genome.fa.s3.2.7.7.80.10.50.1000.23.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  23  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)
9535270--9535796	263	2.0	266	89	2	810	39	20	15	24	1.91
9539965--9540009	23	2.0	23	100	0	90	44	11	4	40	1.60
9542437--9542462	9	2.9	9	100	0	52	57	0	0	42	0.98
9542537--9542593	27	2.2	25	81	12	62	63	1	0	35	1.05
9560318--9560363	23	2.0	23	83	8	58	39	0	4	56	1.19
9561254--9561319	28	2.3	29	81	5	80	42	6	1	50	1.36
9561293--9561335	21	2.2	19	83	8	50	41	4	2	51	1.35
9581026--9581062	19	1.9	19	100	0	74	37	16	18	27	1.92
9581398--9581441	16	2.8	16	82	10	54	40	0	2	56	1.11
9593001--9593071	30	2.4	30	88	4	99	61	12	4	21	1.47
9610367--9610489	54	2.3	53	84	6	162	54	1	6	37	1.36
9610367--9610461	25	3.7	24	71	22	68	52	2	7	37	1.41
9611161--9611186	2	13.0	2	100	0	52	0	50	0	50	1.00
9616603--9616643	18	2.2	20	86	8	59	36	19	2	41	1.65
9620235--9620324	46	2.0	46	88	0	135	35	13	20	31	1.91
9631923--9631980	22	2.7	22	78	7	66	50	1	1	46	1.22
9632354--9632416	21	3.1	21	95	4	112	49	0	3	47	1.17
9634602--9634730	15	8.5	15	68	23	74	47	2	1	48	1.24
9634604--9634655	27	2.0	26	92	3	86	51	1	1	44	1.23
9634651--9634684	16	2.1	16	94	0	59	41	2	0	55	1.15
9634911--9634943	8	4.1	8	100	0	66	48	0	0	51	1.00
9640918--9640950	2	16.5	2	100	0	66	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9645939--9645989	21	2.4	22	74	9	52	45	5	1	47	1.38
9646148--9646208	26	2.4	24	76	15	59	59	0	6	34	1.24
9646221--9646273	23	2.2	25	87	9	76	28	1	1	67	1.11
9647501--9647556	23	2.5	22	74	5	60	21	3	12	62	1.45
9662536--9662570	13	2.7	13	86	0	52	48	2	0	48	1.16
9662536--9662573	18	2.1	18	85	9	51	50	2	0	47	1.15
9666308--9666357	22	2.3	22	96	0	91	30	28	30	12	1.92
9668690--9668727	2	19.0	2	100	0	76	0	50	0	50	1.00
9680119--9680163	15	2.9	16	84	15	60	73	0	20	6	1.05
9691285--9691478	48	4.1	48	92	4	313	4	59	20	15	1.53
9696027--9696069	19	2.4	18	81	14	54	58	0	6	34	1.25
9730086--9730121	2	17.5	2	94	5	63	50	0	2	47	1.15
9751687--9751761	39	1.9	39	97	0	141	26	10	25	37	1.89
9761716--9761754	2	20.0	2	94	5	71	0	51	0	48	1.00
9767583--9767749	82	2.0	82	96	0	307	29	14	19	36	1.92
9777546--9777578	3	11.0	3	93	0	57	36	30	0	33	1.58
9789009--9789067	25	2.4	25	100	0	118	55	6	20	16	1.63
9791991--9792034	2	22.0	2	95	0	70	45	50	4	0	1.22
9792699--9792723	13	1.9	13	100	0	50	8	28	0	64	1.22
9794797--9795101	100	3.1	98	84	4	434	48	11	14	25	1.76
9794768--9795101	98	3.4	95	82	6	380	50	10	13	25	1.74
9800436--9800469	2	17.0	2	87	0	50	0	44	2	52	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9817820--9817872	25	2.1	25	92	0	88	26	28	1	43	1.65
9836494--9836519	2	13.0	2	100	0	52	0	50	0	50	1.00
9848488--9848542	27	2.0	27	82	6	67	36	14	14	34	1.87
9853668--9853713	23	2.0	23	87	8	67	60	4	30	4	1.35
9854987--9855655	340	2.0	341	85	2	905	25	21	13	39	1.89
9855837--9855896	30	2.0	30	90	0	93	26	18	15	40	1.90
9877419--9877443	12	2.1	12	100	0	50	24	28	16	32	1.96
9881485--9881524	21	1.9	21	100	0	80	40	5	15	40	1.68
9882311--9882344	5	6.8	5	86	0	50	17	55	0	26	1.42
9882311--9882349	15	2.6	15	87	0	51	15	56	0	28	1.40
9882516--9882541	2	13.0	2	100	0	52	50	0	0	50	1.00
9891564--9891590	2	13.5	2	100	0	54	0	48	0	51	1.00
9892122--9892174	21	2.4	24	78	15	60	37	3	5	52	1.43
9904734--9904787	25	2.1	27	79	10	67	5	25	1	66	1.23
9915360--9915385	2	13.0	2	100	0	52	0	50	0	50	1.00
9919873--9919904	17	1.9	17	93	6	57	0	68	12	18	1.20
