genome.fa.s3.2.7.7.80.10.50.1000.15.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  15  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)
5312032--5312070	16	2.4	17	87	12	55	56	0	2	41	1.13
5313205--5313257	26	2.0	26	92	7	90	39	7	20	32	1.81
5318005--5318052	8	5.8	8	88	9	60	22	2	27	47	1.62
5318023--5318052	4	7.5	4	100	0	60	26	0	23	50	1.50
5322541--5322571	3	10.3	3	100	0	62	32	32	0	35	1.58
5329154--5329179	2	13.0	2	100	0	52	50	0	0	50	1.00
5330220--5330254	2	17.5	2	100	0	70	51	0	0	48	1.00
5338607--5338645	2	19.5	2	89	0	60	51	0	2	46	1.14
5346880--5346913	6	5.7	6	100	0	68	85	14	0	0	0.60
5347239--5347272	6	5.7	6	92	0	59	0	52	0	47	1.00
5353549--5353606	15	4.1	14	73	8	55	48	5	0	46	1.24
5359712--5360707	333	3.0	334	93	0	1692	30	17	14	38	1.89
5365328--5365441	56	2.0	57	84	5	151	35	16	13	34	1.88
5366660--5366689	2	15.0	2	92	0	51	46	3	0	50	1.18
5367546--5367638	31	3.0	31	92	4	145	35	13	10	39	1.80
5367886--5367920	12	2.8	13	91	8	56	54	0	0	45	0.99
5367891--5367945	13	3.9	14	73	15	51	47	1	1	49	1.23
5371735--5371810	27	2.8	27	73	11	66	46	0	1	52	1.08
5374324--5374402	41	1.9	41	89	0	122	37	25	2	34	1.70
5381123--5381172	19	2.6	19	81	12	50	22	0	6	72	1.07
5392261--5392285	2	12.5	2	100	0	50	52	0	48	0	1.00
5397026--5397075	20	2.4	21	90	6	75	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5397026--5397074	11	4.6	11	73	17	50	51	0	0	48	1.00
5397304--5397329	10	2.6	10	100	0	52	73	0	15	11	1.11
5398216--5398424	107	2.0	107	87	1	303	35	15	5	43	1.70
5409140--5409175	8	4.5	8	85	0	54	44	0	11	44	1.39
5409876--5409959	33	2.6	32	85	9	107	29	3	0	66	1.08
5409903--5409964	19	3.0	22	71	20	62	29	3	0	67	1.06
5410451--5410479	2	14.5	2	100	0	58	51	0	0	48	1.00
5426884--5426949	35	1.9	35	87	9	100	28	0	10	60	1.30
5426885--5426960	35	2.2	34	83	6	91	30	2	10	56	1.47
5431757--5431789	16	2.1	16	94	0	57	42	9	0	48	1.35
5432432--5432478	22	2.2	20	81	7	58	17	29	4	48	1.65
5437636--5437666	3	10.7	3	93	6	55	0	32	0	67	0.91
5437947--5437980	17	2.0	17	94	0	59	61	0	14	23	1.33
5438609--5438660	15	3.5	15	86	0	77	40	17	0	42	1.49
5442166--5442190	2	12.5	2	100	0	50	52	0	0	48	1.00
5452992--5453033	21	2.1	20	86	8	59	59	9	0	30	1.29
5459366--5459411	5	9.0	5	81	13	58	19	4	0	76	0.96
5459370--5459411	20	2.1	20	90	0	66	19	4	0	76	0.96
5460628--5460664	16	2.3	17	81	13	51	75	0	5	18	0.99
5464132--5464168	10	3.8	10	82	17	51	67	0	0	32	0.91
5464984--5465043	30	2.0	30	93	0	102	51	8	15	25	1.70
5466303--5466385	41	2.0	41	92	0	139	40	9	21	27	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5468961--5468993	2	16.5	2	93	0	57	45	0	3	51	1.16
5486317--5486360	21	2.0	23	86	8	65	38	0	6	54	1.27
5488597--5488634	19	2.1	18	90	5	58	47	5	0	47	1.24
5496971--5497013	18	2.2	20	80	12	54	18	2	9	69	1.26
5498967--5499030	22	2.9	22	78	0	83	46	29	6	17	1.72
5500012--5500074	33	1.9	33	90	0	99	36	12	11	39	1.79
5501741--5501821	35	2.3	35	83	6	103	24	0	16	59	1.37
5516394--5516517	23	5.5	23	85	2	171	35	32	11	20	1.88
5516394--5516601	22	9.4	22	79	6	181	37	29	12	20	1.89
5516393--5516517	45	2.8	45	97	1	232	36	32	11	20	1.88
5516529--5516584	21	2.7	21	74	0	67	37	26	17	17	1.93
5516711--5516836	60	2.1	60	83	5	155	48	16	4	30	1.67
5521523--5521583	29	2.1	28	84	3	77	32	22	11	32	1.90
5521450--5522269	404	2.0	408	88	3	1206	34	19	9	36	1.85
5524560--5524617	15	3.9	15	82	8	82	29	34	5	31	1.79
5524557--5524622	30	2.2	30	91	0	114	30	33	4	31	1.78
