genome.fa.s3.2.7.7.80.10.50.1000.24.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  24  of  32  ( 3795 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)
4098724--4098803	34	2.2	36	82	10	94	62	0	0	37	0.95
4098720--4098796	11	7.0	11	72	19	63	62	0	0	37	0.96
4099021--4099063	19	2.3	18	84	4	50	39	0	0	60	0.97
4099132--4099170	18	2.2	18	85	0	51	46	0	0	53	1.00
4101487--4101539	3	17.7	3	96	0	97	66	0	1	32	1.03
4101792--4101839	25	1.9	25	91	8	80	41	12	4	41	1.62
4104114--4104149	19	2.0	17	89	10	54	47	0	0	52	1.00
4104107--4104188	16	5.3	15	69	22	53	43	1	0	54	1.07
4106073--4106135	29	2.2	29	94	0	108	41	9	14	34	1.78
4123960--4124016	28	2.0	28	83	6	71	56	0	0	43	0.99
4123980--4124043	23	2.9	22	75	9	67	54	0	0	45	0.99
4131651--4131680	2	15.0	2	100	0	60	50	0	0	50	1.00
4134929--4134984	7	8.0	7	79	13	62	39	0	0	60	0.97
4134952--4134994	21	2.0	22	90	4	70	30	0	0	69	0.88
4134954--4135002	21	2.3	21	85	3	62	30	0	4	65	1.11
4135780--4135823	16	2.8	16	83	16	56	52	0	0	47	1.00
4136433--4136469	13	2.7	14	80	20	51	43	0	0	56	0.99
4139314--4139347	15	2.4	14	90	9	52	52	0	0	47	1.00
4140487--4140534	14	3.4	14	82	2	60	62	0	0	37	0.95
4141264--4141337	26	3.0	26	76	7	73	51	0	1	47	1.09
4141542--4141575	2	17.5	2	93	6	61	50	0	0	50	1.00
4142494--4142518	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4142872--4142905	2	17.0	2	87	0	50	50	5	0	44	1.26
4144943--4144971	2	14.5	2	100	0	58	48	0	0	51	1.00
4148978--4149032	28	1.9	29	96	3	103	21	23	9	45	1.80
4152599--4152703	52	2.0	52	98	0	201	33	19	26	20	1.96
4153802--4153827	2	13.0	2	100	0	52	50	0	0	50	1.00
4156483--4156664	92	2.0	92	97	0	346	35	23	11	29	1.90
4161113--4161168	17	3.3	17	74	0	58	1	19	0	78	0.84
4161821--4161863	18	2.5	16	79	17	50	6	4	4	83	0.89
4163251--4163369	40	3.0	40	93	4	215	46	2	11	39	1.54
4163251--4163367	38	3.0	38	96	2	207	47	2	11	38	1.54
4164197--4164231	14	2.5	14	86	13	54	88	0	2	8	0.61
4165360--4165393	17	2.0	17	88	11	52	61	26	11	0	1.30
4171687--4171721	17	2.1	17	89	5	54	51	0	0	48	1.00
4171699--4171738	20	2.1	19	85	4	53	50	0	0	50	1.00
4172015--4172054	14	2.8	14	88	3	53	42	5	2	50	1.37
4172210--4172243	3	11.3	3	93	0	59	29	0	2	67	1.05
4177270--4177311	2	21.0	2	100	0	84	50	0	0	50	1.00
4181579--4181608	3	10.0	3	100	0	60	33	0	0	66	0.92
4184131--4184170	20	2.1	18	86	9	53	45	0	2	52	1.14
4185583--4185625	22	2.2	18	80	19	50	55	2	2	39	1.25
4185596--4185630	16	2.1	18	89	10	56	62	0	0	37	0.95
4185624--4185677	22	2.4	22	84	6	72	55	1	0	42	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4190288--4190312	12	2.1	12	100	0	50	0	0	8	92	0.40
4200320--4200361	2	21.0	2	100	0	84	50	0	0	50	1.00
4202030--4202097	20	3.5	19	74	18	59	47	0	0	52	1.00
4202030--4202130	34	2.8	37	77	19	97	40	0	0	59	0.97
4202903--4202947	21	2.0	24	83	12	60	42	0	0	57	0.98
4203542--4203587	18	2.5	19	79	6	51	47	0	0	52	1.00
4204341--4204443	52	2.0	52	90	3	163	26	16	31	26	1.97
4204875--4205104	78	2.9	78	83	1	273	23	13	34	29	1.93
4205048--4205306	130	2.0	130	83	4	324	23	15	34	26	1.94
4205440--4205565	26	4.9	26	70	11	98	20	18	37	23	1.94
4205406--4205625	77	2.8	77	82	5	237	22	17	33	27	1.96
4205642--4205703	26	2.4	26	88	0	88	25	17	38	17	1.92
4205719--4205771	26	2.0	26	85	0	70	33	13	28	24	1.93
4205752--4205875	52	2.4	52	83	0	140	29	18	27	24	1.98
4205636--4206216	207	2.8	206	75	8	559	28	16	29	25	1.97
4205920--4205979	26	2.3	26	88	2	86	30	15	31	23	1.95
