genome.fa.s329.2.7.7.80.10.50.1000.20.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: Scaffold329
Parameters: 2 7 7 80 10 50 1000
Length:  4121247

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  20  of  25  ( 2930 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)
3148507--3148577	31	2.3	31	90	0	115	32	21	11	35	1.89
3149880--3149904	11	2.3	11	100	0	50	40	8	8	44	1.63
3154492--3154551	29	2.0	30	93	3	104	45	15	13	26	1.83
3156188--3156324	50	2.7	51	89	1	195	42	12	13	31	1.82
3158192--3158471	154	1.8	151	81	6	341	35	19	16	28	1.93
3159332--3159381	20	2.5	20	83	6	57	56	18	4	22	1.58
3159514--3159544	16	1.9	16	100	0	62	32	19	6	41	1.77
3164875--3164921	23	2.0	23	95	0	85	21	25	12	40	1.89
3167481--3167869	52	7.3	53	71	13	212	30	24	11	32	1.91
3167478--3167870	51	7.4	52	71	15	232	30	25	11	32	1.91
3167858--3167929	28	2.6	28	86	0	90	23	33	19	23	1.97
3167478--3167979	267	1.9	267	88	3	769	29	26	12	31	1.93
3171279--3171458	52	3.5	52	96	0	326	28	17	18	34	1.94
3171467--3171491	13	1.9	13	100	0	50	36	16	16	32	1.90
3171532--3171598	33	2.0	33	88	0	98	40	13	11	34	1.81
3171554--3171578	13	1.9	13	100	0	50	32	16	16	36	1.90
3173158--3173268	55	2.0	55	94	0	195	19	20	9	50	1.74
3178589--3178631	21	2.0	21	82	8	52	27	2	0	69	1.00
3178591--3178631	10	3.8	11	81	15	50	26	2	0	70	0.99
3183694--3184060	60	6.1	60	72	3	256	30	19	15	34	1.93
3187149--3187205	22	2.7	21	72	20	55	63	0	1	35	1.05
3187375--3187426	24	2.2	24	82	6	61	57	0	1	40	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3188207--3188394	14	13.4	14	68	25	80	56	1	2	39	1.18
3188209--3188303	5	19.8	5	67	16	58	56	1	1	41	1.13
3188199--3188277	41	2.0	42	85	12	112	58	0	1	40	1.06
3188218--3188328	30	3.6	30	70	25	79	57	1	1	38	1.20
3189070--3189095	13	2.0	13	100	0	52	38	0	0	61	0.96
3190242--3190266	2	12.5	2	100	0	50	48	0	0	52	1.00
3190401--3190435	2	17.5	2	100	0	70	48	0	0	51	1.00
3192864--3192925	2	34.5	2	73	20	57	56	0	43	0	0.99
3192864--3192925	5	11.5	6	77	17	57	56	0	43	0	0.99
3192871--3192918	24	1.9	26	87	8	73	56	0	43	0	0.99
3196143--3196221	32	2.4	33	85	2	97	56	0	2	40	1.12
3196176--3196225	18	3.0	18	73	26	56	60	0	2	38	1.09
3196763--3196800	16	2.3	17	86	4	51	68	2	0	28	1.03
3197493--3197543	19	2.7	19	76	11	52	76	1	7	13	1.09
3201420--3201473	20	2.7	20	85	0	72	53	0	38	7	1.29
3201411--3201452	5	8.4	5	89	0	66	64	0	33	2	1.07
3201776--3201816	20	2.0	20	86	9	57	46	19	7	26	1.76
3219398--3219657	130	2.0	128	91	3	423	25	13	21	39	1.90
3220089--3220143	9	6.1	9	81	8	67	1	14	1	81	0.85
3220103--3220143	21	2.1	19	90	9	64	0	14	0	85	0.60
3220610--3220647	17	2.2	18	90	4	60	28	23	15	31	1.96
3225510--3225538	2	14.5	2	100	0	58	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)
3226234--3226313	24	3.3	25	76	18	80	23	5	1	70	1.15
3228373--3229411	519	2.0	519	100	0	2078	36	16	12	34	1.86
3230965--3230989	5	5.0	5	100	0	50	60	0	0	40	0.97
3231925--3231985	23	2.7	23	81	0	68	34	1	3	60	1.23
3232626--3232668	22	2.0	22	90	4	70	37	6	0	55	1.27
3237960--3237994	18	1.9	18	88	0	52	40	0	2	57	1.14
3238453--3238487	17	2.1	17	94	0	61	60	0	5	34	1.21
3238921--3238960	20	2.0	20	85	9	55	60	0	0	40	0.97
3239183--3239214	16	2.0	16	93	0	55	59	3	25	12	1.48
3247469--3247504	18	2.1	17	89	5	54	33	0	0	66	0.92
3247944--3247988	23	2.0	23	91	4	74	53	6	0	40	1.27
3248838--3248936	22	4.8	22	67	26	65	49	0	2	48	1.12
3248849--3248931	26	2.8	32	72	27	83	49	0	2	48	1.14
3248894--3248953	18	3.3	18	86	13	79	51	0	1	46	1.10
