genome.fa.s9634.2.7.7.80.10.50.1000.17.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  17  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)
3749697--3749734	18	2.1	18	95	0	67	36	5	34	23	1.78
3753371--3753408	19	2.0	19	90	10	60	10	50	0	39	1.37
3755645--3755675	16	1.9	16	93	0	53	6	38	9	45	1.63
3759156--3759182	3	9.0	3	100	0	54	0	33	0	66	0.92
3764131--3764166	2	18.0	2	100	0	72	50	0	0	50	1.00
3764433--3764460	14	2.0	14	100	0	56	50	7	7	35	1.57
3767506--3767565	28	2.1	28	100	0	120	38	11	10	40	1.75
3772550--3772594	15	3.1	15	93	3	74	24	24	8	42	1.83
3773686--3773743	30	1.9	30	89	0	89	43	1	5	50	1.35
3774550--3774668	33	3.3	37	82	8	131	40	36	10	13	1.78
3775729--3775765	18	2.1	18	89	0	56	51	10	5	32	1.60
3776152--3776201	25	2.0	25	92	0	82	44	20	8	28	1.79
3776290--3776334	13	3.4	14	74	20	51	13	15	26	44	1.83
3776318--3776364	20	2.3	20	92	0	76	19	21	19	40	1.92
3776692--3776745	6	9.0	6	81	0	54	18	3	22	55	1.58
3776698--3776745	18	2.7	18	90	0	69	18	4	22	54	1.61
3776686--3776737	24	2.2	24	96	0	95	19	3	26	50	1.65
3776686--3776752	24	2.8	24	88	0	80	16	5	23	53	1.65
3778735--3778788	24	2.2	24	83	0	72	40	18	20	20	1.91
3779705--3779752	19	2.5	19	82	0	60	31	16	22	29	1.96
3779749--3779801	19	2.7	20	88	2	72	35	13	16	33	1.88
3779771--3779815	19	2.3	19	84	7	54	31	13	17	37	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3779805--3779887	20	4.2	20	76	0	85	18	13	22	45	1.84
3779827--3779909	40	2.1	40	82	8	98	19	15	21	43	1.88
3779904--3779953	19	2.6	19	87	3	55	22	16	30	32	1.95
3782022--3782266	120	2.0	122	82	9	295	42	8	17	31	1.79
3787326--3787516	96	2.0	96	85	6	262	33	19	17	29	1.95
3787548--3787601	2	27.5	2	96	3	101	50	0	0	50	1.00
3801990--3802060	18	3.9	18	78	14	83	19	15	35	29	1.93
3801990--3802060	36	2.0	36	86	5	99	19	15	35	29	1.93
3803217--3803255	21	1.9	20	89	5	60	35	12	17	33	1.88
3806746--3806787	2	21.5	2	95	4	77	50	0	0	50	1.00
3810116--3810175	20	3.0	20	97	0	111	65	0	33	1	1.03
3810106--3810164	10	5.8	10	73	16	50	64	0	33	1	1.04
3810100--3810175	40	1.9	39	86	7	109	64	0	34	1	1.02
3810942--3811471	264	2.0	263	97	0	1006	36	13	20	30	1.90
3813693--3813736	23	1.9	23	85	0	61	36	0	6	56	1.26
3815564--3815597	9	3.6	10	88	11	54	41	0	0	58	0.98
3817147--3817185	17	2.2	18	86	4	53	51	7	2	38	1.44
3817548--3817583	18	1.9	19	88	5	56	8	36	0	55	1.30
3821392--3821713	165	1.9	166	93	1	558	42	3	8	45	1.51
3822058--3822082	2	12.5	2	100	0	50	52	0	0	48	1.00
3822769--3822817	25	2.0	25	95	0	89	36	16	16	30	1.91
3828186--3828238	3	17.0	3	84	7	61	60	0	3	35	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3828438--3829560	259	4.5	252	84	6	1260	35	16	13	33	1.89
3828382--3829350	259	3.8	258	86	4	1314	35	16	14	34	1.89
3832506--3832555	17	3.1	17	68	26	54	54	22	4	20	1.61
3832506--3832566	31	1.9	31	86	3	86	55	21	3	19	1.57
3832850--3832911	30	2.1	30	100	0	124	53	0	0	46	1.00
3832862--3832926	30	2.2	30	82	0	76	49	0	9	41	1.35
3832850--3832911	2	33.0	2	87	12	96	53	0	0	46	1.00
3834646--3835097	221	2.0	226	90	3	709	13	23	19	43	1.87
3836289--3836359	15	4.7	15	78	0	79	23	26	7	42	1.80
3836294--3836359	30	2.2	30	88	0	96	25	24	6	43	1.77
3836853--3836904	22	2.4	22	96	0	95	28	9	21	40	1.84
3838185--3838228	18	2.5	17	82	10	52	29	45	0	25	1.54
3843840--3843966	62	2.0	62	92	3	211	33	27	9	29	1.88
3853714--3853753	21	1.9	21	89	0	62	25	40	25	10	1.86
3862598--3862636	18	2.1	19	85	4	53	28	5	0	66	1.12
3863459--3863504	2	23.0	2	100	0	92	50	0	0	50	1.00
