genome.fa.s2.2.7.7.80.10.50.1000.26.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  26  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)
3976931--3976997	33	2.0	33	88	0	98	25	14	16	43	1.86
3979503--3979673	51	3.3	51	80	4	207	29	25	11	33	1.91
3979656--3979737	28	2.9	28	82	7	96	24	31	17	26	1.97
3982228--3982297	34	2.1	34	91	0	113	42	18	11	27	1.84
3984707--3985254	156	3.5	157	79	8	555	39	22	16	21	1.92
3986835--3986895	27	2.2	28	82	8	72	77	6	0	16	0.98
3986835--3986897	29	2.3	27	83	10	74	76	6	0	17	0.99
3988614--3989281	79	8.6	78	72	12	399	27	25	13	33	1.93
3988606--3989281	158	4.3	157	83	3	753	28	25	13	33	1.93
3989100--3989233	70	1.9	70	83	3	171	26	27	11	34	1.91
3989190--3989335	78	1.9	79	84	4	197	27	28	13	30	1.94
3990984--3991051	19	3.9	19	78	21	85	33	13	14	38	1.85
3991005--3991029	13	1.9	13	100	0	50	36	16	16	32	1.90
3990986--3991048	32	2.0	32	96	0	117	33	14	15	36	1.88
3991091--3991116	13	2.0	13	100	0	52	30	15	15	38	1.88
3991071--3991137	33	2.0	33	88	0	98	25	14	16	43	1.86
3993595--3993667	27	2.7	27	87	6	94	23	34	21	20	1.97
3993650--3993820	51	3.3	51	79	4	198	29	26	11	32	1.92
3993803--3993884	28	2.9	28	82	7	96	24	31	17	26	1.97
4000005--4000788	55	13.9	54	80	10	802	27	29	20	22	1.99
3999999--4000788	110	7.0	110	82	9	928	27	29	20	22	1.99
3999999--4000788	165	4.7	165	81	11	898	27	29	20	22	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4001687--4001747	27	2.2	28	82	8	72	77	6	0	16	0.98
4001687--4001749	29	2.3	27	83	10	74	76	6	0	17	0.99
4003466--4004132	79	8.6	77	71	14	377	28	25	13	33	1.93
4003458--4004132	158	4.3	157	83	3	744	28	25	13	33	1.93
4004041--4004186	78	1.9	79	84	4	197	27	28	13	30	1.94
4005835--4005902	19	3.9	19	78	21	85	33	13	14	38	1.85
4005856--4005880	13	1.9	13	100	0	50	36	16	16	32	1.90
4005837--4005899	32	2.0	32	96	0	117	33	14	15	36	1.88
4005942--4005967	13	2.0	13	100	0	52	30	15	15	38	1.88
4005922--4005988	33	2.0	33	88	0	98	25	14	16	43	1.86
4008446--4008518	27	2.7	27	87	6	94	23	34	21	20	1.97
4008501--4008671	51	3.3	51	77	4	189	28	26	11	32	1.92
4008654--4008735	28	2.9	28	82	7	96	24	31	17	26	1.97
4010467--4010893	167	2.6	164	82	7	513	51	10	11	27	1.70
4010467--4010933	166	2.8	167	83	6	554	51	10	11	26	1.70
4013042--4013066	13	1.9	13	100	0	50	36	16	16	32	1.90
4013022--4013090	32	2.1	33	86	2	95	36	11	15	36	1.84
4013128--4013152	13	1.9	13	100	0	50	32	16	16	36	1.90
4013141--4013289	52	2.9	51	83	4	190	34	18	16	30	1.92
4014580--4014631	19	2.7	20	87	6	79	42	15	13	28	1.85
4018669--4018699	15	2.1	15	93	0	53	48	16	22	12	1.80
4020778--4020815	13	2.9	13	96	0	67	34	18	15	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4024901--4024936	13	2.8	13	91	0	63	30	11	19	38	1.86
4025047--4025096	21	2.4	22	83	9	61	32	20	0	48	1.50
4026914--4026987	21	3.5	21	85	3	96	35	13	16	35	1.88
4027023--4027090	19	3.9	19	78	21	85	35	11	14	38	1.83
4027044--4027068	13	1.9	13	100	0	50	36	16	16	32	1.90
4027025--4027087	32	2.0	32	96	0	117	34	12	15	36	1.86
4027130--4027155	13	2.0	13	100	0	52	30	15	15	38	1.88
4027110--4027176	33	2.0	33	88	0	98	25	14	16	43	1.86
4029626--4029698	27	2.7	27	85	6	94	23	31	21	23	1.98
4029681--4029855	52	3.3	52	79	3	208	29	27	12	31	1.92
4041934--4042059	51	2.4	50	81	7	144	32	23	11	31	1.91
4042046--4042115	27	2.5	28	86	9	99	27	31	20	21	1.98
4042101--4042273	52	3.3	52	79	6	197	30	26	11	31	1.91
4041934--4042273	105	3.2	102	72	10	299	30	26	12	31	1.92
4041929--4042381	212	2.1	212	86	4	646	29	27	13	30	1.94
4042284--4042487	78	2.6	79	82	3	234	24	30	16	28	1.97
