genome.fa.s1129.2.7.7.80.10.50.1000.17.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  17  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)
3250122--3250191	30	2.4	30	95	2	124	41	5	12	40	1.67
3250642--3250710	27	2.4	29	81	11	72	42	2	20	34	1.67
3250929--3250963	18	1.9	18	88	0	52	17	17	34	31	1.93
3251379--3251409	2	15.5	2	93	0	53	3	0	45	51	1.17
3255057--3255096	20	2.0	21	95	5	73	25	20	22	32	1.98
3256197--3256268	21	3.6	20	83	5	83	30	15	25	29	1.96
3258108--3258166	26	2.4	25	83	10	77	50	0	0	49	1.00
3260241--3260271	2	15.5	2	100	0	62	48	0	0	51	1.00
3263885--3263944	31	1.9	31	93	0	102	36	10	26	26	1.88
3267691--3267754	30	2.1	30	83	11	78	3	29	0	67	1.06
3273624--3273775	57	2.5	63	78	17	192	31	22	16	29	1.96
3273648--3273766	57	2.1	56	92	1	193	31	21	16	29	1.96
3282325--3282484	65	2.5	65	90	3	252	31	21	17	29	1.96
3283952--3284001	20	2.5	20	83	3	66	28	16	26	30	1.96
3292195--3292236	11	3.8	11	96	0	66	42	9	30	16	1.80
3298034--3298083	24	2.1	24	85	7	66	60	14	2	24	1.45
3301726--3301762	16	2.2	18	85	9	51	78	2	5	13	1.03
3308240--3308289	24	2.1	24	85	7	66	60	14	2	24	1.45
3309114--3309813	135	5.2	134	84	3	917	32	19	19	29	1.96
3313927--3313960	17	2.0	17	100	0	68	35	0	29	35	1.58
3317791--3317952	81	2.0	81	93	0	279	40	20	14	24	1.90
3318478--3318575	42	2.2	45	80	12	114	22	8	3	66	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3321182--3321446	100	2.7	99	84	3	320	33	15	17	33	1.92
3322419--3323427	84	12.0	84	82	2	1031	31	24	18	25	1.98
3322419--3323446	253	4.1	252	81	2	1103	31	24	18	25	1.97
3326297--3326336	21	1.9	21	94	0	71	15	17	5	62	1.49
3328024--3329145	563	2.0	563	96	0	2091	33	20	18	27	1.96
3339232--3339272	19	2.2	18	86	4	55	56	0	0	43	0.99
3340837--3340887	22	2.3	22	80	6	59	35	33	3	27	1.75
3341001--3341045	22	2.1	21	91	4	72	8	15	6	68	1.36
3341001--3341045	21	2.1	22	91	4	74	8	15	6	68	1.36
3355207--3355289	18	4.7	19	76	15	81	33	9	10	45	1.72
3355204--3355289	35	2.5	34	85	9	111	33	9	11	45	1.73
3355219--3355271	17	3.1	17	75	20	56	39	9	11	39	1.74
3357768--3357819	27	1.9	27	92	0	86	21	11	23	44	1.84
3358311--3358348	20	1.9	20	94	0	67	31	26	10	31	1.90
3359043--3359100	22	2.7	21	79	12	57	50	0	34	15	1.45
3359041--3359100	21	2.8	22	76	5	68	48	0	33	18	1.48
3361819--3363000	186	6.3	186	83	2	1327	33	15	12	39	1.85
3361819--3362990	372	3.1	371	84	2	1463	33	15	12	38	1.85
3361839--3363000	558	2.1	556	84	2	1508	32	15	12	39	1.85
3367984--3368025	21	2.0	21	90	4	68	59	0	7	33	1.25
3372335--3372419	31	2.7	31	79	0	98	43	28	10	17	1.82
3377067--3377889	139	6.0	139	83	5	960	25	18	23	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3377081--3377844	281	2.7	277	83	4	943	25	18	23	32	1.97
3378799--3378904	42	2.5	42	76	11	126	22	20	33	23	1.98
3380620--3380664	23	1.9	24	86	4	65	64	0	0	35	0.94
3380918--3381038	61	2.0	61	88	3	181	24	33	24	16	1.96
3386190--3386216	10	2.7	10	100	0	54	59	22	18	0	1.38
3388128--3388165	15	2.5	15	91	0	58	42	23	10	23	1.85
3393985--3394027	19	2.3	18	80	11	50	46	0	0	53	1.00
3395369--3395414	5	9.6	5	81	9	51	21	4	0	73	1.00
3395370--3395419	14	3.6	13	81	10	55	20	6	0	74	1.03
3395369--3395414	19	2.4	20	82	17	62	21	4	0	73	1.00
3397726--3397754	14	2.0	15	93	6	51	62	27	3	6	1.37
3399678--3399757	23	3.6	22	76	5	90	23	23	26	26	2.00
3405303--3405346	21	2.1	21	87	8	63	9	20	11	59	1.59
3405303--3405338	11	3.4	11	96	3	65	8	25	8	58	1.55
3406250--3406306	20	2.8	21	83	2	71	31	24	19	24	1.98
