genome.fa.s25.2.7.7.80.10.50.1000.1.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  1  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)
2757--2815	29	2.0	29	93	0	100	11	44	6	37	1.68
6118--6150	15	2.2	15	94	0	57	39	0	12	48	1.40
6493--6522	15	1.9	16	93	6	53	36	6	6	50	1.55
6659--6698	12	3.3	12	83	10	55	80	7	0	12	0.91
6659--6695	13	2.9	13	92	4	58	81	5	0	13	0.86
7402--7465	15	3.9	16	73	16	51	42	0	0	57	0.98
7439--7563	16	8.2	16	67	16	52	38	2	1	57	1.21
7478--7561	16	5.2	16	71	8	64	40	3	1	54	1.25
8285--8318	9	3.8	9	84	0	50	32	2	0	64	1.08
9430--9469	2	21.5	2	80	14	50	50	2	0	47	1.14
9934--9961	2	14.0	2	100	0	56	50	0	0	50	1.00
10864--10910	18	2.5	20	73	20	55	68	0	31	0	0.90
11021--11057	12	3.2	12	88	7	58	35	0	0	64	0.94
11024--11057	11	3.0	11	95	4	59	35	0	0	64	0.94
11728--11753	13	2.0	13	100	0	52	53	0	0	46	1.00
11735--11775	19	2.2	18	87	12	57	48	0	0	51	1.00
11945--11982	18	2.1	19	85	5	51	36	5	5	52	1.47
12889--12914	6	4.3	6	100	0	52	65	0	0	34	0.93
14646--14671	7	3.7	7	100	0	52	30	15	42	11	1.82
15381--15408	13	2.2	13	100	0	56	46	0	25	28	1.53
15697--15729	9	3.8	9	88	4	50	75	0	0	24	0.80
15683--15738	17	3.2	18	78	12	55	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
19685--19712	14	2.0	14	100	0	56	35	14	7	42	1.73
20672--20946	143	1.9	143	95	0	496	36	12	10	40	1.78
20972--21015	4	10.5	4	80	9	52	75	2	0	22	0.92
20983--21015	9	3.8	9	88	4	50	75	0	0	24	0.80
20991--21024	17	1.9	18	88	5	52	70	0	0	29	0.87
21939--21972	2	17.0	2	100	0	68	50	50	0	0	1.00
22674--22706	2	16.5	2	100	0	66	51	0	0	48	1.00
30310--30354	2	22.5	2	100	0	90	51	0	0	48	1.00
32951--32996	5	9.0	5	92	2	65	23	0	73	2	0.94
35578--35639	21	2.9	22	75	18	67	30	1	0	67	1.00
35581--35639	20	2.8	23	80	14	65	30	1	0	67	1.00
36914--36953	3	13.3	3	94	0	71	30	0	2	67	1.04
37362--37386	6	4.2	6	100	0	50	36	16	16	32	1.90
37387--37444	2	29.5	2	75	3	55	51	1	6	39	1.39
37887--37918	2	16.0	2	93	0	55	50	0	3	46	1.17
38459--38488	15	2.0	15	93	0	51	56	13	3	26	1.52
40383--40439	30	1.9	30	88	0	87	45	1	1	50	1.22
40988--41031	14	3.1	15	80	9	56	65	4	2	27	1.23
41263--41309	23	2.0	23	91	0	76	42	2	2	53	1.25
41251--41318	27	2.5	27	80	4	75	44	2	1	51	1.25
44115--44153	2	19.5	2	100	0	78	51	0	48	0	1.00
44737--44919	50	3.7	50	83	5	199	35	14	17	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49305--49490	50	3.7	50	86	0	255	31	17	22	28	1.96
49945--49975	3	10.3	3	100	0	62	67	0	32	0	0.91
50029--50061	4	8.2	4	93	0	57	21	0	24	54	1.45
51052--51081	2	15.0	2	92	0	51	46	0	3	50	1.18
51948--52005	21	2.7	22	84	7	66	53	0	0	46	1.00
52672--52743	19	4.0	19	77	12	80	36	0	0	63	0.94
53961--53990	2	15.0	2	100	0	60	50	0	0	50	1.00
54089--54129	21	2.0	21	100	0	82	21	4	19	53	1.63
54308--54394	42	2.1	42	100	0	174	33	22	9	34	1.86
55312--55481	50	3.4	50	92	0	277	32	15	21	31	1.94
58175--58708	267	2.0	267	91	0	852	27	23	14	34	1.94
59901--59949	19	2.6	19	80	0	62	30	22	24	22	1.99
60219--60389	50	3.4	50	86	1	245	33	18	19	28	1.96
60602--60641	20	2.0	20	100	0	80	60	5	20	15	1.53
62392--62443	16	3.3	15	74	12	50	69	1	0	28	0.99
62376--62451	32	2.6	30	82	12	86	69	1	0	28	0.96
62387--62451	32	2.1	31	85	8	87	69	1	0	29	0.98
