genome.fa.s11.2.7.7.80.10.50.1000.26.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: 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  26  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)
4366995--4367056	29	2.3	26	91	8	97	61	4	0	33	1.17
4371658--4371708	23	2.2	24	82	10	61	52	1	0	45	1.12
4371981--4372062	31	2.6	31	80	7	85	58	2	1	37	1.19
4371951--4372031	29	2.7	29	75	17	76	56	2	2	38	1.26
4373423--4373456	9	3.8	9	92	0	59	85	0	2	11	0.71
4373786--4373836	13	4.2	12	82	10	59	27	3	1	66	1.20
4374281--4374359	37	2.1	39	83	9	101	39	1	0	59	1.06
4374744--4374787	15	2.9	15	83	12	63	40	0	0	59	0.98
4381990--4382028	19	2.0	20	90	5	62	53	0	7	38	1.30
4382759--4382784	4	6.5	4	100	0	52	76	0	23	0	0.78
4386567--4386594	2	14.0	2	100	0	56	50	0	0	50	1.00
4386809--4386881	29	2.4	29	76	15	69	54	0	2	42	1.14
4388508--4388535	3	9.3	3	100	0	56	32	0	0	67	0.91
4389003--4389061	11	5.9	11	77	18	58	67	0	0	32	0.91
4389001--4389061	17	3.6	17	77	14	65	67	0	0	32	0.91
4389025--4389054	15	1.9	15	93	6	51	66	0	0	33	0.92
4391588--4391613	2	13.0	2	100	0	52	0	0	50	50	1.00
4392329--4392354	3	8.7	3	100	0	52	34	0	0	65	0.93
4394846--4394875	2	15.0	2	100	0	60	50	0	0	50	1.00
4398910--4399067	11	15.2	10	65	22	60	41	2	4	51	1.35
4398942--4399067	10	12.4	9	69	25	67	42	2	3	51	1.33
4398910--4399067	21	7.7	21	67	19	84	41	2	4	51	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4398988--4399085	20	4.8	21	75	14	98	39	4	3	53	1.36
4400333--4400413	38	2.3	36	79	12	89	56	0	1	41	1.07
4400341--4400420	15	5.5	15	69	19	53	57	0	1	41	1.07
4400377--4400425	24	2.1	24	88	11	75	59	0	0	40	0.98
4400329--4400436	45	2.4	43	76	13	112	54	0	0	44	1.06
4400989--4401040	25	2.0	26	85	3	70	48	1	1	48	1.24
4401020--4401047	11	2.5	11	100	0	56	32	0	0	67	0.91
4401197--4401266	11	6.4	11	79	11	72	67	0	0	32	0.91
4401213--4401271	25	2.3	26	77	16	61	64	1	0	33	1.04
4401294--4401339	17	2.7	17	80	19	60	63	0	0	36	0.95
4401301--4401339	15	2.5	15	87	8	51	64	0	0	35	0.94
4401859--4401936	32	2.4	33	85	8	106	53	0	1	44	1.08
4401881--4401931	16	3.2	16	75	10	59	54	0	0	45	0.99
4402314--4402350	2	18.5	2	100	0	74	51	0	48	0	1.00
4419103--4419148	23	2.0	22	83	4	56	47	0	6	45	1.28
4419216--4419259	21	2.1	21	87	8	63	52	0	2	45	1.13
4419246--4419277	15	2.0	17	88	11	50	65	0	0	34	0.93
4419795--4419827	8	4.1	8	88	11	50	0	3	9	87	0.63
4423006--4423037	2	16.0	2	100	0	64	50	0	50	0	1.00
4429145--4429174	12	2.5	12	94	0	51	80	20	0	0	0.72
4434021--4434058	20	1.9	20	94	0	67	39	0	0	60	0.97
4435096--4435135	21	1.9	21	89	0	62	65	2	2	30	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4435127--4435152	11	2.4	11	100	0	52	73	0	0	26	0.84
4437880--4437915	2	18.0	2	88	0	54	50	0	0	50	1.00
4437881--4437922	12	3.5	12	86	0	57	50	2	0	47	1.14
4439947--4439980	2	17.0	2	93	0	59	47	0	2	50	1.16
4443371--4443405	17	2.1	17	89	5	54	25	2	0	71	1.00
4445221--4445245	3	8.3	3	100	0	50	68	0	0	32	0.90
4445879--4445943	23	2.8	23	79	6	69	46	7	1	44	1.41
4445879--4445942	24	2.7	23	78	9	76	45	7	1	45	1.42
4445879--4445991	51	2.3	47	83	6	127	45	7	2	45	1.45
4446223--4446273	16	3.2	16	78	8	59	50	7	0	41	1.31
4446222--4446276	17	3.4	17	73	14	53	52	7	0	40	1.29
4449996--4450021	2	13.0	2	100	0	52	50	0	0	50	1.00
4456107--4456167	24	2.6	25	75	19	67	19	0	14	65	1.27
4456858--4456903	17	2.8	17	80	12	60	43	0	0	56	0.99
4465680--4465917	50	4.8	50	94	0	404	28	21	18	31	1.97
