genome.fa.s11.2.7.7.80.10.50.1000.25.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  25  of  29  ( 3461 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)
4147768--4147797	2	15.0	2	100	0	60	50	0	0	50	1.00
4148263--4148302	21	1.9	21	85	10	55	40	0	0	60	0.97
4149536--4149613	30	2.6	29	81	4	93	52	2	5	39	1.37
4149667--4149695	15	1.9	15	100	0	58	27	0	0	72	0.85
4151506--4151723	34	6.5	34	85	5	282	40	27	7	24	1.82
4151504--4151723	67	3.3	67	88	1	323	40	27	7	24	1.82
4155787--4155849	19	3.3	19	90	0	90	34	19	17	28	1.94
4156151--4156367	34	6.4	34	81	6	244	41	26	7	25	1.81
4156149--4156367	68	3.2	67	84	1	285	41	26	7	25	1.81
4156149--4156367	102	2.2	101	87	5	316	41	26	7	25	1.81
4162312--4162350	3	13.0	3	100	0	78	33	0	0	66	0.92
4164096--4164122	2	13.5	2	100	0	54	48	0	0	51	1.00
4168497--4168542	23	1.9	25	86	8	69	13	21	2	63	1.40
4173847--4173898	26	2.0	26	100	0	104	26	19	15	38	1.91
4178727--4178781	7	8.1	7	80	15	55	30	0	0	69	0.89
4178723--4178780	11	5.0	11	77	10	53	29	0	0	70	0.87
4179386--4179446	28	2.2	27	83	16	72	54	0	0	45	1.00
4179383--4179448	19	3.3	19	76	23	73	50	0	0	50	1.00
4179374--4179459	38	2.3	38	78	11	97	47	0	0	52	1.00
4179417--4179476	22	2.8	23	71	21	58	46	0	0	53	1.00
4179798--4179900	45	2.3	45	77	15	106	53	4	1	39	1.33
4180717--4180759	14	3.1	14	80	12	52	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4181334--4181394	22	2.8	21	79	16	70	50	0	1	47	1.10
4181637--4181678	20	2.0	21	90	4	68	59	0	0	40	0.97
4181710--4181748	18	2.2	18	86	9	53	43	0	0	56	0.99
4181743--4181801	14	4.4	14	72	12	52	55	0	0	44	0.99
4181827--4181866	21	1.9	21	85	10	55	57	0	0	42	0.98
4181839--4181944	27	4.2	24	75	17	85	60	0	0	39	0.97
4181849--4181889	17	2.3	19	87	8	59	60	0	0	39	0.96
4181862--4181951	11	8.4	10	74	14	65	60	0	0	40	0.97
4181841--4181951	54	2.1	53	86	8	154	59	0	0	40	0.97
4181862--4181944	31	2.6	31	78	3	103	60	0	0	39	0.97
4181862--4181951	21	4.2	21	73	12	76	60	0	0	40	0.97
4186009--4186048	21	1.9	19	85	14	53	37	0	0	62	0.95
4188163--4188204	18	2.4	19	88	11	63	30	4	0	64	1.14
4188368--4188408	17	2.4	19	80	19	54	41	0	0	58	0.98
4188380--4188418	17	2.2	18	86	4	53	51	2	0	46	1.14
4188687--4188866	75	2.4	75	94	2	310	45	15	19	20	1.85
4190780--4190823	22	2.0	22	100	0	88	13	22	18	45	1.84
4192055--4192121	19	3.7	18	77	20	68	53	0	2	43	1.16
4192080--4192121	18	2.3	19	84	12	52	54	0	4	40	1.21
4192090--4192149	24	2.5	25	81	13	72	58	0	1	40	1.08
4195556--4195596	2	21.5	2	90	9	68	48	0	0	51	1.00
4196086--4196148	20	3.0	21	84	6	67	41	0	1	57	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4197499--4197547	24	2.0	24	84	7	64	71	0	2	26	0.97
4197783--4197825	21	2.0	21	91	8	70	27	27	11	32	1.92
4198088--4198160	22	4.1	18	75	24	66	38	0	1	60	1.06
4198088--4198153	18	3.3	19	81	16	64	37	0	1	60	1.06
4198747--4198785	20	2.0	20	85	5	53	46	0	2	51	1.14
4199250--4199286	10	3.7	10	88	0	56	54	0	0	45	1.00
4199574--4199617	12	3.4	12	81	12	52	45	0	0	54	0.99
4199574--4199626	27	2.0	28	88	7	83	49	0	0	50	1.00
4202232--4202302	35	2.0	35	81	10	83	57	0	1	40	1.07
4203871--4203906	3	12.0	3	100	0	72	66	0	0	33	0.92
4204959--4205004	22	2.0	23	84	12	60	60	0	2	36	1.09
4205748--4205806	3	19.7	3	89	0	91	66	0	3	30	1.08
4208460--4208494	3	11.7	3	100	0	70	65	0	0	34	0.93
4208952--4208980	14	2.1	14	100	0	58	44	0	6	48	1.29
4209993--4210046	25	2.1	26	86	6	74	55	0	0	44	0.99