3408748--3408787	21	1.9	21	90	10	64	57	17	7	17	1.62
3408886--3408963	20	3.8	21	81	3	79	33	25	16	24	1.96
3409657--3409710	27	2.0	27	100	0	108	29	3	25	40	1.73
3410015--3410063	23	2.1	24	92	3	82	51	12	20	16	1.76
3412446--3412479	17	1.9	18	88	5	52	20	0	8	70	1.13
3418134--3418173	21	1.9	21	89	0	62	77	0	22	0	0.77
3418139--3418192	17	3.3	17	80	12	60	70	0	27	1	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3420250--3421474	256	4.8	256	86	1	1583	34	13	16	35	1.88
3420250--3421458	513	2.4	512	86	1	1650	34	13	16	35	1.88
3430173--3430242	21	3.5	20	71	28	67	25	25	21	27	1.99
3430173--3430270	40	2.5	40	89	3	153	24	26	19	29	1.98
3436465--3436514	23	2.2	23	96	0	91	16	20	28	36	1.93
3441007--3441035	5	5.8	5	100	0	58	79	0	0	20	0.74
3441277--3442066	55	14.4	55	84	5	870	30	20	16	31	1.95
3442290--3442407	37	3.2	36	75	4	128	22	22	16	39	1.91
3444458--3444504	2	23.5	2	100	0	94	48	0	0	51	1.00
3449285--3449374	45	2.0	45	82	0	108	35	22	12	30	1.90
3451799--3451864	34	1.9	34	87	6	98	25	21	6	46	1.74
3467794--3468002	109	1.9	109	87	4	307	25	18	27	28	1.98
3473552--3473692	20	7.0	20	69	7	88	34	24	11	30	1.90
3473677--3473764	20	4.5	20	73	9	74	27	20	12	39	1.88
3473553--3473744	40	4.8	41	76	5	149	32	21	11	33	1.90
3473865--3473903	16	2.5	15	84	8	51	28	5	0	66	1.12
3474642--3474695	24	2.2	24	96	0	99	20	16	20	42	1.89
3474870--3474900	3	10.3	3	92	0	53	64	0	32	3	1.09
3476970--3477005	18	2.0	18	94	0	63	55	25	2	16	1.55
3477276--3477331	20	2.8	20	88	0	85	42	23	17	16	1.88
3477495--3477531	17	2.2	17	90	4	58	62	16	0	21	1.33
3478965--3479018	21	2.6	21	81	0	63	24	16	31	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3479031--3479071	21	2.0	21	90	0	64	29	9	36	24	1.87
3479205--3479250	4	11.5	4	80	0	56	67	4	2	26	1.21
3479480--3479525	21	2.2	21	84	0	56	36	34	10	17	1.85
3479644--3479736	42	2.2	42	84	0	114	19	17	34	29	1.94
3481238--3481307	20	3.5	20	88	0	95	48	17	14	20	1.81
3481354--3481397	20	2.2	20	83	0	52	18	11	18	52	1.74
3481871--3481908	20	2.0	20	84	5	51	44	13	15	26	1.83
3481879--3481961	20	4.2	20	69	13	64	36	18	21	24	1.95
3481887--3481968	40	2.1	39	81	6	94	34	18	20	26	1.96
3481985--3482029	20	2.2	21	84	11	58	31	8	28	31	1.88
3483528--3483693	60	2.8	60	81	1	199	39	5	22	31	1.77
3491398--3491599	95	2.1	95	89	0	305	35	16	16	30	1.92
3493236--3493459	85	2.6	84	82	5	261	34	19	17	28	1.95
3494114--3494220	54	2.0	54	88	3	162	35	20	17	26	1.95
3496392--3496448	29	2.0	29	82	3	71	56	10	1	31	1.44
3496799--3496840	22	1.9	22	90	0	66	45	0	0	54	0.99
3498992--3499025	2	17.0	2	100	0	68	50	0	0	50	1.00
3503770--3503817	19	2.5	19	96	0	87	39	0	6	54	1.26
3511761--3511799	21	1.9	20	89	5	60	33	25	15	25	1.95
3526154--3526194	19	2.2	19	90	0	64	24	24	21	29	1.99
3550316--3550352	19	1.9	19	88	0	56	45	13	13	27	1.81
3574132--3574190	23	2.7	23	84	10	70	5	8	10	76	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3574141--3574191	23	2.2	24	89	10	79	5	7	11	74	1.21
3574766--3574791	3	8.7	3	100	0	52	65	0	0	34	0.93
3581031--3581062	6	5.7	6	96	3	50	71	0	9	18	1.12
3581027--3581063	12	3.5	11	86	13	51	72	0	8	18	1.08
3582010--3582063	24	2.2	24	83	6	74	9	7	11	72	1.29
3582915--3583103	83	2.3	83	84	5	240	24	19	31	24	1.98
3583081--3583215	48	2.7	49	75	5	130	26	14	27	31	1.95
3582891--3583396	265	1.9	265	88	0	753	25	17	30	26	1.97
3583212--3583368	83	1.9	83	81	5	192	28	18	29	23	1.98
3583185--3583381	83	2.4	83	73	3	191	26	18	29	25	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