genome.fa.s3.2.7.7.80.10.50.1000.11.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  11  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)
3978023--3978056	11	3.1	11	95	0	59	38	23	20	17	1.93
3978526--3978558	17	2.0	17	88	5	50	15	6	18	60	1.54
3979211--3979239	12	2.5	12	94	5	51	17	0	0	82	0.66
3983372--3983410	21	1.9	19	90	10	60	51	0	7	41	1.31
3983508--3983553	15	2.8	17	74	16	51	47	2	4	45	1.34
3990313--3990381	26	2.9	22	78	16	75	44	0	4	50	1.21
3992783--3992812	9	3.4	9	90	9	53	90	0	0	10	0.47
3992783--3992812	8	3.6	8	95	4	51	90	0	0	10	0.47
3993204--3993229	3	8.7	3	100	0	52	34	0	0	65	0.93
3993387--3993424	15	2.5	15	84	16	51	42	0	2	55	1.14
3997196--3997225	9	3.3	9	95	0	51	43	16	13	26	1.85
3997377--3997457	40	2.0	40	83	6	103	41	16	18	23	1.89
4008804--4008833	2	15.0	2	100	0	60	0	50	0	50	1.00
4008833--4008857	2	12.5	2	100	0	50	48	0	0	52	1.00
4011085--4011208	60	2.1	60	87	0	176	27	13	20	37	1.91
4011118--4011208	32	3.0	30	71	18	89	28	13	20	37	1.90
4011104--4011203	28	3.4	28	73	15	94	29	15	21	35	1.93
4011721--4011769	25	1.9	26	83	4	64	28	6	0	65	1.16
4019036--4019135	51	2.0	51	91	0	164	36	9	5	50	1.56
4026159--4026204	21	2.2	22	88	7	69	67	0	10	21	1.21
4027816--4027842	4	6.8	4	100	0	54	51	0	22	25	1.48
4047179--4047244	4	16.5	4	83	0	78	40	0	9	50	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4047184--4047244	10	6.1	10	90	0	95	40	0	8	50	1.32
4047179--4047245	16	4.3	16	86	7	102	40	0	10	49	1.37
4047180--4047242	30	2.1	30	100	0	126	39	0	9	50	1.35
4049681--4049839	79	2.0	79	86	0	219	22	22	17	37	1.94
4051226--4051263	15	2.5	15	84	16	51	42	0	2	55	1.14
4051553--4051594	14	2.9	14	80	20	50	45	0	4	50	1.23
4052480--4052512	2	16.5	2	100	0	66	51	0	0	48	1.00
4059584--4059718	49	2.8	48	84	8	152	37	4	2	55	1.35
4059584--4059715	50	2.8	48	85	7	155	36	4	3	56	1.35
4060026--4060067	16	2.6	16	92	7	68	38	0	0	61	0.96
4060093--4060137	7	6.3	7	82	5	54	33	0	2	64	1.06
4060091--4060132	15	2.9	15	80	16	52	33	0	2	64	1.07
4060091--4060138	14	3.5	13	81	15	60	35	0	2	62	1.07
4067182--4067216	3	11.7	3	100	0	70	68	0	0	31	0.90
4068117--4068164	23	2.0	25	84	8	64	56	0	18	25	1.42
4068929--4069007	30	2.7	29	86	3	97	26	7	5	60	1.45
4077571--4077604	16	2.2	16	89	5	52	38	0	0	61	0.96
4082309--4082383	35	2.1	35	100	0	150	30	20	13	36	1.91
4089110--4089741	150	4.1	150	78	8	614	29	8	20	41	1.82
4089061--4089741	100	6.7	100	79	8	626	29	9	19	41	1.82
4089061--4089756	50	13.7	49	76	9	520	29	9	19	42	1.82
4089902--4089955	22	2.5	21	77	19	65	16	9	3	70	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4089929--4089982	18	3.1	18	76	12	58	16	9	3	70	1.28
4089929--4089995	35	1.9	35	82	11	84	17	11	2	67	1.35
4095287--4095385	34	3.0	33	82	4	101	29	11	22	37	1.88
4100545--4101006	235	2.0	233	85	5	630	29	14	21	34	1.93
4113376--4113414	6	6.5	6	90	0	51	58	2	0	38	1.12
4113376--4113414	12	3.2	12	92	0	60	58	2	0	38	1.12
4115571--4115609	2	19.5	2	94	0	69	48	0	51	0	1.00
4115613--4115639	3	9.0	3	100	0	54	33	0	33	33	1.58
4120115--4120143	2	15.0	2	92	7	51	48	0	0	51	1.00
4122691--4122743	26	2.0	27	85	3	72	66	0	1	32	1.03
4124614--4124651	20	1.9	20	94	0	67	31	0	18	50	1.47
4129233--4129282	27	2.0	26	84	11	68	36	8	18	38	1.80
4129285--4129484	27	7.6	27	72	8	160	32	10	15	42	1.81
4129239--4129436	54	3.7	54	74	8	172	30	10	16	41	1.82
4129239--4129454	27	8.0	27	75	7	118	31	9	16	42	1.81
4129457--4129574	62	1.9	62	81	6	141	33	11	16	38	1.84