3865056--3865211	7	22.4	7	69	1	89	43	32	3	21	1.68
3865056--3865147	42	2.2	42	90	3	141	44	32	2	20	1.64
3865068--3865156	21	4.2	21	77	5	99	43	33	3	19	1.67
3866641--3866711	23	3.3	23	66	22	73	29	19	23	26	1.98
3866653--3866727	17	4.1	17	71	18	60	26	16	26	30	1.96
3866643--3866748	40	2.7	40	96	0	194	31	15	25	28	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3866778--3866809	16	2.0	16	93	0	55	15	12	21	50	1.77
3868747--3869136	195	2.0	195	89	1	593	26	20	28	25	1.99
3869972--3870079	55	2.0	55	83	0	135	33	20	17	28	1.95
3873276--3873380	37	2.8	37	82	0	129	41	14	13	30	1.84
3873656--3873701	24	2.0	23	83	12	58	19	6	4	69	1.28
3873759--3873784	2	13.0	2	100	0	52	50	0	0	50	1.00
3873844--3873914	21	3.5	20	77	9	65	15	5	1	77	1.02
3877947--3878483	183	2.9	183	94	0	959	27	20	21	30	1.98
3879640--3879753	36	3.2	34	71	9	86	25	16	14	43	1.85
3879624--3879798	72	2.4	75	84	8	218	26	18	13	41	1.87
3879640--3879835	72	2.7	72	82	8	177	26	17	15	40	1.89
3879814--3879949	39	3.2	39	66	25	103	27	22	13	37	1.91
3879869--3880187	105	3.1	104	90	3	493	31	20	11	37	1.88
3880087--3880162	36	2.1	36	90	0	116	22	21	15	40	1.90
3880362--3880782	105	4.0	104	87	4	582	33	27	18	20	1.96
3880362--3880781	205	2.0	211	87	4	604	33	27	17	20	1.96
3881701--3881765	24	2.8	23	78	15	62	24	3	4	67	1.24
3881761--3881871	36	3.0	36	81	10	116	27	2	0	68	1.09
3881846--3881937	13	7.8	11	74	13	69	14	4	1	80	0.92
3881852--3881925	24	3.3	22	73	15	53	13	5	1	79	0.96
3881895--3881948	21	2.6	21	82	5	65	14	3	0	81	0.82
3881819--3881949	5	27.0	5	70	21	59	18	3	0	77	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3885175--3887397	130	17.1	130	79	4	2047	29	17	20	32	1.95
3885290--3887397	261	8.1	261	81	5	2040	30	17	20	32	1.95
3886509--3886696	45	4.3	44	67	15	129	29	17	19	32	1.95
3888105--3888719	45	13.8	45	79	4	588	42	20	15	21	1.89
3888712--3888828	37	3.1	36	81	6	117	46	10	21	22	1.81
3889735--3889806	19	4.1	18	79	16	71	4	22	0	73	1.00
3889735--3889776	8	4.8	9	91	8	61	0	28	0	71	0.86
3889738--3889834	6	15.8	6	71	20	51	4	19	0	76	0.95
3889781--3889843	5	12.4	5	79	14	67	3	14	1	80	0.90
3889740--3889839	24	4.1	23	72	17	78	4	18	1	77	0.99
3889787--3889827	14	2.8	14	88	7	55	4	14	0	80	0.87
3889740--3889843	10	9.6	10	72	13	64	3	18	0	76	0.98
3889780--3889840	14	4.3	13	75	17	50	3	13	1	81	0.88
3889786--3889843	25	2.3	25	85	5	82	3	13	1	81	0.91
3890303--3890330	14	2.0	14	100	0	56	28	14	0	57	1.38
3893312--3893339	2	14.0	2	100	0	56	50	0	0	50	1.00
3893597--3893649	18	2.9	18	85	0	79	22	18	33	24	1.97
3903491--3903523	15	2.2	15	94	0	57	30	33	21	15	1.94
3903668--3903702	12	2.9	12	91	0	52	37	25	5	31	1.80
3904078--3904219	64	2.2	64	82	7	164	28	21	16	33	1.95
3908353--3908405	18	2.9	18	85	0	79	22	18	33	24	1.97
3908563--3908595	2	16.0	2	93	6	57	48	3	0	48	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3909034--3909092	20	3.0	20	70	22	52	30	25	8	35	1.86
3910220--3910262	23	1.9	22	90	4	68	37	9	20	32	1.85
3910240--3910276	19	1.9	19	94	0	65	37	10	13	37	1.80
3909811--3910720	462	2.0	462	98	0	1775	41	13	14	30	1.84
3911692--3911753	23	2.7	23	82	0	79	33	25	24	16	1.95
3912784--3912833	2	25.0	2	100	0	100	50	0	0	50	1.00
3916154--3916211	2	29.0	2	100	0	116	50	0	0	50	1.00
3918499--3918572	2	37.0	2	97	0	139	51	0	0	48	1.00
3918569--3918616	24	2.0	24	87	0	69	33	6	12	47	1.66
3918599--3918626	14	2.0	14	100	0	56	42	7	7	42	1.59

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