genome.fa.s71.2.7.7.80.10.50.1000.25.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: Scaffold71
Parameters: 2 7 7 80 10 50 1000
Length:  5741892

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   

This is table  25  of  33  ( 3929 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)
4110026--4110064	20	1.9	20	84	5	51	61	0	0	38	0.96
4110208--4110248	21	1.9	21	85	5	55	78	4	0	17	0.93
4110614--4110668	26	2.1	26	83	6	67	47	5	3	43	1.44
4110687--4110713	3	9.0	3	100	0	54	66	0	0	33	0.92
4113715--4113748	17	2.0	18	88	11	54	29	0	2	67	1.05
4115848--4115891	15	3.0	15	78	15	56	29	0	0	70	0.88
4116268--4116338	34	2.0	37	84	13	96	46	0	1	52	1.09
4127899--4127955	2	28.5	2	87	0	78	42	5	1	50	1.35
4128692--4128762	26	2.8	24	72	19	63	59	0	2	38	1.12
4128861--4128892	2	16.0	2	93	0	55	46	0	3	50	1.17
4129050--4129119	20	3.5	21	79	14	69	50	1	0	48	1.09
4130364--4130412	21	2.4	20	77	16	55	51	0	0	48	1.00
4133688--4133738	2	25.0	2	92	4	84	49	1	1	47	1.24
4138905--4138980	36	2.1	36	100	0	152	50	18	10	21	1.76
4142747--4142818	36	2.0	36	100	0	144	27	11	25	36	1.90
4146464--4146557	16	5.5	17	75	11	68	42	1	0	56	1.06
4146464--4146557	33	2.8	33	75	15	93	42	1	0	56	1.06
4148617--4148683	31	2.3	29	80	12	82	43	0	1	55	1.09
4148617--4148719	31	3.4	30	78	12	79	44	1	1	51	1.23
4148920--4148988	26	2.8	24	76	19	70	43	0	0	56	0.99
4148925--4148979	23	2.3	23	78	12	58	45	0	0	54	0.99
4148932--4148989	23	2.5	22	73	15	55	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4151173--4151199	3	9.0	3	100	0	54	66	0	0	33	0.92
4151941--4151970	12	2.5	12	94	0	51	50	20	10	20	1.76
4154671--4154698	14	2.0	14	100	0	56	42	7	21	28	1.79
4156627--4156660	17	1.9	18	88	5	52	41	0	0	58	0.98
4156906--4156989	29	2.9	29	80	13	84	61	1	0	36	1.04
4156919--4156989	29	2.4	30	82	11	85	60	1	0	38	1.06
4156937--4157004	29	2.3	28	80	16	75	61	1	0	36	1.05
4157476--4157513	13	3.0	13	84	7	51	55	2	2	39	1.28
4158032--4158090	28	2.1	29	90	3	93	37	6	10	45	1.65
4159291--4159317	2	13.5	2	100	0	54	0	48	0	51	1.00
4159317--4159359	2	21.5	2	100	0	86	48	0	0	51	1.00
4159518--4159562	19	2.3	21	81	14	60	31	2	0	66	1.04
4159586--4159646	28	2.3	27	78	13	65	60	1	3	34	1.23
4159672--4159743	34	2.1	34	82	12	85	54	0	2	43	1.15
4170296--4170375	40	2.0	40	97	0	151	35	16	20	28	1.94
4171630--4171727	2	49.5	2	73	13	51	41	4	7	46	1.50
4171727--4171752	2	13.0	2	100	0	52	50	50	0	0	1.00
4173942--4173988	15	3.1	14	77	22	51	48	0	0	51	1.00
4174214--4174251	20	1.9	20	84	10	51	52	0	5	42	1.24
4178714--4178747	2	17.0	2	100	0	68	50	0	0	50	1.00
4180674--4180701	2	14.0	2	100	0	56	50	0	0	50	1.00
4180701--4180732	2	16.0	2	100	0	64	50	0	50	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4186494--4186520	2	13.5	2	100	0	54	0	51	0	48	1.00
4187667--4187784	62	1.9	62	85	3	166	37	0	6	55	1.33
4187853--4187882	14	2.1	15	93	6	53	76	0	20	3	0.92
4187830--4187882	23	2.3	22	83	6	61	79	0	16	3	0.88
4187883--4187929	16	2.8	17	77	9	60	31	0	8	59	1.27
4188395--4188450	15	3.6	16	79	13	64	41	0	0	58	0.98
4188378--4188452	33	2.3	32	74	19	75	41	1	1	56	1.16
4189756--4189803	2	24.0	2	91	0	78	45	0	4	50	1.21
4196372--4196413	21	1.9	23	85	9	61	50	0	0	50	1.00
4197157--4197202	15	2.9	15	83	6	56	60	0	0	39	0.97
4197279--4197319	12	3.6	11	87	12	57	60	0	2	36	1.10
4197267--4197350	10	8.7	9	79	18	73	58	1	1	39	1.14
4197308--4197342	18	1.9	18	100	0	70	60	0	0	40	0.97
4200268--4200365	49	1.9	52	83	6	130	43	2	1	53	1.19
