genome.fa.s8356.2.7.7.80.10.50.1000.3.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  3  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)
357813--357864	25	2.1	25	88	0	77	32	9	11	46	1.73
360497--360538	22	1.9	22	85	0	57	45	0	0	54	0.99
360758--360827	12	5.6	12	74	25	65	24	4	24	47	1.70
360741--360823	26	3.2	26	98	0	157	22	4	27	44	1.73
368551--368601	2	26.0	2	90	4	77	54	0	45	0	0.99
371369--371434	31	2.1	33	88	5	100	42	7	13	36	1.73
372351--372405	27	2.0	27	96	0	101	36	16	0	47	1.47
377611--377671	22	2.8	22	78	14	72	40	24	14	19	1.89
378847--378989	5	27.8	5	85	12	184	40	0	0	58	1.03
378850--378989	41	3.4	40	83	11	185	40	0	0	58	1.03
378850--378986	36	3.8	35	84	8	186	40	0	0	58	1.03
385835--385882	24	1.9	26	84	16	66	37	12	18	31	1.88
395281--395324	21	2.1	21	91	0	70	38	4	2	54	1.33
395624--395666	16	2.9	16	86	10	56	53	0	0	46	1.00
395625--395660	16	2.2	17	95	5	65	47	0	0	52	1.00
406331--406383	21	2.5	21	87	9	72	28	16	16	37	1.91
413329--413387	20	2.8	21	82	10	59	35	18	10	35	1.85
416332--416362	10	3.1	10	100	0	62	41	9	19	29	1.83
419215--419273	24	2.4	24	97	2	109	18	6	42	32	1.77
422686--422750	29	2.3	29	89	5	98	44	7	7	40	1.62
424681--424795	41	2.8	41	84	6	126	22	41	6	28	1.80
434038--434197	65	2.5	64	88	8	236	30	21	16	31	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
438640--438691	24	2.2	24	85	0	68	9	15	26	48	1.76
438661--438711	14	3.9	14	73	19	56	9	11	21	56	1.63
438627--438707	34	2.4	34	78	12	94	12	14	22	50	1.76
438650--438711	24	2.6	24	94	0	106	9	12	22	54	1.67
438651--438701	10	4.7	10	80	17	57	7	11	25	54	1.63
439374--439402	15	1.9	15	100	0	58	24	13	34	27	1.93
439714--439817	36	2.9	36	100	0	208	20	13	19	47	1.82
439871--439944	10	7.6	10	69	22	59	10	12	20	56	1.65
439876--439940	16	4.1	16	87	0	103	9	13	21	55	1.66
439875--439936	32	1.9	32	96	0	115	11	12	20	54	1.68
440010--440050	16	2.7	16	85	7	59	12	9	17	60	1.57
440155--440205	21	2.5	19	79	14	57	35	15	15	33	1.90
440274--440325	20	2.7	20	84	3	70	38	19	3	38	1.70
441645--441692	19	2.5	20	86	3	62	31	14	6	47	1.69
443076--443123	21	2.5	18	75	18	51	25	14	20	39	1.91
443084--443131	21	2.3	21	96	0	87	25	12	18	43	1.85
443128--443192	20	3.3	20	84	2	78	29	18	12	40	1.87
445413--445449	15	2.5	15	90	0	65	29	35	18	16	1.93
445562--445633	28	2.6	28	97	2	137	19	22	16	41	1.90
445658--445692	12	2.9	12	95	0	61	40	25	2	31	1.70
445992--446168	64	2.8	64	85	1	221	25	19	22	32	1.97
452351--452456	15	7.1	15	91	0	176	31	33	21	13	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
452351--452456	30	3.5	30	97	0	203	31	33	21	13	1.92
452532--452621	26	3.3	27	75	15	87	21	20	13	45	1.84
452543--452613	26	2.7	26	89	8	99	19	21	15	43	1.87
452629--452674	12	3.8	12	91	0	56	39	26	6	28	1.81
452629--452675	24	2.0	24	87	8	69	38	25	6	29	1.81
452642--452675	12	2.8	12	95	0	59	41	26	2	29	1.70
456384--456436	20	2.7	19	85	5	61	37	18	9	33	1.83
457071--457147	40	1.9	40	84	5	102	49	2	18	29	1.61
459983--460038	29	1.9	29	96	0	103	17	1	39	41	1.60
480272--480314	21	2.0	21	90	0	68	37	20	25	16	1.93
484807--484860	28	1.9	28	88	0	81	53	1	3	40	1.29
486724--486748	2	12.5	2	100	0	50	48	0	0	52	1.00
487648--487674	2	13.5	2	100	0	54	48	0	0	51	1.00
488570--488610	3	14.0	3	89	5	57	39	0	0	60	0.96
488570--488612	21	2.0	21	95	0	77	39	0	0	60	0.97
