genome.fa.s3.2.7.7.80.10.50.1000.26.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: 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  26  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)
4553683--4553755	17	4.2	17	77	8	76	43	1	1	53	1.17
4558337--4558406	21	3.4	21	81	11	74	58	0	0	41	0.98
4560984--4561017	3	11.3	3	93	0	59	64	2	32	0	1.08
4561081--4561163	39	2.1	39	82	4	96	38	16	19	25	1.92
4564023--4564062	20	2.0	21	90	9	66	40	0	0	60	0.97
4573387--4573433	19	2.2	21	85	14	62	42	0	0	57	0.98
4573917--4573981	17	3.6	17	71	17	51	24	3	3	69	1.17
4574306--4574349	18	2.4	19	77	11	56	50	0	0	50	1.00
4574439--4574485	16	2.9	16	72	12	51	74	0	23	2	0.93
4574532--4574568	18	2.1	18	89	0	56	45	2	5	45	1.40
4574596--4574653	23	2.7	21	77	12	73	20	1	5	72	1.13
4574596--4574650	21	2.6	19	81	18	65	20	1	5	72	1.13
4574849--4574881	16	2.0	17	88	5	50	69	0	0	30	0.88
4575748--4575785	12	3.0	13	85	14	53	39	0	0	60	0.97
4577472--4577527	15	3.4	18	65	27	52	51	0	3	44	1.18
4577462--4577552	30	3.1	29	86	9	114	49	0	4	46	1.22
4579145--4579181	19	1.9	19	88	0	56	48	2	2	45	1.30
4580744--4580786	17	2.5	17	88	7	61	51	0	0	48	1.00
4580787--4580854	30	2.3	30	80	14	79	51	2	1	44	1.25
4581679--4581706	2	14.0	2	100	0	56	50	0	0	50	1.00
4582463--4582506	16	2.6	17	78	10	54	43	6	4	45	1.51
4583703--4583751	25	2.0	25	83	0	62	44	12	2	40	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4587549--4587650	42	2.4	42	80	0	123	37	10	22	29	1.88
4587618--4587730	58	1.9	58	89	3	174	29	11	18	40	1.86
4589962--4589986	2	12.5	2	100	0	50	48	0	52	0	1.00
4591185--4591213	8	3.6	8	100	0	58	10	13	37	37	1.79
4594743--4594767	5	5.0	5	100	0	50	20	40	20	20	1.92
4595555--4595597	2	21.5	2	100	0	86	0	48	0	51	1.00
4600384--4600413	2	15.0	2	100	0	60	0	0	50	50	1.00
4600993--4601085	9	9.9	9	69	20	57	63	0	2	34	1.07
4600988--4601046	21	2.8	22	80	10	70	64	0	3	32	1.10
4600988--4601098	20	5.8	19	72	18	79	63	0	1	34	1.05
4600993--4601094	48	2.1	50	81	7	120	63	0	1	34	1.05
4601038--4601094	21	2.6	22	78	10	64	63	0	0	36	0.95
4601042--4601095	14	3.8	14	76	13	56	62	0	0	37	0.95
4605843--4605889	24	2.0	24	83	8	60	46	0	0	53	1.00
4606263--4606315	13	4.2	13	76	13	56	39	1	0	58	1.09
4606291--4606362	37	1.9	37	83	8	92	52	0	0	47	1.00
4606748--4606778	13	2.4	13	94	0	53	16	3	9	70	1.26
4615887--4616063	59	3.0	59	97	0	327	35	17	12	33	1.88
4618635--4618664	2	15.0	2	100	0	60	50	0	0	50	1.00
4621121--4621151	3	10.3	3	92	0	53	67	3	0	29	1.06
4622235--4622269	17	1.9	19	88	11	56	68	0	0	31	0.90
4622720--4622784	32	2.0	34	85	11	91	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4622768--4622805	11	3.4	11	92	3	58	36	0	2	60	1.11
4622702--4622805	16	6.8	16	65	21	53	39	0	0	59	1.04
4623241--4623476	131	1.8	130	91	0	364	33	9	7	50	1.62
4623548--4623589	19	2.3	18	84	15	59	61	0	2	35	1.09
4624077--4624167	43	2.1	43	95	0	164	17	30	14	37	1.90
4625520--4625559	2	20.0	2	100	0	80	50	0	0	50	1.00
4627180--4627206	14	1.9	14	100	0	54	37	18	14	29	1.91
4633345--4633395	26	2.0	26	81	14	61	58	1	0	39	1.09
4634040--4634077	19	2.1	19	85	5	51	26	2	0	71	1.00
4634159--4634199	17	2.3	19	83	12	59	60	0	0	39	0.96
4634162--4634232	27	2.7	27	74	10	83	57	0	0	42	0.98
4634439--4634487	21	2.4	20	80	12	55	46	0	0	53	1.00
4634447--4634490	21	2.1	21	87	8	63	43	0	0	56	0.99
4634772--4634805	2	17.0	2	100	0	68	50	0	0	50	1.00
4636276--4636306	3	10.3	3	100	0	62	35	0	0	64	0.94
