genome.fa.s3.2.7.7.80.10.50.1000.9.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: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  13963513

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   

This is table  9  of  29  ( 3437 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)
3164977--3165022	22	2.1	22	84	4	58	45	2	4	47	1.34
3170074--3170115	21	2.0	22	85	4	59	26	7	4	61	1.42
3180033--3180565	194	2.7	195	81	8	643	49	2	3	43	1.35
3180332--3180387	26	2.2	26	83	6	69	51	1	5	41	1.35
3180528--3180610	15	5.6	14	78	12	78	54	2	0	43	1.13
3180543--3180607	22	2.9	22	80	8	78	55	1	0	43	1.09
3185148--3185182	3	11.7	3	93	0	61	65	2	0	31	1.07
3187766--3187880	33	3.4	35	89	6	164	33	26	12	26	1.92
3187799--3187895	35	2.9	34	84	4	106	37	24	12	25	1.91
3189727--3189903	90	2.0	90	82	2	221	28	28	15	28	1.96
3189987--3190196	80	2.6	80	84	1	251	32	23	9	34	1.86
3190535--3190572	17	2.2	18	85	4	51	21	0	13	65	1.26
3197110--3197140	15	2.1	15	93	0	53	48	6	16	29	1.70
3206849--3206937	36	2.5	36	83	1	99	30	15	19	34	1.93
3213446--3213474	14	2.0	15	93	6	51	20	13	17	48	1.81
3225400--3225433	15	2.3	15	89	0	50	44	5	17	32	1.73
3225509--3225579	29	2.4	29	88	0	106	50	9	29	9	1.68
3225843--3225940	35	2.8	34	83	9	117	26	15	13	44	1.83
3237145--3237185	22	1.9	21	90	5	64	39	0	24	36	1.56
3238538--3238577	20	2.0	20	85	5	53	70	5	2	22	1.19
3238574--3238616	16	2.7	16	82	10	52	62	11	0	25	1.29
3244549--3244587	19	2.0	20	90	5	62	71	7	0	20	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3244583--3244625	15	2.8	15	80	16	52	60	11	0	27	1.31
3257460--3257503	13	3.2	15	75	18	51	54	0	0	45	0.99
3257442--3257495	16	3.4	16	78	14	51	46	0	0	53	1.00
3257461--3257527	28	2.4	28	82	9	75	59	0	0	40	0.97
3260074--3260120	18	2.6	18	80	12	53	55	0	27	17	1.42
3265761--3265840	28	2.9	28	81	1	99	31	16	17	35	1.92
3268780--3268845	35	1.9	34	82	14	82	27	21	13	37	1.91
3271688--3271766	38	2.1	38	82	0	95	35	25	11	27	1.90
3273996--3274038	20	2.2	20	87	4	61	48	11	4	34	1.60
3274647--3274703	29	2.0	29	89	0	87	47	15	12	24	1.80
3281065--3281117	18	2.8	19	77	13	56	33	1	0	64	1.05
3293893--3293933	18	2.2	19	86	4	57	68	7	0	24	1.15
3299887--3300029	75	1.9	74	85	1	196	39	4	9	47	1.55
3300112--3300195	35	2.3	38	78	10	95	36	0	3	59	1.15
3300269--3300324	26	2.2	26	83	0	67	33	5	17	42	1.72
3307466--3307496	7	4.4	7	95	0	53	48	0	51	0	1.00
3309498--3309704	105	2.0	105	81	5	249	24	7	21	46	1.76
3309858--3309910	21	2.5	22	78	6	72	49	16	11	22	1.78
3336081--3336117	18	2.1	18	100	0	74	43	0	27	29	1.55
3337708--3337821	7	16.4	7	69	16	60	0	31	1	66	1.02
3337722--3337818	25	3.8	25	82	6	106	0	29	2	68	1.01
3337709--3337811	11	9.9	10	72	19	68	0	30	1	67	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3338635--3338909	60	4.6	59	86	4	340	35	18	12	33	1.88
3338635--3338909	118	2.3	120	85	6	364	35	18	12	33	1.88
3341979--3342022	21	2.0	22	86	4	63	61	9	0	29	1.27
3352266--3352316	21	2.4	21	80	3	57	13	11	25	49	1.76
3352416--3352535	22	5.5	22	75	5	91	46	20	9	24	1.79
3352416--3352571	43	3.6	43	74	1	141	44	23	10	21	1.82
3352418--3352578	87	1.9	87	86	0	232	44	24	9	21	1.83
3352417--3352596	87	2.1	87	82	2	227	43	23	10	22	1.84
3358898--3358935	9	4.3	9	80	6	51	10	5	0	84	0.77
3358904--3358936	17	1.9	17	100	0	66	12	9	0	78	0.95
3363689--3363964	60	4.6	59	86	1	363	32	12	18	36	1.88
3363689--3363964	119	2.3	119	87	2	385	32	12	18	36	1.88
3366272--3366308	18	2.1	18	100	0	74	43	0	27	29	1.55
3370671--3371058	59	6.7	59	80	8	388	33	19	14	32	1.92
