genome.fa.s25.2.7.7.80.10.50.1000.15.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  15  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)
2804722--2804775	27	2.0	26	85	3	72	68	1	0	29	1.00
2804663--2804759	35	2.8	34	79	11	108	58	2	1	38	1.16
2804799--2804843	24	1.9	23	90	4	72	0	24	0	75	0.80
2804789--2804829	13	2.9	15	79	17	52	0	24	0	75	0.80
2804801--2804851	24	2.2	24	82	3	59	3	25	0	70	1.04
2805457--2805496	20	2.1	19	86	13	55	42	2	2	52	1.28
2807612--2807680	34	2.0	34	97	0	129	21	17	24	36	1.95
2812522--2812568	2	23.5	2	91	0	76	53	2	0	44	1.12
2819791--2819833	17	2.3	18	80	15	52	55	0	0	44	0.99
2821580--2821605	5	5.2	5	100	0	52	80	0	0	19	0.71
2828192--2828227	2	18.0	2	100	0	72	0	0	50	50	1.00
2829429--2829491	19	3.0	21	81	9	67	42	0	0	57	0.99
2829454--2829488	14	2.4	15	90	4	54	45	0	0	54	0.99
2830832--2830880	17	2.8	18	78	12	57	38	2	0	59	1.09
2832124--2832173	14	3.6	14	77	0	55	66	4	0	30	1.10
2832224--2832257	14	2.4	14	90	5	50	47	0	0	52	1.00
2832599--2832712	11	9.7	11	69	23	56	42	1	0	54	1.16
2832589--2832684	33	3.1	33	81	14	98	45	0	2	52	1.12
2832613--2832662	19	3.0	17	76	18	52	44	0	2	54	1.11
2832578--2832684	15	7.3	15	74	11	87	46	0	1	51	1.11
2834266--2834306	21	2.0	21	85	9	57	68	0	0	31	0.90
2834283--2834399	8	14.6	8	69	21	59	58	2	0	38	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2834349--2834399	23	2.2	23	82	0	66	60	1	1	35	1.19
2838550--2838590	21	1.9	22	90	5	66	34	0	0	65	0.93
2838563--2838610	13	3.6	13	81	10	53	33	0	0	66	0.92
2839672--2839721	21	2.3	21	86	3	64	34	0	4	62	1.14
2843592--2843624	2	16.5	2	100	0	66	48	0	0	51	1.00
2855464--2855502	2	19.5	2	100	0	78	51	0	0	48	1.00
2856039--2856072	3	11.3	3	93	0	59	61	0	0	38	0.96
2856357--2856381	13	1.9	13	100	0	50	44	0	0	56	0.99
2856550--2856590	3	13.7	3	100	0	82	31	0	0	68	0.90
2863226--2863274	2	25.0	2	95	4	91	48	0	51	0	1.00
2866401--2866448	16	2.9	16	84	6	51	50	4	0	45	1.21
2868434--2868461	2	14.0	2	100	0	56	50	0	0	50	1.00
2870231--2870278	2	24.0	2	100	0	96	50	0	0	50	1.00
2876121--2876147	2	13.5	2	100	0	54	48	0	0	51	1.00
2876619--2876649	6	5.2	6	100	0	62	83	0	0	16	0.64
2877343--2877642	100	3.0	100	95	0	548	28	16	35	20	1.94
2878566--2878686	60	2.0	60	91	0	197	38	8	23	29	1.84
2881370--2881406	18	2.1	18	100	0	74	27	24	16	32	1.96
2883371--2883409	20	2.0	20	90	9	64	46	7	0	46	1.31
2895596--2895675	33	2.4	34	75	4	83	41	2	0	56	1.13
2895623--2895672	21	2.5	21	81	15	61	42	0	0	58	0.98
2896823--2896849	1	27.0	1	100	0	54	100	0	0	0	0.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2901754--2901790	18	2.1	18	90	10	58	45	0	0	54	1.00
2901719--2901800	21	4.0	22	68	17	61	40	1	0	58	1.06
2902108--2902142	18	1.9	18	88	0	52	51	2	2	42	1.31
2903749--2903794	18	2.6	17	81	15	58	60	4	0	34	1.16
2903810--2903844	17	2.1	17	88	0	52	48	11	0	40	1.39
2904649--2904718	26	2.8	26	80	12	67	57	1	1	40	1.17
2904670--2904718	24	2.0	24	84	8	62	55	2	2	40	1.23
2911592--2911622	16	1.9	16	100	0	62	38	12	35	12	1.82
2913957--2913999	15	2.9	14	82	6	50	51	2	30	16	1.57
2914092--2914134	6	6.8	6	82	10	50	83	0	11	4	0.78
2914092--2914135	13	3.5	12	84	6	52	81	0	11	6	0.86
2914092--2914134	19	2.3	19	84	8	52	83	0	11	4	0.78
2914746--2914831	42	2.1	41	86	2	118	44	8	2	45	1.46
2915035--2915069	7	4.9	7	89	6	52	17	28	31	22	1.96
2915897--2915942	19	2.4	19	81	3	56	65	6	2	26	1.28
2915895--2915954	16	3.8	16	75	16	61	60	6	1	31	1.33
