genome.fa.s1129.2.7.7.80.10.50.1000.55.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  55  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)
12486833--12487165	68	4.9	68	91	0	540	29	15	24	30	1.95
12489401--12489466	24	2.8	24	76	2	80	28	22	24	24	1.99
12489580--12489647	24	2.8	24	95	0	118	30	26	23	19	1.98
12493471--12493514	21	2.0	22	91	4	72	27	31	20	20	1.97
12494271--12494361	24	3.8	24	85	4	112	26	25	26	21	2.00
12499183--12499240	24	2.3	24	82	5	71	29	22	22	25	1.99
12499189--12499238	24	2.1	24	92	0	82	28	24	24	24	2.00
12501848--12501915	27	2.5	26	78	21	70	11	27	1	58	1.42
12506100--12506332	68	3.4	68	89	0	358	28	14	25	31	1.94
12506100--12506362	68	3.9	68	87	1	357	28	14	25	31	1.94
12506315--12506470	80	1.9	81	82	6	192	37	12	21	27	1.90
12511084--12511235	55	2.8	55	89	2	225	32	13	19	34	1.91
12511500--12511950	68	6.6	68	89	0	650	28	14	23	33	1.94
12513902--12513947	18	2.5	18	86	10	58	0	32	21	45	1.52
12513915--12513962	18	2.6	19	83	6	55	4	29	18	47	1.67
12515503--12515546	23	2.0	23	90	4	72	22	25	27	25	2.00
12515513--12515562	22	2.2	23	82	10	59	20	30	22	28	1.98
12518939--12518979	13	3.2	13	100	0	82	51	29	0	19	1.47
12524943--12524986	21	2.2	20	84	12	54	22	13	11	52	1.72
12541083--12541125	22	2.0	22	90	0	68	53	13	0	32	1.41
12541073--12541815	54	13.6	54	78	8	761	52	12	0	34	1.43
12541185--12541265	32	2.5	32	95	0	144	55	11	0	33	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12541249--12541291	22	2.0	22	100	0	86	51	13	0	34	1.42
12541251--12541299	22	2.2	22	88	3	71	55	14	0	30	1.40
12541073--12541883	220	3.7	220	95	0	1421	52	12	0	34	1.43
12541305--12541353	22	2.2	22	85	3	62	55	12	0	32	1.37
12541073--12541811	166	4.5	162	79	8	764	52	12	0	34	1.43
12541409--12541468	18	3.6	18	71	17	65	56	11	0	31	1.35
12541581--12541654	22	3.2	22	70	16	60	55	17	0	27	1.42
12541689--12541731	22	2.0	22	100	0	86	51	13	0	34	1.42
12541691--12541739	22	2.2	22	88	3	71	55	14	0	30	1.40
12541073--12541883	86	9.9	82	76	15	339	52	12	0	34	1.43
12541840--12542085	45	5.3	45	84	7	264	49	2	0	48	1.12
12541830--12542083	60	4.0	66	86	6	207	49	3	0	47	1.17
12541906--12542085	15	12.0	15	92	0	279	48	0	0	51	1.00
12541865--12542085	30	7.2	30	87	7	320	49	0	0	49	1.07
12549818--12549922	52	2.0	52	100	0	210	17	17	24	40	1.90
12551138--12551166	12	2.3	13	94	5	51	27	0	3	68	1.05
12552698--12552861	24	7.4	22	77	11	133	50	6	1	42	1.38
12552728--12552863	24	6.0	24	83	10	171	49	5	1	43	1.36
12554268--12554315	13	3.6	13	75	5	51	47	0	4	47	1.21
12556543--12556586	23	1.9	23	90	0	70	34	15	22	27	1.95
12556743--12556808	29	2.3	29	81	0	78	31	6	6	56	1.48
12556766--12556873	48	2.2	48	90	0	171	31	2	9	56	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12556795--12556843	19	2.6	19	86	0	71	34	4	8	53	1.50
12556761--12556818	29	2.0	29	93	0	98	27	3	10	58	1.47
12556744--12556895	77	2.0	77	86	2	216	33	3	7	54	1.48
12556814--12556913	29	3.4	29	84	2	139	36	3	7	54	1.43
12556924--12557035	29	4.0	29	81	9	124	31	10	8	50	1.66
12558231--12558260	15	2.0	15	93	0	51	26	13	10	50	1.73
12564066--12564129	25	2.6	25	92	7	105	50	7	20	21	1.73
12571689--12571714	13	2.0	13	100	0	52	7	30	0	61	1.24
12575736--12575941	111	1.9	111	88	4	317	35	16	15	32	1.90
12577322--12577362	16	2.6	16	92	0	64	39	21	0	39	1.54
12583487--12583534	20	2.6	19	87	9	64	29	22	14	33	1.94
12591656--12591978	54	6.0	54	81	0	333	36	19	15	28	1.93
12600168--12600202	18	1.9	18	88	11	54	17	2	2	77	1.02
12609355--12609589	59	4.0	59	81	5	206	36	25	21	17	1.94
12609429--12609596	59	2.8	59	84	3	214	38	26	19	16	1.92
12619198--12619305	47	2.3	47	98	0	207	31	16	1	50	1.56
