genome.fa.s79.2.7.7.80.10.50.1000.25.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: Scaffold79
Parameters: 2 7 7 80 10 50 1000
Length:  4189514

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   

This is table  25  of  26  ( 3105 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)
3751933--3751965	11	3.2	11	87	12	52	84	0	15	0	0.61
3754977--3755054	18	4.4	17	75	12	59	57	0	0	42	0.98
3754970--3755054	27	3.2	28	76	12	83	57	0	0	42	0.98
3761325--3761405	31	2.9	27	72	13	81	46	1	3	48	1.27
3761319--3761415	27	3.5	27	72	13	90	43	2	4	50	1.33
3765499--3765536	2	19.0	2	100	0	76	50	0	50	0	1.00
3767061--3767106	23	2.0	23	83	8	58	45	0	0	54	0.99
3767311--3767335	12	2.1	12	100	0	50	36	0	0	64	0.94
3767746--3767793	16	3.0	17	74	20	50	56	0	2	41	1.11
3767788--3767856	11	6.9	10	77	11	61	57	0	1	40	1.07
3767737--3767825	22	4.0	21	70	12	63	58	0	2	39	1.11
3767764--3767821	27	2.1	26	84	15	73	55	0	3	41	1.17
3767805--3767908	33	3.1	34	77	12	92	58	0	0	40	1.04
3789338--3789378	20	2.0	20	90	0	64	43	19	9	26	1.82
3792225--3792278	23	2.3	25	75	18	62	55	1	1	40	1.21
3792382--3792428	18	2.8	17	80	6	51	40	2	0	57	1.11
3795183--3795225	21	2.0	21	86	0	59	44	2	0	53	1.13
3797694--3797720	2	13.5	2	100	0	54	51	0	0	48	1.00
3798304--3798350	17	2.8	16	81	9	58	48	0	0	51	1.00
3798376--3798415	20	2.0	21	85	14	57	57	7	0	35	1.27
3799435--3799474	2	20.0	2	89	0	62	50	0	2	47	1.14
3802223--3802252	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)
3802841--3802872	2	16.0	2	100	0	64	50	0	0	50	1.00
3807584--3807637	23	2.4	22	84	12	74	40	0	0	59	0.98
3807584--3807643	22	2.7	22	80	10	68	41	0	0	58	0.98
3807595--3807662	32	2.2	31	81	2	73	50	0	0	50	1.00
3808131--3808281	49	3.0	47	76	5	131	29	8	19	41	1.81
3808160--3808281	49	2.4	49	83	5	156	28	9	23	37	1.87
3812655--3812859	50	4.1	50	82	0	221	29	14	18	37	1.91
3812655--3812859	100	2.0	100	84	1	268	29	14	18	37	1.91
3814184--3814253	29	2.3	29	76	14	70	50	1	0	48	1.09
3814276--3814330	27	2.0	28	85	3	76	36	0	1	61	1.06
3814296--3814355	23	2.6	22	76	7	57	40	3	0	56	1.16
3814337--3814399	14	4.1	16	71	24	55	52	0	1	46	1.10
3814388--3814445	21	2.9	20	75	14	57	62	0	1	36	1.06
3820088--3820247	5	32.2	5	64	14	55	39	0	0	59	1.07
3820090--3820170	17	4.8	17	75	13	53	37	1	1	60	1.13
3820198--3820250	17	3.1	17	76	13	63	37	0	0	62	0.96
3826019--3826072	16	3.4	16	84	0	72	29	0	29	40	1.57
3827340--3827406	31	2.1	33	83	10	86	35	0	0	64	0.94
3827550--3827591	3	14.0	3	100	0	84	66	0	0	33	0.92
3831725--3831764	20	2.0	20	100	0	80	45	0	0	55	0.99
3831803--3831849	23	2.0	23	84	8	60	51	0	0	48	1.00
3832110--3832140	2	15.5	2	93	0	53	48	0	3	48	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3832358--3832387	6	5.0	6	95	0	51	16	63	0	20	1.31
3836875--3836911	3	12.3	3	100	0	74	64	0	0	35	0.94
3837837--3837880	2	22.0	2	80	0	52	52	4	0	43	1.22
3838206--3838236	8	3.9	8	100	0	62	38	0	0	61	0.96
3838478--3838509	2	16.0	2	100	0	64	50	0	0	50	1.00
3844060--3844088	14	2.0	15	93	6	51	34	0	13	51	1.42
3847412--3847444	16	2.1	16	94	0	57	42	18	27	12	1.85
3847731--3847764	17	1.9	18	94	5	61	70	0	0	29	0.87
3851283--3851362	33	2.4	32	84	14	108	52	0	1	46	1.08
3851330--3851393	20	3.4	20	70	22	57	53	0	1	45	1.10
3852136--3852162	3	9.0	3	100	0	54	33	0	33	33	1.58
3854977--3855062	44	2.0	44	88	4	129	43	8	17	31	1.78
3856140--3856169	2	15.0	2	100	0	60	0	50	0	50	1.00
3861758--3861798	15	2.8	15	75	17	50	60	0	7	31	1.24
