genome.fa.s220.2.7.7.80.10.50.1000.15.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: Scaffold220
Parameters: 2 7 7 80 10 50 1000
Length:  3999181

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   

This is table  15  of  19  ( 2201 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)
3213567--3213601	2	17.5	2	100	0	70	51	0	0	48	1.00
3213681--3213712	2	16.0	2	100	0	64	50	0	0	50	1.00
3216871--3216958	36	2.4	36	81	3	106	14	19	20	45	1.85
3216869--3217007	72	1.9	72	81	8	167	11	20	20	46	1.82
3220120--3220190	26	2.7	26	85	12	83	42	0	0	57	0.98
3220973--3220999	3	9.0	3	100	0	54	33	0	0	66	0.92
3221476--3221530	26	2.1	26	86	6	76	60	1	3	34	1.25
3221553--3221623	22	3.2	22	74	14	58	46	1	0	52	1.09
3222064--3222126	25	2.4	27	81	5	67	44	0	0	55	0.99
3222069--3222148	27	3.0	27	77	15	76	46	0	0	53	1.00
3222102--3222139	16	2.4	16	82	4	51	44	0	0	55	0.99
3222087--3222160	30	2.4	30	78	14	80	45	0	0	54	1.00
3222150--3222199	24	2.1	24	85	3	66	42	2	0	56	1.11
3222787--3222847	20	3.0	20	75	4	59	52	0	3	44	1.17
3222803--3222854	26	2.0	26	85	7	70	46	0	5	48	1.26
3223277--3223319	13	3.5	13	78	15	56	69	0	0	30	0.88
3223274--3223324	15	3.5	15	82	15	63	68	0	0	31	0.90
3223282--3223322	8	5.1	8	85	14	50	73	0	0	26	0.84
3223321--3223378	30	2.0	29	86	10	82	48	13	1	36	1.53
3223510--3223536	2	13.5	2	100	0	54	51	0	0	48	1.00
3227716--3227784	22	3.0	22	76	14	61	62	0	0	37	0.96
3227725--3227791	23	2.9	23	78	10	73	59	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3227862--3227907	18	2.7	17	75	21	51	54	0	0	45	0.99
3227868--3227903	18	1.9	19	88	5	56	58	0	0	41	0.98
3227874--3227922	24	2.0	24	84	7	64	55	0	0	44	0.99
3227898--3227939	21	2.2	20	87	12	61	47	0	2	50	1.14
3227942--3227974	13	2.4	14	90	5	50	27	0	0	72	0.85
3227904--3228012	48	2.3	48	78	7	114	33	0	1	65	1.04
3227951--3228013	26	2.5	24	82	12	74	28	0	1	69	0.97
3227936--3228012	39	2.0	39	82	14	97	28	0	1	70	0.96
3233107--3233169	22	3.0	21	77	13	74	50	0	0	49	1.00
3233536--3233569	3	11.3	3	100	0	68	35	0	0	64	0.94
3233660--3233710	4	13.2	4	76	15	54	72	0	27	0	0.85
3233675--3233713	7	5.4	7	81	6	51	79	0	20	0	0.73
3233765--3233802	11	3.5	11	86	10	51	21	0	5	73	1.02
3236012--3236077	13	4.8	13	70	10	51	30	1	1	66	1.10
3236362--3236447	32	2.6	33	82	12	106	60	0	1	38	1.04
3236375--3236440	18	3.9	18	70	25	54	59	0	1	39	1.07
3238370--3238404	2	17.5	2	100	0	70	48	0	0	51	1.00
3240227--3240268	12	3.2	13	83	13	50	40	0	0	59	0.97
3240227--3240267	13	3.0	14	82	13	50	39	0	0	60	0.96
3240421--3240487	25	2.8	23	78	8	62	46	0	0	53	1.00
3240438--3240487	25	2.0	25	88	0	73	50	0	0	50	1.00
3241639--3241676	12	3.0	13	84	7	51	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)
3242200--3242241	22	2.0	22	85	4	59	47	2	4	45	1.36
3242135--3242279	73	2.0	71	84	8	184	45	2	8	42	1.50
3243073--3243114	20	2.0	21	86	4	59	40	0	0	59	0.97
3243895--3243989	50	1.9	50	93	0	163	49	3	3	44	1.34
3244010--3244052	16	2.5	17	88	11	61	67	0	0	32	0.91
3248781--3248938	79	2.0	80	92	2	264	40	6	17	34	1.77
3258121--3258180	27	2.2	26	85	11	77	56	0	0	43	0.99
3264425--3264475	27	1.9	26	88	4	75	56	0	0	43	0.99
3264444--3264493	16	3.1	16	74	5	55	56	2	0	42	1.11
3264428--3264502	26	2.8	27	77	4	62	53	1	0	45	1.08
3264496--3264548	7	7.9	7	76	23	60	39	0	0	60	0.97
3264465--3264532	22	2.9	24	81	12	70	45	1	0	52	1.09
3264496--3264548	18	2.7	20	85	11	65	39	0	0	60	0.97
3266580--3266636	17	3.2	17	78	9	53	54	0	0	45	0.99