4129561--4129607	24	1.9	25	86	4	69	44	12	14	27	1.82
4129589--4129845	127	2.0	127	98	0	496	31	15	12	40	1.84
4131198--4131273	38	2.0	38	94	0	134	43	11	9	35	1.73
4132911--4132967	9	6.2	9	73	4	51	49	0	5	45	1.24
4132941--4132967	9	3.0	9	100	0	54	55	0	0	44	0.99
4137229--4137347	63	1.9	63	85	0	166	48	12	15	23	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4137982--4138026	20	2.2	20	84	0	54	62	8	22	6	1.48
4138758--4138987	71	3.0	70	69	24	178	37	2	1	58	1.21
4138828--4138934	22	4.9	22	79	8	94	42	0	0	57	1.05
4138775--4138945	84	2.0	84	81	12	197	38	1	1	59	1.13
4138864--4138917	27	2.0	26	86	10	74	37	1	0	61	1.07
4138568--4139269	153	4.5	154	78	11	661	38	2	3	55	1.30
4139190--4139287	42	2.4	40	85	10	128	44	2	1	52	1.19
4139411--4139444	15	2.3	15	85	14	52	50	0	0	50	1.00
4139412--4139446	16	2.2	16	95	5	63	48	0	0	51	1.00
4149318--4149347	14	2.1	15	93	6	53	46	0	0	53	1.00
4151038--4151079	21	2.0	20	86	4	57	78	0	14	7	0.95
4154314--4154343	2	15.0	2	100	0	60	50	0	0	50	1.00
4155506--4155549	6	7.7	6	87	5	56	11	2	0	86	0.66
4155506--4155544	7	5.6	7	82	11	53	12	0	0	87	0.55
4155506--4155538	16	2.1	16	94	5	59	12	0	0	87	0.53
4156249--4156278	12	2.6	12	94	5	53	50	0	6	43	1.28
4160623--4160647	12	2.1	12	100	0	50	24	0	0	76	0.80
4163152--4163283	68	1.9	68	92	0	219	41	6	16	35	1.73
4177220--4177248	3	9.7	3	100	0	58	0	31	34	34	1.58
4177885--4177910	2	13.0	2	100	0	52	50	0	50	0	1.00
4179678--4179718	18	2.3	19	83	8	59	56	0	0	43	0.99
4184864--4184897	13	2.6	13	85	0	50	79	0	20	0	0.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4191322--4191369	25	1.9	25	82	0	60	72	2	16	8	1.18
4196517--4196549	15	2.1	16	88	5	50	48	0	0	51	1.00
4206860--4206986	53	2.4	54	84	5	150	46	12	10	30	1.75
4207167--4207254	25	3.5	25	71	10	72	42	13	18	26	1.87
4207154--4207242	25	3.5	26	71	10	76	42	13	12	31	1.81
4211771--4211807	18	2.1	18	95	5	67	21	27	0	51	1.48
4213127--4213184	30	1.9	30	86	6	82	53	3	3	39	1.35
4219248--4219277	3	10.0	3	92	0	51	63	0	3	33	1.11
4224231--4224606	126	3.0	125	79	7	368	32	15	18	32	1.93
4224228--4224668	63	7.0	62	75	11	311	32	15	19	32	1.92
4225792--4225841	24	2.1	24	92	0	82	48	34	4	14	1.62
4240219--4240275	30	1.9	30	88	0	87	38	5	5	50	1.47
4240219--4240283	30	2.2	30	85	0	85	38	6	4	50	1.48
4243750--4243778	2	14.5	2	100	0	58	48	0	0	51	1.00
4248985--4249156	35	4.9	35	81	5	181	41	18	20	19	1.91
4248985--4249156	69	2.5	70	83	5	215	41	18	20	19	1.91
4255269--4255390	35	3.5	35	85	1	136	43	17	22	17	1.88
4261891--4261945	15	3.7	15	85	0	74	40	5	20	34	1.75
4262085--4262306	58	3.8	58	73	17	194	34	3	1	59	1.25
4262168--4262446	39	7.1	39	65	22	109	29	2	1	66	1.11
4262177--4262246	24	3.1	24	73	19	78	34	0	0	65	0.93
4262277--4262361	33	2.6	32	86	3	107	29	1	0	69	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4262150--4262325	54	3.2	53	73	12	181	31	2	1	63	1.19
4262308--4262412	14	7.6	14	68	15	58	28	1	0	68	1.06
4262094--4262325	114	2.0	114	97	0	437	32	3	1	62	1.22
4262260--4262422	72	2.2	75	80	9	174	30	1	1	66	1.13
4262380--4262422	20	2.2	20	87	4	61	30	0	0	69	0.88
4262388--4262440	20	2.7	20	91	5	81	24	1	0	73	0.93
4262315--4262447	24	5.4	25	68	15	66	27	2	0	69	1.05
4262333--4262453	50	2.4	50	77	11	133	29	2	0	66	1.10
4263435--4263495	25	2.5	23	79	15	61	57	3	0	39	1.15
4263337--4263482	53	2.7	54	82	10	167	54	2	2	40	1.29

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