genome.fa.s4.2.7.7.80.10.50.1000.19.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  19  of  31  ( 3628 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)
4258454--4258538	32	2.7	32	78	12	88	32	0	0	67	0.91
4260003--4260045	23	1.9	23	85	4	61	44	4	0	51	1.22
4260078--4260144	32	2.1	32	81	10	75	35	1	4	58	1.28
4262647--4262684	13	2.9	13	77	14	51	50	0	5	44	1.24
4266895--4266939	19	2.2	21	88	7	67	28	0	0	71	0.87
4267265--4267303	2	19.5	2	89	0	60	48	5	0	46	1.24
4267797--4267849	20	2.8	20	80	11	58	54	1	0	43	1.11
4267781--4267836	22	2.5	23	71	23	57	50	1	0	48	1.11
4267834--4267877	9	5.0	9	86	13	65	75	0	0	25	0.81
4267824--4267877	17	3.1	17	91	2	81	72	0	0	27	0.85
4268629--4268653	2	12.5	2	100	0	50	48	0	0	52	1.00
4268658--4268699	21	2.0	20	90	4	66	42	0	0	57	0.99
4268654--4268780	27	4.4	27	67	20	69	41	0	0	57	1.04
4268689--4268735	15	2.9	17	73	23	55	51	0	0	48	1.00
4268689--4268759	32	2.2	32	85	7	90	47	0	1	50	1.09
4268745--4268777	11	3.0	11	91	8	50	36	0	0	63	0.95
4269875--4269902	2	14.0	2	100	0	56	50	0	0	50	1.00
4270230--4270292	27	2.3	27	79	15	76	55	1	0	42	1.09
4270722--4270760	11	3.5	11	82	6	51	51	0	0	48	1.00
4270725--4270789	25	2.5	28	85	14	86	47	1	0	50	1.10
4271948--4271979	6	5.3	6	96	0	55	59	18	21	0	1.38
4276661--4276691	5	6.2	5	92	0	53	3	19	0	77	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4278606--4278658	27	2.0	27	88	0	79	47	0	1	50	1.12
4278960--4279000	6	6.7	6	97	2	73	14	2	0	82	0.76
4279129--4279158	14	2.1	14	93	0	51	53	0	0	46	1.00
4279183--4279243	25	2.5	25	76	12	72	54	0	1	44	1.10
4282024--4282068	3	15.0	3	100	0	90	33	0	0	66	0.92
4283164--4283201	19	2.1	19	90	5	60	47	2	0	50	1.15
4283895--4283947	2	27.0	2	88	3	81	49	0	0	50	1.00
4284845--4284875	2	15.5	2	100	0	62	48	0	0	51	1.00
4285796--4285852	27	2.1	27	83	0	69	38	3	21	36	1.70
4285903--4285935	9	3.7	9	95	0	57	45	18	33	3	1.65
4290575--4290631	27	2.1	27	86	0	78	40	3	19	36	1.69
4290682--4290714	9	3.7	9	95	0	57	45	18	33	3	1.65
4292940--4292980	20	2.0	20	85	0	55	51	0	0	48	1.00
4293865--4293911	2	23.5	2	100	0	94	48	0	0	51	1.00
4294140--4294180	2	20.5	2	94	0	73	51	0	2	46	1.14
4295104--4295129	5	5.2	5	100	0	52	19	0	80	0	0.71
4295413--4295446	18	1.9	17	88	5	50	55	0	5	38	1.24
4306553--4306592	2	20.0	2	100	0	80	50	0	0	50	1.00
4306961--4307020	24	2.5	24	78	8	68	53	0	0	46	1.00
4306968--4307037	35	2.1	32	81	7	77	51	0	0	48	1.00
4307726--4307754	3	9.7	3	100	0	58	65	0	0	34	0.93
4308445--4308484	21	2.0	21	90	5	64	47	0	2	50	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4310417--4310538	24	5.2	24	75	17	98	39	0	0	59	1.09
4310477--4310518	11	3.8	11	78	12	50	30	0	0	69	0.89
4310472--4310529	22	2.7	22	76	12	66	34	0	0	65	0.93
4310501--4310542	15	2.9	15	80	16	52	38	0	0	61	0.96
4310755--4310799	17	2.6	17	83	13	56	44	0	0	55	0.99
4310769--4310808	21	2.0	21	85	5	55	45	0	0	55	0.99
4313510--4313554	18	2.6	17	82	6	54	20	0	46	33	1.51
4313564--4314150	303	1.9	305	87	2	860	32	13	20	34	1.91
4327921--4327968	24	2.0	23	84	11	62	50	25	25	0	1.50
4328761--4328789	12	2.5	12	94	5	51	44	34	0	20	1.52
4334068--4334217	37	4.1	37	100	0	300	40	8	32	18	1.80
4339243--4339285	19	2.2	19	83	8	50	62	0	0	37	0.95
4340227--4340293	16	3.9	17	73	13	57	38	1	0	59	1.06
4340642--4340668	14	1.9	14	100	0	54	51	3	0	44	1.19
4341009--4341049	20	2.0	22	90	9	68	53	0	2	43	1.13
4341210--4341272	18	3.6	18	71	18	51	53	0	0	46	1.00