2916629--2916653	12	2.1	12	100	0	50	40	16	0	44	1.47
2921587--2921642	27	2.1	27	96	0	103	41	17	8	32	1.81
2922455--2922482	3	9.3	3	100	0	56	32	0	0	67	0.91
2922690--2922722	10	3.0	11	86	13	50	39	0	0	60	0.97
2922683--2922722	22	1.9	22	85	10	57	37	0	0	62	0.95
2922879--2922927	17	2.9	16	79	8	62	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2931361--2931391	16	1.9	16	100	0	62	38	12	35	12	1.82
2932649--2932674	3	8.7	3	100	0	52	69	0	0	30	0.89
2932670--2932706	4	9.2	4	100	0	74	75	0	0	24	0.80
2933918--2933956	12	3.3	12	85	3	53	89	0	10	0	0.48
2934840--2934874	7	4.9	7	89	6	52	17	28	31	22	1.96
2935548--2935578	13	2.4	13	94	0	53	83	0	16	0	0.64
2936345--2936369	12	2.1	12	100	0	50	40	16	0	44	1.47
2941407--2941462	27	2.1	27	96	0	103	41	17	8	32	1.81
2942274--2942298	3	8.3	3	100	0	50	32	0	0	68	0.90
2942505--2942537	10	3.0	11	86	13	50	39	0	0	60	0.97
2942498--2942537	22	1.9	22	85	10	57	37	0	0	62	0.95
2942693--2942741	17	2.9	16	76	8	53	34	0	0	65	0.93
2947359--2947388	13	2.4	13	94	5	53	43	3	0	53	1.17
2951032--2951071	20	2.0	20	90	9	64	35	12	15	37	1.85
2951498--2951632	69	2.0	68	85	4	182	31	11	11	44	1.78
2953995--2954042	17	2.9	17	87	3	71	58	0	0	41	0.98
2955328--2955357	2	15.0	2	92	0	51	50	3	0	46	1.18
2957467--2957503	17	2.2	16	90	4	56	59	0	0	40	0.97
2957559--2957606	22	2.2	22	82	14	55	43	2	0	54	1.12
2958185--2958227	21	2.0	22	86	4	61	46	0	4	48	1.22
2963094--2963198	30	3.5	30	78	2	113	35	28	3	32	1.75
2963221--2963292	29	2.5	29	81	4	83	34	8	23	33	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2963497--2963526	2	15.0	2	92	0	51	53	0	46	0	1.00
2967917--2967969	12	4.2	13	81	11	65	43	0	0	56	0.99
2967919--2967968	26	2.0	24	84	7	64	42	0	0	58	0.98
2968551--2968592	19	2.2	19	83	12	50	54	0	4	40	1.21
2971251--2971304	23	2.3	23	80	3	63	38	14	11	35	1.82
2982532--2982556	2	12.5	2	100	0	50	0	0	48	52	1.00
2991047--2991087	7	5.9	7	86	8	57	63	0	0	36	0.95
2991039--2991088	14	3.6	14	80	20	52	62	0	0	38	0.96
2991059--2991114	8	6.3	9	80	15	64	64	0	0	35	0.94
2991046--2991116	16	4.2	16	73	18	54	63	0	0	36	0.95
2997808--2997848	21	2.0	20	86	13	57	29	0	4	65	1.13
2997896--2997949	23	2.3	23	77	20	58	44	0	0	55	0.99
2999328--2999397	21	3.4	20	76	9	61	50	0	0	50	1.00
2999601--2999636	18	1.9	18	88	5	54	58	0	2	38	1.13
2999600--2999637	20	2.0	20	85	15	53	60	0	2	36	1.11
3000387--3000429	19	2.3	18	84	8	50	44	0	0	55	0.99
3003531--3003565	2	17.5	2	100	0	70	51	0	0	48	1.00
3004206--3004245	21	1.9	21	94	0	71	60	0	2	37	1.11
3004236--3004278	21	2.0	21	86	8	61	69	0	0	30	0.88
3006520--3006548	2	14.5	2	100	0	58	51	48	0	0	1.00
3009936--3009982	13	3.5	13	79	2	58	46	0	8	44	1.33
3013630--3013691	32	1.9	33	86	3	90	41	0	3	54	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3013660--3013713	19	2.8	20	85	5	74	35	0	0	64	0.94
3014209--3014252	2	22.0	2	95	0	79	50	2	0	47	1.13
3015625--3015702	22	3.4	23	68	16	56	37	0	5	57	1.21
3015806--3015842	18	2.0	19	85	15	51	35	5	0	59	1.20
3017048--3017115	22	3.0	23	91	8	113	33	8	0	57	1.30
3017048--3017116	24	3.1	22	91	8	106	34	8	0	56	1.30
3020281--3020311	11	2.8	11	90	0	53	61	0	0	38	0.96
3022927--3022974	16	3.1	16	84	3	53	66	0	0	33	0.92
3022946--3022975	15	2.0	15	93	0	51	76	0	0	23	0.78
3023321--3023359	2	19.5	2	100	0	78	51	0	0	48	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   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56