4210070--4210362	147	2.0	147	91	2	484	39	7	5	46	1.56
4211307--4211368	22	2.8	22	70	15	56	53	0	0	46	1.00
4211811--4211869	3	19.7	3	100	0	118	66	0	0	33	0.92
4212965--4213006	22	1.9	22	90	0	66	50	0	2	47	1.14
4215392--4215426	2	17.5	2	100	0	70	48	0	0	51	1.00
4216065--4216108	2	22.5	2	95	4	81	50	0	0	50	1.00
4217285--4217377	32	2.8	32	82	15	109	60	2	1	36	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4217285--4217336	18	3.1	18	75	25	60	59	1	0	38	1.08
4217291--4217374	6	13.7	6	71	21	59	59	2	1	36	1.18
4217330--4217379	19	2.3	23	87	12	72	62	2	2	34	1.18
4219473--4219516	20	2.2	20	87	0	61	11	50	4	34	1.59
4219535--4219966	220	2.0	220	97	0	819	23	18	23	35	1.96
4222190--4222235	21	2.1	22	84	4	58	30	19	30	19	1.97
4223593--4223623	2	15.5	2	100	0	62	0	48	0	51	1.00
4227073--4227102	4	7.5	4	100	0	60	50	26	0	23	1.50
4238133--4238206	29	2.7	27	80	19	82	50	0	0	50	1.00
4238148--4238180	17	1.9	17	88	11	50	48	0	0	51	1.00
4239758--4239913	76	2.0	77	88	1	233	21	18	14	44	1.86
4253925--4254014	4	25.0	4	77	20	83	50	21	0	28	1.49
4253926--4254038	18	6.2	18	87	4	145	50	15	0	33	1.45
4253930--4254036	10	10.3	10	77	7	79	50	15	0	33	1.45
4254012--4254038	4	6.8	4	100	0	54	51	0	0	48	1.00
4253930--4254030	14	7.2	14	87	0	112	50	16	0	32	1.46
4254657--4254706	22	2.3	21	83	12	66	42	0	2	56	1.11
4254682--4254734	19	2.8	18	75	13	54	47	1	0	50	1.12
4254773--4254814	22	1.9	22	95	0	75	54	0	0	45	0.99
4264687--4264767	12	7.2	12	73	17	75	65	0	1	33	1.01
4264681--4264770	19	5.1	17	77	10	74	65	0	1	33	1.00
4265626--4265665	19	2.1	19	86	9	55	37	15	0	47	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4267102--4267131	15	1.9	16	93	6	53	63	0	3	33	1.11
4267322--4267373	24	2.1	25	85	3	70	67	0	1	30	1.02
4267596--4267636	21	1.9	22	85	14	59	60	0	7	31	1.24
4267676--4267725	26	1.9	26	84	8	66	50	4	2	44	1.32
4282091--4282115	3	8.3	3	100	0	50	32	0	32	36	1.58
4284662--4284693	2	16.0	2	100	0	64	50	0	0	50	1.00
4298264--4298288	2	12.5	2	100	0	50	52	48	0	0	1.00
4298288--4298312	2	12.5	2	100	0	50	52	0	0	48	1.00
4298372--4298409	19	2.0	19	94	0	67	57	0	2	39	1.12
4298423--4298464	12	3.3	12	86	6	57	33	0	0	66	0.92
4311100--4311130	3	10.3	3	100	0	62	67	0	0	32	0.91
4311473--4311508	12	3.0	12	91	0	54	55	2	0	41	1.14
4315746--4315803	14	4.0	16	75	18	56	44	0	0	55	0.99
4316152--4316198	24	2.0	24	86	0	67	51	0	0	48	1.00
4316421--4316453	3	11.0	3	100	0	66	66	0	0	33	0.92
4316611--4316655	3	15.0	3	100	0	90	66	0	0	33	0.92
4316836--4316880	18	2.3	20	85	7	58	20	4	6	68	1.29
4316932--4317003	23	3.2	22	75	9	65	37	1	6	54	1.36
4317125--4317171	18	2.6	18	86	3	58	55	0	0	44	0.99
4319523--4319553	3	10.3	3	100	0	62	67	0	0	32	0.91
4328356--4328380	2	12.5	2	100	0	50	52	0	0	48	1.00
4328572--4328605	2	17.0	2	93	0	59	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4328769--4328795	2	13.5	2	100	0	54	0	0	48	51	1.00
4329032--4329059	4	7.0	4	100	0	56	50	0	0	50	1.00
4329501--4329527	2	13.5	2	100	0	54	48	0	0	51	1.00
4344913--4344958	23	2.0	23	86	4	65	36	0	2	60	1.09
4346938--4346984	19	2.5	19	79	6	60	63	0	0	36	0.94
4349947--4349982	3	12.0	3	100	0	72	33	0	0	66	0.92
4351023--4351058	18	2.0	18	100	0	72	27	38	11	22	1.88
4353276--4353308	2	16.5	2	100	0	66	51	0	0	48	1.00
4359830--4359896	32	2.1	33	83	8	84	38	0	0	61	0.96
4365056--4365207	76	2.0	75	94	1	268	21	26	16	35	1.94

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