4341554--4341585	17	1.9	17	93	6	57	21	0	0	78	0.76
4341767--4341807	15	2.8	15	82	14	50	63	0	4	31	1.15
4346702--4346727	7	3.7	7	100	0	52	69	0	0	30	0.89
4346709--4346785	29	2.6	29	85	2	109	54	7	1	36	1.38
4354934--4354992	31	1.9	31	85	0	82	38	3	22	35	1.71
4355975--4356034	15	3.8	15	78	20	52	55	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4356374--4356406	17	1.9	17	88	11	50	30	0	0	69	0.88
4356631--4356655	2	12.5	2	100	0	50	52	0	0	48	1.00
4357004--4357057	25	2.1	26	83	10	67	50	1	0	48	1.11
4358991--4359059	37	2.0	33	88	11	102	46	13	10	30	1.75
4360823--4360862	2	20.0	2	84	0	53	50	2	0	47	1.14
4362446--4362527	14	6.4	13	69	17	55	36	0	1	62	1.03
4362459--4362526	33	2.0	36	85	8	97	33	0	1	64	1.02
4362467--4362532	19	3.6	17	74	11	60	34	0	1	63	1.04
4363377--4363419	18	2.2	20	92	8	72	20	4	0	74	1.00
4364076--4364113	15	2.5	15	83	16	51	76	0	0	23	0.79
4364354--4364403	22	2.3	21	86	3	73	54	0	0	46	1.00
4365540--4365613	29	2.7	27	75	17	80	47	0	0	52	1.00
4365878--4365951	19	3.9	17	75	20	60	51	0	1	47	1.09
4365877--4365931	24	2.3	24	78	6	58	54	0	0	45	0.99
4365880--4365941	20	2.7	23	74	23	60	53	0	0	46	1.00
4365947--4365993	21	2.3	21	85	10	62	55	0	0	44	0.99
4365954--4366003	21	2.4	22	80	10	59	60	0	2	38	1.09
4366884--4366963	30	2.5	35	76	21	93	42	0	0	57	0.98
4366861--4366963	19	5.1	19	68	23	68	41	0	0	58	0.98
4366855--4366964	44	2.5	44	77	21	122	42	0	0	57	0.98
4366980--4367051	15	4.4	18	78	18	61	38	1	0	59	1.06
4366988--4367051	14	4.4	14	81	11	67	40	0	0	59	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4367363--4367788	231	1.9	221	79	12	479	34	7	7	49	1.61
4369667--4369705	2	19.5	2	100	0	78	48	0	0	51	1.00
4372854--4372906	26	2.0	28	85	7	74	30	3	0	66	1.10
4377497--4377553	20	2.8	20	77	17	55	35	3	3	57	1.33
4379883--4379952	14	4.6	14	70	16	59	47	4	2	45	1.37
4379868--4379957	47	1.9	47	95	0	162	46	4	3	45	1.39
4380649--4380679	2	15.5	2	100	0	62	51	0	0	48	1.00
4383047--4383085	2	19.5	2	100	0	78	48	0	0	51	1.00
4384473--4384505	17	2.1	17	88	11	52	45	0	0	54	0.99
4385751--4385793	17	2.5	17	82	17	54	48	6	0	44	1.29
4385964--4386000	18	1.9	19	89	10	58	56	2	0	40	1.13
4386202--4386293	10	9.0	11	78	13	67	71	1	26	1	0.99
4386243--4386267	6	4.2	6	100	0	50	68	0	32	0	0.90
4386215--4386291	26	3.1	26	78	14	74	74	1	23	1	0.97
4393758--4393796	2	19.5	2	94	0	69	2	0	48	48	1.15
4402115--4402179	35	1.9	35	87	6	98	50	0	0	49	1.00
4402172--4402251	35	2.3	33	81	8	88	51	0	1	47	1.08
4402173--4402256	34	2.4	34	77	16	84	50	0	1	48	1.08
4404550--4404593	15	3.0	14	80	9	52	79	2	18	0	0.83
4404550--4404589	21	1.9	21	90	10	64	77	2	20	0	0.88
4405680--4405741	13	4.3	15	77	18	62	46	0	0	53	1.00
4406015--4406046	3	10.3	3	93	6	55	31	3	0	65	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4406742--4406807	30	2.2	31	83	8	91	46	3	10	39	1.54
4406742--4406822	30	2.7	29	81	7	90	45	2	12	39	1.55
4407813--4407851	18	2.3	17	86	8	53	33	0	5	61	1.18
4409893--4409972	42	2.0	42	85	5	110	55	6	20	18	1.64
4410115--4410183	28	2.5	29	79	9	83	55	2	0	42	1.15
4414566--4414637	35	2.1	35	89	5	110	62	1	6	29	1.30
4414570--4414645	35	2.1	35	87	2	107	61	1	3	32	1.22
4414709--4414945	109	2.1	111	83	5	284	40	8	11	39	1.72
4414993--4415022	2	15.5	2	93	6	53	50	0	0	50	1.00
4415539--4415573	7	4.9	7	89	3	52	42	0	0	57	0.99

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