4201357--4201399	15	2.8	15	82	3	50	62	0	2	34	1.08
4208766--4208790	2	12.5	2	100	0	50	52	0	48	0	1.00
4209163--4209210	22	2.2	22	85	7	62	43	0	0	56	0.99
4209806--4209860	19	2.8	20	75	8	58	38	5	1	54	1.34
4212013--4212057	2	22.5	2	100	0	90	51	0	0	48	1.00
4213991--4214044	2	27.0	2	100	0	108	50	0	50	0	1.00
4214610--4214662	21	2.5	22	77	17	60	47	0	0	52	1.00
4214904--4214938	14	2.5	13	86	13	52	28	0	0	71	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4215455--4215560	36	2.9	36	79	8	115	55	1	0	41	1.17
4215408--4215560	74	2.1	74	80	11	172	54	1	1	42	1.20
4215455--4215527	17	4.2	17	74	10	58	57	1	0	41	1.07
4217015--4217065	16	3.1	16	73	15	59	56	1	0	41	1.10
4217017--4217068	17	3.1	17	72	22	56	59	1	0	38	1.08
4217017--4217076	19	3.4	19	71	19	67	60	1	0	38	1.07
4218264--4218300	20	2.0	20	89	10	60	0	8	5	86	0.70
4219060--4219111	21	2.4	22	83	3	61	53	0	0	46	1.00
4220328--4220372	2	22.5	2	95	0	81	46	0	0	53	1.00
4221794--4221847	23	2.5	22	84	6	65	46	0	7	46	1.31
4221794--4221848	22	2.5	23	82	5	69	45	0	7	47	1.30
4222260--4222328	35	2.0	35	100	0	138	17	17	11	53	1.72
4222552--4222584	16	2.1	16	88	11	50	18	6	6	69	1.30
4231137--4231169	2	16.5	2	100	0	66	48	0	51	0	1.00
4240285--4240309	2	12.5	2	100	0	50	48	0	0	52	1.00
4242596--4242621	2	13.0	2	100	0	52	50	0	0	50	1.00
4243373--4243402	2	15.0	2	100	0	60	50	0	0	50	1.00
4245910--4245942	17	1.9	17	88	11	50	27	3	0	69	1.03
4245937--4245996	10	6.0	10	75	14	52	50	0	0	50	1.00
4245938--4246009	18	4.1	19	76	15	66	51	0	0	48	1.00
4246520--4246636	53	2.2	53	82	7	132	46	4	1	47	1.32
4247614--4247653	16	2.6	15	88	7	62	55	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4249038--4249081	3	14.7	3	100	0	88	65	0	0	34	0.93
4251100--4251136	1	37.0	1	88	0	56	0	94	0	5	0.30
4253491--4253572	24	3.6	24	73	14	75	43	0	0	56	0.99
4253495--4253590	38	2.5	40	76	11	101	43	0	0	56	0.99
4253556--4253603	24	2.0	24	87	0	69	56	0	2	41	1.11
4253817--4253901	23	4.0	21	73	16	61	69	4	0	25	1.08
4253833--4253901	28	2.5	27	81	9	77	69	5	0	24	1.10
4254525--4254552	2	14.0	2	100	0	56	50	0	0	50	1.00
4260371--4260442	27	2.7	27	80	10	85	51	1	0	47	1.09
4268866--4268915	25	2.0	25	88	0	73	70	0	0	30	0.88
4269667--4269713	15	3.2	15	74	14	53	55	2	0	42	1.12
4270033--4270057	2	12.5	2	100	0	50	52	0	0	48	1.00
4271679--4271725	3	15.7	3	95	0	85	31	0	36	31	1.58
4272070--4272123	2	27.0	2	96	0	99	50	1	0	48	1.11
4274133--4274158	2	13.0	2	100	0	52	50	50	0	0	1.00
4276523--4276565	20	2.0	20	82	8	50	60	2	0	37	1.10
4277270--4277308	2	20.5	2	84	10	55	48	0	2	48	1.15
4277477--4277577	18	5.4	19	70	20	63	60	0	0	39	0.97
4277448--4277515	25	2.6	26	78	17	70	66	1	0	32	1.01
4277453--4277560	10	10.7	10	72	17	64	62	0	0	37	0.95
4279275--4279339	29	2.2	30	83	5	78	55	4	0	40	1.21
4279648--4279709	28	2.1	29	85	11	83	41	1	0	56	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4280710--4280744	17	2.0	18	88	5	54	54	0	0	45	0.99
4287974--4288022	14	3.4	14	77	5	53	40	0	2	57	1.10
4289522--4289566	20	2.2	21	84	11	58	48	2	0	48	1.13
4290784--4290837	28	2.0	27	85	3	72	48	0	1	50	1.11
4291401--4291463	27	2.3	28	78	13	69	41	0	3	55	1.16
4291425--4291493	20	3.9	18	70	27	58	40	0	0	59	0.97
4291341--4291474	66	2.0	68	80	11	150	38	0	4	56	1.19
4291422--4291505	27	3.2	26	75	14	84	40	0	0	59	0.97
4292832--4292873	19	2.2	20	86	4	59	45	0	0	54	0.99
4292864--4292944	29	2.9	28	73	10	69	53	0	0	46	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   30   31   32   
          33