genome.fa.s3.2.7.7.80.10.50.1000.20.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  20  of  32  ( 3795 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)
3241004--3241047	11	4.1	11	80	13	56	68	0	2	29	1.02
3241275--3241337	29	2.2	29	82	5	74	61	3	0	34	1.12
3241400--3241462	32	2.0	32	87	6	94	52	1	0	46	1.10
3241413--3241460	16	2.9	17	72	27	50	50	2	0	47	1.12
3242324--3242380	24	2.5	24	94	5	100	56	26	3	14	1.54
3243028--3243062	18	2.0	18	88	5	54	62	2	0	34	1.10
3243027--3243085	21	2.9	20	74	18	59	61	1	0	37	1.07
3244386--3244426	18	2.3	18	86	0	64	68	0	0	31	0.90
3246730--3246785	24	2.2	26	84	9	71	46	0	5	48	1.25
3247889--3247928	19	2.0	20	85	4	55	72	0	0	27	0.85
3248274--3248320	16	2.8	17	83	9	60	65	0	0	34	0.93
3248287--3248340	11	5.0	11	79	18	60	62	0	0	37	0.95
3248287--3248339	16	3.4	16	81	2	54	64	0	0	35	0.94
3248976--3249011	2	18.0	2	88	11	56	47	0	2	50	1.15
3252960--3252997	19	2.0	19	89	0	58	52	2	0	44	1.14
3254736--3254776	20	2.0	21	90	4	66	36	0	7	56	1.27
3255392--3255439	24	2.0	24	95	0	87	6	29	6	58	1.47
3256234--3256387	36	4.3	36	79	2	157	18	41	16	24	1.89
3258008--3258033	2	13.0	2	100	0	52	50	0	0	50	1.00
3258989--3259028	13	3.1	13	85	0	53	50	0	2	47	1.14
3261431--3261485	24	2.3	24	75	12	58	58	3	0	38	1.16
3261641--3261673	16	2.1	16	88	5	50	30	0	0	69	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3261647--3261729	42	2.0	41	84	13	107	48	0	2	49	1.14
3261935--3261993	26	2.3	27	82	11	70	44	3	1	50	1.28
3270409--3270448	20	2.0	20	85	9	55	35	5	0	60	1.19
3278042--3278072	7	4.4	7	95	0	53	41	29	16	12	1.85
3278034--3278072	21	1.9	20	84	5	51	41	30	15	12	1.85
3278029--3278078	21	2.5	20	75	18	50	42	26	16	16	1.88
3289308--3289336	2	14.5	2	100	0	58	0	48	0	51	1.00
3289336--3289372	2	18.5	2	100	0	74	48	0	0	51	1.00
3291553--3291588	2	18.0	2	100	0	72	50	0	50	0	1.00
3291881--3291915	18	1.9	18	88	11	54	28	40	0	31	1.57
3293405--3293473	28	2.5	27	79	11	70	37	1	0	60	1.06
3293397--3293462	17	3.9	17	76	23	52	34	0	0	65	0.93
3293497--3293549	20	2.7	19	80	16	63	37	3	0	58	1.16
3293928--3294072	73	2.0	70	86	5	202	45	14	17	22	1.85
3294166--3294243	24	3.4	24	79	8	74	44	0	0	55	0.99
3294174--3294243	22	3.1	24	82	8	76	47	0	0	52	1.00
3296441--3296473	4	8.2	4	93	0	57	51	21	0	27	1.48
3296455--3296498	2	22.0	2	85	0	61	50	6	0	43	1.29
3296441--3296497	12	4.8	12	88	0	60	50	12	0	36	1.40
3296443--3296493	16	3.2	16	91	0	75	50	11	0	37	1.39
3299233--3299357	6	21.2	6	68	18	59	58	0	1	40	1.08
3299267--3299365	29	3.5	28	72	16	89	58	0	1	40	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3299262--3299347	45	1.9	44	86	11	122	58	0	1	40	1.06
3299233--3299352	51	2.4	51	78	10	122	58	0	1	40	1.08
3299260--3299357	40	2.5	40	78	9	103	58	0	1	40	1.05
3299233--3299373	56	2.6	53	72	16	114	57	0	2	40	1.11
3302484--3302533	21	2.5	20	81	12	57	32	2	4	62	1.25
3302539--3302581	14	3.1	14	74	12	52	58	0	2	39	1.11
3303225--3303281	22	2.5	23	80	11	73	45	0	0	54	0.99
3303355--3303396	17	2.6	16	81	7	57	35	0	0	64	0.94
3303877--3303906	11	2.7	11	89	0	51	86	0	13	0	0.57
3309268--3309294	2	13.5	2	100	0	54	51	0	0	48	1.00
3310588--3310636	22	2.1	25	88	11	77	30	2	0	67	1.02
3314221--3314309	30	2.9	30	85	12	112	57	0	5	37	1.22
3319159--3319217	9	6.2	10	86	11	72	72	0	0	27	0.84
3319165--3319217	3	18.0	3	81	18	67	71	0	0	28	0.86
3323910--3324246	181	1.8	183	91	5	554	34	17	13	34	1.89