3266616--3266660	17	2.6	17	82	0	54	46	0	0	53	1.00
3267090--3267128	3	13.0	3	94	0	69	30	0	2	66	1.05
3270636--3270685	3	16.7	3	100	0	100	68	0	0	32	0.90
3273028--3273071	23	1.9	23	86	9	63	50	0	0	50	1.00
3273370--3273397	2	14.0	2	100	0	56	50	0	0	50	1.00
3275075--3275132	17	3.7	17	75	22	56	56	0	1	41	1.09
3275122--3275172	22	2.3	22	93	6	86	41	0	0	58	0.98
3276413--3276451	2	19.5	2	100	0	78	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3281013--3281037	11	2.3	11	100	0	50	44	0	8	48	1.32
3281350--3281385	17	2.0	18	89	10	56	58	0	0	41	0.98
3286201--3286242	21	2.0	21	90	9	68	61	0	0	38	0.96
3286201--3286256	20	2.7	20	81	10	60	62	0	0	37	0.95
3290641--3290693	25	2.1	26	96	3	99	30	3	3	62	1.30
3299557--3299613	23	2.4	24	79	5	71	50	0	0	49	1.00
3299557--3299607	17	3.3	15	82	17	52	50	0	0	49	1.00
3302597--3302625	13	2.1	14	93	6	51	89	0	10	0	0.48
3302951--3302982	3	10.3	3	93	6	55	34	0	0	65	0.93
3303964--3304012	17	2.9	16	75	6	53	46	2	0	51	1.12
3303979--3304046	25	2.6	25	77	13	66	44	0	0	55	0.99
3304018--3304059	22	1.9	22	90	0	66	35	0	0	64	0.94
3304032--3304068	17	2.2	17	90	9	58	32	0	0	67	0.91
3304018--3304074	16	3.6	16	81	6	62	35	0	0	64	0.93
3315433--3315538	17	5.9	18	69	16	78	48	0	0	50	1.07
3319739--3319836	48	2.0	50	94	4	173	35	5	8	51	1.54
3319999--3320049	2	25.5	2	95	0	93	49	0	0	50	1.00
3320116--3320153	13	3.0	13	84	3	51	50	0	0	50	1.00
3321179--3321313	42	3.2	42	93	3	220	45	11	22	20	1.83
3321616--3321659	16	2.8	16	79	3	54	59	2	0	38	1.10
3322156--3322190	2	17.5	2	93	0	61	0	0	45	54	0.99
3322792--3322833	21	2.0	22	95	4	77	19	26	30	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3323827--3323951	39	3.2	39	75	10	128	57	4	7	31	1.44
3325961--3326001	14	2.8	15	85	10	50	31	0	0	68	0.90
3325878--3326228	185	1.9	185	85	4	494	43	3	2	49	1.36
3326902--3326937	4	9.0	4	93	0	54	69	0	0	30	0.89
3327625--3327687	5	13.2	5	73	9	60	39	0	1	58	1.07
3327633--3327691	19	3.2	19	72	11	59	37	0	0	62	0.95
3327632--3327685	28	1.9	28	88	0	81	42	0	0	57	0.98
3327641--3327696	18	3.1	18	76	5	67	41	0	0	58	0.98
3328003--3328031	2	14.5	2	100	0	58	48	0	0	51	1.00
3329049--3329498	224	2.0	224	89	3	690	52	8	4	35	1.52
3330585--3330609	13	1.9	13	100	0	50	80	4	16	0	0.87
3332513--3332683	87	2.0	82	85	7	227	34	10	15	39	1.81
3337357--3337402	19	2.4	18	86	10	65	39	15	21	23	1.92
3338898--3338936	19	2.2	19	90	9	64	51	5	0	43	1.24
3338908--3338974	19	3.5	19	79	20	61	53	1	0	44	1.09
3338926--3338974	13	3.8	13	81	7	64	55	0	0	44	0.99
3339891--3339972	44	1.9	42	85	14	114	50	1	0	48	1.08
3340328--3340364	3	13.0	3	88	11	60	32	0	0	67	0.91
3341117--3341156	15	2.7	16	77	14	50	52	0	0	47	1.00
3341184--3341247	20	3.2	20	71	6	67	46	0	0	53	1.00
3341169--3341271	40	2.7	40	82	7	115	46	0	1	51	1.12
3344408--3344434	2	13.5	2	100	0	54	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3348128--3348162	10	3.5	10	88	11	54	68	0	0	31	0.90
3348700--3348729	2	15.0	2	92	0	51	53	0	0	46	1.00
3349651--3349696	11	4.2	12	78	15	55	67	0	0	32	0.91
3349646--3349695	20	2.6	18	79	17	55	66	0	0	34	0.92
3353078--3353179	50	2.0	51	92	1	170	37	27	6	28	1.82
3358155--3358187	2	16.5	2	100	0	66	0	48	0	51	1.00
3358223--3358270	6	8.2	6	93	4	80	0	18	0	81	0.70
3359367--3359424	21	2.8	21	84	10	66	43	0	0	56	0.99
3359367--3359410	18	2.4	19	85	7	65	47	0	0	52	1.00
3359405--3359446	8	5.4	8	81	16	52	23	0	0	76	0.79

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19