3248940--3248980	16	2.6	16	78	21	50	60	2	0	36	1.10
3249146--3249179	16	2.1	17	88	5	52	55	23	14	5	1.61
3249177--3249244	16	4.2	16	75	0	55	50	23	10	16	1.75
3250841--3250879	16	2.5	15	80	12	51	35	0	2	61	1.10
3252299--3252347	26	2.0	24	84	8	62	46	0	0	53	1.00
3252604--3252645	11	3.4	12	81	12	50	45	0	0	54	0.99
3252713--3252758	18	2.5	19	82	10	51	39	0	2	58	1.10
3252991--3253035	19	2.4	19	82	17	58	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3253003--3253078	20	3.8	20	72	6	57	55	0	0	44	0.99
3255539--3255577	20	1.9	21	85	15	55	43	0	2	53	1.14
3256773--3256827	29	2.0	27	85	7	74	52	0	3	43	1.18
3257075--3257125	19	2.6	20	81	9	52	35	1	0	62	1.06
3257531--3257606	10	7.4	11	71	19	58	57	0	0	42	0.98
3257562--3257606	13	4.0	12	78	21	53	60	0	0	40	0.97
3257544--3257668	59	2.1	59	80	11	141	55	0	0	44	1.05
3258004--3258056	17	2.9	18	78	21	65	30	1	1	66	1.13
3258444--3258488	23	2.0	22	91	4	72	51	4	2	42	1.34
3259378--3259479	16	6.4	15	72	11	53	52	0	2	44	1.16
3259437--3259506	16	4.6	14	76	15	59	61	1	0	37	1.05
3259454--3259522	31	2.4	29	80	17	83	56	2	0	40	1.14
3259619--3259662	17	2.7	16	86	6	61	47	25	18	9	1.77
3259610--3259682	16	4.5	16	75	3	74	47	23	16	12	1.80
3259943--3260002	16	3.8	16	71	8	52	55	0	0	45	0.99
3260759--3260820	18	3.6	17	77	14	65	62	0	0	37	0.95
3260776--3260824	15	3.1	15	81	16	62	55	0	0	44	0.99
3260759--3260824	33	2.0	33	88	5	98	59	0	0	40	0.98
3262180--3262232	28	2.0	26	85	7	70	49	3	0	47	1.19
3266178--3266288	57	1.9	56	84	10	145	26	10	10	52	1.69
3266214--3266291	28	2.8	29	77	16	83	24	10	12	52	1.70
3266183--3266665	58	8.4	58	70	8	227	28	12	10	49	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3272111--3272137	2	13.5	2	100	0	54	0	48	0	51	1.00
3276417--3276442	11	2.4	11	100	0	52	42	0	19	38	1.51
3277413--3277463	20	2.5	21	81	12	61	37	3	0	58	1.16
3277488--3277546	27	2.3	25	80	16	68	30	3	1	64	1.20
3277557--3277598	18	2.3	18	84	8	50	33	2	2	61	1.21
3277647--3277709	20	3.0	22	82	13	71	50	0	0	49	1.00
3277624--3277698	34	2.2	35	81	11	93	50	0	0	49	1.00
3277649--3277708	26	2.3	27	80	11	72	51	0	0	48	1.00
3281146--3281240	30	3.0	32	65	20	90	36	10	21	31	1.87
3281146--3281275	63	2.1	63	89	0	197	36	9	24	30	1.87
3281956--3282013	23	2.5	24	94	5	109	41	5	15	37	1.70
3286651--3286705	23	2.3	24	96	3	103	40	5	14	40	1.69
3289552--3289606	28	1.9	29	85	3	76	63	0	0	36	0.95
3289887--3289946	14	4.4	14	75	10	61	55	1	6	36	1.36
3290224--3290261	19	2.0	19	85	10	51	42	5	0	52	1.24
3290707--3290746	21	1.9	21	84	0	53	30	20	10	40	1.85
3291451--3291475	13	1.9	13	100	0	50	40	0	0	60	0.97
3291894--3291936	21	2.0	21	86	8	61	41	0	0	58	0.98
3293211--3293252	21	2.0	21	90	0	66	28	11	14	45	1.80
3295174--3295256	16	5.2	16	77	11	80	55	6	1	37	1.32
3295177--3295256	32	2.5	32	83	4	99	55	6	1	37	1.33
3296276--3296305	2	15.0	2	100	0	60	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)
3296419--3296457	18	2.2	18	86	9	53	43	0	0	56	0.99
3296996--3297043	20	2.4	21	86	6	64	0	8	12	79	0.94
3296996--3297056	20	3.0	20	81	9	61	0	9	9	80	0.91
3302326--3302379	16	3.4	16	72	7	56	40	0	0	59	0.98
3302322--3302408	32	2.8	30	80	15	81	41	0	1	57	1.06
3304322--3304348	2	13.5	2	100	0	54	51	0	0	48	1.00
3305073--3305128	28	2.0	28	89	6	87	58	0	0	41	0.98
3306047--3306081	11	3.2	11	100	0	70	25	54	8	11	1.64
3307011--3307036	12	2.2	12	100	0	52	50	7	0	42	1.31
3308132--3308170	19	2.1	19	85	9	53	61	0	0	38	0.96

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