genome.fa.s8.2.7.7.80.10.50.1000.21.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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  21  of  33  ( 3942 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)
3273492--3273557	23	2.7	25	81	6	73	37	0	0	62	0.96
3282291--3282550	50	5.2	50	84	2	317	33	19	16	31	1.94
3286928--3287133	50	4.1	50	88	1	306	27	18	21	32	1.97
3289864--3289891	6	4.7	6	100	0	56	0	53	0	46	1.00
3290997--3291022	2	13.0	2	100	0	52	50	0	0	50	1.00
3296074--3296099	3	8.7	3	100	0	52	65	0	34	0	0.93
3297209--3297244	16	2.3	15	86	9	54	58	0	0	41	0.98
3297679--3297709	2	15.5	2	93	0	53	48	0	3	48	1.17
3302272--3302313	12	3.3	12	78	21	50	52	0	0	47	1.00
3302292--3302351	8	7.1	8	71	17	50	51	0	0	48	1.00
3302272--3302334	13	4.9	13	74	12	51	50	0	0	49	1.00
3302270--3302351	26	3.2	26	83	6	89	51	0	0	48	1.00
3309993--3310052	26	2.4	25	86	5	77	45	8	10	36	1.68
3310008--3310063	26	2.1	26	86	6	76	48	10	12	28	1.74
3310318--3310347	5	5.8	5	92	7	51	60	0	0	40	0.97
3310377--3310420	20	2.1	22	87	8	65	47	0	0	52	1.00
3312843--3312894	22	2.6	19	82	11	61	38	1	0	59	1.08
3312927--3312978	16	3.2	17	81	5	54	38	0	1	59	1.08
3322136--3322174	4	9.8	4	100	0	78	51	0	0	48	1.00
3322907--3322969	2	32.5	2	80	6	76	49	6	0	44	1.28
3323949--3323983	17	2.0	17	88	5	52	34	0	0	65	0.93
3324690--3324731	17	2.5	17	81	14	52	33	4	2	59	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3324760--3325018	139	1.9	139	79	10	300	36	7	3	51	1.49
3325774--3325966	106	1.8	106	86	2	280	34	11	10	43	1.76
3327146--3327184	20	2.0	20	89	0	60	5	23	0	71	1.05
3328701--3328735	18	1.9	18	94	0	61	80	2	17	0	0.84
3330462--3330508	19	2.3	20	85	10	60	42	0	0	57	0.98
3331821--3331855	2	17.5	2	100	0	70	0	51	0	48	1.00
3333699--3333731	2	17.0	2	93	6	59	48	0	0	51	1.00
3333888--3333914	2	13.5	2	100	0	54	51	0	0	48	1.00
3337005--3337050	2	23.0	2	100	0	92	50	0	0	50	1.00
3337050--3337079	2	15.5	2	93	6	53	50	0	50	0	1.00
3337493--3337558	20	3.5	18	78	13	62	53	0	0	46	1.00
3339506--3339531	2	13.0	2	100	0	52	50	0	50	0	1.00
3339709--3339764	26	2.2	25	81	9	60	46	1	0	51	1.11
3340778--3340811	13	2.4	14	85	14	52	76	0	2	20	0.92
3341401--3341462	21	2.7	23	75	14	65	51	1	0	46	1.10
3341477--3341525	21	2.6	18	77	22	55	38	2	0	59	1.09
3341568--3341648	25	3.3	25	68	14	69	53	3	2	40	1.32
3341634--3341674	14	2.9	14	81	0	55	58	2	0	39	1.11
3342376--3342448	31	2.3	32	88	2	112	31	12	13	42	1.81
3342336--3342534	76	2.6	75	86	6	247	29	13	11	45	1.78
3348110--3348136	2	13.5	2	100	0	54	51	0	0	48	1.00
3348764--3348815	21	2.5	22	81	9	65	59	1	0	38	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3350035--3350102	28	2.4	28	83	13	95	58	1	2	36	1.22
3353095--3353120	3	8.7	3	100	0	52	69	30	0	0	0.89
3353757--3353783	2	13.5	2	100	0	54	48	0	0	51	1.00
3355119--3355159	2	20.5	2	100	0	82	48	0	0	51	1.00
3355909--3355933	2	12.5	2	100	0	50	52	0	0	48	1.00
3356321--3356426	41	2.8	35	73	22	90	54	0	0	45	0.99
3356335--3356423	42	2.2	40	80	13	101	56	0	0	43	0.99
3356337--3356440	38	2.8	38	81	10	108	56	0	0	43	0.99
3356356--3356414	26	2.5	23	81	10	66	52	0	0	47	1.00
3356374--3356428	20	2.9	20	72	17	55	54	0	0	45	0.99
3361685--3361714	2	15.0	2	92	0	51	46	0	3	50	1.18
3370188--3370295	53	2.0	53	89	7	164	27	17	25	29	1.97
3370764--3370819	21	2.5	22	77	16	62	62	0	0	37	0.95
3370764--3370821	22	2.7	22	81	13	75	62	0	0	37	0.96
3370866--3370910	16	2.9	16	87	6	67	60	2	0	37	1.09
