genome.fa.s8.2.7.7.80.10.50.1000.27.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  27  of  33  ( 3942 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)
4839687--4839730	23	2.0	22	90	4	70	65	0	0	34	0.93
4840447--4840546	28	4.0	24	72	22	82	59	0	1	40	1.04
4840572--4840610	11	3.1	13	82	17	55	53	0	0	46	1.00
4841763--4841840	40	1.9	41	82	10	97	48	0	2	48	1.15
4841827--4841866	20	2.1	19	85	4	53	52	0	2	45	1.14
4842534--4842609	19	4.4	19	75	21	78	59	0	0	40	0.98
4842536--4842624	24	3.7	23	75	18	81	58	0	0	41	0.98
4842534--4842609	11	7.6	11	70	26	62	59	0	0	40	0.98
4842537--4842624	11	7.2	11	73	18	59	57	0	0	42	0.98
4842547--4842620	26	2.9	26	71	16	66	59	0	0	40	0.97
4843029--4843059	2	15.5	2	100	0	62	51	0	0	48	1.00
4845015--4845074	20	3.2	19	81	11	70	53	0	0	46	1.00
4845011--4845052	18	2.4	18	81	18	61	57	0	0	42	0.99
4849719--4849743	4	6.2	4	100	0	50	76	0	0	24	0.80
4849910--4849948	14	2.7	15	88	4	62	10	5	0	84	0.76
4849914--4849947	13	2.5	13	90	4	50	8	2	0	88	0.62
4850405--4850476	28	2.6	27	76	8	74	65	0	0	34	0.93
4851046--4851129	42	2.1	38	82	8	96	52	0	0	47	1.00
4853553--4853614	11	5.6	11	73	22	51	30	0	0	69	0.89
4853564--4853606	12	3.5	13	81	12	63	27	0	0	72	0.85
4853553--4853606	24	2.2	25	93	6	94	29	0	0	70	0.88
4854713--4854749	2	18.5	2	94	0	65	48	0	2	48	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4856267--4856307	19	2.1	19	86	13	57	56	4	0	39	1.21
4858082--4858116	17	2.1	16	89	5	52	34	0	0	65	0.93
4858553--4858591	16	2.5	15	84	12	51	53	0	0	46	1.00
4861301--4861353	16	3.4	16	84	5	63	66	0	1	32	1.03
4861387--4861467	24	3.2	25	70	19	69	51	0	0	48	1.00
4862081--4862141	25	2.4	26	75	13	63	32	1	0	65	1.02
4864240--4864281	17	2.4	18	88	7	61	57	0	7	35	1.26
4864242--4864281	18	2.3	17	86	4	53	60	0	7	32	1.25
4864199--4864573	208	1.8	202	82	6	486	49	2	8	40	1.45
4864445--4864490	16	2.8	16	86	6	56	56	0	4	39	1.19
4865901--4866154	130	2.0	129	93	0	436	38	22	12	25	1.90
4869656--4869725	27	2.5	28	81	11	81	55	0	1	42	1.08
4871291--4871342	16	3.2	16	80	2	59	53	9	5	30	1.57
4874106--4874147	14	3.0	14	86	6	59	28	2	0	69	1.01
4874406--4874472	23	2.9	23	72	26	61	52	0	0	47	1.00
4874408--4874489	21	3.8	21	79	17	87	53	0	1	45	1.08
4877106--4877134	2	14.5	2	100	0	58	0	51	0	48	1.00
4885470--4885592	61	2.0	61	96	0	228	33	11	14	40	1.82
4886781--4886806	2	13.0	2	100	0	52	50	0	0	50	1.00
4908962--4909007	17	2.6	18	83	13	60	58	0	0	41	0.98
4908942--4909038	14	6.4	16	70	20	59	57	1	0	41	1.05
4908943--4909034	32	2.9	32	77	9	91	59	1	0	39	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4908955--4909052	32	3.4	27	76	19	83	57	1	0	41	1.05
4909204--4909265	23	2.6	25	76	21	62	37	0	0	62	0.95
4909330--4909382	26	2.0	26	100	0	106	39	7	11	41	1.69
4911546--4911587	15	2.8	16	79	17	54	47	2	0	50	1.14
4915897--4915990	43	2.2	41	85	12	120	40	0	1	58	1.05
4915903--4915993	41	2.2	41	81	11	114	40	0	1	58	1.05
4915950--4916018	27	2.6	26	76	17	70	42	1	0	56	1.08
4917073--4917153	25	3.4	25	77	5	78	62	1	0	35	1.03
4917102--4917153	23	2.2	23	86	6	68	69	1	0	28	0.99
4917812--4917867	27	2.0	29	82	6	71	55	8	3	32	1.48
4918441--4918554	59	1.9	59	81	16	139	49	0	1	48	1.17
4918520--4918576	22	2.8	20	82	14	73	52	0	0	47	1.00
4919137--4919188	22	2.3	23	74	12	54	40	0	0	59	0.97
4928054--4928128	23	3.5	22	76	20	56	49	0	1	49	1.09
4935425--4935477	23	2.5	22	84	9	65	0	24	0	75	0.80
