genome.fa.s1129.2.7.7.80.10.50.1000.2.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   79   80   
          81   82   83   84   85   86   87   88   89   

This is table  2  of  89  ( 10573 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)
237392--237669	36	7.7	36	90	0	430	19	27	23	30	1.98
241592--241620	2	14.5	2	100	0	58	48	0	0	51	1.00
248883--248919	6	6.2	6	100	0	74	35	48	16	0	1.46
248917--248950	5	6.8	5	89	0	50	26	32	41	0	1.56
248916--248950	10	3.5	10	92	0	61	28	31	40	0	1.57
248916--248953	15	2.5	15	86	0	58	28	31	39	0	1.57
249714--249767	28	1.9	28	100	0	108	38	20	0	40	1.53
249543--249802	5	52.4	5	86	11	304	40	4	0	55	1.22
249544--249830	19	16.2	17	78	14	135	39	4	0	56	1.22
258828--258882	28	2.0	28	92	0	92	34	14	18	32	1.91
259951--259994	22	2.0	23	86	4	63	68	4	2	25	1.20
263032--263075	22	2.0	23	86	4	63	68	4	2	25	1.20
269788--269818	6	5.2	6	100	0	62	35	48	16	0	1.46
269815--269848	5	6.8	5	93	0	50	35	26	38	0	1.57
270448--271274	5	167.8	5	87	10	724	33	8	0	58	1.28
270448--271275	23	36.9	22	80	15	367	33	8	0	58	1.28
270454--271280	18	47.7	17	79	17	286	33	8	0	58	1.28
280280--280334	28	2.0	28	88	0	83	32	14	18	34	1.91
280487--280550	31	2.1	31	82	2	76	45	20	14	20	1.85
297161--297203	8	5.5	8	77	5	52	58	0	0	41	0.98
302383--302419	6	6.0	6	90	3	56	67	2	0	29	1.04
302378--302417	12	3.3	12	89	6	55	72	5	0	22	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
302946--302996	17	3.0	17	68	8	50	37	3	7	50	1.50
302927--302996	34	2.1	34	88	0	104	35	7	7	50	1.57
305017--305046	13	2.4	12	94	5	51	6	36	20	36	1.79
310501--310548	21	2.4	20	80	10	53	58	14	6	20	1.58
311469--311525	30	1.9	30	85	0	78	40	26	28	5	1.77
311744--311814	24	2.9	24	87	2	79	39	15	18	26	1.90
311762--311814	24	2.2	24	96	0	97	37	18	18	24	1.94
312313--312425	35	3.2	34	86	5	154	41	23	1	33	1.65
313421--313532	35	3.2	35	84	0	143	35	0	20	42	1.58
323950--324106	71	2.2	70	90	1	251	36	12	10	40	1.77
326712--326744	2	16.5	2	100	0	66	51	0	0	48	1.00
329694--329833	59	2.4	58	75	7	138	37	15	9	38	1.79
330042--330163	60	2.0	60	82	6	149	36	16	16	31	1.91
333344--333380	19	1.9	19	94	0	65	32	29	16	21	1.95
333425--333476	20	2.6	21	75	9	54	28	21	19	30	1.97
333463--333516	20	2.7	20	91	0	90	42	16	20	20	1.89
333505--333552	20	2.4	20	85	0	69	27	29	20	22	1.99
334608--334644	14	2.5	15	86	8	58	54	21	18	5	1.64
336880--336976	20	4.8	20	88	0	122	34	19	17	28	1.95
337015--337076	20	3.1	20	92	0	106	11	19	22	46	1.81
337020--337092	20	3.7	19	83	3	74	13	17	24	43	1.86
337015--337092	40	2.0	40	84	5	104	14	17	24	43	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
337214--337248	14	2.5	14	100	0	70	48	20	0	31	1.50
337145--337320	81	2.1	81	81	15	191	49	17	2	31	1.59
338691--338730	21	2.0	20	86	13	57	30	15	30	25	1.95
338618--338738	42	2.9	42	75	9	138	25	19	32	23	1.97
339216--339259	20	2.2	20	91	0	70	52	22	9	15	1.71
339250--339301	20	2.6	19	88	11	77	44	25	17	13	1.85
339296--339333	19	2.0	19	94	0	67	50	31	13	5	1.63
339343--339417	33	2.2	34	83	2	89	14	16	20	49	1.80
339409--339477	20	3.5	20	95	0	120	20	20	26	33	1.97
339409--339496	20	4.4	20	86	2	81	19	18	26	36	1.94
341393--341460	21	3.4	20	82	6	84	51	22	13	13	1.75
341849--341899	22	2.3	22	86	0	75	21	13	43	21	1.87
342099--342203	20	5.2	20	82	5	113	30	20	20	28	1.98
342099--342203	40	2.6	41	81	4	133	30	20	20	28	1.98
342225--342270	19	2.4	19	85	3	56	21	17	30	30	1.96
