genome.fa.s9634.2.7.7.80.10.50.1000.30.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  30  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)
6177225--6177259	16	2.1	18	89	10	56	25	8	0	65	1.21
6179317--6179355	15	2.6	15	95	0	69	20	23	20	35	1.96
6180083--6180120	10	3.8	10	80	13	51	10	10	44	34	1.73
6180076--6180120	20	2.2	20	96	0	81	8	11	46	33	1.70
6183294--6183344	15	3.4	15	76	15	52	41	3	15	39	1.66
6183290--6183360	30	2.4	30	86	9	101	46	5	14	33	1.67
6183552--6183600	21	2.4	20	83	12	64	36	0	2	61	1.08
6183585--6183655	30	2.2	33	82	7	85	45	0	5	49	1.26
6183734--6183786	20	2.7	20	75	16	56	49	1	0	49	1.12
6188985--6189274	148	2.0	145	90	4	458	34	10	15	40	1.81
6205276--6205303	2	14.0	2	100	0	56	50	0	0	50	1.00
6205598--6205657	30	2.0	30	84	9	79	30	23	8	38	1.84
6206234--6206288	20	2.8	20	94	0	83	21	34	18	25	1.96
6206627--6206691	32	2.0	32	96	0	121	18	18	15	47	1.82
6208714--6208843	58	2.2	58	81	9	140	40	14	10	35	1.80
6210811--6210874	12	5.3	12	67	14	51	25	18	7	48	1.75
6210799--6210874	24	3.2	24	92	0	125	22	18	9	50	1.75
6211069--6211137	23	3.0	22	72	2	57	46	14	11	27	1.79
6215746--6215780	18	1.9	18	88	0	52	37	11	20	31	1.88
6217064--6217101	20	2.0	20	89	5	60	50	7	13	28	1.69
6218363--6218419	20	2.9	19	79	7	60	29	21	15	33	1.94
6223761--6224038	139	2.0	139	94	0	493	40	15	11	32	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6229238--6229289	19	2.7	19	87	0	77	26	19	34	19	1.95
6229286--6229394	57	1.9	56	83	9	141	28	19	22	30	1.98
6235409--6235461	22	2.3	23	83	6	63	45	0	1	52	1.11
6235432--6235683	137	1.8	136	82	9	325	40	7	5	45	1.58
6235678--6235707	2	15.0	2	92	0	51	46	0	0	53	1.00
6237698--6237728	16	1.9	16	93	0	53	45	16	0	38	1.47
6238355--6238478	31	4.0	32	68	10	78	26	28	25	19	1.99
6239294--6239456	29	5.6	29	82	5	213	39	21	4	34	1.73
6239300--6239455	57	2.7	56	88	4	222	40	20	4	34	1.73
6239465--6239509	19	2.4	19	84	0	63	26	33	22	17	1.96
6245613--6245665	25	2.1	25	89	0	79	47	13	5	33	1.66
6245724--6245800	31	2.5	31	78	2	82	28	31	25	14	1.95
6246583--6246717	29	4.6	29	82	3	171	37	21	5	36	1.76
6246583--6246717	60	2.3	60	85	2	184	37	21	5	36	1.76
6249837--6249867	16	2.0	15	93	6	53	83	0	16	0	0.64
6254441--6254665	73	3.1	71	83	6	290	31	20	12	36	1.90
6254442--6254624	36	5.0	36	64	9	120	31	19	10	38	1.86
6261734--6261781	21	2.3	21	85	7	62	60	2	0	37	1.09
6265477--6265516	18	2.2	18	86	8	55	17	30	27	25	1.97
6269562--6269587	13	2.0	13	100	0	52	15	30	7	46	1.74
6273654--6273702	10	4.8	11	80	16	61	57	0	0	42	0.99
6273662--6273700	13	3.2	13	82	17	57	56	0	0	43	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6273654--6273702	15	3.3	15	85	5	64	57	0	0	42	0.99
6274159--6274260	37	2.8	37	89	0	141	30	14	14	40	1.86
6275013--6276089	106	10.3	106	88	3	1516	23	18	24	33	1.97
6275795--6276089	94	3.0	96	83	6	369	24	17	24	33	1.96
6276992--6277046	22	2.5	22	100	0	110	23	12	27	36	1.91
6277627--6277699	7	9.9	7	71	21	51	1	12	6	79	0.99
6277640--6277709	15	4.6	14	81	15	68	0	14	7	78	0.95
6277640--6277711	16	4.7	15	80	16	76	0	15	6	77	0.96
6277640--6277711	31	2.3	31	83	6	92	0	15	6	77	0.96
6282090--6282157	26	2.7	25	81	6	75	70	2	4	22	1.18
6282188--6282250	21	3.0	21	77	15	67	63	3	3	30	1.25
6282931--6283020	37	2.4	37	86	0	117	30	13	14	42	1.84
6284551--6284593	20	2.2	20	82	0	50	32	20	13	32	1.92
6284855--6284892	3	13.0	3	94	5	69	31	0	0	68	0.90
6287244--6287279	19	1.9	19	94	5	65	33	5	5	55	1.46
6290172--6290231	21	2.8	21	87	2	84	80	3	13	3	0.97
