genome.fa.s3.2.7.7.80.10.50.1000.25.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: 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  25  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)
4299506--4299553	21	2.2	21	85	14	71	56	20	4	18	1.58
4299513--4299555	21	2.1	21	95	4	79	53	18	6	20	1.67
4300509--4300550	17	2.5	17	88	3	59	64	0	2	33	1.07
4300509--4300559	8	6.2	8	80	19	61	62	0	1	35	1.06
4300509--4300558	25	2.1	22	89	10	73	64	0	2	34	1.05
4300509--4300550	6	7.5	6	79	15	54	64	0	2	33	1.07
4301161--4301221	17	3.5	17	76	12	54	50	0	0	49	1.00
4301171--4301227	22	2.5	22	81	10	62	49	0	0	50	1.00
4301196--4301263	28	2.4	27	78	14	66	57	0	4	38	1.19
4301669--4301888	27	8.1	27	82	6	151	27	36	20	15	1.93
4301680--4301896	81	2.7	81	83	2	267	26	35	21	16	1.94
4301680--4301888	54	3.9	54	81	3	251	26	36	21	15	1.94
4312234--4312295	32	1.9	33	93	3	108	51	1	0	46	1.10
4313246--4313322	22	3.5	22	81	8	93	49	5	10	35	1.59
4313239--4313357	22	5.3	22	71	8	71	47	3	10	38	1.56
4317221--4317251	16	1.9	16	93	0	53	51	3	0	45	1.17
4320937--4320992	28	2.0	27	89	3	85	48	0	0	51	1.00
4326624--4326668	20	2.3	20	88	7	67	17	15	20	46	1.84
4327777--4327834	29	2.0	29	93	3	98	58	6	3	31	1.41
4328100--4328188	31	2.8	31	86	5	115	50	1	0	48	1.08
4345045--4345093	17	2.9	17	77	20	57	24	6	10	59	1.53
4349460--4349517	21	2.8	21	73	17	59	50	0	1	48	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4357610--4357664	28	2.0	28	85	7	76	34	0	1	63	1.05
4357710--4357765	23	2.5	23	77	11	62	57	0	1	41	1.09
4358130--4358179	25	2.0	25	92	4	82	56	0	0	44	0.99
4358127--4358181	7	8.3	7	80	11	62	60	0	0	40	0.97
4358118--4358190	32	2.2	32	80	7	85	49	0	4	46	1.21
4362467--4362501	2	17.5	2	100	0	70	51	0	0	48	1.00
4362654--4362714	19	3.2	18	77	15	61	57	0	0	42	0.98
4362636--4362714	17	4.5	17	76	16	65	58	0	0	41	0.98
4362667--4362720	17	3.2	18	82	10	60	61	0	0	38	0.96
4362650--4362720	18	4.1	17	74	15	65	60	0	0	39	0.97
4363743--4363786	3	14.7	3	95	0	79	65	0	34	0	0.93
4371552--4371606	28	2.0	28	100	0	110	23	10	21	43	1.84
4375369--4375402	2	17.0	2	100	0	68	50	0	0	50	1.00
4375810--4375839	10	3.0	10	90	0	51	53	0	0	46	1.00
4375804--4375905	53	1.9	52	80	11	118	50	0	0	48	1.07
4381314--4381352	21	1.9	20	84	5	51	51	0	0	48	1.00
4384270--4384304	16	2.1	17	94	5	63	25	0	17	57	1.40
4390673--4390702	15	1.9	16	93	6	53	46	6	6	40	1.56
4391039--4391073	17	2.1	17	88	0	52	42	5	2	48	1.41
4392218--4392268	24	2.2	22	83	13	59	62	1	0	35	1.06
4397668--4397692	4	6.2	4	100	0	50	76	0	0	24	0.80
4399833--4399927	19	5.3	19	69	21	78	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4400565--4400605	20	2.1	19	86	13	57	60	0	0	39	0.96
4401417--4401443	3	9.0	3	100	0	54	66	0	0	33	0.92
4402513--4402572	25	2.3	27	80	5	70	73	1	0	25	0.93
4411257--4411296	20	2.0	20	90	0	62	80	0	15	5	0.88
4411940--4411984	22	2.0	22	87	8	65	46	0	4	48	1.22
4414824--4414857	17	2.0	17	88	0	50	58	0	0	41	0.98
4414824--4414888	29	2.2	29	81	5	69	60	3	1	35	1.22
4415541--4415621	27	3.1	26	82	8	101	38	0	0	61	0.96
4415561--4415601	20	2.0	20	90	9	66	41	0	0	58	0.98
4415565--4415613	22	2.2	22	85	7	64	34	0	0	65	0.93
4415568--4415615	11	4.3	11	76	12	53	35	0	0	64	0.94
4416544--4416573	2	15.0	2	92	0	51	53	0	46	0	1.00
4421196--4421249	20	2.7	20	88	0	81	33	14	16	35	1.90
4421298--4421322	13	1.9	13	100	0	50	40	12	16	32	1.84
4422061--4422097	16	2.3	16	90	0	56	45	0	0	54	1.00
