genome.fa.s258.2.7.7.80.10.50.1000.17.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: Scaffold258
Parameters: 2 7 7 80 10 50 1000
Length:  5730937

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   

This is table  17  of  25  ( 2900 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)
3973170--3973212	2	21.5	2	95	0	77	48	2	0	48	1.14
3973858--3973913	3	18.7	3	92	0	94	30	1	1	66	1.12
3978675--3978705	3	10.3	3	92	0	53	64	3	32	0	1.09
3988421--3988470	2	25.0	2	100	0	100	0	50	0	50	1.00
3991022--3991139	60	2.0	60	91	3	193	32	15	20	32	1.93
3995353--3995384	3	10.7	3	100	0	64	31	0	0	68	0.90
3995751--3995784	2	17.0	2	100	0	68	0	50	0	50	1.00
3996352--3996389	19	2.0	19	94	0	67	60	0	0	39	0.97
4004818--4004857	15	2.8	15	78	21	50	35	0	0	65	0.93
4004819--4004857	12	2.9	14	85	14	55	33	0	0	66	0.92
4006395--4006437	14	3.1	14	79	0	50	41	0	0	58	0.98
4020239--4020265	2	13.5	2	100	0	54	51	0	0	48	1.00
4024037--4024061	2	12.5	2	100	0	50	48	0	0	52	1.00
4024194--4024227	2	17.0	2	100	0	68	50	0	0	50	1.00
4027207--4027235	14	2.0	15	93	6	51	37	0	0	62	0.96
4027609--4027634	2	13.0	2	100	0	52	50	0	0	50	1.00
4028467--4028504	3	12.7	3	100	0	76	65	0	0	34	0.93
4028503--4028532	3	10.0	3	100	0	60	33	0	0	66	0.92
4029093--4029118	2	13.0	2	100	0	52	50	0	0	50	1.00
4033116--4033157	2	21.0	2	95	0	75	47	0	52	0	1.00
4034034--4034076	22	2.0	22	86	9	61	46	0	0	53	1.00
4037471--4037511	2	20.5	2	100	0	82	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)
4047986--4048014	3	9.7	3	100	0	58	31	0	0	68	0.89
4048932--4049005	36	2.0	38	82	10	91	60	5	0	33	1.19
4049180--4049213	13	2.6	14	86	13	54	82	0	2	14	0.79
4049901--4049982	32	2.9	27	74	23	78	50	0	0	50	1.00
4049902--4049952	22	2.3	22	76	6	59	50	0	0	49	1.00
4049916--4049969	15	3.4	16	82	9	67	46	0	0	53	1.00
4052289--4052313	12	2.1	12	100	0	50	24	8	0	68	1.16
4056918--4057013	8	11.4	9	68	18	64	58	0	0	41	0.98
4056918--4057002	12	7.1	13	66	20	51	58	0	0	41	0.98
4056954--4056988	17	1.9	19	88	11	56	51	0	0	48	1.00
4056951--4057013	25	2.5	25	85	12	85	53	0	0	46	1.00
4056929--4057013	33	2.5	33	80	10	84	56	0	0	43	0.99
4057615--4057660	24	1.9	24	86	0	65	43	17	2	36	1.61
4058975--4058999	2	12.5	2	100	0	50	52	0	0	48	1.00
4059304--4059342	11	3.5	11	89	0	60	0	12	5	82	0.83
4059304--4059345	21	2.0	22	86	9	61	0	11	7	80	0.88
4059955--4059985	4	7.8	4	100	0	62	74	0	0	25	0.82
4060233--4060258	2	13.0	2	100	0	52	50	0	0	50	1.00
4061072--4061116	20	2.2	21	84	4	56	42	13	6	37	1.70
4061298--4061332	18	2.0	18	88	5	54	40	0	0	60	0.97
4062049--4063270	152	7.9	152	86	3	1753	37	12	10	39	1.77
4062043--4063287	304	4.0	304	94	3	2204	37	12	10	39	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4062049--4065989	625	6.2	615	81	10	4215	38	12	10	39	1.77
4063102--4063479	192	2.0	192	94	2	670	36	12	11	39	1.80
4063292--4064400	152	7.2	152	86	3	1581	37	12	10	38	1.78
4062796--4064753	496	4.0	492	86	5	2289	37	12	10	39	1.78
4063292--4064408	304	3.6	304	93	4	1876	37	12	10	39	1.78
4064223--4064600	192	2.0	192	91	1	623	37	12	10	39	1.78
4064413--4065208	152	5.2	151	84	2	1058	38	11	10	39	1.75
4064099--4064735	344	1.9	344	90	1	1017	38	12	10	38	1.77
4063917--4064904	496	2.0	496	93	0	1672	37	12	10	39	1.77
4064413--4065208	304	2.6	304	92	0	1306	38	11	10	39	1.75
4065215--4065989	303	2.6	303	91	1	1268	38	10	9	40	1.73
4065213--4066006	152	5.2	152	85	1	1067	38	11	9	40	1.74
4065821--4066186	192	1.9	192	91	0	597	38	11	9	40	1.75
4066424--4066453	10	3.1	10	90	9	53	50	0	0	50	1.00