4470290--4470525	50	4.7	50	83	4	269	32	20	16	30	1.95
4470290--4470527	100	2.4	100	84	1	298	32	20	16	31	1.94
4477215--4477239	1	25.0	1	100	0	50	0	0	100	0	0.00
4482403--4482435	17	2.0	17	88	5	50	51	0	3	45	1.16
4482904--4482936	10	3.0	11	86	13	50	69	0	0	30	0.88
4483908--4483947	18	2.1	20	86	9	57	70	10	0	20	1.16
4484022--4484118	8	10.1	10	70	21	50	71	4	0	24	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4484022--4484108	22	4.4	21	75	21	82	71	4	0	24	1.05
4484063--4484117	8	6.1	9	78	18	53	76	3	0	20	0.94
4484086--4484117	8	4.0	8	95	0	55	78	0	0	21	0.76
4484031--4484117	16	5.2	16	71	23	63	73	3	0	22	0.98
4484141--4484179	21	1.9	20	84	5	51	74	7	0	17	1.05
4493982--4494016	6	5.8	6	100	0	70	51	0	48	0	1.00
4493983--4494021	18	2.2	18	90	0	60	53	2	43	0	1.14
4501727--4501759	17	2.0	17	88	5	50	54	0	0	45	0.99
4503240--4503284	20	2.3	20	85	7	58	68	11	0	20	1.19
4503360--4503457	9	10.1	10	70	21	59	71	4	0	24	1.03
4503360--4503455	22	4.9	21	75	20	84	71	4	0	23	1.03
4503391--4503456	19	3.6	17	74	20	62	75	3	0	21	0.93
4503480--4503517	20	1.9	20	84	10	51	73	7	0	18	1.06
4513303--4513337	6	5.8	6	100	0	70	51	0	48	0	1.00
4513304--4513342	18	2.2	18	90	0	60	53	2	43	0	1.14
4517822--4517861	2	20.5	2	94	5	73	0	50	0	50	1.00
4517948--4517987	15	2.7	15	81	11	55	40	0	0	60	0.97
4518276--4518321	18	2.5	18	82	3	56	47	0	0	52	1.00
4518295--4518324	12	2.6	11	90	10	51	56	0	0	43	0.99
4521493--4521526	6	5.7	6	100	0	68	32	0	17	50	1.47
4529877--4529914	18	2.1	19	90	5	60	52	0	0	47	1.00
4530169--4530206	16	2.4	16	83	16	53	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)
4530991--4531019	12	2.3	13	94	5	51	34	0	3	62	1.12
4535669--4535713	21	2.1	22	84	12	58	48	2	0	48	1.13
4537112--4537148	11	3.5	11	82	17	51	72	0	0	27	0.84
4537107--4537151	19	2.2	19	84	11	54	68	0	0	31	0.89
4537910--4537938	2	14.5	2	100	0	58	48	0	0	51	1.00
4538861--4538892	6	5.3	6	92	0	55	34	0	0	65	0.93
4548803--4548845	2	22.5	2	90	9	72	53	0	0	46	1.00
4561634--4561663	15	1.9	16	93	6	53	20	0	0	80	0.72
4562843--4562870	2	14.0	2	100	0	56	50	0	50	0	1.00
4567200--4567234	2	18.0	2	88	5	54	48	2	0	48	1.16
4567826--4567886	31	2.1	28	85	11	79	62	1	1	34	1.15
4568746--4568800	15	3.7	16	81	16	57	45	0	0	54	0.99
4568757--4568808	20	2.6	21	81	9	63	46	0	0	53	1.00
4576266--4576336	27	2.6	28	86	6	92	46	23	5	23	1.74
4578216--4578261	21	2.1	22	88	4	67	19	28	19	32	1.96
4581477--4581505	2	14.5	2	100	0	58	51	0	0	48	1.00
4584408--4584477	33	2.1	34	80	15	85	54	1	0	44	1.09
4585686--4585720	2	17.5	2	93	0	61	51	0	2	45	1.16
4587101--4587193	39	2.4	39	100	0	186	13	21	26	37	1.91
4589477--4589506	2	15.0	2	100	0	60	50	0	0	50	1.00
4591790--4591840	2	25.5	2	100	0	102	49	0	0	50	1.00
4593338--4593400	32	2.0	32	100	0	126	28	15	19	36	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4593475--4593507	2	16.5	2	100	0	66	48	0	0	51	1.00
4593640--4593678	15	2.6	15	84	8	53	28	17	7	46	1.76
4598675--4598704	5	6.0	5	92	0	51	76	0	23	0	0.78
4599269--4599294	5	5.2	5	100	0	52	57	0	0	42	0.98
4599893--4599948	19	2.7	21	84	13	64	39	0	0	60	0.97
4599912--4599988	35	2.2	36	79	11	88	38	0	1	59	1.06
4599912--4599990	12	6.8	12	67	25	53	40	0	1	58	1.06
4600127--4600199	37	1.9	39	83	10	98	52	4	0	43	1.20
4605188--4605306	59	2.0	60	95	1	213	23	17	5	52	1.66
4608485--4608513	2	14.5	2	100	0	58	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