genome.fa.s9462.2.7.7.80.10.50.1000.16.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: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  20687664

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   90   91   

This is table  16  of  91  ( 10815 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)
3185361--3185406	18	2.6	18	92	0	74	17	50	19	13	1.78
3185415--3185461	10	5.5	8	82	14	51	14	34	27	23	1.94
3185418--3185451	15	2.1	16	89	10	52	11	35	29	23	1.90
3186738--3186773	18	2.0	18	88	0	54	52	0	16	30	1.44
3187918--3188007	23	3.8	24	82	4	112	24	16	20	38	1.92
3192440--3192494	3	18.0	3	84	3	74	34	0	1	63	1.05
3194296--3194345	23	2.0	26	85	11	70	46	2	0	52	1.12
3194838--3194880	17	2.4	18	84	3	52	25	2	0	72	0.97
3199194--3199264	14	5.1	14	80	13	74	80	5	14	0	0.89
3199194--3199259	13	5.0	13	81	9	62	80	4	15	0	0.87
3199216--3199262	9	5.0	9	82	10	58	85	2	12	0	0.70
3199199--3199262	22	2.8	22	83	9	67	82	3	14	0	0.78
3199222--3199260	7	5.4	7	87	6	60	87	0	12	0	0.55
3199199--3199263	31	2.1	32	82	2	78	83	3	13	0	0.77
3201456--3201678	114	2.0	113	93	0	383	31	16	21	29	1.96
3204569--3204633	22	3.0	22	82	14	82	29	0	3	67	1.05
3204578--3204678	31	3.3	30	78	13	98	34	0	3	61	1.15
3208214--3208248	4	8.8	4	100	0	70	25	0	0	74	0.82
3222846--3222886	17	2.4	17	91	0	64	12	26	0	60	1.31
3223527--3223567	13	3.3	13	80	10	50	21	4	2	70	1.18
3223734--3223767	4	8.2	4	87	6	50	23	2	0	73	0.97
3223734--3223768	13	2.8	13	91	4	54	22	2	0	74	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3223716--3223780	28	2.5	27	78	16	75	27	3	0	69	1.03
3228384--3228434	19	2.6	19	81	3	57	33	27	13	25	1.94
3228444--3228593	77	1.9	77	90	0	237	38	16	16	28	1.91
3228898--3228947	20	2.5	20	90	0	73	12	20	26	42	1.86
3228857--3229007	77	2.0	77	87	0	221	19	17	21	41	1.90
3233379--3233414	15	2.4	15	95	0	63	25	36	8	30	1.85
3235523--3235556	9	3.9	9	84	7	52	61	2	0	35	1.11
3235519--3235557	17	2.4	17	95	4	71	61	5	0	33	1.18
3236628--3236679	21	2.4	21	77	3	59	23	0	32	44	1.54
3236669--3236716	21	2.2	23	85	14	75	22	0	25	52	1.48
3237168--3237194	4	6.8	4	100	0	54	22	0	0	77	0.76
3237190--3237247	30	1.9	30	93	6	100	39	3	5	51	1.41
3237473--3237503	15	2.1	15	100	0	62	45	12	12	29	1.80
3237841--3237919	32	2.5	33	79	10	101	49	0	11	39	1.39
3238402--3238882	226	2.1	228	95	1	858	44	7	8	39	1.62
3238951--3239423	180	2.6	181	88	2	684	42	13	17	26	1.86
3239344--3239390	20	2.4	19	82	10	67	53	10	17	19	1.72
3239353--3239395	20	2.3	19	88	11	63	51	11	16	20	1.75
3238951--3239423	181	2.6	180	88	3	691	42	13	17	26	1.86
3241590--3241633	21	2.1	21	91	0	70	40	11	31	15	1.83
3241667--3241732	33	2.0	33	90	0	105	28	0	48	22	1.51
3243522--3243570	19	2.6	19	93	0	80	30	2	10	57	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3243689--3245050	198	6.9	198	97	0	2498	36	15	17	30	1.91
3246528--3246608	3	27.0	3	79	0	90	35	6	33	24	1.81
3246516--3246592	36	2.1	36	92	0	127	36	9	33	20	1.85
3247800--3247833	16	2.1	16	88	0	50	47	8	20	23	1.78
3248198--3248268	21	3.3	21	80	7	79	33	4	22	39	1.74
3248193--3248254	21	2.8	22	82	7	81	35	4	22	37	1.76
3248193--3248263	23	3.2	23	76	13	76	33	4	22	39	1.74
3251422--3251486	25	2.6	25	80	0	85	35	9	13	41	1.77
3251826--3251898	23	3.2	23	81	11	87	34	4	20	41	1.72
3252172--3252221	25	2.0	25	96	0	91	26	8	22	44	1.80
3252898--3252984	39	2.2	39	95	0	156	48	20	13	17	1.81
3253405--3253477	23	3.2	23	84	0	92	34	4	20	41	1.72
3253405--3253502	46	2.1	45	81	7	108	33	6	17	42	1.74
3253835--3253907	23	3.2	23	84	0	92	34	4	20	41	1.72
