genome.fa.s8356.2.7.7.80.10.50.1000.16.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: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12862612

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   

This is table  16  of  56  ( 6656 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)
3156220--3156496	149	1.9	149	81	7	348	37	14	14	33	1.87
3156351--3157074	199	3.7	199	80	8	867	38	14	15	31	1.88
3156450--3157014	184	3.0	185	80	8	679	37	15	15	31	1.89
3158704--3158751	19	2.5	19	96	0	87	31	6	10	52	1.60
3161222--3161908	191	3.5	191	84	5	792	38	15	15	30	1.89
3163923--3163955	17	1.9	17	88	11	50	66	6	0	27	1.15
3164397--3164452	21	2.6	21	75	10	51	69	1	1	26	1.08
3165001--3165097	49	2.0	49	97	0	185	38	19	2	40	1.64
3167371--3167416	20	2.3	20	88	3	67	43	0	36	19	1.51
3171746--3171804	22	2.6	22	82	10	75	22	3	6	67	1.29
3178894--3179332	134	3.3	133	78	9	437	30	15	19	33	1.93
3179809--3180029	111	2.0	110	95	0	397	36	15	13	34	1.87
3180244--3180359	20	5.7	20	66	13	56	32	19	22	25	1.97
3179920--3180593	234	2.9	234	86	0	929	35	17	14	32	1.90
3180258--3180359	42	2.5	41	83	3	132	34	19	22	23	1.97
3190096--3190178	2	41.5	2	100	0	166	50	0	0	49	1.00
3191065--3191128	12	5.3	12	71	14	51	4	18	1	75	1.06
3194340--3194379	21	1.9	21	85	10	55	30	12	2	55	1.50
3196114--3196158	23	2.0	23	81	0	54	71	0	13	15	1.15
3196276--3196331	7	7.6	7	74	18	51	78	1	7	12	1.02
3196280--3196331	14	3.5	14	77	12	59	78	1	7	11	1.02
3196371--3196413	9	4.8	9	82	0	59	74	4	2	18	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3196361--3196391	14	2.2	14	100	0	62	74	0	6	19	1.03
3196371--3196413	18	2.4	18	92	0	68	74	4	2	18	1.10
3197449--3197474	12	2.2	12	100	0	52	80	0	0	19	0.71
3197531--3197632	31	3.2	31	81	13	109	42	4	3	49	1.43
3197530--3197632	33	3.2	31	76	12	102	42	4	3	48	1.42
3197627--3197788	37	4.4	36	83	9	211	43	4	3	48	1.40
3197596--3197787	73	2.6	74	83	8	207	43	4	3	48	1.39
3200021--3200056	16	2.2	17	90	5	56	61	0	0	38	0.96
3200828--3200883	22	2.5	22	80	11	62	58	3	7	30	1.42
3202091--3202216	60	2.1	61	81	1	146	34	11	18	35	1.86
3204090--3204124	16	2.2	16	100	0	70	65	5	17	11	1.43
3204090--3204131	16	2.6	16	92	0	57	64	4	16	14	1.45
3213971--3213997	14	1.9	14	100	0	54	7	22	3	66	1.33
3217538--3217647	8	14.0	8	82	14	115	76	0	14	9	1.02
3217544--3217659	17	8.3	14	76	19	68	77	0	14	7	0.98
3217558--3217647	9	10.1	9	82	12	98	78	0	13	7	0.94
3217524--3217663	46	3.0	45	83	7	156	75	0	16	7	1.02
3217558--3217661	8	12.8	8	76	12	70	78	0	14	6	0.94
3218570--3219403	105	7.9	105	95	0	1425	36	18	23	21	1.95
3219347--3219412	20	3.3	20	67	14	55	45	12	19	22	1.83
3222363--3222450	44	2.0	44	97	0	167	35	18	4	42	1.71
3223444--3223480	3	11.7	3	88	11	56	62	0	0	37	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3223547--3223628	22	3.7	22	79	6	94	31	19	19	29	1.96
3226758--3226925	83	2.0	83	95	0	300	40	8	11	39	1.72
3226778--3226947	83	2.0	83	85	4	227	42	7	12	36	1.72
3227501--3227544	2	22.0	2	95	0	79	47	0	2	50	1.13
3233803--3233840	19	2.0	19	90	10	60	13	31	31	23	1.93
3234654--3234714	32	1.9	32	86	3	88	27	14	21	36	1.93
3234640--3234767	31	4.1	31	76	6	132	26	16	21	35	1.94
3239530--3239692	88	1.9	88	84	2	220	21	17	23	37	1.94
3241715--3241790	21	3.6	21	74	0	71	25	21	22	31	1.98
3250212--3250245	17	2.1	16	88	5	50	76	0	8	14	1.01
3252750--3252830	24	3.5	24	69	17	64	20	23	24	30	1.99
3254354--3254397	21	2.1	21	86	0	61	9	40	15	34	1.79
3255043--3255070	2	14.0	2	100	0	56	50	0	0	50	1.00
3255517--3255554	20	1.9	20	94	0	67	31	34	15	18	1.92