3326418--3326457	21	1.9	21	90	10	64	60	0	0	40	0.97
3327381--3327410	1	30.0	1	93	0	51	0	96	3	0	0.21
3331389--3331437	25	2.0	25	83	0	62	51	0	0	48	1.00
3342301--3342346	14	3.1	14	84	6	56	58	0	2	39	1.10
3344455--3345442	494	2.0	494	97	0	1877	30	18	18	32	1.95
3347802--3347831	15	2.0	15	100	0	60	53	0	0	46	1.00
3347802--3347841	15	2.7	14	88	7	53	60	0	2	37	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3349311--3349336	2	13.0	2	100	0	52	50	0	0	50	1.00
3354326--3354357	12	2.7	12	90	0	55	18	40	25	15	1.90
3354359--3354404	12	3.6	12	78	16	56	43	4	13	39	1.63
3354360--3354416	27	2.1	27	90	0	87	40	5	19	35	1.74
3355768--3355818	25	2.0	25	81	7	59	54	3	3	37	1.37
3361920--3362003	15	5.4	15	70	8	60	0	34	7	58	1.26
3361960--3362051	33	2.8	33	86	0	121	0	30	11	57	1.35
3361926--3362066	48	2.9	48	81	9	144	0	31	11	57	1.34
3361993--3362066	15	4.7	15	79	9	67	0	28	13	58	1.36
3362502--3362531	2	15.0	2	100	0	60	50	0	0	50	1.00
3363826--3363854	2	15.0	2	92	7	51	48	0	51	0	1.00
3364269--3364314	24	1.9	24	82	8	58	63	0	0	36	0.95
3365054--3365109	21	2.6	22	69	8	53	51	0	0	48	1.00
3365370--3365440	23	3.0	23	80	11	65	39	1	1	57	1.16
3366728--3366780	19	2.8	18	85	8	61	54	0	0	45	0.99
3366733--3366783	18	2.6	19	87	9	68	58	0	0	41	0.98
3366912--3366966	25	2.2	25	87	6	76	45	0	0	54	0.99
3366957--3366999	17	2.5	17	84	0	50	53	0	4	41	1.21
3367085--3367131	15	3.1	15	75	22	53	65	6	0	27	1.16
3368099--3368198	11	9.1	11	75	14	91	34	0	1	65	1.00
3368101--3368170	36	2.0	35	94	2	122	31	0	1	67	1.00
3368110--3368226	24	4.7	23	69	18	67	34	0	0	64	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3368099--3368215	47	2.5	47	79	5	114	35	0	0	64	1.00
3368097--3368225	52	2.5	51	75	19	126	34	0	0	64	0.99
3368148--3368226	33	2.4	32	76	2	86	34	0	0	65	0.93
3368101--3368233	13	10.7	13	73	11	59	32	0	0	66	0.97
3371756--3371785	1	30.0	1	93	0	51	0	0	96	3	0.21
3376411--3376437	1	27.0	1	100	0	54	0	0	0	100	0.00
3385573--3385606	2	17.0	2	87	0	50	0	44	5	50	1.26
3389526--3389571	15	3.1	15	76	20	51	41	0	2	56	1.11
3391765--3391806	21	2.0	21	86	9	59	61	2	0	35	1.09
3391755--3391786	15	2.0	17	88	11	50	62	3	0	34	1.11
3394103--3394191	45	2.0	45	91	4	144	29	6	24	39	1.81
3396312--3396345	12	2.8	12	86	0	50	70	0	0	29	0.87
3397026--3397077	26	2.0	26	84	0	68	36	1	0	61	1.07
3397252--3397294	14	3.1	14	87	9	61	37	4	0	58	1.19
3397310--3397354	24	2.0	22	82	8	54	53	0	4	42	1.21
3398504--3398530	6	4.5	6	100	0	54	62	0	0	37	0.95
3401131--3401190	31	1.9	31	86	3	84	46	0	1	51	1.10
3401180--3401213	17	2.0	18	88	11	54	47	0	0	52	1.00
3403649--3403717	20	3.5	20	71	13	63	37	2	0	59	1.12
3408759--3408794	2	18.0	2	100	0	72	50	0	0	50	1.00
3410743--3411118	191	2.0	191	95	0	680	33	15	13	36	1.88
3417294--3417323	15	1.9	16	93	6	53	63	0	0	36	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3421317--3421348	4	8.2	4	93	6	57	53	0	0	46	1.00
3421585--3421644	16	3.9	15	75	12	52	41	1	1	55	1.20
3421822--3421859	18	2.1	18	100	0	76	50	5	7	36	1.54
3424795--3424839	14	3.0	15	83	9	56	48	0	0	51	1.00
3426091--3426126	18	1.9	19	88	5	56	36	0	0	63	0.94
3430010--3430036	2	13.5	2	100	0	54	51	0	0	48	1.00
3430464--3430497	17	2.0	17	88	0	50	47	0	5	47	1.26
3430896--3430952	29	2.0	29	82	6	71	43	5	3	47	1.43
3431961--3432009	21	2.3	21	75	0	53	53	0	2	44	1.12
3433126--3433155	2	15.0	2	100	0	60	0	50	0	50	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