genome.fa.s4.2.7.7.80.10.50.1000.16.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  16  of  31  ( 3628 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)
3797608--3797689	40	2.0	40	97	0	155	20	34	1	43	1.60
3805518--3805544	3	9.0	3	100	0	54	66	0	0	33	0.92
3806226--3806278	26	2.0	26	92	0	88	37	13	1	47	1.54
3806230--3806285	26	2.2	26	83	0	67	42	12	1	42	1.53
3810486--3810537	27	1.9	27	84	7	70	50	1	0	48	1.12
3810497--3810545	14	3.5	15	78	13	59	48	0	2	48	1.12
3810499--3810556	27	2.1	27	81	6	64	51	0	1	46	1.11
3810647--3810705	28	2.1	29	81	9	68	42	0	0	57	0.98
3810629--3810754	68	1.9	68	84	9	172	50	0	0	48	1.06
3810626--3810765	64	2.2	60	75	18	140	52	0	0	46	1.05
3810772--3810956	76	2.4	76	84	8	232	50	0	2	46	1.19
3810807--3810930	38	3.2	38	68	16	101	52	0	0	45	1.12
3810918--3810988	33	2.2	33	87	10	101	50	0	1	47	1.09
3811406--3811498	48	1.9	49	82	10	120	43	2	0	54	1.12
3811480--3811547	21	3.1	22	82	12	70	39	0	1	58	1.07
3811352--3811654	126	2.5	116	81	11	349	43	2	0	52	1.23
3811487--3811547	22	2.8	20	77	15	68	36	0	1	62	1.05
3812146--3812765	87	6.9	92	83	5	682	41	7	16	34	1.78
3816168--3816200	16	2.0	17	94	5	59	48	0	12	39	1.40
3816264--3816341	37	2.2	35	84	11	104	46	0	0	53	1.00
3816282--3816368	28	3.1	28	67	20	67	51	0	0	48	1.00
3817750--3817779	16	1.9	15	93	6	51	53	3	0	43	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3828083--3828112	2	15.0	2	100	0	60	0	50	0	50	1.00
3828356--3828389	15	2.1	17	89	10	54	44	0	0	55	0.99
3828503--3828549	14	3.4	14	80	11	60	48	0	0	51	1.00
3828503--3828544	15	2.9	15	79	10	52	47	0	0	52	1.00
3829657--3829687	15	2.1	15	94	5	55	16	25	12	45	1.83
3830063--3830100	3	12.7	3	94	0	67	0	31	2	65	1.06
3831160--3831186	2	13.5	2	100	0	54	51	48	0	0	1.00
3833468--3833576	56	1.9	56	86	0	155	28	1	28	41	1.66
3833529--3833558	12	2.4	12	94	5	51	20	0	40	40	1.52
3833511--3833591	34	2.4	34	82	0	99	25	3	30	39	1.73
3835303--3835583	139	2.0	139	92	0	472	32	11	21	34	1.89
3838516--3838627	34	3.3	34	92	0	188	24	4	35	35	1.76
3843612--3843683	9	8.0	9	72	20	53	47	0	0	52	1.00
3843621--3843671	15	3.4	16	78	10	63	47	0	0	52	1.00
3843640--3843682	19	2.3	18	80	11	50	48	0	0	51	1.00
3844747--3844791	2	22.5	2	100	0	90	48	0	51	0	1.00
3844943--3844982	2	20.0	2	100	0	80	0	50	0	50	1.00
3845882--3845949	33	2.1	33	91	5	111	48	8	7	35	1.62
3846870--3846913	14	3.1	14	86	0	52	43	4	4	47	1.44
3846880--3846913	7	4.9	7	88	0	50	44	2	0	52	1.16
3848224--3848258	2	17.5	2	93	0	61	48	48	2	0	1.16
3849198--3849243	15	3.1	15	81	12	58	6	23	0	69	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3850306--3850377	32	2.4	29	81	9	83	56	1	1	40	1.16
3850396--3850451	27	2.1	26	83	3	67	46	0	1	51	1.11
3851140--3851170	2	15.5	2	93	0	53	51	0	0	48	1.00
3858734--3858783	2	25.5	2	77	18	52	44	2	4	50	1.32
3859108--3859143	2	18.5	2	94	5	65	50	0	0	50	1.00
3865493--3865517	8	3.1	8	100	0	50	36	0	12	52	1.39
3866131--3866156	2	13.0	2	100	0	52	0	50	0	50	1.00
3873301--3873560	130	2.0	130	98	0	502	40	11	22	26	1.88
3875991--3876037	21	2.2	21	100	0	94	17	8	0	74	1.05
3876664--3876705	19	2.2	20	91	4	68	66	0	2	30	1.04
3880965--3881008	22	1.9	24	86	9	65	29	2	0	68	1.02
3882708--3882806	49	2.0	49	98	0	189	9	10	28	52	1.65
3882791--3882819	2	14.5	2	100	0	58	0	0	51	48	1.00
3887319--3887413	47	2.0	47	100	0	190	38	25	12	23	1.90
3890213--3890245	3	11.0	3	100	0	66	66	0	0	33	0.92
