genome.fa.s11.2.7.7.80.10.50.1000.27.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  27  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)
4608692--4608725	3	11.3	3	100	0	68	32	0	0	67	0.91
4608975--4609004	14	2.1	15	93	6	53	56	0	0	43	0.99
4609950--4610045	48	2.0	47	97	2	183	45	4	10	39	1.58
4620431--4620465	2	17.5	2	100	0	70	51	0	0	48	1.00
4620465--4620489	2	12.5	2	100	0	50	52	0	48	0	1.00
4622794--4622828	14	2.6	14	90	4	54	40	8	0	51	1.33
4623020--4623102	23	3.5	23	76	12	80	51	0	0	48	1.00
4623038--4623092	18	3.0	18	81	2	56	56	0	0	43	0.99
4623312--4623361	25	2.0	25	88	3	75	46	0	0	54	1.00
4624728--4624766	18	2.2	18	85	0	51	38	12	0	48	1.42
4625159--4625184	13	2.0	13	100	0	52	7	38	30	23	1.83
4627131--4627222	31	3.2	31	66	23	92	52	3	3	41	1.34
4627131--4627244	54	2.1	54	91	0	183	52	4	2	40	1.35
4630344--4630398	28	2.0	27	85	7	74	47	0	1	50	1.11
4631119--4631153	3	12.0	3	93	6	63	65	0	0	34	0.93
4640148--4640180	5	6.6	5	100	0	66	42	18	0	39	1.50
4650276--4650365	45	2.0	45	95	0	162	35	18	16	28	1.93
4651859--4651892	2	17.0	2	100	0	68	50	0	0	50	1.00
4653582--4653615	2	17.0	2	100	0	68	50	0	0	50	1.00
4659065--4659099	14	2.5	14	90	0	52	60	5	17	17	1.55
4659110--4659143	12	2.8	12	81	0	50	76	2	17	2	1.04
4661966--4662003	18	2.1	18	100	0	76	55	0	39	5	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4662067--4662098	2	16.0	2	93	0	55	46	0	3	50	1.17
4662624--4662696	22	3.3	21	71	19	60	38	1	2	57	1.22
4663419--4663452	3	11.3	3	100	0	68	67	0	0	32	0.91
4666268--4666294	2	13.5	2	100	0	54	51	0	48	0	1.00
4675245--4675272	2	14.0	2	100	0	56	50	0	0	50	1.00
4676572--4676640	29	2.4	29	81	11	72	42	1	1	55	1.18
4676572--4676633	30	2.1	30	82	11	74	41	1	1	54	1.19
4680264--4680288	2	12.5	2	100	0	50	52	0	0	48	1.00
4680288--4680316	2	14.5	2	100	0	58	51	0	48	0	1.00
4685548--4685587	20	2.0	21	85	5	55	32	7	7	52	1.58
4686975--4687001	12	2.2	12	100	0	54	25	7	40	25	1.82
4688944--4688984	19	2.2	18	91	4	64	39	0	0	60	0.96
4689791--4689834	22	2.0	22	90	0	70	56	6	11	25	1.58
4690276--4690331	20	2.8	20	83	0	67	26	1	7	64	1.29
4690279--4690371	20	4.7	20	72	7	64	31	2	8	58	1.40
4690375--4690415	21	1.9	22	85	5	57	31	4	2	60	1.30
4690435--4690488	11	5.2	11	70	20	53	37	1	1	59	1.19
4690435--4690489	21	2.6	22	88	11	89	36	1	3	58	1.26
4690481--4690542	21	3.0	21	79	6	65	38	3	8	50	1.48
4692946--4693082	21	6.5	20	72	19	100	39	0	0	59	1.02
4692943--4693005	29	2.1	29	79	8	72	46	0	0	53	1.00
4693007--4693076	9	7.4	9	74	19	54	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4699830--4699875	23	2.0	23	83	8	58	52	0	0	47	1.00
4702369--4702398	2	15.0	2	92	0	51	50	3	0	46	1.18
4706189--4706240	20	2.6	19	82	17	61	48	0	0	51	1.00
4706194--4706254	20	3.1	18	77	17	50	47	0	0	52	1.00
4706441--4706489	2	24.5	2	100	0	98	51	0	48	0	1.00
4706986--4707016	13	2.3	14	94	5	55	35	0	0	64	0.94
4707184--4707231	17	2.8	17	75	6	53	37	0	0	62	0.95
4723801--4723857	23	2.4	25	77	17	66	43	0	5	50	1.24
4729863--4729891	1	29.0	1	100	0	58	0	0	100	0	0.00
4736133--4736183	14	3.4	14	76	23	59	50	0	0	49	1.00
4736172--4736230	20	2.9	19	82	7	64	32	1	0	66	1.02
4736172--4736215	21	2.2	21	88	8	65	29	0	0	70	0.88
4736172--4736230	21	2.9	20	80	12	59	32	1	0	66	1.02
4739778--4739805	2	14.0	2	100	0	56	50	0	0	50	1.00
4745186--4745241	27	2.1	26	96	3	103	33	3	16	46	1.64
4748531--4748571	21	2.0	21	90	0	64	78	0	0	21	0.76
