genome.fa.s2012.2.7.7.80.10.50.1000.2.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: VEPZ01002012.1 Hibiscus syriacus cultivar Beakdansim tig00004111_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  773058

Tables:   1   2   3   

This is table  2  of  3  ( 324 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)
328781--328849	23	3.0	23	82	6	68	46	0	2	50	1.16
329019--329079	23	2.6	23	82	12	63	47	0	1	50	1.10
329287--329368	42	2.0	42	85	0	110	52	13	10	23	1.72
335386--336342	4	239.8	4	97	0	1828	49	24	0	25	1.56
345733--345793	27	2.3	27	85	0	77	31	13	13	42	1.82
346369--346536	89	1.9	90	82	1	212	39	10	10	39	1.74
352079--352108	15	2.0	15	100	0	60	13	20	6	60	1.55
353418--353572	60	2.6	60	81	0	166	47	6	14	31	1.70
360063--360103	16	2.6	16	88	3	57	34	21	7	36	1.82
370581--370759	90	2.0	91	89	1	279	45	4	11	39	1.60
384429--384860	174	2.5	173	85	3	562	35	18	20	25	1.95
399441--399509	30	2.3	30	94	0	120	23	18	24	33	1.97
399744--399782	16	2.4	16	95	0	69	41	0	5	53	1.23
399741--399785	16	2.5	19	75	24	60	44	0	4	51	1.21
400420--400446	14	1.9	14	100	0	54	88	11	0	0	0.50
401307--401370	23	2.7	23	82	4	74	40	3	4	51	1.38
401371--401417	25	1.9	24	82	4	58	57	2	0	40	1.11
401461--401509	18	2.8	18	81	6	57	48	0	0	51	1.00
401686--401712	14	1.9	14	100	0	54	37	22	22	18	1.95
402804--402853	2	26.5	2	88	11	79	50	0	0	50	1.00
402811--402853	17	2.5	17	96	0	77	48	0	0	51	1.00
402804--402853	19	2.6	19	93	0	91	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)
402903--402972	27	2.7	26	85	8	90	38	1	8	51	1.41
402941--402994	19	2.6	19	82	11	63	48	0	3	48	1.19
402903--402972	26	2.7	27	82	8	85	38	1	8	51	1.41
402903--403001	27	4.2	24	68	19	64	41	1	6	51	1.33
403103--403166	3	21.3	3	81	9	69	32	0	3	64	1.10
403113--403174	20	3.1	19	73	11	61	29	1	3	66	1.17
403083--403174	8	12.7	7	78	14	57	32	2	2	63	1.19
404459--404501	17	2.4	18	85	14	63	16	2	4	76	1.05
406279--406323	19	2.4	19	92	3	74	11	13	8	66	1.44
409644--410332	164	4.2	165	90	2	1032	30	24	21	23	1.99
411048--411090	2	21.5	2	100	0	86	48	0	0	51	1.00
411100--411173	38	1.9	38	86	2	103	39	4	9	47	1.55
411074--411178	39	2.7	39	81	8	110	40	4	7	46	1.53
411141--411209	25	2.9	23	80	16	70	39	1	8	50	1.42
411178--411233	19	2.8	20	78	8	69	42	0	3	53	1.18
411333--411396	3	21.3	3	78	12	69	31	0	3	65	1.08
411334--411396	13	4.9	13	80	17	62	31	0	3	65	1.09
412644--412686	12	3.4	12	87	6	50	25	2	2	69	1.12
412706--412751	13	3.4	14	76	8	51	13	2	6	78	1.04
412702--412744	17	2.4	18	85	14	63	16	2	4	76	1.05
412766--412813	16	3.2	16	72	19	50	18	8	0	72	1.08
412852--412876	3	8.3	3	100	0	50	32	0	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
413257--413392	37	3.8	36	85	9	179	42	13	13	29	1.84
413743--413785	18	2.5	17	85	7	61	25	4	2	67	1.22
414048--414103	9	6.2	9	74	14	53	21	3	1	73	1.08
414288--414319	2	16.0	2	100	0	64	50	0	0	50	1.00
416914--416952	8	5.0	8	84	6	53	10	17	12	58	1.61
418067--418113	13	3.4	13	78	21	51	80	8	10	0	0.89
418074--418133	16	3.9	16	73	20	56	80	8	11	0	0.92
418069--418131	29	2.1	30	85	8	85	80	7	11	0	0.89
418731--418774	22	2.0	22	91	8	72	38	22	11	27	1.88
419209--419244	18	2.0	18	94	0	63	16	8	33	41	1.78
419680--419784	37	2.9	37	92	1	176	24	21	14	39	1.91
419814--419891	37	2.1	38	87	2	113	28	20	12	38	1.89
419698--419951	102	2.5	102	95	0	454	29	20	12	37	1.89
419851--420020	65	2.6	65	93	0	297	31	18	12	37	1.88