3255574--3255625	26	2.0	26	96	0	95	23	23	21	32	1.98
3258051--3258107	21	2.7	21	77	20	57	28	8	31	31	1.87
3258124--3258202	20	3.9	20	77	8	70	24	15	25	35	1.94
3258125--3258202	41	1.9	41	86	5	113	24	14	25	35	1.93
3258125--3258202	21	3.8	21	79	3	79	24	14	25	35	1.93
3258324--3258359	11	3.3	11	96	0	63	36	5	8	50	1.56
3264836--3264909	32	2.3	32	71	0	76	32	4	18	44	1.69
3269111--3269184	39	2.0	35	87	12	105	31	16	13	39	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3269424--3269640	118	1.8	118	90	0	353	28	10	15	45	1.79
3275671--3275759	24	3.7	24	77	5	90	44	17	11	25	1.82
3280348--3280468	57	2.1	57	81	0	134	28	27	10	33	1.90
3283939--3283964	2	13.0	2	100	0	52	50	0	0	50	1.00
3289040--3289079	21	1.9	21	89	0	62	10	25	40	25	1.86
3289061--3289120	23	2.7	23	80	10	72	16	23	38	21	1.93
3297439--3297477	15	2.6	15	91	0	60	35	0	17	46	1.49
3297635--3297705	24	3.0	24	85	6	99	19	23	25	30	1.98
3302866--3302908	17	2.5	17	88	3	59	41	11	9	37	1.74
3304622--3304749	21	6.1	21	79	7	145	32	21	21	23	1.98
3304633--3304768	21	6.6	21	76	13	88	33	21	22	22	1.97
3304633--3304775	62	2.3	62	91	2	225	33	20	22	23	1.97
3304758--3304915	21	7.6	21	81	9	180	23	22	24	29	1.99
3304675--3304857	62	3.0	60	80	8	147	29	20	24	25	1.99
3304758--3304940	42	4.4	42	83	9	205	23	21	23	31	1.99
3304764--3304949	21	8.9	22	77	12	99	24	22	23	30	1.99
3305033--3305063	6	5.2	6	100	0	62	35	48	16	0	1.46
3305562--3305610	6	8.5	6	95	2	66	0	16	57	26	1.40
3305731--3305888	21	7.6	21	83	8	180	28	24	22	24	1.99
3305706--3305888	42	4.4	42	80	9	187	30	23	21	24	1.99
3305878--3305929	20	2.6	20	100	0	104	23	21	17	38	1.93
3305917--3306116	21	9.6	21	81	7	228	24	22	22	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3306623--3306700	22	3.5	22	73	16	79	41	6	5	47	1.51
3306624--3306707	45	1.9	43	90	4	132	40	5	5	47	1.52
3309491--3309858	185	2.0	184	92	0	619	36	17	17	27	1.93
3316301--3316363	17	3.4	19	78	17	78	49	1	0	49	1.10
3316631--3316706	2	38.0	2	97	0	143	50	1	0	48	1.09
3317184--3317221	2	19.0	2	100	0	76	50	0	0	50	1.00
3319556--3319699	57	2.6	57	81	9	156	38	7	9	43	1.66
3319666--3319789	58	2.2	57	82	4	142	42	4	11	41	1.62
3322144--3322182	15	2.6	15	87	0	60	20	23	25	30	1.98
3327677--3327780	29	3.6	28	79	12	102	39	12	10	37	1.78
3327680--3327765	31	2.9	30	82	6	104	40	12	10	36	1.78
3332435--3332498	23	2.8	23	85	0	83	26	25	26	21	2.00
3332514--3332818	97	3.1	97	93	4	506	36	24	14	24	1.93
3333301--3333341	21	2.0	21	90	0	64	9	36	31	21	1.86
3333367--3333407	21	2.0	21	90	0	64	17	21	29	31	1.96
3342396--3342435	21	1.9	21	89	0	62	10	25	40	25	1.86
3342416--3342467	22	2.3	24	71	15	58	19	21	38	21	1.94
3348953--3349016	23	2.8	22	83	4	74	26	26	25	21	2.00
3349032--3349352	103	3.1	103	97	0	597	37	23	12	25	1.91
3349898--3349940	21	2.0	21	86	0	59	18	23	25	32	1.97
3358756--3358892	39	3.5	38	84	5	159	48	13	5	31	1.66
3358910--3359073	40	4.2	39	77	8	163	40	15	6	37	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3358910--3359073	39	4.2	40	79	9	187	40	15	6	37	1.74
3359100--3359210	39	2.9	38	85	6	143	43	12	3	40	1.60
3359115--3359217	39	2.7	39	90	1	163	41	13	4	39	1.66
3359263--3359578	117	2.7	117	78	6	302	43	11	6	37	1.68
3359279--3359578	58	5.1	58	82	4	291	43	11	7	37	1.69
3359709--3359822	45	2.8	40	80	13	140	40	18	7	33	1.80
3359728--3359846	45	2.6	45	84	7	161	39	17	7	35	1.78
3360045--3360077	14	2.3	15	89	5	50	57	15	3	24	1.52
3362112--3362151	20	2.0	20	95	0	71	52	5	12	30	1.60
3367051--3367096	21	2.2	21	92	3	76	30	21	26	21	1.99

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