12619331--12619402	19	3.7	19	79	1	72	30	15	9	44	1.78
12619663--12619697	17	2.1	16	89	5	52	45	22	0	31	1.53
12621608--12621750	71	2.0	71	100	0	286	43	14	13	27	1.84
12624486--12624534	11	4.3	11	76	7	53	40	0	0	59	0.98
12624678--12624745	20	3.4	19	84	8	82	44	1	0	54	1.09
12624721--12624773	27	1.9	28	84	3	72	37	1	1	58	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12624678--12624745	21	3.4	20	84	6	84	44	1	0	54	1.09
12625114--12625178	33	2.0	33	90	0	103	35	10	10	43	1.75
12626279--12626340	23	2.7	23	75	9	63	22	14	11	51	1.74
12635445--12635485	19	2.2	19	90	0	64	39	14	17	29	1.89
12636039--12636602	67	8.4	67	85	1	731	32	15	23	28	1.95
12636039--12636906	134	6.3	134	77	9	823	33	14	23	28	1.94
12636039--12636906	201	4.2	200	77	8	767	33	14	23	28	1.94
12636586--12636772	81	2.3	81	84	1	241	37	10	22	28	1.88
12636732--12636906	67	2.6	67	92	2	280	33	13	25	27	1.94
12636434--12637068	296	2.1	296	88	0	923	35	13	22	28	1.92
12636861--12637204	81	4.3	81	86	0	447	37	11	22	28	1.89
12636861--12637260	81	4.9	81	84	1	444	37	11	23	28	1.89
12637290--12637419	46	2.7	46	84	4	152	46	8	20	24	1.78
12639158--12639194	2	18.5	2	100	0	74	51	0	0	48	1.00
12642016--12642259	67	3.6	66	84	5	319	32	14	23	29	1.94
12642016--12642259	133	1.8	135	86	4	359	32	14	23	29	1.94
12642210--12642496	80	3.6	80	84	3	364	35	12	22	28	1.91
12642451--12642701	67	3.7	67	91	1	396	32	15	23	28	1.95
12642652--12643033	81	4.7	81	85	0	471	36	10	23	29	1.88
12643235--12643352	46	2.6	46	77	10	118	42	12	17	27	1.86
12647592--12647723	30	4.4	30	83	0	156	34	19	21	24	1.96
12647592--12647723	60	2.2	60	86	0	174	34	19	21	24	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12649807--12649851	15	3.1	15	90	3	74	66	0	0	33	0.92
12650342--12650440	44	2.2	44	81	0	117	28	23	18	30	1.97
12650208--12650785	121	4.8	121	89	0	852	28	19	20	31	1.97
12650080--12650785	241	2.9	241	86	2	926	28	18	21	31	1.97
12651928--12651957	2	15.0	2	100	0	60	50	0	0	50	1.00
12653245--12653303	12	4.7	12	78	17	66	15	1	3	79	0.94
12653244--12653318	23	3.3	22	74	5	69	18	1	5	74	1.08
12653245--12653303	18	3.5	17	73	17	59	15	1	3	79	0.94
12660241--12660501	51	5.1	51	81	4	290	27	22	16	33	1.95
12660241--12660501	105	2.5	102	80	3	290	27	22	16	33	1.95
12660241--12660545	156	2.0	156	79	5	330	27	22	16	33	1.96
12660494--12660664	55	3.1	55	93	0	297	26	25	14	33	1.94
12661660--12661726	8	8.0	8	79	15	64	13	8	0	77	0.98
12661672--12661741	27	2.7	26	82	8	81	14	10	0	75	1.04
12661678--12661741	25	2.5	26	82	10	78	14	10	0	75	1.06
12665239--12665266	8	3.5	8	100	0	56	50	10	0	39	1.37
12671694--12671724	16	1.9	16	100	0	62	35	32	6	25	1.82
12681648--12681673	11	2.4	11	100	0	52	15	38	7	38	1.76
12685136--12685206	35	2.0	35	100	0	142	46	11	16	25	1.80
12686053--12686086	18	1.9	18	88	5	52	20	29	20	29	1.98
12694415--12694561	79	1.9	80	98	1	287	39	18	6	36	1.76
12695083--12695127	23	2.0	23	86	0	63	28	26	26	17	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12700951--12700996	23	2.0	23	95	0	83	32	13	13	41	1.82
12712089--12712199	30	3.6	30	86	4	141	35	9	22	32	1.87
12715001--12715067	30	2.2	30	84	5	82	46	11	16	25	1.81
12716240--12716285	20	2.3	20	85	3	58	36	0	23	39	1.55
12717713--12717825	34	3.4	34	75	9	135	33	7	23	35	1.82
12717747--12717884	30	4.5	30	81	7	168	34	11	22	31	1.90
12717709--12717861	64	2.4	64	96	0	279	34	9	21	34	1.85
12717747--12717921	30	5.7	30	78	9	147	33	12	23	30	1.92
12724413--12724467	15	3.7	15	75	4	58	40	20	20	20	1.92
12724387--12724466	29	2.8	29	86	3	101	38	17	20	23	1.93

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