9920350--9920396	24	2.0	24	91	0	76	46	10	21	21	1.81
9925540--9925653	54	2.1	54	90	4	178	29	21	22	25	1.99
9940478--9940949	229	2.1	230	80	3	522	29	17	25	27	1.97
9953486--9953533	8	5.9	8	78	4	51	64	0	0	35	0.94
9953474--9953556	18	4.8	17	78	12	64	67	0	0	32	0.91
9953476--9953556	17	4.7	18	78	17	66	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)
9954062--9954106	13	3.4	14	82	11	51	55	0	0	44	0.99
9954062--9954106	18	2.6	18	80	19	60	55	0	0	44	0.99
9954155--9954212	24	2.6	24	84	12	72	58	1	0	39	1.08
9955873--9955969	41	2.3	41	96	1	176	46	1	11	41	1.47
9956567--9956630	32	2.0	31	87	3	92	31	6	7	54	1.54
9956539--9956630	29	3.1	29	77	9	85	35	6	8	48	1.60
9956629--9956779	76	2.0	76	86	0	212	41	8	7	43	1.63
9956719--9956776	31	1.9	31	89	3	91	43	8	3	44	1.51
9956872--9956900	15	1.9	15	100	0	58	44	0	0	55	0.99
9962744--9962768	3	8.3	3	100	0	50	32	0	0	68	0.90
9967909--9967971	28	2.2	28	100	0	126	22	19	17	41	1.90
9972240--9972276	7	5.3	7	100	0	74	13	13	45	27	1.81
9988268--9988376	51	2.1	53	84	6	143	22	8	51	17	1.72
9988515--9988574	19	3.3	19	68	13	63	43	25	18	13	1.86
9988516--9988593	35	2.2	35	100	0	156	42	24	17	15	1.88
9988535--9988595	16	3.6	16	68	12	50	40	24	16	18	1.90
9993280--9993310	3	10.3	3	92	0	53	35	32	32	0	1.58
10001915--10001959	21	2.3	21	85	11	60	53	4	0	42	1.21
10005605--10005642	19	2.1	19	85	9	53	60	2	0	36	1.11
10011860--10011945	9	9.6	9	74	14	70	22	41	1	34	1.61
10011860--10011951	6	15.3	6	81	0	76	21	41	2	34	1.66
10011860--10011945	24	3.6	24	87	0	118	22	41	1	34	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10036391--10036446	28	2.0	27	86	3	76	73	1	7	17	1.15
10037143--10037171	2	15.0	2	92	7	51	51	0	48	0	1.00
10041181--10042214	497	2.1	503	84	6	1319	29	22	16	32	1.95
10043853--10043882	3	10.0	3	100	0	60	66	0	0	33	0.92
10044137--10044326	60	3.2	60	71	20	193	35	5	0	58	1.24
10044231--10044297	23	2.8	23	76	12	64	32	1	0	65	1.02
10044146--10044362	115	1.9	114	94	0	380	32	5	0	61	1.25
10044231--10044297	25	2.8	25	80	12	72	32	1	0	65	1.02
10044420--10044494	25	3.0	25	75	9	64	29	1	1	68	1.06
10044481--10044512	15	2.1	15	94	0	55	31	0	0	68	0.90
10046037--10046078	15	2.7	15	85	3	57	19	0	0	80	0.70
10046037--10046078	20	2.1	20	86	8	59	19	0	0	80	0.70
10046042--10046077	11	3.3	11	88	11	56	16	0	0	83	0.65
10058355--10058410	2	28.0	2	88	0	85	3	46	0	50	1.19
10059414--10059468	21	2.6	21	82	8	67	49	3	1	45	1.30
10059426--10059475	21	2.4	21	82	0	64	48	2	0	50	1.12
10059461--10059532	28	2.6	28	77	14	78	33	2	0	63	1.08
10060790--10060831	18	2.3	19	80	16	52	47	0	4	47	1.23
10061477--10061513	2	18.5	2	88	0	56	2	45	2	48	1.30
10075738--10075771	5	6.8	5	93	0	59	44	17	38	0	1.49
10088446--10088478	2	16.5	2	100	0	66	48	0	0	51	1.00
10100006--10100066	29	2.1	28	84	3	77	34	32	4	27	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10101575--10101622	12	4.0	12	83	0	69	54	2	0	43	1.12
10101575--10101630	24	2.4	24	81	3	69	55	1	0	42	1.10
10102392--10102439	16	2.9	17	80	17	57	50	2	0	47	1.12
10113438--10114762	282	4.7	282	96	0	2357	43	8	8	40	1.64
10113438--10114762	566	2.3	565	95	1	2368	43	8	8	40	1.64
10115813--10115848	2	18.0	2	100	0	72	50	0	0	50	1.00
10124994--10125054	28	2.3	27	83	10	74	49	8	3	39	1.49
10125663--10125868	25	7.6	27	70	15	86	33	8	11	46	1.70
10125771--10125902	25	5.2	24	74	13	95	34	9	11	44	1.73
10125665--10125875	29	7.8	27	69	17	118	33	9	11	45	1.72

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