490147--490181	9	3.5	10	88	11	54	51	2	0	45	1.16
496277--496359	29	2.9	29	96	0	148	38	21	12	27	1.89
499579--499645	27	2.4	27	75	2	71	55	0	7	37	1.28
509571--509596	9	2.9	9	100	0	52	23	11	11	53	1.69
522667--522704	20	1.9	19	89	5	58	36	23	18	21	1.95
529444--529598	28	5.6	27	75	11	116	48	10	1	39	1.47
532005--532156	85	1.8	79	86	8	214	26	5	16	51	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
537468--537875	199	2.0	204	86	6	571	38	16	23	21	1.92
540357--540387	14	2.3	13	94	5	53	51	16	0	32	1.44
543684--543756	23	3.2	23	84	0	101	49	19	17	13	1.80
543684--543765	23	3.6	23	84	0	92	48	20	17	13	1.80
553576--553724	73	2.0	74	98	1	291	33	17	10	38	1.84
554165--554460	64	4.6	64	81	7	296	31	15	18	34	1.92
563011--563036	13	2.0	13	100	0	52	7	7	15	69	1.35
574876--574923	20	2.5	20	86	3	62	18	22	22	35	1.96
583648--583761	30	3.8	30	72	6	90	16	33	22	27	1.96
584902--584955	23	2.3	23	78	9	56	25	24	5	44	1.75
594066--594094	14	2.1	14	100	0	58	34	6	13	44	1.71
599514--599557	22	2.0	22	95	0	79	22	6	13	56	1.61
601474--601543	3	23.3	3	71	11	54	37	1	1	60	1.15
601460--601548	29	3.2	26	79	16	90	34	2	1	61	1.15
601472--601543	12	5.1	14	71	25	62	37	1	1	59	1.15
602566--602598	7	4.7	7	100	0	66	42	0	0	57	0.98
602631--602672	16	2.7	16	77	3	50	23	2	16	57	1.51
607973--608018	21	2.2	20	84	3	56	23	6	15	54	1.64
619258--619302	9	5.2	9	79	15	51	80	0	8	11	0.92
620294--620507	54	3.9	55	90	5	330	31	15	24	27	1.96
620303--620552	108	2.3	108	84	6	317	31	16	24	27	1.96
620472--620675	105	1.9	106	83	3	259	30	22	24	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
620303--620781	55	8.9	53	82	8	259	30	20	24	25	1.98
622710--622757	25	2.0	24	83	4	60	25	6	16	52	1.67
625237--625279	16	2.5	17	77	7	52	41	4	2	51	1.35
626271--626309	7	5.7	7	90	3	62	43	0	2	53	1.14
626875--626916	18	2.3	18	84	8	50	57	11	0	30	1.35
628504--628550	18	2.5	19	80	13	53	68	4	0	27	1.08
634154--634183	5	6.0	5	100	0	60	20	80	0	0	0.72
634155--634190	15	2.4	15	90	0	54	22	75	2	0	0.94
635218--635286	30	2.3	30	79	0	84	28	21	23	26	1.99
639202--639261	31	1.9	31	93	0	102	40	6	10	43	1.64
639757--639894	20	6.8	20	79	6	161	13	23	23	39	1.91
639757--639894	61	2.3	61	93	2	233	13	23	23	39	1.91
639825--639963	41	3.4	42	90	4	203	15	21	23	39	1.91
639842--639916	21	3.6	21	72	18	75	13	22	28	36	1.92
639825--639979	41	3.8	41	91	3	199	16	20	23	40	1.91
639907--639972	19	3.3	19	70	12	60	18	18	21	42	1.89
640055--640130	6	13.5	6	92	1	99	30	51	18	0	1.47
640089--640133	5	8.6	5	97	2	72	24	55	20	0	1.43
640645--640679	6	5.8	6	86	0	52	2	17	48	31	1.61
640775--641076	41	7.4	41	91	4	502	36	24	21	17	1.94
640755--641076	82	3.9	82	99	0	626	36	24	21	17	1.94
641065--641183	41	2.9	41	92	0	202	36	26	19	18	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
640755--641117	123	2.9	122	84	6	489	36	24	21	17	1.94
640777--641158	123	3.1	121	80	6	419	36	25	21	17	1.94
641427--641474	18	2.5	19	77	19	55	62	0	0	37	0.95
641458--641507	20	2.6	19	74	17	50	58	2	0	40	1.10
641473--641537	22	2.8	23	84	9	71	53	1	0	44	1.09
641468--641537	24	3.0	24	79	10	81	52	1	0	45	1.09
641498--641573	36	2.1	36	83	9	93	57	1	0	40	1.07
641554--641601	14	3.8	14	69	25	52	58	0	0	41	0.98
641549--641596	23	2.3	20	80	19	62	56	0	0	43	0.99
641591--641624	16	2.1	16	88	0	50	64	2	0	32	1.08

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