3371851--3371895	2	22.5	2	100	0	90	48	0	0	51	1.00
3377836--3377870	17	2.1	17	88	0	52	60	0	2	37	1.12
3377851--3377908	30	1.9	30	86	6	82	39	1	3	55	1.27
3378603--3378652	18	2.8	17	83	16	66	38	0	0	62	0.96
3378612--3378709	45	2.4	38	73	20	97	42	1	1	55	1.13
3380721--3380819	51	1.9	52	81	2	119	10	7	55	27	1.59
3381177--3381222	15	3.3	15	73	14	53	15	0	58	26	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3382016--3382055	21	2.0	20	85	14	55	65	15	7	12	1.47
3384533--3384612	40	2.0	40	97	2	153	47	13	11	27	1.77
3386623--3386650	2	14.0	2	100	0	56	50	0	0	50	1.00
3388898--3388941	2	22.0	2	95	0	79	0	52	0	47	1.00
3388941--3388982	2	21.0	2	95	0	75	50	47	0	2	1.14
3395343--3395450	54	2.0	54	100	0	216	18	35	9	37	1.83
3398087--3398127	2	21.0	2	87	5	57	46	0	2	51	1.14
3398073--3398149	29	2.5	31	73	16	79	41	6	2	49	1.42
3405770--3405812	21	2.0	21	82	8	52	53	2	4	39	1.34
3413655--3413712	29	2.0	29	96	0	107	20	12	25	41	1.87
3419366--3419430	33	1.9	35	85	14	93	52	3	0	44	1.16
3419413--3419484	20	3.8	18	73	19	58	59	2	1	36	1.20
3420335--3420372	15	2.4	16	82	13	51	44	0	0	55	0.99
3423757--3423831	15	5.0	16	68	12	52	50	0	0	49	1.00
3429066--3429098	2	17.0	2	93	6	59	48	0	0	51	1.00
3429559--3429858	152	2.0	149	92	2	494	37	9	9	43	1.70
3431246--3431274	2	14.5	2	100	0	58	48	0	0	51	1.00
3431795--3431834	2	20.5	2	94	5	73	50	0	0	50	1.00
3432072--3432108	16	2.3	16	90	0	56	48	2	5	43	1.40
3434305--3434340	16	2.2	17	90	5	56	41	0	0	58	0.98
3436491--3436521	3	10.0	3	93	6	53	67	0	0	32	0.91
3437265--3437304	6	6.5	6	91	2	53	20	2	0	77	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3437421--3437458	19	2.0	20	84	5	51	71	0	5	23	1.07
3437749--3437786	2	19.0	2	100	0	76	50	0	0	50	1.00
3438994--3439027	2	17.0	2	87	0	50	47	0	5	47	1.26
3440616--3440656	20	2.0	20	86	9	57	75	2	0	21	0.92
3441470--3441514	20	2.4	19	85	7	56	48	0	2	48	1.13
3441855--3441887	3	11.0	3	93	0	57	63	0	3	33	1.10
3443481--3443526	23	2.0	22	83	4	56	56	0	0	43	0.99
3450789--3450877	45	2.0	45	95	0	160	37	40	8	13	1.76
3460479--3460511	3	11.0	3	100	0	66	33	0	0	66	0.92
3468149--3468202	14	3.5	16	78	17	60	59	0	0	40	0.98
3468156--3468202	14	3.1	15	84	9	69	57	0	0	42	0.98
3468167--3468211	23	2.0	23	86	8	65	51	0	0	48	1.00
3468767--3468809	3	14.3	3	100	0	86	67	0	0	32	0.91
3469837--3469862	3	8.7	3	100	0	52	34	0	0	65	0.93
3473524--3473729	104	2.0	104	98	1	396	38	16	17	27	1.91
3492974--3493141	82	2.0	82	100	0	336	48	13	20	17	1.80
3499245--3499291	13	3.5	13	72	16	51	42	10	6	40	1.65
3499294--3499319	12	2.2	12	100	0	52	23	26	34	15	1.94
3503936--3503982	13	3.5	13	72	16	51	42	10	6	40	1.65
3511308--3511349	21	2.0	21	81	9	50	33	2	7	57	1.39
3511670--3511720	13	4.0	13	80	10	61	49	0	0	50	1.00
3511669--3511718	25	2.0	24	88	11	73	46	0	0	54	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3511876--3511912	11	3.2	12	85	14	51	48	0	0	51	1.00
3514208--3514233	2	13.0	2	100	0	52	50	0	0	50	1.00
3518444--3518529	2	45.0	2	75	13	56	44	2	0	53	1.13
3518435--3518529	22	4.3	22	71	14	79	43	2	1	53	1.19
3518445--3518553	36	3.0	35	78	12	105	45	3	0	50	1.19
3519331--3519360	5	6.0	5	100	0	60	20	40	0	40	1.52
3519430--3519492	17	3.9	15	74	22	56	50	0	0	49	1.00
3520244--3520270	2	13.5	2	100	0	54	48	0	0	51	1.00
3520314--3520349	3	12.3	3	94	5	65	69	0	0	30	0.89
3520509--3520558	19	2.6	19	87	3	64	64	2	0	34	1.05

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