5524836--5524892	15	3.8	15	84	9	80	12	40	29	17	1.86
5524835--5524898	30	2.1	30	94	0	110	10	40	29	18	1.85
5527615--5527650	7	5.1	7	100	0	72	44	27	0	27	1.55
5529042--5529104	26	2.4	26	79	10	74	44	4	15	34	1.68
5529154--5529216	26	2.5	26	86	2	83	55	1	6	36	1.35
5529154--5529239	25	3.4	25	80	1	73	53	4	5	36	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5529207--5529247	22	1.9	22	90	5	66	51	12	2	34	1.52
5529207--5529253	22	2.1	22	84	7	60	51	14	4	29	1.62
5536102--5536132	14	2.1	15	94	5	55	77	6	9	6	1.12
5538404--5538472	21	3.4	21	82	6	70	43	30	1	24	1.63
5538515--5538556	21	2.0	21	95	0	75	47	26	0	26	1.52
5538565--5538658	21	4.5	20	69	13	64	44	20	8	26	1.80
5538809--5538853	20	2.2	20	84	4	54	46	31	8	13	1.74
5548699--5548752	28	2.0	27	85	10	74	38	1	0	59	1.08
5549214--5549263	26	1.9	26	88	8	75	54	0	0	46	1.00
5551383--5551428	21	2.2	21	88	0	65	34	32	8	23	1.86
5551614--5551656	3	14.3	3	87	0	59	67	2	27	2	1.15
5551835--5551889	27	2.0	27	92	0	92	45	10	12	30	1.77
5570968--5571053	30	3.2	26	70	20	61	67	2	1	29	1.10
5571033--5571335	8	34.2	9	62	26	71	63	0	1	33	1.10
5571045--5571439	10	39.1	10	63	24	66	63	0	2	33	1.11
5571031--5571111	31	2.6	32	77	15	87	69	0	2	28	1.02
5571030--5571134	33	3.1	31	69	25	79	66	0	2	29	1.12
5571030--5571496	70	6.9	69	66	21	188	63	0	2	33	1.12
5571158--5571334	6	29.0	6	67	21	59	64	0	1	33	1.05
5571071--5571516	112	4.0	112	94	4	758	63	0	2	34	1.11
5571071--5571516	223	2.0	225	94	4	787	63	0	2	34	1.11
5571104--5571504	13	28.6	15	65	27	93	62	0	2	34	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5571306--5571525	60	3.8	60	76	16	230	61	0	2	35	1.14
5571661--5571719	15	3.9	15	88	0	73	32	27	8	32	1.87
5573217--5573263	23	2.0	23	87	0	67	61	2	10	25	1.39
5577137--5577224	43	2.0	43	97	0	167	63	14	4	17	1.46
5587681--5587750	28	2.5	28	92	2	113	30	0	7	62	1.21
5598723--5598769	19	2.4	20	86	10	62	76	0	10	12	1.02
5598723--5598776	27	2.0	27	89	3	83	75	0	9	14	1.03
5601431--5601485	27	2.0	28	89	7	85	36	7	9	47	1.63
5601442--5601495	27	2.0	27	85	0	72	37	11	7	44	1.68
5606811--5606866	11	5.4	11	75	10	55	66	0	3	30	1.09
5606833--5607454	316	2.0	315	83	6	794	52	2	3	40	1.33
5614364--5614416	20	2.7	20	78	0	61	32	20	9	37	1.85
5616271--5616305	16	2.2	16	94	0	61	65	11	2	20	1.37
5619203--5619306	34	3.1	34	81	2	120	22	14	30	32	1.93
5630585--5630656	36	2.0	36	86	0	99	33	13	20	31	1.92
5632040--5632069	16	1.9	15	93	6	51	13	3	16	66	1.37
5634043--5634081	20	2.0	20	84	0	51	43	12	7	35	1.72
5651180--5651328	78	1.9	79	87	1	219	42	10	7	39	1.68
5651271--5651384	57	2.0	57	89	1	176	39	10	10	39	1.74
5658870--5658910	20	2.0	20	90	0	64	46	14	19	19	1.84
5676337--5676424	39	2.2	39	93	2	149	40	25	18	15	1.90
5678802--5678839	2	19.0	2	94	0	67	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5685743--5685830	40	2.2	40	91	0	149	54	20	1	23	1.51
5688660--5688831	31	5.3	31	81	11	134	55	4	21	18	1.60
5714390--5714431	18	2.3	19	79	4	50	14	0	23	61	1.32
5715504--5715591	44	2.0	44	81	0	104	42	9	13	35	1.76
5723122--5723175	27	2.0	27	96	0	99	31	22	7	38	1.82
5723321--5723345	6	4.2	6	100	0	50	36	0	0	64	0.94
5724706--5724763	24	2.5	22	76	17	64	56	8	5	29	1.51
5725140--5725174	18	1.9	18	88	0	52	20	11	17	51	1.75
5736567--5736597	6	5.2	6	92	0	53	32	3	32	32	1.74
5752463--5752487	12	2.1	12	100	0	50	36	16	32	16	1.90

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