genome.fa.s4.2.7.7.80.10.50.1000.21.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  21  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)
4576496--4576545	23	2.2	23	88	0	73	50	0	0	50	1.00
4576629--4576715	11	7.5	11	75	12	68	64	2	1	32	1.13
4576628--4576698	25	3.0	25	81	8	85	64	2	1	30	1.16
4576631--4576708	36	2.2	37	80	13	92	65	2	1	30	1.14
4577358--4577392	14	2.3	16	90	9	56	65	0	0	34	0.93
4577620--4577648	15	2.0	15	93	6	51	58	0	0	41	0.98
4577648--4577689	16	2.6	16	84	3	57	45	0	0	54	0.99
4577689--4577738	21	2.6	19	75	15	50	42	2	0	56	1.11
4577838--4577876	11	3.5	11	89	6	60	38	0	0	61	0.96
4577844--4577876	6	5.7	6	92	7	59	36	0	0	63	0.95
4578451--4578492	16	2.6	17	81	11	52	42	0	0	57	0.99
4580061--4580165	52	2.0	53	88	1	158	41	10	4	42	1.60
4580936--4580979	22	2.0	22	86	0	61	36	2	0	61	1.09
4581442--4581488	23	2.1	22	84	11	60	42	0	4	53	1.20
4581451--4581505	23	2.3	23	84	9	67	43	0	7	49	1.30
4583653--4583683	11	2.8	11	95	0	53	87	0	12	0	0.55
4588488--4588528	20	2.2	17	87	12	55	51	0	0	48	1.00
4589873--4589897	2	12.5	2	100	0	50	48	0	0	52	1.00
4590004--4590046	19	2.2	19	87	8	59	44	0	4	51	1.22
4604337--4604371	5	6.6	5	87	12	52	77	2	0	20	0.90
4605136--4605177	20	2.1	20	90	0	66	42	14	9	33	1.78
4605208--4605239	16	2.1	16	88	11	50	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4605216--4605257	21	2.0	21	85	0	57	64	0	0	35	0.94
4609185--4609235	26	2.0	26	100	0	102	33	11	7	47	1.69
4617539--4617618	36	2.2	36	91	4	126	33	30	13	22	1.93
4617553--4617613	18	3.4	18	64	8	52	36	27	14	21	1.93
4620774--4620818	23	2.0	23	81	0	54	46	8	2	42	1.47
4626169--4626233	13	4.6	13	69	23	51	49	0	1	49	1.10
4626143--4626232	44	2.0	44	100	0	180	48	0	2	48	1.13
4626160--4626224	29	2.2	31	78	10	73	52	0	1	46	1.10
4626146--4626224	15	5.2	16	75	13	78	49	0	2	48	1.14
4626714--4626752	18	2.2	17	95	4	69	82	0	7	10	0.86
4630869--4630926	28	2.1	28	84	12	75	53	0	0	46	1.00
4630869--4630932	27	2.3	28	81	13	78	53	0	1	45	1.10
4631679--4631728	21	2.3	21	77	19	57	54	4	0	42	1.19
4632194--4632243	20	2.4	21	77	12	59	32	2	4	62	1.25
4638530--4638556	2	13.5	2	100	0	54	48	0	0	51	1.00
4638847--4638884	11	3.5	11	82	3	51	71	0	0	28	0.87
4639309--4639356	23	2.0	24	88	4	71	31	0	2	66	1.03
4639822--4639938	8	14.0	8	71	22	64	35	0	0	64	1.00
4639824--4639907	18	4.8	17	80	12	82	36	0	1	61	1.04
4639828--4639936	46	2.3	46	81	10	116	34	0	0	64	1.00
4639894--4639936	9	4.1	10	85	14	52	27	0	0	72	0.85
4639894--4639943	11	4.7	11	85	12	61	30	0	0	70	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4640150--4640197	22	2.2	22	84	0	60	50	0	4	45	1.21
4640388--4640426	20	2.0	20	84	0	51	58	0	0	41	0.98
4640472--4640496	11	2.3	11	100	0	50	48	20	0	32	1.50
4640646--4640684	16	2.4	16	86	0	60	51	0	2	46	1.14
4640692--4640732	18	2.3	18	86	0	55	39	0	0	60	0.96
4640680--4640729	24	2.1	24	85	14	68	40	0	0	60	0.97
4642079--4642118	20	2.0	20	90	9	64	70	0	0	30	0.88
4642124--4642167	22	2.0	22	86	0	61	43	6	0	50	1.29
4642145--4642246	29	3.4	29	73	21	77	39	1	0	58	1.09
4642162--4642246	31	2.8	30	79	13	93	37	1	0	61	1.04
4642167--4642249	29	2.7	30	79	7	96	39	1	0	59	1.05
4646713--4646744	16	1.9	16	93	6	55	0	6	0	93	0.34
4646713--4646744	12	2.8	12	95	4	57	0	6	0	93	0.34
4648846--4648893	24	2.0	24	91	0	78	45	0	0	54	0.99
4653508--4653580	20	3.6	20	81	3	101	35	13	19	31	1.91
4653526--4653601	21	3.7	21	80	3	100	42	11	17	28	1.84
