genome.fa.s8242.2.7.7.80.10.50.1000.16.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: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  16962412

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   

This is table  16  of  73  ( 8740 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)
3407772--3407816	14	3.3	13	80	20	56	71	0	20	8	1.12
3407772--3407817	13	3.3	14	74	20	51	71	0	19	8	1.11
3411482--3411617	59	2.3	58	80	7	168	27	16	25	30	1.97
3411718--3411843	47	2.8	45	89	5	191	38	7	22	31	1.83
3413500--3413553	19	2.7	19	85	8	63	31	18	20	29	1.96
3413541--3413593	20	2.7	20	100	0	106	30	16	26	26	1.97
3413514--3413612	42	2.3	43	79	8	114	34	14	23	28	1.93
3413943--3414097	55	2.8	55	93	1	265	37	11	16	34	1.85
3417664--3417836	91	1.9	90	83	11	228	27	18	24	30	1.98
3424393--3424432	21	1.9	21	90	10	64	37	7	0	55	1.29
3429069--3429183	20	5.6	21	74	15	89	33	15	23	26	1.95
3429070--3429183	22	5.5	21	81	9	119	34	15	23	26	1.95
3429070--3429183	42	2.7	42	85	6	151	34	15	23	26	1.95
3429505--3429779	55	5.0	55	88	2	399	34	11	18	35	1.87
3433871--3434001	55	2.4	55	97	0	244	33	12	17	36	1.87
3433871--3434018	55	2.7	55	90	2	181	33	12	18	35	1.88
3433871--3434040	55	3.1	55	87	4	166	34	12	17	34	1.88
3440156--3440209	26	2.0	27	82	10	67	72	7	7	12	1.28
3440201--3440251	10	5.0	10	75	13	50	76	0	3	19	0.94
3440202--3440238	11	3.2	12	85	14	51	83	0	2	13	0.74
3440282--3440328	17	2.7	17	81	12	60	72	0	12	14	1.13
3440588--3440642	2	28.0	2	80	10	60	52	1	3	41	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3440611--3440688	20	3.7	21	77	16	65	62	0	6	30	1.20
3440607--3440671	25	2.6	25	85	7	78	63	0	3	33	1.10
3440636--3440702	21	3.1	20	72	19	55	67	0	4	28	1.10
3440593--3440670	14	5.4	14	78	15	63	60	0	2	37	1.11
3453723--3453763	21	2.1	20	86	13	59	73	9	2	14	1.19
3453821--3453868	18	2.8	17	75	9	53	75	0	10	14	1.06
3453894--3453977	36	2.3	36	84	8	100	67	4	4	22	1.28
3453967--3454029	18	3.5	18	75	12	58	74	0	3	22	0.96
3460920--3460947	2	14.0	2	100	0	56	50	0	0	50	1.00
3467879--3468110	6	37.3	6	81	13	249	37	0	60	0	1.06
3470249--3470290	20	2.1	20	100	0	84	14	19	16	50	1.79
3471861--3471913	28	2.0	26	82	10	63	52	32	0	15	1.42
3477662--3478127	41	11.4	41	70	12	165	36	16	16	30	1.91
3477662--3478153	82	6.0	81	78	4	418	36	16	16	31	1.90
3477775--3478139	163	2.2	163	85	2	484	36	15	16	31	1.90
3478796--3478884	5	17.8	5	95	0	142	41	0	34	23	1.55
3478875--3479143	5	53.8	5	98	0	502	40	0	38	21	1.54
3480606--3481050	58	7.7	58	93	0	743	35	20	11	32	1.88
3480600--3481050	115	3.9	116	92	1	755	35	20	11	32	1.88
3480606--3481050	173	2.6	174	92	1	743	35	20	11	32	1.88
3484445--3484474	15	2.0	15	100	0	60	46	6	0	46	1.29
3484930--3485209	117	2.4	117	89	4	426	35	19	11	33	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3484930--3485209	58	4.8	58	89	3	422	35	19	11	33	1.87
3487982--3488013	2	16.0	2	100	0	64	50	0	0	50	1.00
3489704--3489735	12	2.7	12	95	0	55	53	21	0	25	1.46
3496918--3496966	24	1.9	24	88	12	71	44	6	0	48	1.27
3497126--3497343	105	2.1	107	97	1	413	54	15	12	18	1.71
3499068--3499146	3	26.3	3	92	5	133	65	1	0	32	1.00
3499357--3499808	111	4.1	111	86	2	620	29	15	23	31	1.95
3500930--3501015	17	5.6	15	70	26	56	8	15	2	74	1.15
3500950--3500988	11	3.6	10	86	13	51	2	20	0	76	0.90
3500950--3500993	22	2.0	23	90	4	72	4	18	0	77	0.94
3504533--3504569	8	4.2	9	83	16	51	70	0	0	29	0.88
3512634--3512685	3	17.3	3	100	0	104	65	0	0	34	0.93
3519176--3519529	5	69.8	5	66	20	105	16	9	1	73	1.15