4205966--4206083	52	2.3	51	83	4	146	26	18	30	24	1.98
4206004--4206214	78	2.7	77	85	4	255	27	17	31	24	1.97
4206325--4206355	15	2.0	16	93	6	55	41	6	32	19	1.77
4208526--4208724	98	2.0	98	100	0	398	32	21	18	28	1.96
4214251--4214293	22	2.0	22	90	0	68	51	0	2	46	1.13
4216787--4216839	22	2.4	21	84	12	63	35	1	0	62	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4216785--4216848	21	2.9	22	82	13	71	37	1	0	60	1.06
4216785--4216849	22	2.8	22	77	11	60	38	1	0	60	1.07
4216815--4216895	42	1.9	41	82	9	101	44	0	1	54	1.08
4220238--4220423	89	2.1	89	100	0	372	38	20	16	24	1.92
4223493--4223552	20	3.0	20	75	15	54	28	1	1	68	1.09
4223493--4223534	10	4.1	10	87	12	50	28	0	0	71	0.86
4225102--4225141	19	2.1	19	100	0	80	15	10	30	45	1.78
4231022--4231048	2	13.5	2	100	0	54	51	0	48	0	1.00
4231940--4232015	29	2.6	30	81	6	77	51	0	0	48	1.00
4232804--4232880	19	3.9	19	75	17	68	45	2	5	46	1.39
4232944--4233014	35	2.0	37	86	5	101	45	4	1	49	1.30
4233274--4233301	2	14.0	2	100	0	56	50	0	0	50	1.00
4240005--4240060	19	2.8	19	79	15	69	58	0	0	41	0.98
4240005--4240058	20	2.7	21	77	8	67	59	0	0	40	0.98
4240657--4240714	29	2.0	30	83	6	75	46	0	1	51	1.11
4240674--4240729	29	1.9	29	82	7	69	51	0	1	46	1.11
4242706--4242749	2	22.0	2	100	0	88	50	0	0	50	1.00
4247809--4247836	14	2.0	14	100	0	56	21	14	14	50	1.78
4249547--4249645	38	2.5	38	81	4	99	43	1	0	55	1.06
4249574--4249658	32	2.6	33	78	10	86	45	1	0	52	1.08
4249590--4249684	43	2.2	44	83	10	117	43	0	1	55	1.06
4249583--4249657	38	2.0	38	84	5	98	49	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4249616--4249700	44	1.9	44	83	4	109	44	2	1	51	1.21
4250448--4250482	13	2.8	12	87	8	52	85	11	2	0	0.69
4250448--4250482	12	2.9	12	91	0	52	85	11	2	0	0.69
4252966--4253041	35	2.2	35	95	0	134	52	3	10	32	1.54
4252966--4253025	20	3.2	20	64	22	58	53	5	10	31	1.56
4253203--4253235	16	2.1	16	88	5	50	51	0	0	48	1.00
4253263--4253306	23	1.9	23	85	0	61	47	0	0	52	1.00
4253823--4253898	16	4.8	16	70	20	52	51	0	1	47	1.09
4256905--4256939	2	17.5	2	100	0	70	51	0	0	48	1.00
4258505--4258587	42	2.0	41	82	13	100	46	0	0	53	1.00
4259738--4259776	3	13.0	3	100	0	78	66	0	0	33	0.92
4260470--4260531	18	3.7	18	72	24	64	50	0	0	50	1.00
4260486--4260536	23	2.3	22	83	12	61	47	0	0	52	1.00
4260504--4260553	19	2.6	20	71	9	50	42	0	0	58	0.98
4263033--4263085	26	2.0	27	85	7	72	47	0	0	52	1.00
4263819--4263863	21	2.1	22	83	4	56	57	0	0	42	0.98
4263858--4263895	18	2.2	18	85	4	51	39	10	0	50	1.37
4265048--4265129	36	2.2	38	85	10	107	57	0	1	41	1.06
4273086--4273115	3	10.0	3	100	0	60	66	0	0	33	0.92
4277080--4277126	23	2.0	23	95	0	85	25	10	14	48	1.76
4277747--4277814	11	5.8	12	72	26	56	41	0	1	57	1.08
4277742--4277795	21	2.6	21	77	11	74	37	0	3	59	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4278296--4278350	20	2.8	20	80	0	65	45	0	3	50	1.19
4278556--4278595	2	20.0	2	86	0	53	47	2	5	45	1.38
4279332--4279383	17	2.8	18	74	11	52	50	0	0	50	1.00
4281777--4281843	19	3.8	19	74	22	74	38	17	8	34	1.82
4281799--4281823	13	1.9	13	100	0	50	40	16	8	36	1.77
4281782--4281842	32	1.9	32	96	0	113	39	19	8	32	1.81
4283642--4283702	17	3.5	17	77	8	52	52	1	1	44	1.20
4285972--4286022	17	2.7	19	79	14	61	58	0	0	41	0.98
4291485--4291523	20	2.0	20	84	0	51	35	25	15	23	1.94
4294426--4294464	2	19.5	2	100	0	78	48	0	0	51	1.00

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