419734--420051	167	1.9	169	92	1	541	29	20	12	37	1.89
420839--421670	105	8.0	105	91	1	1278	34	25	17	22	1.96
422218--422353	37	3.8	36	85	9	179	42	13	13	29	1.84
422711--422753	18	2.5	17	85	7	61	25	4	2	67	1.22
423354--423386	9	3.7	9	100	0	66	21	0	0	78	0.75
427245--427307	21	3.0	21	92	0	99	30	9	9	50	1.66
428606--428641	18	1.9	19	94	5	65	47	2	0	50	1.15
431035--431088	2	27.0	2	100	0	108	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)
431086--431117	4	8.0	4	100	0	64	25	0	0	75	0.81
436501--436535	2	17.5	2	100	0	70	51	0	0	48	1.00
437095--437171	37	2.1	37	100	0	154	27	22	28	22	1.99
452663--452721	31	1.9	31	85	0	82	44	8	8	38	1.65
457525--457557	2	17.0	2	93	6	59	48	0	0	51	1.00
462364--462418	26	2.0	29	89	10	89	52	3	0	43	1.18
462384--462423	21	1.9	21	84	0	53	55	0	2	42	1.13
463422--463449	14	2.0	14	100	0	56	21	42	28	7	1.79
463388--463435	10	4.8	10	79	5	53	31	35	22	10	1.88
463437--463488	23	2.3	23	86	0	68	26	26	36	9	1.87
463444--463496	23	2.3	24	83	9	74	30	24	33	11	1.90
463557--463616	23	2.6	23	86	5	77	10	36	26	26	1.88
463599--463631	14	2.4	14	94	0	57	6	30	39	24	1.79
463618--463674	10	5.7	10	76	15	64	10	24	36	28	1.88
463618--463675	20	2.9	20	92	0	98	10	25	36	27	1.89
463714--463771	29	2.0	29	90	6	91	22	24	37	15	1.93
472427--472614	99	1.9	99	92	3	315	48	11	9	30	1.69
482453--482754	150	2.0	151	99	0	597	21	18	15	44	1.87
484401--484449	16	3.1	16	90	0	80	57	20	12	10	1.64
485474--485558	34	2.5	34	82	0	107	52	21	12	12	1.72
485504--485535	14	2.3	14	100	0	64	50	28	15	6	1.68
485487--485520	10	3.4	10	95	0	59	55	23	11	8	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
489310--489339	15	2.0	15	100	0	60	53	0	0	46	1.00
489346--489386	21	2.0	21	85	9	57	68	4	12	14	1.36
504419--504452	17	2.1	17	88	5	52	32	17	17	32	1.94
516676--516721	21	2.2	20	82	14	58	36	4	4	54	1.40
521611--521653	17	2.5	17	82	14	52	34	0	2	62	1.08
521741--521796	27	2.1	27	86	6	78	30	10	25	33	1.90
523631--523785	60	2.6	60	77	9	163	32	24	7	35	1.83
529884--529924	20	2.0	20	90	0	64	46	7	21	24	1.77
541590--541634	23	1.9	24	86	4	65	42	4	8	44	1.56
544984--545050	16	4.3	16	92	3	102	10	10	19	59	1.58
544982--545042	32	1.9	32	96	0	113	8	13	22	55	1.64
545112--545144	16	2.1	16	100	0	66	12	12	18	57	1.64
548177--548298	64	1.9	64	88	3	183	23	16	23	36	1.94
551041--551108	32	2.2	32	86	2	93	38	5	7	48	1.55
552886--552936	25	2.1	23	82	7	57	35	0	9	54	1.33
555981--556015	16	2.2	16	89	0	52	54	28	8	8	1.60
555985--556028	16	2.8	16	89	0	61	47	36	9	6	1.62
556745--556818	32	2.3	32	81	2	87	33	24	16	25	1.95
560811--560850	18	2.2	18	86	4	53	42	0	0	57	0.98
561197--561241	21	2.2	21	84	11	58	40	2	0	57	1.11
562008--562260	134	1.9	134	82	7	316	30	12	14	42	1.83
583566--583602	14	2.6	14	100	0	74	56	8	21	13	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
590352--590469	43	2.8	42	79	5	139	49	1	0	48	1.17
595419--595452	17	2.1	17	89	10	54	38	11	17	32	1.86
607853--607899	18	2.6	18	82	0	58	4	29	17	48	1.65
607909--607945	18	2.1	18	89	0	56	8	29	16	45	1.76
607909--608020	48	2.3	48	79	0	125	7	32	16	43	1.75
607965--608102	30	4.6	30	88	0	186	3	31	21	42	1.70
610156--610189	17	1.9	17	88	5	50	38	0	0	61	0.96
614509--614538	12	2.5	12	100	0	60	43	0	0	56	0.99
616912--616957	3	15.3	3	90	0	74	30	2	2	65	1.16
620989--621041	27	2.0	27	92	7	90	16	16	3	62	1.47

Tables:   1   2   3