3370770--3371058	53	5.2	53	75	13	267	33	19	14	32	1.92
3370667--3371058	168	2.3	170	85	7	488	33	19	14	32	1.92
3378786--3378845	21	2.8	21	84	2	66	18	6	28	46	1.74
3378785--3378859	22	3.5	22	81	3	71	21	8	24	46	1.77
3378904--3378957	22	2.4	23	84	3	74	38	25	7	27	1.83
3378904--3378965	23	2.7	23	85	2	81	38	24	8	29	1.84
3382882--3382920	20	2.0	20	94	0	69	38	17	10	33	1.84
3383556--3383595	21	2.0	20	85	5	53	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3386343--3386418	38	2.0	38	94	0	134	32	32	9	25	1.87
3388570--3388618	20	2.5	20	96	0	89	0	28	0	71	0.86
3388572--3388621	16	3.2	16	83	8	59	0	26	0	74	0.83
3393897--3393942	23	2.0	23	100	0	92	34	17	8	39	1.80
3399692--3399740	16	3.3	16	67	21	52	59	16	2	22	1.47
3399686--3399746	28	2.4	25	77	17	70	62	14	1	21	1.41
3411794--3411844	18	2.8	18	85	14	61	31	1	1	64	1.15
3414106--3414243	72	1.9	72	83	0	177	23	26	11	38	1.89
3417754--3417778	9	2.8	9	100	0	50	12	0	0	88	0.53
3418141--3418511	76	4.9	76	83	2	444	22	14	26	36	1.92
3421706--3421820	31	3.5	31	72	17	95	36	19	15	28	1.92
3421712--3421788	39	2.0	38	87	2	109	35	18	16	29	1.93
3421813--3421873	26	2.5	25	84	7	63	27	27	21	22	1.99
3422510--3422573	23	2.8	23	92	0	110	26	25	23	25	2.00
3422561--3422734	46	3.8	46	77	5	172	26	30	13	29	1.94
3422561--3422712	23	6.7	23	77	4	137	25	30	14	30	1.95
3422662--3422849	104	1.8	104	88	0	286	27	30	14	27	1.95
3422861--3422913	23	2.3	23	86	0	70	32	28	9	30	1.88
3422924--3422982	23	2.6	23	86	0	82	18	23	16	40	1.91
3423031--3423089	23	2.6	23	83	0	64	27	35	8	28	1.86
3423054--3423104	23	2.2	23	85	0	66	25	37	9	27	1.87
3423989--3424036	24	2.0	24	84	8	62	35	2	4	58	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3429817--3429847	1	31.0	1	100	0	62	0	0	0	100	0.00
3444672--3444727	29	1.9	30	82	13	73	64	3	3	28	1.27
3455773--3455834	22	2.9	20	76	11	61	19	9	24	46	1.79
3455725--3456184	203	2.3	203	82	2	566	21	10	23	43	1.84
3459854--3460086	69	3.4	69	82	5	222	34	24	9	31	1.88
3459937--3460112	69	2.6	69	84	1	183	36	23	7	32	1.83
3459856--3460178	92	3.5	91	75	4	256	34	25	8	31	1.86
3459854--3460236	23	16.7	23	70	5	164	34	25	8	31	1.86
3460080--3460236	69	2.3	69	87	0	215	34	27	7	31	1.83
3460548--3460613	26	2.5	26	90	2	96	50	4	15	30	1.64
3465369--3465840	236	2.0	236	85	4	632	27	22	15	34	1.94
3488573--3488605	17	1.9	17	93	0	57	51	0	21	27	1.48
3491073--3491134	21	3.0	21	85	0	79	37	16	17	29	1.92
3493088--3493121	12	2.8	12	86	4	50	17	5	0	76	0.98
3502339--3502387	23	2.0	24	88	7	73	26	8	4	61	1.42
3503510--3503593	23	3.5	24	87	6	109	30	10	19	39	1.85
3507688--3507755	21	3.0	23	85	8	104	26	23	20	29	1.99
3508105--3508156	23	2.4	21	78	12	59	28	28	7	34	1.85
3508111--3508187	23	3.3	23	79	12	86	27	31	7	33	1.85
3508271--3508354	23	3.7	23	73	23	88	26	32	8	33	1.86
3507995--3508400	217	1.9	217	79	8	468	26	29	11	33	1.91
3516027--3516064	12	3.2	12	88	3	51	42	2	2	52	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3517234--3517266	8	3.9	9	88	11	52	0	0	90	9	0.44
3521737--3521780	22	2.0	23	86	4	63	61	0	4	34	1.16
3522038--3522194	83	1.9	84	89	2	244	19	21	29	29	1.98
3550499--3550546	21	2.2	21	88	3	69	31	12	20	35	1.90
3552159--3552209	21	2.4	21	93	0	93	37	21	9	31	1.86
3554271--3554307	9	3.9	9	89	10	56	83	2	2	10	0.84
3556926--3557027	31	3.3	31	78	6	100	37	13	2	46	1.59
3565426--3565470	20	2.3	20	84	3	56	55	4	4	35	1.40
3567784--3567817	11	3.1	11	86	0	50	67	17	5	8	1.37
3569873--3569900	2	14.0	2	100	0	56	50	0	0	50	1.00

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