4425793--4425826	2	17.0	2	100	0	68	50	0	0	50	1.00
4430686--4430710	13	1.9	13	100	0	50	40	12	16	32	1.84
4431126--4431192	16	4.2	16	73	17	50	20	7	22	49	1.74
4431155--4431224	15	4.5	15	71	5	50	21	14	20	44	1.86
4431166--4431230	15	4.2	16	70	5	53	16	15	24	43	1.87
4431207--4431330	53	2.3	55	80	8	139	29	15	16	37	1.90
4434268--4434333	32	2.2	31	84	10	84	50	0	3	46	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4434340--4434397	30	2.0	29	89	3	89	60	3	1	34	1.24
4434866--4434947	29	2.9	28	78	12	78	46	0	0	53	1.00
4441525--4441559	15	2.3	15	85	0	52	62	0	0	37	0.95
4441500--4441555	21	2.7	21	83	8	71	58	0	0	41	0.98
4441554--4441593	18	2.3	17	87	12	55	57	5	0	37	1.21
4441552--4441599	23	2.1	22	84	3	60	58	4	0	37	1.18
4451382--4451440	5	12.8	5	73	22	58	59	0	0	40	0.97
4452007--4452052	16	2.8	17	74	9	51	45	0	0	54	0.99
4451975--4452056	25	3.4	25	77	12	73	46	0	0	53	1.00
4451975--4452041	16	4.2	16	69	14	50	47	0	0	52	1.00
4451993--4452054	17	3.7	18	72	23	55	45	0	0	54	0.99
4452044--4452187	13	11.5	13	64	25	53	35	0	2	61	1.13
4451991--4452126	31	4.4	30	76	18	120	41	0	0	57	1.09
4458713--4458756	2	22.0	2	95	0	70	45	0	4	50	1.22
4464175--4464202	6	4.7	6	100	0	56	17	14	35	32	1.90
4466412--4466466	29	1.9	28	81	3	65	32	10	7	49	1.65
4467778--4467813	2	18.0	2	100	0	72	50	0	0	50	1.00
4467968--4468034	34	2.0	34	84	0	89	58	2	0	38	1.14
4471137--4471175	3	12.7	3	94	5	69	0	35	0	64	0.94
4477040--4477069	3	10.0	3	100	0	60	33	0	0	66	0.92
4478702--4478756	17	3.4	16	76	11	51	63	0	0	36	0.95
4478710--4478772	17	3.6	18	72	14	60	61	1	0	36	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4479254--4479302	21	2.3	22	86	10	75	36	0	0	63	0.95
4479244--4479301	21	3.1	18	74	16	55	41	0	0	58	0.98
4481330--4481374	15	3.1	15	80	6	56	55	0	0	44	0.99
4481962--4482010	2	24.5	2	100	0	98	51	0	0	48	1.00
4488928--4489090	81	2.0	81	98	0	317	37	13	17	31	1.88
4496185--4496219	2	17.5	2	100	0	70	0	48	0	51	1.00
4496219--4496255	2	18.5	2	100	0	74	48	0	0	51	1.00
4500403--4500463	31	2.0	31	83	6	79	55	1	0	42	1.09
4500402--4500470	19	3.8	18	77	11	68	56	1	0	42	1.08
4502115--4502150	2	18.0	2	91	0	54	0	52	2	44	1.15
4504246--4504309	11	6.2	11	74	20	57	46	6	0	46	1.27
4504238--4504297	30	2.0	30	96	0	111	48	3	0	48	1.18
4505220--4505264	2	22.5	2	86	0	63	48	6	0	44	1.29
4507577--4507623	14	3.6	13	75	11	51	34	6	0	59	1.23
4507627--4507669	18	2.4	19	80	11	54	55	0	0	44	0.99
4510073--4510314	132	1.8	130	91	1	403	37	17	14	30	1.90
4519907--4519946	16	2.6	16	88	4	64	57	0	0	42	0.98
4520189--4520219	2	15.5	2	100	0	62	48	0	0	51	1.00
4520358--4520383	4	6.5	4	100	0	52	73	0	0	26	0.84
4524536--4524614	42	1.9	39	92	7	131	25	5	7	62	1.43
4525085--4525159	21	3.8	21	66	25	56	46	0	0	53	1.00
4525081--4525164	37	2.2	38	80	14	95	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4525081--4525175	39	2.5	37	78	10	95	48	1	0	50	1.07
4524901--4525207	170	1.8	168	84	7	424	48	3	3	43	1.37
4525293--4525354	29	2.1	29	90	0	97	48	0	0	51	1.00
4525296--4525353	13	4.2	13	72	14	53	46	0	0	53	1.00
4526447--4526494	17	2.8	17	71	9	53	58	0	2	39	1.10
4549836--4549870	2	17.5	2	100	0	70	48	0	0	51	1.00
4551059--4551112	18	2.8	18	76	13	54	61	0	0	38	0.96
4551045--4551109	28	2.2	30	83	5	80	56	0	0	43	0.99
4551063--4551114	22	2.3	21	80	9	59	63	0	0	36	0.95
4551219--4551257	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