4066765--4066790	12	2.2	12	100	0	52	42	7	0	50	1.31
4067546--4067580	16	2.2	16	89	0	52	60	2	0	37	1.12
4070816--4070847	16	2.0	16	93	0	55	50	3	0	46	1.17
4075227--4075307	12	6.9	12	71	17	55	53	0	0	46	1.00
4075227--4075318	47	2.0	46	85	6	123	51	0	0	48	1.00
4075986--4076010	2	12.5	2	100	0	50	0	0	48	52	1.00
4076879--4076909	6	5.2	6	96	0	53	51	0	0	48	1.00
4077469--4077562	45	2.1	45	97	0	179	43	10	12	32	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4078068--4078300	116	2.0	117	95	2	423	30	14	17	37	1.90
4079262--4079334	36	2.0	36	97	0	137	36	16	16	30	1.91
4079361--4079399	2	19.5	2	100	0	78	51	0	0	48	1.00
4079944--4080037	46	2.0	46	97	0	179	32	13	21	31	1.92
4080007--4080279	134	2.0	136	87	5	401	35	17	17	29	1.93
4090536--4090613	5	16.2	5	69	21	51	65	0	0	34	0.93
4090539--4090644	13	7.6	14	71	24	64	62	0	0	37	0.96
4090535--4090648	31	3.9	30	79	14	121	63	0	0	36	0.95
4090535--4090648	29	3.9	31	75	14	107	63	0	0	36	0.95
4090534--4090605	11	6.7	11	75	20	64	66	0	0	33	0.92
4091136--4091181	22	2.0	23	83	4	58	52	4	2	41	1.33
4092047--4092076	2	15.0	2	100	0	60	0	50	0	50	1.00
4094547--4094840	146	2.0	146	100	0	588	24	12	23	39	1.90
4103102--4103154	22	2.4	22	80	0	61	5	16	1	75	1.08
4107052--4107157	21	5.1	20	72	7	86	50	5	1	41	1.36
4107342--4107374	16	2.1	16	88	5	50	21	15	0	63	1.30
4108841--4108924	16	5.4	16	71	22	63	42	0	0	57	0.99
4108852--4108935	26	3.5	25	70	25	65	44	0	0	55	0.99
4109756--4109786	2	15.5	2	100	0	62	51	0	48	0	1.00
4110507--4110666	81	2.0	81	92	0	266	23	18	31	25	1.97
4111057--4111086	2	15.0	2	100	0	60	50	0	50	0	1.00
4112831--4112865	2	17.5	2	87	0	52	45	51	0	2	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4113993--4114103	51	2.1	54	93	5	192	44	12	0	43	1.42
4114000--4114101	26	4.0	26	82	12	147	46	13	0	40	1.44
4119168--4119205	2	19.0	2	94	0	67	50	2	0	47	1.15
4122832--4122877	21	2.2	21	100	0	92	32	13	0	54	1.39
4133045--4133072	2	14.0	2	100	0	56	0	50	0	50	1.00
4133363--4133404	19	2.2	19	86	0	57	4	21	0	73	1.01
4135122--4135163	22	1.9	22	85	0	57	35	2	2	59	1.23
4137256--4137300	20	2.3	19	82	14	56	42	0	2	55	1.12
4141024--4141183	83	1.9	82	92	3	268	31	23	30	14	1.94
4142291--4142371	42	1.9	42	87	0	117	53	16	7	23	1.68
4145162--4145188	12	2.2	12	100	0	54	92	0	7	0	0.38
4147760--4147817	26	2.2	26	90	6	91	39	3	27	29	1.73
4156495--4156532	2	19.5	2	94	5	69	50	0	0	50	1.00
4174248--4174291	2	21.5	2	95	4	79	0	47	2	50	1.13
4175829--4175876	14	3.5	15	78	13	50	52	0	0	47	1.00
4177547--4177573	3	9.0	3	100	0	54	66	0	0	33	0.92
4180170--4180219	27	1.9	27	84	8	68	44	6	8	42	1.58
4190140--4190191	26	2.0	26	100	0	104	34	7	30	26	1.85
4196203--4196243	2	20.5	2	100	0	82	51	0	0	48	1.00
4197666--4197720	20	2.8	20	88	5	76	45	0	0	54	0.99
4197666--4197747	20	4.3	19	73	19	64	45	0	0	54	0.99
4198128--4198165	2	19.0	2	100	0	76	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4198481--4198542	22	2.6	24	80	17	76	54	0	0	45	0.99
4198503--4198547	22	2.0	22	83	8	56	60	0	0	40	0.97
4199298--4199348	23	2.2	24	85	3	68	54	0	0	45	0.99
4199488--4199517	15	1.9	16	93	6	53	76	0	0	23	0.78
4200349--4200404	21	2.6	22	77	11	62	44	0	0	55	0.99
4213733--4213771	2	19.5	2	100	0	78	51	0	0	48	1.00
4214137--4214175	7	6.0	7	94	5	57	58	0	0	41	0.98
4214138--4214174	18	2.2	16	90	9	56	59	0	0	40	0.97
4215841--4215874	2	17.0	2	100	0	68	50	0	0	50	1.00
4218462--4218494	10	2.9	12	82	17	52	39	0	0	60	0.97

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