3519186--3519247	28	2.3	27	86	5	81	16	11	0	72	1.12
3519200--3519529	9	35.9	9	68	20	136	17	8	1	73	1.15
3519200--3519334	4	32.2	4	72	23	77	20	5	0	73	1.07
3519146--3519321	63	2.7	64	75	20	161	21	6	0	71	1.13
3519206--3519448	43	5.8	41	75	15	134	18	7	0	72	1.11
3519205--3519457	63	4.0	62	75	19	179	18	7	1	73	1.13
3519186--3519412	29	8.0	28	71	17	93	18	8	0	72	1.12
3519310--3519446	58	2.4	59	82	10	160	16	9	0	73	1.08
3519454--3519501	22	2.1	23	84	3	62	12	14	0	72	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3529813--3529862	22	2.2	24	92	7	86	78	0	12	10	0.98
3529820--3529861	11	3.8	11	77	22	52	83	0	11	4	0.79
3530698--3530868	65	2.7	64	84	6	217	38	18	14	28	1.90
3531656--3531685	2	15.5	2	93	6	53	46	0	0	53	1.00
3532705--3532783	3	24.3	3	80	12	77	32	3	0	63	1.12
3532704--3532771	7	10.1	7	84	9	81	32	1	0	66	1.01
3532879--3532936	15	3.5	17	72	23	52	29	1	0	68	0.99
3532909--3532968	31	1.9	31	87	12	88	21	3	0	75	0.95
3532881--3533035	4	38.2	4	69	23	51	26	3	0	69	1.11
3532892--3533017	48	2.6	50	81	10	136	26	3	0	69	1.09
3532881--3532994	58	1.9	60	82	7	144	24	3	0	71	1.08
3532881--3533017	50	2.7	50	76	11	136	27	2	0	68	1.09
3532881--3533043	50	3.1	51	70	13	123	25	4	0	69	1.11
3533035--3533125	20	4.6	20	70	21	66	15	8	1	74	1.11
3533024--3533098	29	2.6	29	77	8	80	16	6	1	76	1.07
3533022--3533126	24	4.5	23	69	16	65	15	8	0	75	1.09
3533020--3533177	9	17.4	9	68	23	66	13	10	1	74	1.16
3533138--3533187	25	2.0	25	84	7	66	14	10	2	74	1.16
3533138--3533188	26	2.0	25	88	3	75	13	9	1	74	1.15
3533973--3534043	26	2.8	25	69	14	63	53	7	1	38	1.37
3534071--3534134	22	3.0	23	76	10	66	50	4	0	45	1.22
3535863--3535899	14	2.6	14	100	0	74	32	8	13	45	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3537072--3537507	217	2.0	218	99	0	865	29	20	20	28	1.98
3544863--3544902	21	1.9	21	89	0	62	30	7	7	55	1.56
3550207--3550334	59	2.2	59	88	0	184	28	15	25	30	1.96
3550858--3550890	12	2.8	12	90	0	57	27	15	21	36	1.93
3550865--3551032	84	2.0	84	100	0	336	34	14	19	32	1.91
3553533--3553570	16	2.4	16	86	8	51	36	7	18	36	1.80
3553704--3553775	31	2.4	31	85	2	101	27	16	16	38	1.90
3553984--3554024	2	20.5	2	100	0	82	48	0	0	51	1.00
3560868--3560892	2	12.5	2	100	0	50	48	0	0	52	1.00
3561365--3561540	89	2.0	89	92	2	291	38	10	5	45	1.62
3566703--3566853	58	2.6	58	82	6	164	40	5	6	47	1.54
3566720--3566879	87	1.8	86	84	5	214	38	6	6	48	1.55
3566690--3566886	29	6.8	29	75	11	145	38	6	7	48	1.55
3570646--3570822	90	2.0	89	93	1	300	39	10	5	44	1.63
3570784--3570853	20	3.3	21	70	16	63	48	2	4	44	1.37
3585227--3585275	16	2.9	16	77	11	53	40	2	2	55	1.23
3586516--3586630	38	3.0	37	78	8	115	23	20	26	30	1.98
3586529--3586635	39	2.8	38	85	1	133	23	19	26	30	1.98
3586734--3586881	36	4.0	37	75	12	117	48	4	1	45	1.32
3586864--3586905	21	1.9	22	90	9	68	50	2	0	47	1.14
3586773--3586942	2	90.0	2	73	20	118	47	4	1	47	1.32
3587261--3587286	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3590179--3590227	19	2.5	20	78	21	59	24	8	0	67	1.18
3595471--3595519	19	2.5	20	78	21	59	24	8	0	67	1.18
3596154--3596200	24	2.0	23	84	15	62	31	0	31	36	1.58
3597402--3597450	25	1.9	25	83	4	62	44	8	12	34	1.71
3599565--3599598	17	1.9	18	88	5	52	35	0	32	32	1.58
3599810--3599858	24	2.1	24	84	3	64	4	16	6	73	1.19
3600298--3600368	35	2.0	37	88	5	110	33	4	30	30	1.77
3608550--3608599	22	2.3	22	96	0	91	44	0	20	36	1.52
3608572--3608922	195	1.8	195	95	0	639	31	14	18	35	1.90
3619173--3619236	27	2.4	27	81	5	76	9	14	34	42	1.77

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