4638178--4638219	18	2.3	19	80	12	52	30	0	0	69	0.89
4642727--4642802	13	5.4	15	73	16	65	55	0	0	44	0.99
4642719--4642795	14	5.1	16	72	13	56	57	0	0	42	0.99
4642737--4642793	23	2.3	25	85	8	73	56	0	0	43	0.99
4642696--4642794	43	2.3	43	84	8	132	58	0	0	41	0.98
4642770--4642822	13	4.0	13	78	9	54	58	1	0	39	1.09
4642818--4642850	17	1.9	17	93	0	57	66	0	3	30	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4642815--4642873	24	2.5	23	83	8	66	66	1	1	30	1.12
4642987--4643027	13	2.9	15	79	17	52	56	4	2	36	1.34
4643019--4643067	22	2.3	21	85	3	62	55	10	6	28	1.57
4643166--4643226	29	2.1	29	84	6	79	3	14	1	80	0.92
4643166--4643226	10	6.4	9	78	10	50	3	14	1	80	0.92
4644698--4644739	4	10.2	4	94	5	75	0	26	0	73	0.83
4644699--4644739	21	2.0	21	100	0	82	0	24	0	75	0.80
4645015--4645098	41	2.1	39	82	8	98	44	0	1	54	1.07
4645005--4645101	41	2.3	42	74	18	94	43	0	1	55	1.06
4649401--4649441	21	2.0	20	95	4	73	12	9	34	43	1.75
4653444--4653472	3	9.7	3	100	0	58	65	0	0	34	0.93
4664023--4664052	10	2.8	11	90	10	53	36	0	0	63	0.95
4664966--4665013	21	2.2	23	82	14	66	54	0	2	43	1.12
4664978--4665020	21	2.1	20	87	12	61	65	0	0	34	0.93
4665079--4665119	17	2.4	17	87	0	55	29	2	4	63	1.28
4665088--4665120	17	1.9	17	93	0	57	27	3	6	63	1.32
4665109--4665137	15	2.0	15	93	6	51	24	0	0	75	0.80
4665481--4665505	2	12.5	2	100	0	50	52	0	0	48	1.00
4665809--4665852	23	1.9	23	100	0	88	40	29	13	15	1.86
4675599--4675684	45	1.9	45	95	0	154	50	17	18	13	1.79
4678348--4678422	30	2.5	30	78	8	80	60	0	0	40	0.97
4678359--4678434	31	2.3	33	78	13	86	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)
4679411--4679443	3	11.3	3	87	6	50	27	0	3	69	1.03
4680262--4680312	22	2.5	20	76	17	59	35	0	0	64	0.94
4680306--4680418	47	2.5	43	79	14	113	57	0	1	40	1.09
4680324--4680418	41	2.2	43	83	9	115	57	0	2	40	1.10
4680355--4680427	22	3.3	23	69	19	66	54	0	1	43	1.08
4687788--4687826	20	1.9	21	84	5	53	66	17	10	5	1.39
4687788--4687829	19	2.1	21	86	8	61	66	16	11	4	1.40
4691185--4691215	15	2.1	14	94	5	53	67	0	0	32	0.91
4691522--4691564	2	21.5	2	90	0	68	51	2	46	0	1.13
4702463--4702512	23	2.2	23	100	0	100	30	18	18	34	1.94
4703972--4704018	16	3.1	15	78	12	51	55	0	2	42	1.12
4703982--4704014	14	2.3	15	94	5	59	60	0	0	39	0.97
4703989--4704035	20	2.4	19	76	13	51	59	0	0	40	0.97
4704001--4704038	20	1.9	20	89	10	60	52	0	0	47	1.00
4704601--4704673	25	3.0	23	74	20	60	52	5	1	41	1.33
4706453--4706539	45	2.0	42	82	6	102	56	1	0	42	1.07
4706495--4706543	18	2.8	18	80	17	59	55	0	0	44	0.99
4706728--4706761	18	1.9	18	88	5	52	14	14	0	70	1.17
4707427--4707502	21	3.7	21	79	11	70	50	0	0	50	1.00
4707451--4707500	19	2.7	18	81	9	64	52	0	0	48	1.00
4708100--4708184	45	1.9	44	85	7	118	45	4	0	49	1.23
4712103--4712296	103	1.9	104	95	1	354	43	17	14	25	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4714282--4714329	15	3.1	15	78	3	51	43	2	2	52	1.24
4714348--4714388	22	1.9	23	85	14	61	43	0	0	56	0.99
4715009--4715042	2	17.0	2	100	0	68	50	0	0	50	1.00
4716674--4716720	24	2.0	22	84	12	58	42	0	0	57	0.98
4719473--4719497	5	5.0	5	100	0	50	80	0	20	0	0.72
4720214--4720249	2	18.5	2	94	5	65	50	0	0	50	1.00
4721800--4721855	2	28.0	2	100	0	112	50	0	50	0	1.00
4722278--4722310	12	2.8	12	90	4	50	63	0	0	36	0.95
4733182--4733220	10	3.9	10	93	0	60	51	0	48	0	1.00
4736182--4736228	16	2.9	16	78	12	51	59	0	25	14	1.36

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