.0	69	94	0	240	24	14	21	39	1.91
10078871--10078920	12	4.0	12	83	16	66	2	16	2	80	0.91
10078870--10078920	13	4.0	13	85	12	70	3	15	1	78	0.99
10080890--10080940	17	3.1	17	75	11	52	70	0	15	13	1.17
10081869--10081961	35	2.6	32	78	14	78	77	2	6	13	1.06
10081898--10082061	13	12.6	12	67	22	66	72	1	3	23	1.06
10081909--10081935	11	2.5	11	100	0	54	92	0	7	0	0.38
10081921--10081989	24	2.9	24	71	26	65	75	1	2	20	1.01
10081897--10082014	9	13.6	9	71	19	58	75	0	2	21	0.97
10081897--10082014	48	2.5	45	80	10	128	75	0	2	21	0.97
10081955--10082073	39	3.0	40	76	14	122	66	0	2	30	1.11
10081951--10082042	44	2.1	42	86	7	123	68	0	2	29	1.01
10082051--10082109	26	2.3	25	82	11	66	66	3	3	27	1.24
10082052--10082109	27	2.2	26	81	9	64	67	3	3	25	1.22
10083790--10083874	45	1.9	44	83	11	111	38	4	4	51	1.44
10084743--10084809	20	3.3	20	79	4	89	41	17	22	17	1.90
10084760--10084835	21	3.7	21	76	3	91	42	18	23	15	1.89
10084824--10084938	20	5.7	20	82	6	115	31	26	18	24	1.97
10084743--10084835	41	2.3	41	98	0	177	40	18	23	17	1.90
10084821--10084958	41	3.4	41	79	6	154	34	24	17	23	1.96
10085126--10085169	22	2.0	22	91	8	72	22	45	13	18	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10085126--10085177	22	2.5	21	84	12	63	23	44	11	21	1.84
10086810--10086854	18	2.5	18	92	0	81	28	44	13	13	1.81
10087335--10087401	20	3.4	20	81	2	73	38	23	22	14	1.92
10087335--10087437	19	5.6	19	75	14	72	41	23	21	13	1.88
10087449--10087506	14	3.9	14	81	16	71	8	17	24	50	1.74
10087444--10087522	32	2.4	33	93	2	133	10	18	22	48	1.78
10087463--10087580	20	6.4	19	77	11	95	13	19	23	43	1.87
10089428--10089463	14	2.6	14	90	0	54	30	0	22	47	1.52
10089570--10089623	14	3.5	14	75	22	54	48	22	18	11	1.79
10089551--10089628	33	2.4	33	88	0	111	42	23	21	12	1.87

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