62972--63050	38	2.1	37	83	2	95	39	1	2	56	1.21
63071--63111	19	2.2	19	90	0	64	53	0	2	43	1.13
63168--63300	65	2.0	65	80	8	146	40	3	2	54	1.28
63224--63284	14	4.4	14	71	8	52	39	3	0	57	1.15
63187--63309	65	1.9	65	81	6	151	37	3	4	55	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63400--63452	24	2.2	24	90	6	81	41	11	11	35	1.77
63464--63549	38	2.3	38	86	6	113	50	3	3	43	1.36
63531--63563	13	2.4	14	95	5	59	51	0	0	48	1.00
63531--63569	13	2.9	13	85	7	51	53	0	0	46	1.00
63635--63681	20	2.5	20	80	10	55	51	2	0	46	1.13
63861--63922	28	2.3	26	79	17	72	48	4	0	46	1.23
63872--63927	28	2.0	28	89	3	85	44	3	0	51	1.18
64497--64529	5	6.6	5	92	0	57	42	0	36	21	1.53
65207--65252	16	3.0	16	84	12	53	32	0	0	67	0.91
65206--65253	17	2.8	17	81	15	55	33	0	0	66	0.92
78800--78827	2	14.0	2	100	0	56	0	50	0	50	1.00
79091--79165	20	3.8	20	80	0	69	36	12	10	41	1.77
80075--80126	22	2.3	23	90	6	88	17	11	11	59	1.60
88532--88645	49	2.3	49	89	0	165	45	9	5	39	1.59
90295--90334	2	20.0	2	100	0	80	50	0	0	50	1.00
91444--91500	27	2.1	27	90	0	87	47	24	7	21	1.75
95200--95230	16	1.9	16	100	0	62	25	19	22	32	1.97
96016--96089	27	2.8	26	84	11	96	50	8	5	36	1.55
104538--104571	2	17.5	2	93	6	61	50	0	0	50	1.00
106545--107053	152	3.3	150	75	11	455	40	20	14	24	1.89
107616--107650	8	4.4	8	86	13	54	22	0	0	77	0.78
107620--107653	11	3.3	11	92	8	54	23	0	0	76	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
109201--109272	21	3.2	21	75	24	83	52	6	19	20	1.68
109364--109432	17	4.3	16	77	17	72	21	0	4	73	1.00
109412--109525	8	13.8	8	80	12	61	15	0	7	76	1.05
109402--109489	9	11.1	7	86	12	61	14	1	10	73	1.14
109484--109541	19	3.3	19	76	18	70	22	1	0	75	0.89
109363--109523	7	20.9	7	76	17	85	18	0	6	75	1.05
110048--110087	21	1.9	21	85	10	55	35	10	12	42	1.76
110117--110178	16	3.8	16	82	2	79	45	17	11	25	1.82
110117--110178	32	1.9	33	90	3	99	45	17	11	25	1.82
111004--111034	16	1.9	16	100	0	62	51	9	0	38	1.35
111006--111047	16	2.6	16	88	3	57	54	9	0	35	1.33
111048--111100	15	3.4	16	79	7	65	58	5	0	35	1.22
111535--111602	6	11.8	6	82	14	81	48	1	35	14	1.53
111553--111602	15	3.1	15	84	15	73	52	0	34	14	1.42
113058--113093	2	18.0	2	100	0	72	0	50	0	50	1.00
120227--120259	2	17.0	2	93	6	59	51	0	0	48	1.00
121069--121098	6	5.0	6	100	0	60	16	16	0	66	1.25
124131--124174	3	14.7	3	100	0	88	0	31	0	68	0.90
125419--125451	2	16.5	2	100	0	66	51	0	0	48	1.00
125560--125598	20	2.0	20	94	0	69	41	10	5	43	1.61
125674--125733	18	3.0	20	75	18	63	33	0	1	65	1.03
125837--125887	23	2.2	24	80	13	63	37	0	1	60	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
126188--126232	24	1.9	23	81	4	54	22	2	6	68	1.24
132546--132583	2	19.0	2	100	0	76	50	0	0	50	1.00
133250--133284	6	5.8	6	96	0	61	17	28	0	54	1.43
133249--133292	18	2.4	18	84	0	61	18	27	2	52	1.57
137161--137200	2	20.0	2	100	0	80	50	0	0	50	1.00
137431--137490	21	2.9	21	85	5	68	40	0	0	60	0.97
137411--137476	34	2.0	33	81	3	78	42	0	0	57	0.98
137466--137518	18	2.9	17	78	18	54	35	0	0	64	0.94
137492--137560	16	4.4	16	74	18	56	31	0	2	65	1.08
137497--137541	14	3.3	14	81	3	56	33	0	4	62	1.15

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