4935422--4935477	20	2.6	23	80	11	73	0	23	0	76	0.78
4935759--4935823	19	3.6	17	76	23	55	53	0	0	46	1.00
4935782--4935837	21	2.7	19	86	10	67	58	0	0	41	0.98
4935977--4936002	2	13.0	2	100	0	52	50	0	0	50	1.00
4943324--4943355	8	3.8	9	84	16	50	18	0	0	81	0.70
4943324--4943355	12	2.5	13	90	10	57	18	0	0	81	0.70
4949697--4949763	31	2.1	33	83	5	84	31	0	17	50	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4949739--4949778	15	2.7	15	88	7	55	32	0	25	42	1.55
4954792--4954849	27	2.1	27	90	0	89	25	41	1	31	1.66
4955122--4955500	75	5.0	75	90	0	560	29	8	21	40	1.83
4955311--4955438	39	3.4	39	69	10	120	28	9	19	42	1.82
4956145--4956193	23	2.1	23	88	0	71	34	6	0	59	1.22
4957064--4957123	32	1.9	30	83	6	75	41	13	8	36	1.74
4958060--4958194	66	2.0	67	84	1	173	29	14	25	31	1.94
4958369--4958395	2	13.5	2	100	0	54	48	0	0	51	1.00
4963753--4963787	2	17.5	2	100	0	70	51	0	0	48	1.00
4967695--4967737	2	21.5	2	95	0	77	51	0	46	2	1.13
4968658--4968699	16	2.6	16	88	7	59	40	0	4	54	1.21
4968700--4968869	16	10.1	16	67	18	78	44	1	3	50	1.29
4968673--4968766	41	2.3	40	79	15	104	44	0	2	53	1.12
4968720--4968778	25	2.3	26	74	8	68	47	1	0	50	1.11
4968797--4968928	27	4.5	28	67	19	81	43	4	3	48	1.38
4972216--4972253	2	19.0	2	100	0	76	0	50	0	50	1.00
4973836--4973906	23	3.0	23	79	16	76	59	0	0	40	0.98
4974624--4974674	18	2.8	18	80	14	59	54	1	7	35	1.40
4978812--4978836	2	12.5	2	100	0	50	48	0	0	52	1.00
4979471--4979516	23	2.0	23	83	8	58	76	4	0	19	0.96
4989812--4989852	15	2.6	16	84	7	57	39	0	0	60	0.96
4991313--4991539	114	2.0	112	87	4	330	25	18	15	39	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4996912--4996944	2	16.5	2	100	0	66	0	48	0	51	1.00
5005488--5005536	18	2.6	18	80	6	53	36	0	0	63	0.95
5005521--5005595	34	2.3	31	81	6	87	45	2	0	52	1.15
5005500--5005597	11	8.9	11	71	19	71	43	2	0	54	1.12
5006006--5006067	30	2.0	30	87	9	90	62	0	0	37	0.95
5006006--5006063	18	3.5	17	80	17	61	62	0	0	37	0.96
5006484--5006531	20	2.5	20	86	3	62	43	0	0	56	0.99
5007452--5007567	40	2.9	40	80	1	142	27	12	5	55	1.58
5007486--5007561	20	3.8	21	77	16	72	27	11	3	56	1.53
5008373--5008404	11	2.8	12	90	9	50	56	0	0	43	0.99
5009940--5010034	44	2.2	44	96	1	174	27	24	0	48	1.51
5013751--5013811	29	2.0	31	87	6	90	47	8	18	26	1.76
5013826--5013875	9	5.9	9	76	9	52	42	0	2	56	1.11
5014197--5014264	21	3.3	20	75	19	68	54	0	0	45	0.99
5017901--5017943	13	3.2	13	80	12	52	51	0	0	48	1.00
5018476--5018537	24	2.5	25	75	21	60	50	0	0	50	1.00
5018485--5018537	23	2.2	24	81	12	65	47	0	0	52	1.00
5020954--5021621	1	668.0	1	99	0	1309	99	0	0	0	0.05
5022053--5022101	18	2.6	18	80	6	53	36	0	0	63	0.95
5022086--5022178	34	3.0	31	76	11	91	44	2	0	53	1.12
5022065--5022162	11	8.9	11	71	19	71	43	2	0	54	1.12
5022087--5022173	11	7.6	11	74	13	52	41	2	0	56	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5022578--5022669	17	5.5	17	67	20	68	59	1	0	39	1.04
5022570--5022632	30	2.0	31	85	11	85	61	0	0	38	0.96
5022570--5022628	17	3.5	17	82	15	70	61	0	0	38	0.96
5023050--5023097	20	2.5	20	86	3	62	43	0	0	56	0.99
5024015--5024127	20	5.7	20	73	11	97	30	9	2	56	1.45
5024017--5024132	40	2.9	40	78	1	142	29	11	3	56	1.51
5024058--5024124	22	3.2	21	70	19	50	28	10	1	59	1.39
5024937--5024968	11	2.8	12	90	9	50	56	0	0	43	0.99
5026504--5026598	44	2.2	44	96	1	174	27	24	0	48	1.51
5030378--5030427	9	5.9	9	76	9	52	42	0	2	56	1.11

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