genome.fa.s9639.2.7.7.80.10.50.1000.16.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: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  15077257

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  16  of  62  ( 7398 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)
3536054--3536098	23	2.0	23	90	0	72	62	0	31	6	1.21
3536635--3536697	33	1.9	33	83	6	83	47	3	0	49	1.17
3541065--3541126	14	4.5	15	78	13	62	0	37	0	62	0.95
3541100--3541752	232	2.8	232	91	1	1058	33	26	8	31	1.87
3542077--3542187	30	3.7	30	93	1	197	16	38	24	20	1.92
3544130--3544167	20	1.9	20	88	0	58	36	15	13	34	1.87
3544210--3544261	20	2.6	20	96	0	95	46	25	11	17	1.81
3544422--3544468	22	2.1	22	88	0	67	17	42	19	21	1.89
3544802--3544845	20	2.1	21	91	4	72	56	18	9	15	1.65
3544870--3544908	19	2.0	20	85	5	53	28	12	17	41	1.87
3546177--3546270	41	2.3	41	90	0	143	42	15	11	29	1.83
3546436--3546539	42	2.5	42	91	0	163	26	35	17	20	1.94
3546641--3546802	21	7.7	21	69	10	116	19	12	34	33	1.89
3546650--3546802	63	2.4	62	79	4	180	18	13	34	33	1.90
3547152--3547197	21	2.2	21	96	0	83	21	39	17	21	1.93
3547165--3547225	21	2.9	21	87	4	79	19	42	16	21	1.89
3548418--3548453	16	2.2	16	90	0	54	19	0	13	66	1.24
3548518--3548602	19	4.3	20	93	3	138	49	16	15	18	1.80
3548649--3548703	20	2.8	20	85	0	74	23	10	25	40	1.87
3548598--3548677	34	2.4	34	76	0	88	18	13	23	43	1.86
3551198--3551265	24	2.8	24	79	0	73	41	19	14	25	1.89
3552181--3552297	40	2.9	40	82	5	155	38	11	21	28	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3552169--3552299	20	6.6	20	69	16	76	36	11	21	30	1.89
3552313--3552430	20	5.8	20	72	16	82	29	15	22	32	1.95
3556838--3556871	16	2.1	17	88	5	52	52	17	2	26	1.58
3558329--3558361	14	2.2	16	89	10	52	33	27	12	27	1.92
3560259--3560460	109	1.9	109	87	4	300	35	14	19	31	1.91
3580945--3581099	64	2.4	64	77	10	147	36	20	18	25	1.95
3581474--3581583	29	3.8	29	87	2	159	46	15	19	19	1.84
3588306--3588444	29	4.8	29	96	1	253	45	16	20	17	1.86
3592685--3592737	15	3.2	17	72	22	58	52	0	0	47	1.00
3592684--3592775	4	24.5	4	68	12	52	51	0	0	48	1.00
3592684--3592775	6	16.3	6	75	13	52	51	0	0	48	1.00
3592684--3592776	32	2.8	33	78	15	93	51	0	0	48	1.00
3595081--3595119	21	1.9	19	90	10	60	15	12	0	71	1.14
3595289--3595342	21	2.5	22	80	17	60	14	11	3	70	1.29
3597342--3597366	13	1.9	13	100	0	50	40	12	40	8	1.72
3599195--3599440	95	2.7	94	84	11	311	29	19	19	31	1.96
3600556--3600737	72	2.5	72	92	0	301	29	17	10	41	1.84
3600609--3600723	36	3.2	36	66	4	106	29	16	9	44	1.79
3600913--3600998	36	2.4	36	86	0	109	22	23	15	39	1.91
3600734--3601037	101	3.0	101	91	2	473	31	20	13	35	1.91
3601019--3601054	17	2.1	17	94	0	63	33	11	11	44	1.75
3600954--3601119	82	2.0	82	96	0	305	32	19	11	36	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3600865--3601209	183	1.9	184	93	0	602	30	21	11	36	1.89
3601280--3601389	42	2.8	38	82	10	134	25	22	13	38	1.91
3601343--3601522	65	2.7	64	80	10	202	32	20	10	37	1.85
3603256--3603314	22	2.7	21	79	12	66	28	3	1	66	1.18
3603360--3603402	17	2.4	18	84	7	52	23	2	4	69	1.18
3603394--3603532	2	71.5	2	77	16	114	41	4	2	51	1.33
3603762--3603816	21	2.5	22	80	11	60	14	10	3	70	1.28
3611552--3611634	21	3.9	21	78	7	87	21	36	25	16	1.94
3616138--3616167	2	15.0	2	100	0	60	50	0	0	50	1.00
3622358--3622412	28	1.9	29	88	3	85	30	10	3	54	1.52
3622636--3622681	16	2.9	16	83	0	56	30	28	6	34	1.82
3622636--3622700	30	2.1	31	85	5	87	30	27	4	36	1.77
3624230--3624290	23	2.7	23	78	0	68	29	22	27	19	1.98
3624955--3625011	2	28.5	2	100	0	114	50	0	0	49	1.00
