genome.fa.s25.2.7.7.80.10.50.1000.22.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  22  of  56  ( 6609 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)
3890316--3890402	30	2.9	31	81	3	97	28	12	8	50	1.68
3894957--3894987	6	5.2	6	96	0	53	0	70	0	29	0.87
3895024--3895053	10	3.1	10	90	9	53	26	0	0	73	0.84
3899842--3899982	70	2.0	70	81	13	166	37	12	15	34	1.85
3901514--3901585	7	10.1	7	82	8	92	31	0	0	68	0.90
3901503--3901577	5	15.6	5	68	13	50	36	0	0	64	0.94
3901507--3901577	12	5.7	13	75	17	62	35	0	0	64	0.94
3901513--3901584	17	3.8	19	75	20	71	33	0	0	66	0.92
3901503--3901585	29	2.9	29	89	5	116	34	0	0	65	0.93
3901746--3901804	20	2.7	22	78	19	61	62	1	1	33	1.15
3901750--3901804	14	3.8	15	75	20	55	61	1	1	34	1.17
3901737--3901781	11	4.2	11	76	23	51	64	0	0	35	0.94
3902312--3902386	12	6.2	12	74	21	59	5	26	0	68	1.11
3902312--3902355	22	2.0	22	90	0	70	4	27	0	68	1.09
3902316--3902366	22	2.3	21	81	15	59	1	29	0	68	1.00
3903010--3903072	25	2.5	26	74	10	67	61	1	1	34	1.15
3903106--3903206	20	5.0	19	68	20	55	58	1	0	38	1.16
3903093--3903205	22	5.2	21	68	25	67	56	1	0	40	1.16
3903163--3903189	13	2.1	13	100	0	54	55	0	0	44	0.99
3903093--3903208	39	2.7	44	75	17	118	57	1	0	39	1.15
3903372--3903444	32	2.3	32	100	0	146	53	0	0	46	1.00
3903382--3903473	32	3.4	26	81	14	82	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3903416--3903496	24	3.4	24	80	14	71	48	0	0	51	1.00
3903436--3903496	23	2.7	23	80	16	65	45	0	0	54	1.00
3903538--3903608	37	1.9	37	97	0	133	39	9	4	46	1.57
3903540--3903619	37	2.2	37	90	0	124	38	11	6	43	1.66
3903713--3903773	19	3.3	18	73	8	52	49	0	0	50	1.00
3903976--3904007	2	16.0	2	100	0	64	50	0	0	50	1.00
3904048--3904093	25	1.9	23	82	8	56	47	6	0	45	1.28
3904188--3904243	26	2.2	26	83	6	69	62	1	1	33	1.16
3904266--3904323	24	2.4	23	77	8	62	53	3	5	37	1.40
3904316--3904372	20	3.0	21	85	12	70	70	0	0	29	0.88
3905557--3905622	26	2.5	26	75	4	71	45	0	0	54	0.99
3905647--3905686	18	2.3	18	87	12	57	45	0	2	52	1.14
3907111--3907152	21	2.0	21	86	4	59	64	2	16	16	1.40
3907201--3907259	18	3.4	17	78	19	59	49	0	0	50	1.00
3909318--3909362	17	2.6	18	78	3	56	53	0	0	46	1.00
3909811--3909847	2	18.5	2	100	0	74	51	0	0	48	1.00
3910490--3910514	2	12.5	2	100	0	50	48	0	0	52	1.00
3915406--3915436	14	2.3	14	94	5	55	48	0	0	51	1.00
3915542--3915587	11	4.1	11	77	5	56	45	0	0	54	0.99
3915523--3915587	34	1.9	34	83	0	85	46	1	1	50	1.20
3925244--3925282	16	2.3	18	79	20	57	61	0	2	35	1.10
3925249--3925282	16	2.2	16	94	5	61	61	0	2	35	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3925803--3925860	14	4.2	14	76	12	66	41	0	0	58	0.98
3925816--3925875	30	2.1	29	85	14	81	46	0	0	53	1.00
3926063--3926111	15	3.2	16	77	8	57	46	2	0	51	1.12
3937047--3937072	2	13.0	2	100	0	52	50	0	50	0	1.00
3938487--3938511	2	12.5	2	100	0	50	48	0	0	52	1.00
3942904--3942929	2	13.0	2	100	0	52	50	0	0	50	1.00
3943094--3943118	6	4.2	6	100	0	50	68	0	0	32	0.90
3943593--3943626	15	2.2	16	89	5	52	50	2	0	47	1.16
3944538--3944577	20	2.0	21	85	9	57	37	0	0	62	0.95
3944874--3944920	15	2.9	16	72	15	51	27	0	4	68	1.08
3946345--3946379	15	2.4	15	90	4	54	48	0	0	51	1.00
3946903--3946928	2	13.0	2	100	0	52	0	0	50	50	1.00
3949475--3949639	78	2.0	80	87	5	235	49	7	10	32	1.66
3950869--3950944	38	2.0	38	97	0	143	30	6	15	47	1.71
3950962--3951047	27	3.3	27	68	14	81	48	0	1	50	1.08
3950953--3951015	31	1.9	35	84	12	89	49	0	3	47	1.17