4043801--4043857	19	2.9	19	81	2	69	33	14	15	36	1.88
4043907--4043931	13	1.9	13	100	0	50	36	16	16	32	1.90
4044691--4044812	35	3.5	35	86	0	145	45	11	22	20	1.82
4054819--4054972	52	3.0	52	85	1	211	28	14	19	37	1.92
4054991--4055055	19	3.7	19	75	23	79	38	16	12	32	1.86
4054986--4055053	32	2.1	32	97	0	127	36	17	11	33	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4055010--4055034	13	1.9	13	100	0	50	32	16	16	36	1.90
4061143--4061195	19	2.6	20	91	8	81	26	11	15	47	1.79
4061226--4061299	20	3.7	20	82	8	78	29	17	13	39	1.88
4063724--4063775	20	2.6	20	87	6	70	46	17	13	23	1.83
4065792--4065822	15	2.1	15	93	0	53	12	22	16	48	1.80
4069890--4069915	13	2.0	13	100	0	52	30	15	15	38	1.88
4069869--4069933	32	2.0	33	90	6	105	26	12	15	46	1.81
4069964--4070037	20	3.7	20	82	8	78	29	17	13	39	1.88
4074459--4074587	52	2.5	52	96	2	233	29	18	17	34	1.94
4074459--4074607	52	2.9	52	86	7	205	31	17	17	33	1.93
4074596--4074620	13	1.9	13	100	0	50	36	16	16	32	1.90
4074663--4074742	19	4.5	19	77	17	100	36	15	12	36	1.85
4074701--4074757	13	3.9	13	76	24	60	33	15	14	36	1.88
4074682--4074777	32	3.0	32	93	1	165	34	16	13	35	1.88
4075411--4075979	55	10.7	54	74	14	314	36	14	23	25	1.93
4075461--4075783	174	1.9	172	82	3	407	37	14	22	25	1.92
4075684--4076162	92	5.0	92	86	7	652	32	17	24	25	1.96
4075693--4076145	49	9.4	49	79	11	501	32	17	23	25	1.97
4076165--4076381	33	6.8	32	83	8	257	16	17	35	29	1.92
4076165--4076389	65	3.5	64	86	6	330	16	17	37	29	1.91
4076396--4077183	31	23.8	34	76	12	684	31	14	33	20	1.92
4076391--4077183	100	8.0	100	79	11	562	32	14	33	19	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4076391--4077178	131	6.0	128	78	11	556	32	14	33	20	1.92
4076396--4077183	331	2.4	328	88	3	1138	31	14	33	20	1.92
4078428--4078463	18	2.1	17	89	5	54	0	0	16	83	0.65
4085193--4085321	52	2.5	52	96	0	231	28	17	17	35	1.93
4085330--4085354	13	1.9	13	100	0	50	36	16	16	32	1.90
4085376--4085524	19	8.7	19	72	25	109	36	16	12	34	1.87
4085414--4085502	13	5.9	13	72	27	70	33	17	13	34	1.89
4085395--4085522	32	4.0	32	97	1	238	34	17	13	34	1.89
4086156--4086724	55	10.7	54	75	13	350	35	14	24	25	1.94
4086155--4086890	49	14.4	52	73	14	285	33	16	24	25	1.95
4086438--4086907	49	9.8	49	79	11	508	32	18	24	24	1.97
4086438--4086907	92	4.9	92	87	6	670	32	18	24	24	1.97
4086910--4087124	33	6.8	32	82	8	244	17	17	35	29	1.93
4086910--4087124	65	3.4	64	84	7	285	17	17	35	29	1.93
4088040--4088107	32	2.1	32	94	0	118	36	16	11	35	1.85
4088064--4088088	13	1.9	13	100	0	50	32	16	16	36	1.90
4088045--4088128	19	4.7	19	80	18	99	36	16	11	34	1.86
4088679--4089128	142	3.2	139	78	7	434	42	10	10	36	1.73
4088742--4089128	142	2.8	140	81	7	441	43	9	9	37	1.70
4091175--4091200	13	2.0	13	100	0	52	38	15	15	30	1.88
4097290--4097368	20	3.7	20	69	18	59	29	15	16	39	1.89
4099887--4099912	13	2.0	13	100	0	52	38	15	15	30	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4099869--4099933	32	2.0	32	87	6	94	40	18	13	27	1.89
4099918--4100036	51	2.4	51	98	1	231	31	15	18	35	1.92
4102008--4102038	14	2.2	14	94	0	53	3	16	0	80	0.83
4102008--4102049	13	3.2	13	86	10	50	2	16	0	80	0.81
4105143--4105734	155	3.7	157	82	5	649	50	8	10	31	1.65
4107342--4107415	20	3.7	20	81	3	103	35	13	20	31	1.91
4107360--4107435	21	3.7	21	82	3	109	40	11	18	28	1.86
4107342--4107435	41	2.3	41	100	0	188	38	12	19	29	1.89
4107474--4107499	13	2.0	13	100	0	52	38	15	15	30	1.88
4111559--4111589	15	2.1	15	93	0	53	48	16	22	12	1.80

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