342236--342272	19	1.9	19	94	0	65	21	16	29	32	1.95
350634--350684	8	6.8	8	80	10	54	45	1	19	33	1.62
350634--350684	15	3.4	15	80	0	66	45	1	19	33	1.62
350634--350700	22	3.0	22	78	10	64	46	1	17	34	1.58
350637--350700	30	2.1	30	82	5	76	45	1	17	35	1.58
352758--352795	19	2.0	19	100	0	76	31	15	0	52	1.43
355841--355911	15	4.7	15	74	6	63	38	7	21	33	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
356047--356141	24	3.9	24	83	1	109	23	21	24	31	1.98
362924--362997	24	3.0	25	78	4	87	22	21	21	33	1.97
367982--368339	116	3.1	116	82	3	409	27	21	16	35	1.94
369413--369462	22	2.3	21	83	6	64	6	24	0	70	1.10
372736--372830	48	2.0	48	81	4	111	35	21	8	34	1.83
374135--374235	31	3.2	31	77	8	96	63	4	9	21	1.44
374441--374474	17	2.0	17	88	11	52	70	0	8	20	1.13
376335--376406	17	4.2	17	72	13	60	44	6	1	47	1.38
378104--378185	29	2.8	29	100	0	164	25	31	30	12	1.92
378183--378217	13	2.8	13	95	4	63	31	17	37	14	1.89
378232--378405	28	5.8	29	78	13	147	34	20	33	11	1.89
378230--378425	93	2.1	91	94	2	338	34	21	31	12	1.90
378230--378424	61	3.2	64	81	10	230	34	21	31	11	1.90
378456--378560	28	3.8	28	86	11	144	15	30	32	21	1.94
378640--378674	18	1.9	18	100	0	70	28	17	25	28	1.97
378779--378824	23	2.0	23	91	8	76	47	4	39	8	1.54
378834--378865	10	3.1	11	86	13	50	84	0	15	0	0.63
378856--378898	13	3.2	13	76	3	50	60	0	37	2	1.10
379039--379155	41	2.8	40	82	10	110	42	0	12	44	1.42
379078--379163	43	2.0	44	86	11	124	43	0	12	44	1.42
379326--379363	15	2.6	15	91	4	60	36	0	7	55	1.29
381484--381516	17	1.9	17	93	0	57	45	12	6	36	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
381612--381797	25	7.3	25	76	12	157	46	9	2	42	1.47
384610--384668	26	2.3	24	78	16	64	40	3	8	47	1.51
385379--385483	41	2.5	43	78	12	110	48	8	0	41	1.40
385445--385504	27	2.2	28	88	8	88	55	11	0	33	1.36
385449--385513	27	2.5	26	82	12	87	52	12	0	35	1.39
386023--386080	25	2.3	25	79	5	64	22	43	17	17	1.88
386139--386218	29	2.8	29	96	0	142	16	28	33	21	1.95
391568--391602	6	5.8	6	93	0	52	42	2	0	54	1.15
392690--392717	2	14.0	2	100	0	56	50	0	0	50	1.00
393035--393083	21	2.3	20	83	10	62	48	0	0	51	1.00
403451--403504	23	2.4	22	84	6	72	22	31	24	22	1.98
403488--403529	18	2.3	18	91	4	66	23	23	33	19	1.97
407213--407445	90	2.6	90	90	0	367	30	19	15	34	1.93
410721--410766	19	2.7	18	81	15	53	32	2	0	65	1.05
410762--410796	13	2.7	13	91	8	54	51	8	0	40	1.33
410730--410781	19	2.5	21	78	15	63	40	3	0	55	1.18
410721--410768	3	16.7	3	79	16	57	33	2	0	64	1.05
414461--414500	12	3.3	12	85	0	53	20	0	7	72	1.08
415382--415474	43	2.2	43	94	0	159	36	15	13	34	1.87
417041--417113	30	2.4	30	81	0	83	34	30	20	15	1.93
421232--421294	25	2.5	24	82	12	74	15	3	7	73	1.20
421247--421293	12	3.7	13	77	11	53	14	2	8	74	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
434053--434098	21	2.1	23	88	11	71	15	13	15	56	1.68
434180--434241	20	3.0	20	75	15	63	19	8	1	70	1.20
434260--434293	17	1.9	18	88	5	52	17	17	0	64	1.29
434321--434369	13	3.8	13	82	12	57	20	2	0	77	0.87
439499--440032	84	6.4	84	81	4	611	28	25	21	24	1.99
439499--440054	164	3.4	164	86	3	776	28	24	21	24	1.99
439499--440135	164	3.8	159	79	9	598	29	24	21	24	1.99
439499--440148	328	2.0	329	84	5	866	29	24	21	24	1.99
440241--440444	84	2.5	80	79	7	228	29	25	20	24	1.99
440280--440443	84	1.9	85	86	1	231	30	27	19	22	1.98

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   79   80   
          81   82   83   84   85   86   87   88   89