3951309--3951364	22	2.4	23	80	14	62	51	0	3	44	1.18
3951601--3951654	17	3.3	17	70	19	51	53	0	3	42	1.18
3951856--3951926	33	2.1	33	81	7	79	53	1	1	43	1.18
3952357--3952406	2	25.0	2	100	0	100	50	0	0	50	1.00
3954868--3954919	16	3.3	16	78	7	54	32	0	9	57	1.31
3955819--3955854	12	3.1	12	84	8	56	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3955945--3955969	12	2.1	12	100	0	50	48	0	0	52	1.00
3955937--3955973	20	1.9	19	89	10	58	45	0	0	54	1.00
3955941--3955986	22	2.3	19	85	11	56	50	0	0	50	1.00
3959040--3959130	16	5.7	16	68	17	55	48	1	0	50	1.08
3961836--3961877	19	2.3	18	87	4	57	33	4	4	57	1.41
3961923--3961982	30	2.0	30	90	3	93	50	5	3	41	1.41
3961983--3962020	19	2.0	19	100	0	76	47	5	26	21	1.71
3964844--3964896	28	1.9	27	84	3	70	43	1	0	54	1.11
3965473--3965504	16	2.0	16	93	0	55	50	3	0	46	1.17
3968929--3968967	20	2.0	20	85	10	53	58	0	0	41	0.98
3968944--3968969	13	2.0	13	100	0	52	61	0	0	38	0.96
3976521--3976586	28	2.4	28	82	12	75	62	1	3	33	1.20
3976548--3976587	19	2.2	18	90	4	62	62	2	2	32	1.22
3978110--3978165	2	28.0	2	96	0	103	48	0	1	50	1.11
3978247--3978273	14	1.9	14	100	0	54	66	0	0	33	0.92
3978620--3978654	16	2.2	16	89	0	52	28	17	14	40	1.88
3980100--3980137	12	3.2	12	82	14	51	65	0	0	34	0.93
3981088--3981131	23	1.9	23	85	0	61	20	2	9	68	1.28
3981269--3981332	31	2.1	30	86	11	87	32	4	4	57	1.40
3981738--3981780	2	22.5	2	86	9	63	53	0	0	46	1.00
3985823--3985863	3	13.7	3	100	0	82	68	0	0	31	0.90
3992811--3992845	14	2.4	14	90	4	52	8	0	14	77	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3992810--3992848	15	2.6	16	80	16	55	7	0	15	76	0.99
4004141--4004209	2	34.5	2	88	0	102	44	1	4	49	1.31
4006258--4006292	6	5.8	6	96	0	52	40	17	8	34	1.80
4012979--4013015	2	18.5	2	100	0	74	51	0	48	0	1.00
4013291--4013323	13	2.4	14	90	5	50	45	0	0	54	0.99
4018616--4018682	33	2.0	33	94	0	116	38	10	16	34	1.83
4027540--4027697	79	2.0	79	98	0	307	48	11	20	18	1.79
4029558--4029582	2	12.5	2	100	0	50	52	0	48	0	1.00
4034728--4034803	27	2.9	28	70	21	65	53	1	0	44	1.08
4034687--4034795	36	3.1	36	73	10	100	51	0	1	46	1.11
4037255--4037303	20	2.5	18	78	18	53	38	0	0	61	0.96
4037245--4037308	15	3.9	17	78	17	64	42	0	0	57	0.98
4037332--4037371	19	2.3	19	87	12	59	57	0	2	40	1.12
4037544--4037583	13	2.6	17	81	18	52	35	2	2	60	1.24
4038335--4038387	27	2.0	26	81	3	61	52	1	0	45	1.11
4038569--4038624	2	28.0	2	96	0	103	48	0	0	51	1.00
4038573--4038636	8	8.1	8	92	3	67	43	1	0	54	1.09
4039358--4039404	15	2.9	16	90	9	78	63	0	0	36	0.94
4042254--4042292	20	2.0	19	90	5	60	35	7	15	41	1.76
4044855--4044919	33	1.9	34	87	9	98	58	0	0	41	0.98
4044891--4044922	17	1.9	16	93	6	55	50	0	0	50	1.00
4047754--4047785	2	16.0	2	100	0	64	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4051002--4051026	11	2.3	11	100	0	50	56	0	0	44	0.99
4054481--4054505	2	12.5	2	100	0	50	48	0	0	52	1.00
4062443--4062489	16	2.8	16	77	20	51	70	0	2	27	0.99
4062457--4062550	9	10.1	10	70	20	62	60	0	1	38	1.04
4062443--4062552	19	6.2	18	71	19	79	63	0	0	35	1.01
4062425--4062549	27	4.6	28	70	19	86	62	0	0	36	1.01
4062574--4062605	12	2.7	12	95	0	55	0	25	0	75	0.81
4062572--4062609	16	2.4	16	82	4	51	0	21	0	78	0.74
4062572--4062617	17	2.5	19	82	10	60	0	19	0	80	0.71
4062681--4062724	20	2.1	20	87	8	61	63	0	4	31	1.14

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   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56