genome.fa.s2.2.7.7.80.10.50.1000.23.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  23  of  38  ( 4457 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)
3537436--3537461	13	2.0	13	100	0	52	30	15	15	38	1.88
3540010--3540074	13	5.0	13	94	0	112	35	15	18	30	1.92
3540010--3540073	26	2.5	26	100	0	128	34	15	18	31	1.93
3540060--3540138	20	3.7	20	78	15	77	44	15	15	25	1.85
3542153--3542183	15	2.1	15	93	0	53	12	22	16	48	1.80
3543962--3544006	21	2.1	21	84	8	56	22	20	4	53	1.63
3546224--3546249	13	2.0	13	100	0	52	30	15	15	38	1.88
3549086--3549110	13	1.9	13	100	0	50	36	16	8	40	1.77
3553322--3553348	13	2.1	13	100	0	54	29	14	14	40	1.86
3557437--3557488	21	2.4	22	90	6	88	38	9	23	28	1.86
3557534--3557670	53	2.6	53	91	1	229	27	16	18	37	1.92
3557640--3557710	20	3.5	20	77	11	74	29	14	16	39	1.88
3557750--3557790	21	2.0	21	85	9	57	39	9	12	39	1.76
3559897--3559951	20	2.8	20	77	0	56	41	12	12	32	1.81
3568412--3568652	79	3.1	79	93	2	387	32	16	25	25	1.96
3568412--3568699	79	3.6	79	89	4	379	32	15	26	25	1.96
3568631--3568729	51	1.9	51	81	4	119	34	14	24	27	1.94
3568783--3568942	50	3.2	50	82	3	187	40	11	21	26	1.87
3572361--3572415	20	2.8	20	77	0	65	34	7	12	45	1.70
3572332--3572485	71	2.2	70	87	3	220	29	14	12	42	1.83
3572432--3572485	20	2.7	20	97	0	99	35	16	11	37	1.84
3576292--3576376	27	3.0	29	71	15	79	31	28	20	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3576296--3576480	56	3.3	56	83	2	185	35	24	16	23	1.94
3576076--3576472	28	14.2	28	65	11	98	34	22	17	25	1.96
3577228--3577275	20	2.3	20	82	3	60	43	12	14	29	1.82
3577335--3577387	20	2.7	20	85	2	72	28	9	11	50	1.69
3579756--3580063	158	1.9	158	84	3	415	31	26	9	32	1.88
3579745--3580123	79	4.8	80	78	8	373	30	27	10	31	1.90
3581667--3581706	21	1.9	21	89	0	62	45	0	0	55	0.99
3581870--3582349	155	3.1	156	84	2	599	38	19	15	26	1.91
3583195--3583628	156	2.8	156	81	2	503	43	19	10	26	1.83
3584655--3585091	154	2.8	152	79	9	463	50	9	7	33	1.61
3585766--3585867	43	2.4	43	80	11	111	46	17	19	16	1.85
3585862--3585909	24	2.0	24	88	8	71	37	12	31	18	1.88
3585886--3585987	42	2.4	42	81	4	116	44	17	20	17	1.87
3585776--3585988	110	1.9	110	83	5	270	44	15	22	17	1.87
3585886--3586407	86	6.1	84	75	6	300	40	16	23	19	1.91
3586352--3586449	51	1.9	51	80	0	115	40	14	23	21	1.90
3585886--3586490	43	13.9	43	72	9	257	40	16	23	19	1.91
3586561--3586692	44	3.2	41	76	9	110	43	16	23	16	1.88
3586818--3587009	41	4.9	41	73	10	159	41	14	27	16	1.87
3586719--3586989	120	2.2	121	80	3	278	43	15	24	16	1.86
3586832--3587017	78	2.4	79	79	2	205	40	15	26	17	1.89
3586766--3587009	41	6.2	39	72	12	126	43	15	24	16	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3590657--3590708	19	2.7	20	87	6	79	42	15	13	28	1.85
3592687--3592728	18	2.3	19	87	4	59	71	2	9	16	1.23
3593679--3593730	19	2.7	20	87	6	79	42	15	13	28	1.85
3596963--3597030	29	2.2	31	82	12	79	30	27	13	27	1.94
3597207--3597271	33	2.0	32	88	8	96	24	30	9	35	1.87
3597296--3597520	32	7.2	32	72	14	166	28	32	19	20	1.97
3597400--3597518	63	1.9	63	82	6	152	31	30	22	15	1.95
3597305--3597531	33	7.2	32	71	17	115	28	31	20	19	1.97
3597889--3597973	42	2.0	42	82	13	102	23	24	23	28	2.00
3597845--3598016	97	1.8	89	84	9	227	24	24	19	31	1.98
3653789--3654096	158	1.9	158	84	3	415	31	26	9	32	1.88
3653778--3654156	79	4.8	80	78	8	373	30	27	10	31	1.90
3655700--3655739	21	1.9	21	89	0	62	45	0	0	55	0.99
3655903--3656382	155	3.1	156	84	2	599	38	19	15	26	1.91
3657230--3657663	156	2.8	156	81	2	503	43	19	10	26	1.83
3658690--3659126	154	2.8	152	79	9	463	50	9	7	33	1.61