3625848--3625894	19	2.5	19	96	0	85	25	31	17	25	1.97
3629324--3629387	23	2.8	23	85	0	92	29	26	28	15	1.96
3634381--3634449	23	3.0	23	89	0	102	30	26	26	17	1.97
3635106--3635139	2	17.0	2	100	0	68	50	0	0	50	1.00
3639373--3639441	23	3.0	23	78	0	66	28	23	26	21	1.99
3645107--3645221	18	6.4	18	71	19	64	74	2	19	3	1.08
3645107--3645205	27	4.0	23	70	19	74	74	3	19	3	1.08
3647959--3648092	37	3.6	37	74	15	125	33	15	14	36	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3648012--3648105	37	2.5	35	78	11	107	30	15	10	42	1.81
3648058--3648226	67	2.5	66	83	8	184	34	16	10	39	1.82
3648128--3648470	99	3.3	102	74	14	276	35	16	11	37	1.84
3648434--3648552	37	3.4	37	63	19	92	27	19	16	36	1.93
3648148--3648504	105	3.5	100	72	16	273	33	16	12	37	1.86
3648418--3648661	67	3.6	67	88	2	339	30	18	13	36	1.90
3648418--3648661	135	1.8	133	84	3	337	30	18	13	36	1.90
3648783--3649319	139	3.9	139	84	1	655	29	28	17	24	1.97
3649251--3649371	56	2.2	56	86	3	163	28	23	19	28	1.98
3649102--3649514	195	2.1	195	85	2	553	28	26	19	25	1.98
3649297--3649840	139	3.9	139	80	1	581	30	27	16	25	1.97
3648988--3649644	334	2.0	334	83	1	825	29	27	18	25	1.98
3649297--3649821	278	1.9	278	83	1	676	30	27	16	25	1.97
3648829--3649784	473	2.0	473	81	3	1127	29	27	17	25	1.97
3653793--3653848	29	1.9	29	92	0	94	28	12	5	53	1.60
3673787--3673833	9	5.1	9	75	14	51	72	4	2	21	1.12
3673771--3673833	18	3.5	17	81	10	63	69	4	1	23	1.16
3675215--3675679	33	13.9	33	76	9	367	22	20	18	38	1.93
3675221--3675690	233	2.0	234	85	2	631	22	20	18	38	1.93
3675216--3675690	67	7.1	67	84	2	591	22	19	18	38	1.93
3677867--3677928	11	5.4	11	79	11	70	0	17	0	82	0.67
3677867--3677923	18	3.2	18	82	9	80	0	17	0	82	0.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3677875--3677925	8	5.7	9	82	13	61	0	17	0	82	0.67
3678392--3678437	3	15.3	3	95	0	83	2	30	0	67	1.03
3695222--3695334	20	5.7	20	93	0	172	28	21	16	33	1.95
3695221--3695363	60	2.4	60	80	2	153	28	18	17	34	1.94
3695222--3695350	40	3.2	40	85	2	170	29	19	17	34	1.94
3695496--3696040	36	15.1	36	87	4	699	33	17	20	28	1.96
3695496--3696031	108	5.0	107	90	2	788	33	17	20	28	1.96
3696233--3696267	3	11.7	3	100	0	70	34	0	0	65	0.93
3697376--3697481	52	2.0	52	98	0	203	37	13	7	41	1.72
3703203--3703258	12	5.1	12	77	14	50	62	1	0	35	1.06
3703290--3703338	22	2.2	22	85	0	62	46	4	2	46	1.33
3703301--3703448	64	2.3	63	82	11	169	45	7	2	44	1.46
3703365--3703422	28	2.0	30	90	6	93	48	5	3	43	1.42
3703442--3703472	12	2.6	12	94	0	53	41	3	0	54	1.16
3708349--3708392	20	2.2	20	100	0	88	27	9	18	45	1.79
3710285--3710634	174	2.0	173	99	0	691	37	18	21	22	1.94
3711585--3711609	4	6.2	4	100	0	50	24	0	0	76	0.80
3713697--3713969	135	2.0	134	97	2	501	23	16	9	50	1.73
3713926--3713983	30	1.9	30	89	0	89	15	17	8	58	1.61
3714450--3714512	14	4.6	14	79	11	69	15	23	9	50	1.73
3714450--3714512	28	2.3	27	91	5	101	15	23	9	50	1.73
3717439--3717604	54	3.1	53	84	8	194	28	7	21	42	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3718518--3718590	35	2.1	34	82	7	85	26	13	12	47	1.78
3719011--3719689	135	5.0	135	84	4	806	33	16	20	29	1.95
3724496--3724528	13	2.5	13	100	0	66	45	0	18	36	1.49
3724672--3724740	26	2.7	25	77	22	72	76	1	7	14	1.06
3724672--3724740	27	2.7	26	76	17	72	76	1	7	14	1.06
3724724--3724751	6	4.7	6	100	0	56	85	0	14	0	0.59
3725004--3725080	15	4.9	16	77	17	65	59	5	2	32	1.33
3725017--3725080	18	3.7	17	82	12	69	60	6	3	29	1.36
3725011--3725090	15	4.8	15	69	24	54	61	5	2	31	1.31
3725432--3725536	37	2.8	37	85	0	138	30	14	13	41	1.84

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