4653508--4653601	41	2.3	41	98	0	179	39	12	18	29	1.88
4653640--4653665	13	2.0	13	100	0	52	38	15	15	30	1.88
4657727--4657757	15	2.1	15	93	0	53	48	16	22	12	1.80
4659772--4659851	21	3.6	22	73	12	74	25	12	16	46	1.82
4659838--4659876	13	3.0	13	96	0	69	30	17	15	35	1.91
4662318--4662390	20	3.6	20	81	3	101	35	13	19	31	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4662336--4662411	21	3.7	21	80	3	100	42	11	17	28	1.84
4662318--4662411	41	2.3	41	98	0	179	39	12	18	29	1.88
4662450--4662475	13	2.0	13	100	0	52	38	15	15	30	1.88
4665977--4666005	5	5.8	5	100	0	58	82	17	0	0	0.66
4666391--4666437	22	2.1	23	84	11	62	48	4	0	46	1.21
4666405--4666452	11	4.3	11	78	5	51	45	8	2	43	1.45
4667876--4667923	22	2.2	23	82	14	57	75	6	0	18	1.01
4670526--4670576	15	3.4	15	79	15	61	35	0	0	64	0.94
4670614--4670670	20	2.6	23	75	16	66	31	5	0	63	1.17
4670631--4670665	10	3.4	10	88	4	52	28	0	0	71	0.86
4671887--4671915	14	2.0	15	93	6	51	41	0	0	58	0.98
4671849--4671909	25	2.4	25	73	10	70	39	0	0	60	0.97
4672263--4672305	21	2.0	21	91	8	70	44	0	0	55	0.99
4672261--4672337	38	2.1	34	81	15	84	45	0	0	54	0.99
4672763--4672787	2	12.5	2	100	0	50	48	0	0	52	1.00
4673533--4673589	18	3.2	18	68	7	53	54	0	0	45	0.99
4674501--4674531	3	10.3	3	92	0	53	64	3	0	32	1.09
4674811--4674855	2	24.0	2	86	13	69	48	0	0	51	1.00
4674810--4674855	9	4.7	10	84	15	53	47	0	0	52	1.00
4677282--4677362	38	2.3	36	80	15	91	41	0	0	58	0.98
4677331--4677376	24	1.9	24	82	8	58	41	2	0	56	1.11
4677806--4677830	3	8.3	3	100	0	50	36	32	32	0	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4677899--4677925	2	13.5	2	100	0	54	48	0	0	51	1.00
4684736--4684768	17	1.9	17	88	11	50	42	0	0	57	0.98
4684740--4684781	18	2.3	18	84	8	50	42	0	2	54	1.13
4684885--4684930	23	2.0	23	82	0	56	52	4	26	17	1.63
4685079--4685124	16	2.8	17	86	6	67	56	0	0	43	0.99
4685175--4685241	13	5.2	13	70	20	50	58	1	0	40	1.07
4685175--4685291	53	2.2	53	89	1	173	57	3	0	38	1.22
4685732--4685787	11	5.1	11	79	14	62	35	0	0	64	0.94
4685698--4685787	26	3.5	25	78	19	87	42	0	0	57	0.98
4692110--4692137	9	3.1	9	100	0	56	35	42	10	10	1.74
4694152--4694209	16	3.6	16	72	9	55	44	0	0	55	0.99
4694168--4694197	10	3.0	10	90	0	51	46	0	0	53	1.00
4694236--4694298	25	2.6	23	76	16	65	53	0	0	46	1.00
4694390--4694437	19	2.5	19	86	10	62	41	2	0	56	1.11
4695150--4695183	18	1.9	18	94	5	61	44	2	5	47	1.42
4695260--4695294	15	2.5	15	90	9	56	48	2	0	48	1.16
4695906--4696149	123	2.0	124	90	2	384	43	4	6	45	1.52
4696709--4696735	2	13.5	2	100	0	54	51	0	0	48	1.00
4697359--4697404	22	2.1	22	87	0	65	60	2	0	36	1.09
4697676--4697740	18	3.5	18	73	18	62	70	3	0	26	1.01
4698222--4698271	22	2.4	21	81	15	59	52	0	0	48	1.00
4698860--4698894	12	2.7	13	91	8	54	62	2	0	34	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4699269--4699307	19	1.9	19	85	10	51	43	0	2	53	1.14
4699778--4699825	3	16.0	3	95	0	87	68	0	0	31	0.90
4700409--4700489	40	2.0	40	100	0	162	41	4	14	38	1.68
4700971--4701084	38	2.8	39	86	9	158	32	19	7	41	1.78
4701136--4701197	25	2.7	21	77	18	61	37	3	0	59	1.13
4709230--4709270	22	2.0	21	85	9	57	36	2	0	60	1.10
4712795--4712828	3	11.3	3	100	0	68	64	0	0	35	0.94
4713324--4713374	4	12.8	4	95	0	57	39	0	9	50	1.35
4713328--4713386	8	7.4	8	92	0	73	35	0	13	50	1.42
4713332--4713390	12	4.9	12	89	0	82	33	0	15	50	1.44

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