3861750--3861809	7	8.1	7	77	15	59	58	1	10	30	1.41
3861770--3861809	12	3.1	13	89	7	55	57	2	10	30	1.45
3867378--3867442	34	1.9	34	96	0	121	30	24	7	36	1.84
3876203--3876253	14	3.1	18	73	26	67	68	0	11	19	1.20
3876189--3876253	31	2.1	32	97	2	123	72	0	9	18	1.11
3883285--3883323	21	1.9	20	85	15	53	41	2	2	53	1.28
3884710--3884840	52	2.5	52	88	0	208	29	16	18	36	1.92
3884849--3884873	13	1.9	13	100	0	50	36	16	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3884926--3884977	19	2.7	19	93	0	95	40	17	11	30	1.85
3890668--3890752	30	2.8	31	76	16	88	38	4	3	52	1.39
3890973--3891035	24	2.7	23	73	11	56	46	1	0	52	1.10
3891075--3891100	9	2.9	9	100	0	52	80	0	0	19	0.71
3892608--3892691	41	2.0	41	93	0	141	34	19	17	28	1.95
3897965--3897994	2	15.0	2	100	0	60	50	0	0	50	1.00
3898857--3898895	17	2.4	16	86	4	60	43	5	0	51	1.24
3899723--3899752	2	15.0	2	100	0	60	50	0	50	0	1.00
3901983--3902018	18	2.0	18	88	0	54	61	0	2	36	1.11
3903684--3903720	5	7.4	5	87	0	56	0	75	2	21	0.92
3904586--3904625	21	1.9	21	84	0	53	60	2	30	7	1.38
3905884--3905929	21	2.2	21	100	0	92	26	15	28	30	1.96
3905884--3905937	21	2.6	21	93	0	81	24	14	29	31	1.95
3905932--3905973	21	2.0	21	85	0	57	28	16	16	38	1.91
3907786--3907813	2	14.0	2	100	0	56	50	50	0	0	1.00
3916390--3916428	19	2.0	20	90	5	62	74	0	0	25	0.82
3916481--3916505	2	12.5	2	100	0	50	52	0	0	48	1.00
3916727--3916752	4	6.5	4	100	0	52	76	0	0	23	0.78
3919339--3919378	2	20.5	2	94	5	73	52	0	0	47	1.00
3919993--3920021	14	2.0	15	93	6	51	75	0	3	20	0.94
3921916--3921941	2	13.0	2	100	0	52	50	0	0	50	1.00
3925938--3925962	7	3.6	7	100	0	50	12	0	0	88	0.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3929032--3929062	3	10.3	3	100	0	62	32	0	0	67	0.91
3933362--3933396	2	17.5	2	100	0	70	48	0	0	51	1.00
3933758--3933799	2	21.0	2	100	0	84	50	0	0	50	1.00
3936279--3936322	2	22.0	2	95	0	79	47	0	2	50	1.13
3939723--3939756	2	17.5	2	87	6	52	47	2	0	50	1.16
3940665--3940733	28	2.5	28	95	0	120	55	18	7	18	1.66
3940665--3940741	28	2.8	28	90	4	93	53	16	7	22	1.69
3941719--3941752	16	2.2	15	89	5	50	26	0	0	73	0.83
3942674--3942713	2	20.0	2	89	0	53	47	0	47	5	1.24
3944750--3944787	2	19.5	2	83	5	51	47	2	2	47	1.30
3946548--3946615	30	2.3	30	84	0	91	27	10	33	27	1.89
3951356--3951385	10	3.0	10	95	0	51	46	20	3	30	1.66
3951356--3951403	20	2.4	20	79	6	53	43	16	4	35	1.67
3960879--3960918	13	2.8	16	78	21	52	50	0	0	50	1.00
3964547--3964583	2	18.5	2	100	0	74	0	48	0	51	1.00
3972069--3972122	28	2.0	27	92	3	90	44	24	18	12	1.85
3973904--3973941	15	2.6	15	79	4	51	63	0	0	36	0.95
3973922--3973961	21	1.9	21	90	10	64	70	0	0	30	0.88
3977257--3977344	32	2.8	32	82	6	99	40	20	14	23	1.90
3977287--3977359	16	4.6	16	80	0	83	41	21	15	21	1.90
3977256--3977351	48	2.0	48	84	8	124	42	19	13	23	1.87
3978192--3978249	16	3.7	16	83	2	64	44	24	13	17	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3980022--3980061	2	20.0	2	89	0	62	50	5	0	45	1.23
3985985--3986011	2	13.5	2	100	0	54	51	0	0	48	1.00
3988528--3988739	34	6.3	34	82	2	221	29	6	22	41	1.79
3988539--3988739	102	2.0	102	86	0	285	29	6	22	41	1.80
3988523--3988738	68	3.2	69	80	3	251	29	6	22	41	1.78
3996020--3996075	14	3.9	15	81	6	62	44	7	7	41	1.59
3996020--3996093	14	5.2	14	75	3	58	41	5	9	43	1.60
4005378--4005409	3	10.7	3	93	0	55	31	3	0	65	1.08
4007622--4007651	2	15.0	2	100	0	60	50	0	50	0	1.00
4008271--4008298	2	14.0	2	100	0	56	50	50	0	0	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