6290156--6290231	34	2.2	33	80	15	84	76	3	14	5	1.11
6294777--6294821	20	2.2	20	100	0	90	31	15	15	37	1.89
6296387--6296421	18	1.9	18	94	0	61	25	25	22	25	2.00
6297266--6297340	21	3.5	21	75	10	71	29	24	16	30	1.96
6299607--6299638	15	2.1	15	100	0	64	18	40	6	34	1.76
6299766--6299805	20	2.0	21	90	9	66	60	5	0	35	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6299979--6300034	24	2.3	24	81	6	69	44	5	25	25	1.75
6300029--6300069	22	1.9	22	85	5	57	26	2	24	46	1.65
6302464--6302520	17	3.5	17	68	29	52	26	0	3	70	1.03
6308403--6308438	11	3.4	11	96	3	65	36	19	27	16	1.93
6308439--6308495	17	3.4	16	75	15	62	31	28	15	24	1.96
6311114--6311141	12	2.3	12	100	0	56	7	28	21	42	1.79
6312570--6312634	27	2.4	27	94	0	121	35	41	10	12	1.78
6319389--6319457	27	2.6	27	88	0	93	37	8	15	37	1.79
6319457--6319495	19	2.1	19	100	0	78	48	0	10	41	1.37
6320168--6320295	39	3.3	39	87	0	202	15	27	26	30	1.96
6322214--6322286	18	3.8	18	74	13	74	32	30	17	19	1.95
6322207--6322284	40	2.0	40	89	0	120	33	26	17	21	1.96
6329123--6329180	18	2.9	21	80	17	77	29	31	15	24	1.95
6329124--6329186	22	3.0	21	82	13	78	30	28	15	25	1.96
6330663--6330706	20	2.2	20	95	0	79	22	13	18	45	1.84
6335221--6335250	10	3.1	10	95	4	53	20	43	20	16	1.88
6335874--6335908	3	11.7	3	100	0	70	31	0	0	68	0.90
6336330--6336462	39	3.4	39	84	0	176	18	26	24	30	1.98
6338021--6338065	3	15.0	3	100	0	90	33	0	0	66	0.92
6350296--6350397	31	3.3	31	98	0	195	13	27	32	26	1.94
6350300--6350429	31	4.2	31	91	1	179	15	29	30	25	1.96
6353642--6353679	19	2.0	20	85	15	53	21	15	21	42	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6355077--6355131	28	2.0	28	82	3	67	16	10	41	30	1.83
6361516--6361576	24	2.5	24	100	0	122	36	8	39	16	1.78
6363867--6363905	19	2.0	20	85	5	53	30	7	7	53	1.57
6364009--6364131	23	5.2	24	77	5	117	32	22	21	23	1.98
6364014--6364131	46	2.5	47	83	1	139	32	23	20	23	1.98
6369284--6369355	24	3.0	24	79	4	92	29	13	22	34	1.93
6369283--6369357	23	3.2	23	77	3	87	29	13	22	34	1.92
6369506--6369542	15	2.5	15	90	0	56	35	18	5	40	1.74
6373840--6373889	24	2.1	24	85	3	66	38	4	0	58	1.17
6376471--6376523	21	2.7	20	79	5	63	22	0	32	45	1.53
6377031--6377067	18	2.1	18	94	0	65	64	5	0	29	1.15
6380057--6380105	23	2.1	24	88	3	73	20	26	6	46	1.73
6380064--6380115	23	2.3	23	83	9	63	25	21	7	46	1.77
6380800--6380848	24	2.0	25	84	11	66	51	0	2	46	1.12
6383316--6383363	24	2.0	25	83	4	62	6	12	8	72	1.26
6397330--6397375	14	3.3	14	85	8	58	71	10	2	15	1.23
6399867--6399897	10	3.1	10	90	0	53	80	6	0	12	0.89
6400243--6400367	30	4.2	30	84	2	135	52	10	20	16	1.73
6401739--6401800	3	20.3	3	96	3	115	64	0	0	35	0.94
6402558--6402732	20	8.7	20	87	3	190	30	26	18	24	1.98
6402888--6402919	12	2.8	12	95	4	57	15	37	6	40	1.73
6403474--6403527	24	2.2	24	90	0	81	22	16	20	40	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6405995--6406043	20	2.5	20	93	0	80	34	26	22	16	1.95
6406006--6406050	20	2.2	20	96	0	81	42	20	22	15	1.89
6407703--6407794	42	2.2	42	88	1	141	20	15	42	21	1.89
6407730--6407790	21	2.9	21	73	9	70	21	13	42	22	1.87
6408131--6408183	20	2.7	20	87	0	70	33	28	13	24	1.93
6408137--6408231	20	4.8	20	83	3	86	38	23	20	17	1.93
6408196--6408269	19	4.2	19	73	16	86	48	17	17	16	1.81
6408212--6408294	33	2.5	33	92	0	130	51	20	15	12	1.75
6408212--6408305	33	2.8	33	88	3	109	52	22	13	11	1.73
6408306--6408436	19	7.3	19	69	18	75	12	18	22	46	1.83

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