3253835--3253932	46	2.1	45	81	7	108	33	6	17	42	1.74
3253203--3254687	430	3.5	430	98	0	2819	41	7	11	38	1.71
3254265--3254337	23	3.2	23	92	0	110	35	4	21	38	1.73
3257734--3257804	37	1.9	37	97	0	133	26	8	26	38	1.85
3257798--3257874	41	2.0	39	85	10	104	35	6	20	37	1.79
3259682--3259711	2	15.0	2	100	0	60	50	0	0	50	1.00
3267155--3267217	19	3.2	21	80	14	64	53	11	3	31	1.52
3267406--3267457	15	3.6	13	80	19	59	63	1	0	34	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3268293--3268353	31	2.0	31	87	6	88	57	4	11	26	1.54
3286221--3286278	29	2.0	28	83	9	73	48	3	0	48	1.18
3287755--3288406	81	8.1	81	88	1	950	32	22	10	34	1.88
3290754--3290813	31	1.9	31	89	0	93	40	5	10	45	1.60
3291291--3291362	21	3.4	21	73	11	58	59	1	2	36	1.20
3291313--3291496	64	2.8	62	86	8	210	57	1	1	40	1.16
3291356--3291399	24	1.9	23	90	9	63	56	0	0	43	0.99
3291391--3291460	23	2.8	26	85	12	94	52	1	0	45	1.09
3291412--3291502	41	2.2	41	81	11	105	58	1	0	40	1.05
3291449--3291502	23	2.3	23	87	6	74	62	1	0	35	1.06
3298156--3298209	24	2.3	23	79	17	58	40	0	1	57	1.09
3303173--3303215	19	2.2	19	87	4	59	60	0	0	39	0.97
3303930--3303960	2	15.5	2	100	0	62	48	0	0	51	1.00
3305043--3305086	21	2.1	21	83	8	54	45	18	15	20	1.85
3305714--3305781	16	4.9	14	77	18	63	19	4	1	75	1.06
3305716--3305775	21	2.8	21	74	5	57	18	5	1	75	1.07
3305747--3305788	16	2.7	15	76	23	50	21	7	0	71	1.09
3305847--3305886	12	3.2	12	89	10	55	35	7	0	57	1.27
3305879--3305952	2	37.0	2	100	0	148	50	0	0	50	1.00
3306000--3306038	2	20.0	2	94	5	71	48	0	0	51	1.00
3306234--3306309	14	5.1	14	75	23	59	18	13	1	67	1.30
3306258--3306309	14	3.4	15	78	21	63	19	11	1	67	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3310234--3310474	95	2.5	98	86	7	355	34	16	17	31	1.92
3311771--3311851	36	2.2	36	86	2	108	34	18	8	38	1.82
3311864--3312027	36	4.5	37	76	3	109	28	19	12	40	1.87
3311864--3312027	72	2.3	74	78	5	183	28	19	12	40	1.87
3311901--3312161	138	1.9	139	83	2	337	27	18	11	42	1.85
3311771--3312161	174	2.2	174	85	1	532	28	18	11	40	1.86
3312089--3312161	36	2.0	36	89	0	110	24	17	15	42	1.88
3312496--3312534	18	2.2	18	95	0	69	30	20	7	41	1.80
3313824--3313887	9	6.8	9	77	10	56	14	4	0	81	0.85
3313800--3313869	36	1.9	36	82	5	88	17	5	1	75	1.06
3313992--3314033	2	21.0	2	100	0	84	50	0	0	50	1.00
3314245--3314329	33	2.6	34	78	10	88	11	11	2	74	1.17
3314245--3314345	19	5.3	19	74	15	68	12	10	1	74	1.16
3314310--3314371	14	4.1	15	77	20	67	19	9	1	69	1.25
3314552--3314625	38	1.9	38	86	5	105	27	13	43	16	1.85
3317676--3317798	62	2.0	62	100	0	246	26	9	20	43	1.82
3320755--3320813	29	2.0	29	100	0	118	38	0	16	44	1.48
3321126--3321152	2	13.5	2	100	0	54	51	0	0	48	1.00
3324231--3324291	2	30.5	2	96	0	95	49	4	0	45	1.23
3324536--3324607	2	36.0	2	94	5	128	50	1	0	48	1.09
3325877--3325910	7	4.9	7	100	0	68	73	11	0	14	1.10
3329129--3329181	16	3.1	16	77	15	52	26	0	5	67	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3329129--3329195	35	1.9	35	84	6	91	29	0	5	64	1.17
3329173--3329212	16	2.5	16	84	8	55	42	0	2	55	1.13
3330996--3331064	21	3.3	21	91	4	104	18	34	24	21	1.96
3331594--3331698	33	3.2	33	81	9	124	55	4	2	37	1.36
3332078--3332796	125	5.8	125	96	2	1310	31	19	26	22	1.98
3332078--3332796	372	1.9	370	96	2	1325	31	19	26	22	1.98
3332864--3332903	8	5.1	8	81	6	55	37	27	0	35	1.57
3335924--3335981	23	2.6	23	94	5	102	44	12	3	39	1.58
3341368--3341435	31	2.2	31	94	2	118	54	5	5	33	1.49
3341409--3341819	194	2.1	200	83	3	519	48	8	4	38	1.53

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   90   91