3893455--3893493	2	19.5	2	94	0	69	51	0	2	46	1.14
3893493--3893527	2	17.5	2	100	0	70	51	0	48	0	1.00
3893704--3893735	2	16.0	2	100	0	64	50	0	50	0	1.00
3894177--3894206	3	10.0	3	92	0	51	63	33	3	0	1.11
3896409--3896467	31	1.9	29	83	10	73	57	5	1	35	1.31
3896574--3896626	18	2.9	17	77	8	52	45	3	1	49	1.31
3896583--3896616	17	1.9	18	88	5	52	38	2	2	55	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3896689--3896729	3	13.7	3	100	0	82	65	0	0	34	0.93
3897630--3897689	5	11.2	5	84	8	66	53	1	1	43	1.20
3897630--3897689	28	2.2	28	80	14	72	53	1	1	43	1.20
3898248--3898296	20	2.4	21	80	13	57	48	0	0	51	1.00
3899910--3899946	2	18.5	2	100	0	74	48	0	0	51	1.00
3901282--3901327	24	2.0	23	82	4	56	54	2	4	39	1.32
3907430--3907513	42	2.0	42	92	0	141	42	23	8	25	1.82
3910510--3910552	2	21.5	2	100	0	86	51	0	0	48	1.00
3910865--3910917	17	3.2	17	79	12	65	67	1	0	30	1.01
3910850--3910919	17	4.5	15	70	19	54	62	1	1	34	1.13
3911753--3911790	3	13.0	3	88	5	60	31	0	2	65	1.06
3912405--3912456	3	17.3	3	95	0	95	30	0	1	67	1.02
3915592--3915632	20	2.0	21	95	4	75	48	0	0	51	1.00
3916392--3916424	2	16.5	2	100	0	66	51	0	0	48	1.00
3919621--3919685	29	2.3	28	87	10	96	30	0	1	67	1.00
3919640--3919685	17	2.8	17	73	26	53	28	0	0	71	0.86
3919880--3919905	1	26.0	1	100	0	52	0	0	100	0	0.00
3920550--3920599	2	25.5	2	91	4	84	46	2	0	52	1.12
3924489--3924542	27	2.0	27	88	0	81	31	11	9	48	1.70
3925065--3925115	24	2.2	24	86	10	70	35	13	5	45	1.68
3925486--3925514	6	4.8	6	100	0	58	82	0	0	17	0.66
3926166--3926218	25	2.1	26	82	6	65	50	0	1	47	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3928151--3928180	2	15.0	2	100	0	60	50	0	0	50	1.00
3930785--3930810	2	13.0	2	100	0	52	50	0	0	50	1.00
3931934--3931967	17	2.0	17	94	0	59	14	14	35	35	1.87
3932011--3932036	2	13.0	2	100	0	52	50	0	0	50	1.00
3939304--3939330	2	13.5	2	100	0	54	51	0	0	48	1.00
3939679--3939707	2	14.5	2	100	0	58	48	0	0	51	1.00
3939977--3940025	21	2.2	24	85	10	68	48	2	0	48	1.12
3940922--3940951	2	15.0	2	100	0	60	50	0	0	50	1.00
3941313--3941368	29	1.9	29	100	0	112	66	7	5	21	1.37
3947665--3947701	2	18.5	2	100	0	74	48	0	0	51	1.00
3948132--3948348	34	6.4	34	87	1	285	25	7	25	41	1.81
3948135--3948348	67	3.2	68	85	2	297	25	7	25	41	1.81
3948649--3948706	20	3.0	19	89	2	80	31	17	17	34	1.93
3948650--3948713	19	3.3	19	88	2	83	28	17	18	35	1.93
3952779--3952996	34	6.5	34	87	1	296	25	7	26	41	1.81
3952783--3952996	67	3.2	68	86	2	306	25	7	26	41	1.81
3953588--3953619	6	5.2	6	96	3	55	81	0	3	15	0.82
3954672--3955202	179	3.0	174	82	5	617	41	10	9	37	1.73
3956484--3956534	22	2.5	20	83	6	66	52	0	0	47	1.00
3956532--3956585	17	3.1	17	78	10	56	42	0	3	53	1.18
3957311--3957358	23	2.2	21	81	7	51	64	6	2	27	1.28
3957342--3957366	11	2.3	11	100	0	50	56	0	8	36	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3957511--3957535	8	3.1	8	100	0	50	76	0	0	24	0.80
3962825--3962855	2	15.5	2	100	0	62	51	0	0	48	1.00
3963000--3963034	3	11.7	3	100	0	70	65	0	0	34	0.93
3966042--3966080	16	2.4	16	86	4	51	76	7	12	2	1.09
3967793--3967836	2	22.0	2	100	0	88	50	0	0	50	1.00
3968269--3968293	13	1.9	13	100	0	50	44	0	0	56	0.99
3971429--3971469	2	21.0	2	90	5	66	51	0	2	46	1.14
3973564--3973685	59	2.0	62	85	4	169	55	4	13	26	1.57
3978056--3978117	28	2.2	29	80	13	76	35	0	0	64	0.94
3978074--3978116	9	4.7	9	82	5	50	30	0	0	69	0.88

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