3659800--3659901	43	2.4	43	80	11	111	46	17	19	16	1.85
3659896--3659943	24	2.0	24	88	8	71	37	12	31	18	1.88
3659920--3660021	42	2.4	42	81	4	116	44	17	20	17	1.87
3659810--3660022	110	1.9	110	83	5	270	44	15	22	17	1.87
3659920--3660525	43	13.9	43	74	7	258	40	16	23	19	1.91
3659920--3660442	86	6.1	84	75	6	300	40	16	23	19	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3660387--3660484	51	1.9	51	80	0	115	40	14	23	21	1.90
3660596--3660727	44	3.2	41	76	9	110	43	16	23	16	1.88
3660853--3661045	41	4.9	41	73	9	159	41	14	26	16	1.87
3660754--3661025	120	2.2	121	80	3	278	44	15	24	16	1.86
3660867--3661053	79	2.4	79	79	1	205	41	15	26	17	1.89
3660914--3661375	201	2.3	197	76	5	464	42	16	24	17	1.88
3665155--3665322	78	2.2	78	98	0	327	38	14	13	33	1.85
3666642--3666667	13	2.0	13	100	0	52	76	0	7	15	0.99
3666681--3666737	21	2.7	21	97	0	105	33	10	19	36	1.86
3666793--3666860	19	3.9	19	78	21	85	35	11	14	38	1.83
3666814--3666838	13	1.9	13	100	0	50	36	16	16	32	1.90
3666795--3666857	32	2.0	32	96	0	117	34	12	15	36	1.86
3666900--3666925	13	2.0	13	100	0	52	30	15	15	38	1.88
3666880--3666946	33	2.0	33	88	0	98	25	14	16	43	1.86
3669453--3669623	51	3.3	51	80	4	207	29	25	11	33	1.91
3669606--3669687	28	2.9	28	82	7	96	24	31	17	26	1.97
3675879--3675930	19	2.7	20	87	6	79	42	15	13	28	1.85
3678904--3678955	19	2.7	20	87	6	79	42	15	13	28	1.85
3682180--3682263	30	2.8	29	81	15	100	28	26	15	29	1.96
3682207--3682325	31	3.8	32	81	10	147	26	27	15	31	1.95
3682356--3682512	33	4.7	34	75	19	132	22	31	11	35	1.90
3682332--3682514	101	1.8	100	85	3	260	21	31	12	34	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3682522--3682800	33	8.6	33	87	5	392	28	32	17	21	1.96
3682531--3682800	65	4.2	64	88	4	391	28	32	18	20	1.96
3682522--3682793	131	2.1	131	90	2	429	27	32	18	21	1.96
3682793--3683260	49	9.7	49	77	12	479	25	25	17	32	1.96
3682788--3683260	92	5.0	92	86	7	626	24	25	16	32	1.96
3682974--3683316	104	3.4	102	80	12	395	24	24	16	34	1.96
3683170--3683269	52	1.9	52	87	0	146	24	23	17	36	1.95
3683896--3683957	32	1.9	32	90	3	97	33	9	19	37	1.84
3684002--3684026	13	1.9	13	100	0	50	32	16	16	36	1.90
3684015--3684163	52	2.9	52	88	4	221	34	18	16	30	1.93
3691654--3691690	16	2.4	16	90	4	58	78	10	2	8	1.06
3693042--3693175	27	4.5	28	74	17	101	20	38	15	25	1.92
3693000--3693114	60	1.9	60	85	5	160	22	36	13	26	1.92
3692995--3693344	34	10.9	32	72	16	230	20	35	13	31	1.91
3692995--3693218	94	2.4	94	86	6	299	19	35	13	31	1.91
3693093--3693266	61	2.7	62	85	5	224	20	35	13	30	1.91
3693155--3693363	100	2.1	99	90	1	328	20	35	12	31	1.90
3693354--3693702	32	10.9	32	90	1	522	28	36	18	15	1.92
3693691--3694901	92	12.7	92	78	13	862	24	26	17	31	1.97
3693703--3694901	49	25.1	49	78	10	1130	24	25	17	31	1.97
3693703--3694901	190	6.3	187	76	13	850	24	25	17	31	1.97
3694691--3694892	104	1.9	104	87	0	296	22	22	18	36	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3695622--3695647	13	2.0	13	100	0	52	38	15	15	30	1.88
3695603--3695667	33	2.0	33	87	6	96	41	16	13	27	1.87
3703917--3703962	21	2.2	20	81	11	58	32	19	4	43	1.71
3706273--3706326	20	2.6	21	82	2	65	35	11	20	33	1.88
3706377--3706401	13	1.9	13	100	0	50	32	16	20	32	1.94
3706357--3706421	33	2.0	33	87	6	96	40	16	15	27	1.89
3707602--3707686	20	4.7	19	75	20	92	35	11	16	36	1.85
3707603--3707667	33	2.0	33	96	0	121	36	12	16	33	1.87
3707717--3707741	13	1.9	13	100	0	50	32	16	16	36	1.90
3707750--3707880	52	2.5	52	88	0	208	35	19	16	29	1.93

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