4748538--4748571	17	2.0	17	94	0	59	79	0	0	20	0.73
4749367--4749403	16	2.3	17	90	9	60	56	0	2	40	1.13
4751494--4751577	43	2.0	43	92	0	141	40	23	9	26	1.85
4758799--4758838	20	2.1	20	86	9	57	37	0	5	57	1.21
4766155--4766188	2	17.0	2	100	0	68	50	0	0	50	1.00
4767695--4767742	20	2.4	20	82	6	62	37	0	0	62	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4770080--4770109	2	15.0	2	100	0	60	50	0	0	50	1.00
4770173--4770215	3	14.0	3	90	4	68	65	4	0	30	1.13
4772325--4772364	13	2.7	16	81	14	50	52	0	2	45	1.14
4772322--4772370	14	3.3	15	80	13	66	53	0	2	44	1.12
4775348--4775385	4	9.5	4	100	0	76	50	23	0	26	1.50
4776634--4776660	2	13.5	2	100	0	54	51	0	0	48	1.00
4777285--4777337	5	10.4	5	79	4	52	52	0	0	47	1.00
4777285--4777336	11	4.5	11	75	15	52	51	0	0	48	1.00
4781111--4781331	107	2.1	107	93	0	379	33	13	13	40	1.83
4781950--4782000	26	2.0	26	96	0	93	52	15	0	31	1.43
4782034--4782070	2	18.5	2	100	0	74	51	0	0	48	1.00
4784165--4784200	14	2.5	15	90	4	56	47	0	0	52	1.00
4784411--4784464	18	3.1	18	77	17	60	37	0	5	57	1.22
4787678--4787702	2	12.5	2	100	0	50	52	0	48	0	1.00
4787754--4787792	2	20.0	2	89	5	62	48	0	2	48	1.15
4787799--4787827	14	2.0	15	93	6	51	48	6	44	0	1.29
4791952--4792017	8	8.5	8	68	18	50	62	0	0	37	0.96
4791952--4792011	18	3.3	18	82	13	79	63	0	0	36	0.95
4791956--4792014	20	3.0	20	88	9	79	64	0	0	35	0.94
4798879--4798917	20	2.0	20	89	0	60	61	2	0	35	1.10
4799491--4799517	2	13.5	2	100	0	54	0	51	0	48	1.00
4799594--4799648	21	2.5	22	82	8	67	58	0	1	40	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4799611--4799652	21	2.0	21	100	0	84	52	0	0	47	1.00
4799781--4799831	20	2.5	20	77	17	52	45	7	0	47	1.32
4802795--4802916	45	3.0	39	79	15	108	51	0	0	47	1.06
4802789--4802920	21	6.4	22	71	17	97	50	0	0	48	1.06
4803163--4803207	19	2.4	18	85	14	56	44	0	0	55	0.99
4808192--4808225	2	17.0	2	100	0	68	50	0	0	50	1.00
4811139--4811175	18	2.1	18	89	0	56	75	0	16	8	1.02
4823468--4823523	17	3.6	16	72	15	55	37	0	0	62	0.95
4823471--4823558	31	2.9	29	74	22	83	35	0	0	64	0.94
4823470--4823563	40	2.4	39	79	12	102	36	0	0	63	0.94
4823470--4823558	24	3.7	24	71	15	76	35	0	0	64	0.94
4823468--4823558	16	5.9	15	74	13	60	36	0	0	63	0.94
4823677--4823721	6	7.7	6	85	9	58	0	17	0	82	0.68
4823678--4823721	22	2.0	22	86	0	61	0	15	0	84	0.63
4824779--4824834	24	2.5	22	78	13	62	66	1	0	32	1.03
4824785--4824848	33	1.9	34	84	9	87	64	1	0	34	1.03
4827463--4827507	21	2.2	20	88	11	65	66	0	0	33	0.92
4827447--4827504	18	3.1	18	81	13	71	62	1	1	34	1.16
4827593--4827657	21	3.3	21	64	27	61	55	1	0	43	1.09
4827599--4827685	16	5.5	16	67	25	51	54	1	0	44	1.07
4827635--4827695	27	2.3	27	85	5	79	59	0	0	40	0.98
4830864--4830912	26	2.0	26	88	8	75	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4837168--4837327	11	15.0	11	67	19	72	39	1	3	56	1.23
4837169--4837322	43	3.6	43	73	13	120	38	1	3	56	1.24
4837150--4837326	21	8.3	21	69	17	84	38	1	3	55	1.26
4837170--4837324	21	7.2	21	70	17	104	38	1	3	57	1.23
4837571--4837627	28	2.0	28	83	6	71	38	0	0	61	0.96
4837610--4837691	32	2.5	33	84	7	114	46	0	1	52	1.08
4837904--4837941	18	2.1	18	90	5	58	42	2	0	55	1.14
4838344--4838494	16	11.1	14	68	25	67	58	0	1	40	1.06
4838341--4838444	41	2.6	41	81	6	115	59	0	0	40	0.97
4838333--4838500	11	15.8	11	73	15	99	57	0	1	40	1.09

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